Promoter Regions, Genetic
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Gene Expression Regulation
Sp1 Transcription Factor
Gene Expression Regulation, Bacterial
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Transcription Initiation Site
Regulatory Sequences, Nucleic Acid
Electrophoretic Mobility Shift Assay
An electrophoretic technique for assaying the binding of one compound to another. Typically one compound is labeled to follow its mobility during electrophoresis. If the labeled compound is bound by the other compound, then the mobility of the labeled compound through the electrophoretic medium will be retarded.
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
A method for determining the sequence specificity of DNA-binding proteins. DNA footprinting utilizes a DNA damaging agent (either a chemical reagent or a nuclease) which cleaves DNA at every base pair. DNA cleavage is inhibited where the ligand binds to DNA. (from Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
An enzyme that catalyzes the acetylation of chloramphenicol to yield chloramphenicol 3-acetate. Since chloramphenicol 3-acetate does not bind to bacterial ribosomes and is not an inhibitor of peptidyltransferase, the enzyme is responsible for the naturally occurring chloramphenicol resistance in bacteria. The enzyme, for which variants are known, is found in both gram-negative and gram-positive bacteria. EC 220.127.116.11.
Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes.
Sequence Homology, Nucleic Acid
Amino Acid Sequence
5' Flanking Region
A technique for identifying specific DNA sequences that are bound, in vivo, to proteins of interest. It involves formaldehyde fixation of CHROMATIN to crosslink the DNA-BINDING PROTEINS to the DNA. After shearing the DNA into small fragments, specific DNA-protein complexes are isolated by immunoprecipitation with protein-specific ANTIBODIES. Then, the DNA isolated from the complex can be identified by PCR amplification and sequencing.
An enzyme capable of hydrolyzing highly polymerized DNA by splitting phosphodiester linkages, preferentially adjacent to a pyrimidine nucleotide. This catalyzes endonucleolytic cleavage of DNA yielding 5'-phosphodi- and oligonucleotide end-products. The enzyme has a preference for double-stranded DNA.
Enhancer Elements, Genetic
Gene Expression Regulation, Enzymologic
Sequence Analysis, DNA
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.
Polymerase Chain Reaction
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Tumor Cells, Cultured
Recombinant Fusion Proteins
Reverse Transcriptase Polymerase Chain Reaction
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
DNA-Directed RNA Polymerases
Enzymes that catalyze DNA template-directed extension of the 3'-end of an RNA strand one nucleotide at a time. They can initiate a chain de novo. In eukaryotes, three forms of the enzyme have been distinguished on the basis of sensitivity to alpha-amanitin, and the type of RNA synthesized. (From Enzyme Nomenclature, 1992).
A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.
Gene Expression Regulation, Neoplastic
Gene Expression Regulation, Viral
Sp3 Transcription Factor
Artificial Gene Fusion
Polymorphism, Single Nucleotide
DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.
5' Untranslated Regions
Single-Strand Specific DNA and RNA Endonucleases
Enzymes that catalyze the endonucleolytic cleavage of single-stranded regions of DNA or RNA molecules while leaving the double-stranded regions intact. They are particularly useful in the laboratory for producing "blunt-ended" DNA molecules from DNA with single-stranded ends and for sensitive GENETIC TECHNIQUES such as NUCLEASE PROTECTION ASSAYS that involve the detection of single-stranded DNA and RNA.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Repetitive Sequences, Nucleic Acid
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
A class of proteins that were originally identified by their ability to bind the DNA sequence CCAAT. The typical CCAAT-enhancer binding protein forms dimers and consists of an activation domain, a DNA-binding basic region, and a leucine-rich dimerization domain (LEUCINE ZIPPERS). CCAAT-BINDING FACTOR is structurally distinct type of CCAAT-enhancer binding protein consisting of a trimer of three different subunits.
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Gene Expression Regulation, Plant
The intracellular transfer of information (biological activation/inhibition) through a signal pathway. In each signal transduction system, an activation/inhibition signal from a biologically active molecule (hormone, neurotransmitter) is mediated via the coupling of a receptor/enzyme to a second messenger system or to an ion channel. Signal transduction plays an important role in activating cellular functions, cell differentiation, and cell proliferation. Examples of signal transduction systems are the GAMMA-AMINOBUTYRIC ACID-postsynaptic receptor-calcium ion channel system, the receptor-mediated T-cell activation pathway, and the receptor-mediated activation of phospholipases. Those coupled to membrane depolarization or intracellular release of calcium include the receptor-mediated activation of cytotoxic functions in granulocytes and the synaptic potentiation of protein kinase activation. Some signal transduction pathways may be part of larger signal transduction pathways; for example, protein kinase activation is part of the platelet activation signal pathway.
Gene Expression Regulation, Developmental
Genetic Predisposition to Disease
RNA Polymerase II
Gene Expression Regulation, Fungal
Upstream Stimulatory Factors
Plants, Genetically Modified
Transcription Factor AP-1
Cyclic AMP Response Element-Binding Protein
Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.
Gene Expression Profiling
Nucleic Acid Conformation
Sequence Homology, Amino Acid
DNA Restriction Enzymes
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Cell lines whose original growing procedure consisted being transferred (T) every 3 days and plated at 300,000 cells per plate (J Cell Biol 17:299-313, 1963). Lines have been developed using several different strains of mice. Tissues are usually fibroblasts derived from mouse embryos but other types and sources have been developed as well. The 3T3 lines are valuable in vitro host systems for oncogenic virus transformation studies, since 3T3 cells possess a high sensitivity to CONTACT INHIBITION.
Green Fluorescent Proteins
YY1 Transcription Factor
Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.
Regulatory Elements, Transcriptional
NFI Transcription Factors
Proteins that are coded by immediate-early genes, in the absence of de novo protein synthesis. The term was originally used exclusively for viral regulatory proteins that were synthesized just after viral integration into the host cell. It is also used to describe cellular proteins which are synthesized immediately after the resting cell is stimulated by extracellular signals.
Proto-Oncogene Proteins c-jun
Cellular DNA-binding proteins encoded by the c-jun genes (GENES, JUN). They are involved in growth-related transcriptional control. There appear to be three distinct functions: dimerization (with c-fos), DNA-binding, and transcriptional activation. Oncogenic transformation can take place by constitutive expression of c-jun.
Transcription Factor AP-2
Motifs in DNA- and RNA-binding proteins whose amino acids are folded into a single structural unit around a zinc atom. In the classic zinc finger, one zinc atom is bound to two cysteines and two histidines. In between the cysteines and histidines are 12 residues which form a DNA binding fingertip. By variations in the composition of the sequences in the fingertip and the number and spacing of tandem repeats of the motif, zinc fingers can form a large number of different sequence specific binding sites.
Deacetylases that remove N-acetyl groups from amino side chains of the amino acids of HISTONES. The enzyme family can be divided into at least three structurally-defined subclasses. Class I and class II deacetylases utilize a zinc-dependent mechanism. The sirtuin histone deacetylases belong to class III and are NAD-dependent enzymes.
DNA Modification Methylases
Enzymes that are part of the restriction-modification systems. They are responsible for producing a species-characteristic methylation pattern, on either adenine or cytosine residues, in a specific short base sequence in the host cell's own DNA. This methylated sequence will occur many times in the host-cell DNA and remain intact for the lifetime of the cell. Any DNA from another species which gains entry into a living cell and lacks the characteristic methylation pattern will be recognized by the restriction endonucleases of similar specificity and destroyed by cleavage. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms.
Open Reading Frames
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Operator Regions, Genetic
DNA Transposable Elements
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
Oligonucleotide Array Sequence Analysis
Erythroid-Specific DNA-Binding Factors
Tumor Suppressor Proteins
RNA, Small Interfering
Small double-stranded, non-protein coding RNAs (21-31 nucleotides) involved in GENE SILENCING functions, especially RNA INTERFERENCE (RNAi). Endogenously, siRNAs are generated from dsRNAs (RNA, DOUBLE-STRANDED) by the same ribonuclease, Dicer, that generates miRNAs (MICRORNAS). The perfect match of the siRNAs' antisense strand to their target RNAs mediates RNAi by siRNA-guided RNA cleavage. siRNAs fall into different classes including trans-acting siRNA (tasiRNA), repeat-associated RNA (rasiRNA), small-scan RNA (scnRNA), and Piwi protein-interacting RNA (piRNA) and have different specific gene silencing functions.
Proteins whose abnormal expression (gain or loss) are associated with the development, growth, or progression of NEOPLASMS. Some neoplasm proteins are tumor antigens (ANTIGENS, NEOPLASM), i.e. they induce an immune reaction to their tumor. Many neoplasm proteins have been characterized and are used as tumor markers (BIOMARKERS, TUMOR) when they are detectable in cells and body fluids as monitors for the presence or growth of tumors. Abnormal expression of ONCOGENE PROTEINS is involved in neoplastic transformation, whereas the loss of expression of TUMOR SUPPRESSOR PROTEINS is involved with the loss of growth control and progression of the neoplasm.
Kruppel-Like Transcription Factors
Proto-Oncogene Proteins c-ets
Octamer Transcription Factor-1
Hepatocyte Nuclear Factor 4
Genetic Complementation Test
Saccharomyces cerevisiae Proteins
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
Proto-Oncogene Protein c-ets-1
Y-Box-Binding Protein 1
Basic Helix-Loop-Helix Leucine Zipper Transcription Factors
TATA-Box Binding Protein
A general transcription factor that plays a major role in the activation of eukaryotic genes transcribed by RNA POLYMERASES. It binds specifically to the TATA BOX promoter element, which lies close to the position of transcription initiation in RNA transcribed by RNA POLYMERASE II. Although considered a principal component of TRANSCRIPTION FACTOR TFIID it also takes part in general transcription factor complexes involved in RNA POLYMERASE I and RNA POLYMERASE III transcription.
Hepatocyte Nuclear Factor 1
Studies which start with the identification of persons with a disease of interest and a control (comparison, referent) group without the disease. The relationship of an attribute to the disease is examined by comparing diseased and non-diseased persons with regard to the frequency or levels of the attribute in each group.
Cyclic AMP Receptor Protein
A transcriptional regulator in prokaryotes which, when activated by binding cyclic AMP, acts at several promoters. Cyclic AMP receptor protein was originally identified as a catabolite gene activator protein. It was subsequently shown to regulate several functions unrelated to catabolism, and to be both a negative and a positive regulator of transcription. Cell surface cyclic AMP receptors are not included (CYCLIC AMP RECEPTORS), nor are the eukaryotic cytoplasmic cyclic AMP receptor proteins, which are the regulatory subunits of CYCLIC AMP-DEPENDENT PROTEIN KINASES.
Serotonin Plasma Membrane Transport Proteins
Sodium chloride-dependent neurotransmitter symporters located primarily on the PLASMA MEMBRANE of serotonergic neurons. They are different than SEROTONIN RECEPTORS, which signal cellular responses to SEROTONIN. They remove SEROTONIN from the EXTRACELLULAR SPACE by high affinity reuptake into PRESYNAPTIC TERMINALS. Regulates signal amplitude and duration at serotonergic synapses and is the site of action of the SEROTONIN UPTAKE INHIBITORS.
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Transcriptional repression by the Drosophila giant protein: cis element positioning provides an alternative means of interpreting an effector gradient. (1/58449)Early developmental patterning of the Drosophila embryo is driven by the activities of a diverse set of maternally and zygotically derived transcription factors, including repressors encoded by gap genes such as Kruppel, knirps, giant and the mesoderm-specific snail. The mechanism of repression by gap transcription factors is not well understood at a molecular level. Initial characterization of these transcription factors suggests that they act as short-range repressors, interfering with the activity of enhancer or promoter elements 50 to 100 bp away. To better understand the molecular mechanism of short-range repression, we have investigated the properties of the Giant gap protein. We tested the ability of endogenous Giant to repress when bound close to the transcriptional initiation site and found that Giant effectively represses a heterologous promoter when binding sites are located at -55 bp with respect to the start of transcription. Consistent with its role as a short-range repressor, as the binding sites are moved to more distal locations, repression is diminished. Rather than exhibiting a sharp 'step-function' drop-off in activity, however, repression is progressively restricted to areas of highest Giant concentration. Less than a two-fold difference in Giant protein concentration is sufficient to determine a change in transcriptional status of a target gene. This effect demonstrates that Giant protein gradients can be differentially interpreted by target promoters, depending on the exact location of the Giant binding sites within the gene. Thus, in addition to binding site affinity and number, cis element positioning within a promoter can affect the response of a gene to a repressor gradient. We also demonstrate that a chimeric Gal4-Giant protein lacking the basic/zipper domain can specifically repress reporter genes, suggesting that the Giant effector domain is an autonomous repression domain. (+info)
Association of snRNA genes with coiled bodies is mediated by nascent snRNA transcripts. (2/58449)BACKGROUND: Coiled bodies are nuclear organelles that are highly enriched in small nuclear ribonucleoproteins (snRNPs) and certain basal transcription factors. Surprisingly, coiled bodies not only contain mature U snRNPs but also associate with specific chromosomal loci, including gene clusters that encode U snRNAs and histone messenger RNAs. The mechanism(s) by which coiled bodies associate with these genes is completely unknown. RESULTS: Using stable cell lines, we show that artificial tandem arrays of human U1 and U2 snRNA genes colocalize with coiled bodies and that the frequency of the colocalization depends directly on the transcriptional activity of the array. Association of the genes with coiled bodies was abolished when the artificial U2 arrays contained promoter mutations that prevent transcription or when RNA polymerase II transcription was globally inhibited by alpha-amanitin. Remarkably, the association was also abolished when the U2 snRNA coding regions were replaced by heterologous sequences. CONCLUSIONS: The requirement for the U2 snRNA coding region indicates that association of snRNA genes with coiled bodies is mediated by the nascent U2 RNA itself, not by DNA or DNA-bound proteins. Our data provide the first evidence that association of genes with a nuclear organelle can be directed by an RNA and suggest an autogenous feedback regulation model. (+info)
Telomerase reverse transcriptase gene is a direct target of c-Myc but is not functionally equivalent in cellular transformation. (3/58449)The telomerase reverse transcriptase component (TERT) is not expressed in most primary somatic human cells and tissues, but is upregulated in the majority of immortalized cell lines and tumors. Here, we identify the c-Myc transcription factor as a direct mediator of telomerase activation in primary human fibroblasts through its ability to specifically induce TERT gene expression. Through the use of a hormone inducible form of c-Myc (c-Myc-ER), we demonstrate that Myc-induced activation of the hTERT promoter requires an evolutionarily conserved E-box and that c-Myc-ER-induced accumulation of hTERT mRNA takes place in the absence of de novo protein synthesis. These findings demonstrate that the TERT gene is a direct transcriptional target of c-Myc. Since telomerase activation frequently correlates with immortalization and telomerase functions to stabilize telomers in cycling cells, we tested whether Myc-induced activation of TERT gene expression represents an important mechanism through which c-Myc acts to immortalize cells. Employing the rat embryo fibroblast cooperation assay, we show that TERT is unable to substitute for c-Myc in the transformation of primary rodent fibroblasts, suggesting that the transforming activities of Myc extend beyond its ability to activate TERT gene expression and hence telomerase activity. (+info)
Detailed methylation analysis of the glutathione S-transferase pi (GSTP1) gene in prostate cancer. (4/58449)Glutathione-S-Transferases (GSTs) comprise a family of isoenzymes that provide protection to mammalian cells against electrophilic metabolites of carcinogens and reactive oxygen species. Previous studies have shown that the CpG-rich promoter region of the pi-class gene GSTP1 is methylated at single restriction sites in the majority of prostate cancers. In order to understand the nature of abnormal methylation of the GSTP1 gene in prostate cancer we undertook a detailed analysis of methylation at 131 CpG sites spanning the promoter and body of the gene. Our results show that DNA methylation is not confined to specific CpG sites in the promoter region of the GSTP1 gene but is extensive throughout the CpG island in prostate cancer cells. Furthermore we found that both alleles are abnormally methylated in this region. In normal prostate tissue, the entire CpG island was unmethylated, but extensive methylation was found outside the island in the body of the gene. Loss of GSTP1 expression correlated with DNA methylation of the CpG island in both prostate cancer cell lines and cancer tissues whereas methylation outside the CpG island in normal prostate tissue appeared to have no effect on gene expression. (+info)
B-MYB transactivates its own promoter through SP1-binding sites. (5/58449)B-MYB is an ubiquitous protein required for mammalian cell growth. In this report we show that B-MYB transactivates its own promoter through a 120 bp segment proximal to the transcription start site. The B-MYB-responsive element does not contain myb-binding sites and gel-shift analysis shows that SP1, but not B-MYB, protein contained in SAOS2 cell extracts binds to the 120 bp B-myb promoter fragment. B-MYB-dependent transactivation is cooperatively increased in the presence of SP1, but not SP3 overexpression. When the SP1 elements of the B-myb promoter are transferred in front of a heterologous promoter, an increased response to B-MYB results. In contrast, c-MYB, the prototype member of the Myb family, is not able to activate the luciferase construct containing the SP1 elements. With the use of an SP1-GAL4 fusion protein, we have determined that the cooperative activation occurs through the domain A of SP1. These observations suggest that B-MYB functions as a coactivator of SP1, and that diverse combinations of myb and SP1 sites may dictate the responsiveness of myb-target genes to the various members of the myb family. (+info)
Differential stability of the DNA-activated protein kinase catalytic subunit mRNA in human glioma cells. (6/58449)DNA-dependent protein kinase (DNA-PK) functions in double-strand break repair and immunoglobulin [V(D)J] recombination. We previously established a radiation-sensitive human cell line, M059J, derived from a malignant glioma, which lacks the catalytic subunit (DNA-PKcs) of the DNA-PK multiprotein complex. Although previous Northern blot analysis failed to detect the DNA-PKcs transcript in these cells, we show here through quantitative studies that the transcript is present, albeit at greatly reduced (approximately 20x) levels. Sequencing revealed no genetic alteration in either the promoter region, the kinase domain, or the 3' untranslated region of the DNA-PKcs gene to account for the reduced transcript levels. Nuclear run-on transcription assays indicated that the rate of DNA-PKcs transcription in M059J and DNA-PKcs proficient cell lines was similar, but the stability of the DNA-PKcs message in the M059J cell line was drastically (approximately 20x) reduced. Furthermore, M059J cells lack an alternately spliced DNA-PKcs transcript that accounts for a minor (5-20%) proportion of the DNA-PKcs message in all other cell lines tested. Thus, alterations in DNA-PKcs mRNA stability and/or the lack of the alternate mRNA may result in the loss of DNA-PKcs activity. This finding has important implications as DNA-PKcs activity is essential to cells repairing damage induced by radiation or radiomimetric agents. (+info)
Id helix-loop-helix proteins inhibit nucleoprotein complex formation by the TCF ETS-domain transcription factors. (7/58449)The Id subfamily of helix-loop-helix (HLH) proteins plays a fundamental role in the regulation of cellular proliferation and differentiation. Id proteins are thought to inhibit differentiation mainly through interaction with other HLH proteins and by blocking their DNA-binding activity. Members of the ternary complex factor (TCF) subfamily of ETS-domain proteins have key functions in regulating immediate-early gene expression in response to mitogenic stimulation. TCFs form DNA-bound complexes with the serum response factor (SRF) and are direct targets of MAP kinase (MAPK) signal transduction cascades. In this study we demonstrate functional interactions between Id proteins and TCFs. Ids bind to the ETS DNA-binding domain and disrupt the formation of DNA-bound complexes between TCFs and SRF on the c-fos serum response element (SRE). Inhibition occurs by disrupting protein-DNA interactions with the TCF component of this complex. In vivo, the Id proteins cause down-regulation of the transcriptional activity mediated by the TCFs and thereby block MAPK signalling to SREs. Therefore, our results demonstrate a novel facet of Id function in the coordination of mitogenic signalling and cell cycle entry. (+info)
Cooperative binding of heat shock factor to the yeast HSP82 promoter in vivo and in vitro. (8/58449)Previous work has shown that heat shock factor (HSF) plays a central role in remodeling the chromatin structure of the yeast HSP82 promoter via constitutive interactions with its high-affinity binding site, heat shock element 1 (HSE1). The HSF-HSE1 interaction is also critical for stimulating both basal (noninduced) and induced transcription. By contrast, the function of the adjacent, inducibly occupied HSE2 and -3 is unknown. In this study, we examined the consequences of mutations in HSE1, HSE2, and HSE3 on HSF binding and transactivation. We provide evidence that in vivo, HSF binds to these three sites cooperatively. This cooperativity is seen both before and after heat shock, is required for full inducibility, and can be recapitulated in vitro on both linear and supercoiled templates. Quantitative in vitro footprinting reveals that occupancy of HSE2 and -3 by Saccharomyces cerevisiae HSF (ScHSF) is enhanced approximately 100-fold through cooperative interactions with the HSF-HSE1 complex. HSE1 point mutants, whose basal transcription is virtually abolished, are functionally compensated by cooperative interactions with HSE2 and -3 following heat shock, resulting in robust inducibility. Using a competition binding assay, we show that the affinity of recombinant HSF for the full-length HSP82 promoter is reduced nearly an order of magnitude by a single-point mutation within HSE1, paralleling the effect of these mutations on noninduced transcript levels. We propose that the remodeled chromatin phenotype previously shown for HSE1 point mutants (and lost in HSE1 deletion mutants) stems from the retention of productive, cooperative interactions between HSF and its target binding sites. (+info)
IFI44L promoter methylation as a blood biomarker for systemic lupus erythematosus | Annals of the Rheumatic Diseases
Results Significant hypomethylation of two CpG sites within IFI44L promoter, Site1 (Chr1: 79 085 222) and Site2 (Chr1: 79 085 250; cg06872964), was identified in patients with SLE compared with HCs, patients with RA and patients with pSS. In a comparison between patients with SLE and HCs included in the first validation cohort, Site1 methylation had a sensitivity of 93.6% and a specificity of 96.8% at a cut-off methylation level of 75.5% and Site2 methylation had a sensitivity of 94.1% and a specificity of 98.2% at a cut-off methylation level of 25.5%. The IFI44L promoter methylation marker was also validated in an European-derived cohort. In addition, the methylation levels of Site1 and Site2 within IFI44L promoter were significantly lower in patients with SLE with renal damage than those without renal damage. Patients with SLE showed significantly increased methylation levels of Site1 and Site2 during remission compared with active stage. ...
Genome-wide promoter methylation analysis identifies epigenetic silencing of MAPK13 in primary cutaneous melanoma - Gao - 2013 ...
Gao, L., Smit, M. A., van den Oord, J. J., Goeman, J. J., Verdegaal, E. M. E., van der Burg, S. H., Stas, M., Beck, S., Gruis, N. A., Tensen, C. P., Willemze, R., Peeper, D. S. and van Doorn, R. (2013), Genome-wide promoter methylation analysis identifies epigenetic silencing of MAPK13 in primary cutaneous melanoma. Pigment Cell & Melanoma Research, 26: 542-554. doi: 10.1111/pcmr.12096 ...
Novel Cofactors and TFIIA Mediate Functional Core Promoter Selectivity by the Human TAFII150-Containing TFIID Complex |...
The structure of the core promoter region (i.e., DNA sequences flanking the transcription start site and including the TATA, initiator, and downstream elements that interact with the general transcription machinery) of protein-coding genes has an important influence both on the efficiency of basal transcription and on the ability of the core promoter to respond to upstream promoter-bound activators in vivo and in vitro (reviewed in references33, 38, and 46). Although the general transcription machinery has been well characterized, little is known about the factors and mechanisms that control its activity in a core promoter-specific manner. Whereas various factors like E2F, YY1, TFII-I, and USF may regulate transcription not only through upstream promoter elements but also through interactions with the core promoter regions of certain genes (for reviews, see references38 and 50), several components of the basal transcription machinery have intrinsic and more general core promoter-selective ...
Identification of the human DPR core promoter element using machine learning | Nature
The RNA polymerase II (Pol II) core promoter is the strategic site of convergence of the signals that lead to the initiation of DNA transcription1-5, but the downstream core promoter in humans has been difficult to understand1-3. Here we analyse the human Pol II core promoter and use machine learning to generate predictive models for the downstream core promoter region (DPR) and the TATA box. We developed a method termed HARPE (high-throughput analysis of randomized promoter elements) to create hundreds of thousands of DPR (or TATA box) variants, each with known transcriptional strength. We then analysed the HARPE data by support vector regression (SVR) to provide comprehensive models for the sequence motifs, and found that the SVR-based approach is more effective than a consensus-based method for predicting transcriptional activity. These results show that the DPR is a functionally important core promoter element that is widely used in human promoters. Notably, there appears to be a duality between the
Transcriptional promoter of the human α1(V) collagen gene (COL5A1) | Biochemical Journal
We have characterized the 5′ region of the human alpha 1(V) collagen gene (COL5A1). The transcriptional promoter is shown to have a number of features characteristic of the promoters of housekeeping and growth-control-related genes. It lacks obvious TATA and CAAT boxes, has multiple transcription start sites, has a high GC content, lies within a well-defined CpG island and has a number of consensus sites for the potential binding of transcription factor Sp1. This type of promoter structure, while unusual for a collagen gene, is consistent with the broad distribution of expression of COL5A1 and is reminiscent of the promoter structures of the genes encoding type VI collagen, which has a similarly broad distribution of expression. Stepwise deletion of COL5A1 5′ sequences, placed upstream of a heterologous reporter gene, yielded a gradual decrease in promoter activity, indicating that the COL5A1 promoter is composed of an array of cis-acting elements. A minimal promoter region contained ...
Association of CnB 5I/5D promoter gene polymorphism and serum calcineurin levels in early onset of coronary artery disease of...
Our products have been quoted by publications of Association of CnB 5I/5D promoter gene polymorphism and serum calcineurin levels in early onset of coronary artery disease of south Indian cohort from Gene .
Upstream promoter sequences and αCTD mediate stable DNA wrapping within the RNA polymerase-promoter open complex | EMBO Reports
Our results establish that the extent of stable DNA wrapping in RPo depends on the sequence of the promoter and, in particular, on sequence determinants in the upstream region of the promoter (UP elements). The presence of αCTD and an intact α‐linker is required to maintain extensive stable DNA wrapping. Our results further indicate that the sequence of the upstream region of the promoter can affect DNA wrapping even in the absence of αCTD and thus even in the absence of αCTD-DNA interactions. For example, RPo prepared using ΔαCTDI/ΔαCTDII RNAP shows an apparent DNA compaction of 13±0.6 nm at lacUV5(UPfull) but only 4±0.8 nm at lacUV5(ICAP) (Fig 3E,F). We infer that the sequence of the upstream region of the promoter can affect compaction not only through effects on αCTD-DNA interaction but also through other effects. We suggest that these other effects involve intrinsic DNA curvature, noting that UP‐element subsites and UP elements are A/T‐rich sequences (Fig 1A; Ross et al, ...
Dual Luciferase Assay - Molecular Cloning - BioForum
Dual Luciferase Assay - posted in Molecular Cloning: I am planning to do a dual luciferase assay using the firefly and renilla luciferase vectors. Can someone suggest me a ratio for the co-reporter vectors to be added to the transfection mix. Regards Sankella
A Novel Transcriptional Mechanism of Cell Type-Specific Regulation of Vascular Gene Expression by Glucose | Arteriosclerosis,...
The present study describes a novel cell type-specific mechanism of transcriptional regulation of TSP-1 in vascular cells in response to glucose. We report here that unlike our recently identified short promoter region (−280/+66) responsible for the increased THBS1 transcription in ECs, a longer promoter fragment (−1270/+66) is required for THBS1 regulation in HASMCs, as was described for specialized pericytes and mesangial cells.27 Interestingly, glucose responsiveness in ECs was in fact inhibited by the distal fragment of the promoter,10 suggesting the presence of an inhibitory element in this region, which is not active in either VSMCs or mesangial cells.27 The longer promoter region, −1270/+66, responsible for the increased THBS1 transcription in HASMCs contained distinctly different binding elements, as identified by MatInspector, located in the distal end of the promoter. These binding elements had no similarity to those in the EC-specific THBS1 promoter fragment, −280/+66, ...
Artificial Promoters for Metabolic Optimization - DTU Orbit
In this article, we review some of the expression systems that are available for Metabolic Control Analysis and Metabolic Engineering, and examine their advantages and disadvantages in different contexts. In a recent approach, artificial promoters for modulating gene expression in micro-organisms were constructed using synthetic degenerated oligonucleotides. From this work, a promoter library was obtained for Lactococcus lactis, containing numerous individual promoters and covering a wide range of promoter activities. Importantly, the range of promoter activities was covered in small steps of activity change. Promoter libraries generated by this approach allow for optimization of gene expression and for experimental control analysis in a wide range of biological systems by choosing from the promoter library promoters giving, e.g., 25%, 50%, 200%, and 400% of the normal expression level of the gene in question. If the relevant variable (e.g., the flux or yield) is then measured with each of these ...
Can I use the SMARTchoice shRNA Promoter Selection Plate to optimize all of the transduction conditions for my cells of...
No. The Promoter Selection Plate is not meant to be used to establish fundamental lentiviral transduction conditions, such as optimal cell density, in your cells of interest. The purpose of the Promoter Selection Plate is to visually assess relative promoter activity. Basic experimental conditions (such as cell density, with or without serum, Polybrene concentration) should be established prior to transduction of viral particles using the SMARTchoice Promoter Selection Plate. The Promoter Selection Plate contains duplicate wells of serially diluted lentiviral particles representing each promoter so that two separate conditions can be tested simultaneously. After identification of the optimal promoter for your cells of interest, additional transduction optimization should be performed to identify appropriate MOIs for optimal shRNA performance ...
A mammalian promoter model links cis elements to genetic networks | UMIACS
An accurate identification of gene promoters remains an important challenge. Computational approaches for this problem rely on promoter sequence attributes that are believed to be critical for transcription initiation. Here we report a probabilistic model that captures two important properties of promoters, not used by previous methods, viz., the location preference and co-occurrence of promoter elements. Additionally, we found that many of the position-specific DNA elements are strongly linked with the function of the gene product. For instance, a highly conserved motif CCTTT at -1 position is strongly associated with protein synthesis, cellular and tissue development. Our comparative analysis of promoter classes reveals that the promoters devoid of CpG islands are more conserved and have fewer alternative transcription start sites. The discovered links between promoter elements and gene function allows us to infer genetic networks from promoter elements. The web server for the PSPA promoter ...
Viral promoters can initiate expression of toxin genes introduced into Escherichia coli | BMC Biotechnology | Full Text
The expression of recombinant proteins in eukaryotic cells requires the fusion of the coding region to a promoter functional in the eukaryotic cell line. Viral promoters are very often used for this purpose. The preceding cloning procedures are usually performed in Escherichia coli and it is therefore of interest if the foreign promoter results in an expression of the gene in bacteria. In the case molecules toxic for humans are to be expressed, this knowledge is indispensable for the specification of safety measures. We selected five frequently used viral promoters and quantified their activity in E. coli with a reporter system. Only the promoter from the thymidine kinase gene from HSV1 showed no activity, while the polyhedrin promoter from baculovirus, the early immediate CMV promoter, the early SV40 promoter and the 5 LTR promoter from HIV-1 directed gene expression in E. coli. The determination of transcription start sites in the immediate early CMV promoter and the polyhedrin promoter confirmed the
Regulation of Cell Type-Specific Mouse FcεRI β-Chain Gene Expression by GATA-1 Via Four GATA Motifs in the Promoter | The...
In this study, we indicated that the mouse β-chain promoter is functional only in PT18 mouse mast cell line, but not in monomacrophage and lymphoma cell lines. By using a series of 5′-deletion promoter constructs, the cell type-specific promoter was assigned within −69/+103, although a slight decrease in the promoter activity was observed by the deletion of −116/−70. This may suggest the presence of additional cis-enhancing elements recognizing the deleted region. Anyway, by EMSA using antitranscription factor Abs and various competitive oligonucleotides, GATA-1 protein was identified to bind the promoter region (−61/+3) of the β-chain where three possible GATA-1-binding (−53/−48, −46/−51, and −42/−47) and a single possible GATA-1-binding site (−31/−26) are present. Furthermore, reporter assay using PT18 cells (β-chain+, GATA-1+) and coexpression analysis using CV-1 cells (β-chain−, GATA-1−) indicated that those four GATA-1 sites are required for full ...
Structural and functional characterization of the human and mouse fibulin-1 gene promoters: role of Sp1 and Sp3 | Biochemical...
Fibulin-1 is a multifunctional extracellular protein involved in diverse biological processes including cardiovascular development, haemostasis and cancer. To investigate the transcriptional regulation of the gene encoding fibulin-1 we cloned and analysed about 4.0kb of the 5′-flanking regions of both the human and mouse fibulin-1 genes. The human and mouse fibulin-1 promoters share little sequence similarity except for a short region of approx. 150-170bp immediately upstream of the translation start site. The conserved region contains a TATA-like sequence (ATAATT) and multiple consensus binding sites for Sp1 and activator protein 2 (AP-2). That the short conserved region in each gene confers basal promoter activity is demonstrated by transient transfections of promoter deletion constructs for both the human and mouse genes into cells that express fibulin-1 constitutively. Co-transfections of promoter constructs with expression plasmids for Sp1, Sp3 and Sp4 into Drosophila SL2 cells indicate ...
A functional p53-responsive intronic promoter is contained within the by A Zauberman, D Flusberg et al.
The mdm2 gene is a target for transcriptional activation by the p53 tumor suppressor gene product. Previous work has revealed that the mouse mdm2 gene contains two promoters: one is located upstream to the gene and is active in the absence of p53, the other resides within the first intron and requires p53 for transcriptional activity. To determine whether this unique promoter activation pattern is biologically important, we investigated the structure and function of the corresponding region of the human mdm2 (hmdm2) gene. We report here that the hmdm2 gene also contains an intronic, p53-dependent promoter. The structural features of this promoter are highly conserved between mouse and man, as opposed to the lack of conservation of the first exon. This promoter is triggered in vivo in the presence of activated wild type p53, leading to the production of novel mRNA species. The intronic hmdm2 promoter contains two tandem p53 binding elements. Deletion analysis suggests that optimal promoter
Interleukin-6 and Mevastatin Regulate Plasminogen Activator Inhibitor-1 Through CCAAT/Enhancer-Binding Protein-δ |...
IL-6 induces PAI-1 mRNA and protein accumulation.13,19 Although several transcription factor binding sites were identified in PAI-1 promoter, no classic inflammatory response element was found. Because promoter activity was increased by IL-6, the IL-6-responsive region was explored. The deletion and site mutation of the region from −239 to −210 bp decreased ,80% of the IL-6-inducible promoter activity, indicating that the region is critical for response. A computer-based database analysis indicated there is a putative C/EBP binding site (−226 to −212 bp). The promoters of most IL-6-inducible acute-phase protein genes have been characterized with C/EBP binding motifs.11 Using competition experiments, EMSA supershift analysis, and DNase I footprinting analysis, a C/EBP motif on PAI-1 promoter was verified, and 3 members of C/EBP family including α, β, and δ were involved in the DNA-protein complex formation. C/EBPβ was involved in the formation of 3 complexes because single-copy ...
EPD The Eukaryotic Promoter Database
Core promoter element analysis is performed in order to investigate the quality of the promoter collection. It exploits the fact that certain DNA motifs preferentially occur at characteristic distances from a TSS. For instance, the TATA-box occurs in a narrow region centered about 28 bp upstream of the TSS whereas the CCAAT-box occurs in a much wider area with a peak frequency at position −80. Based on these observations, we would expect a high-quality promoter collection to show high peaks for both sequence motifs. In addition, a narrow TATA-box peak at −28 would indicate precise TSS mapping. This analysis has been performed using OProf. Readers are encouraged to repeat this anlysis and perform others in order to check for the quality of the promoter list. TATA-box: this core promoter element is normally found 28 bp upstream the transcription start site. The following plot shows that EPDnew promoter collection has a more focused TATA-box distribution compared to Gramene annotation ...
A new member of the leucine zipper class of proteins that binds to the HLA DR alpha promoter | Science
Several mutants derived from transformed human B cell lines are defective in expressing major histocompatibility complex (MHC) class II genes. The failure to express a class II gene in at least one such mutant line has been mapped to the MHC class II X box, a conserved transcriptional element in the promoter region. A complementary DNA encoding a DNA-binding protein (human X box binding protein, hXBP-1) whose target is the human DR alpha X box and the 3 flanking region has now been cloned. This complementary DNA encoded a protein with structural similarities to the c-jun proto-oncogene product, and its target sequence was closely related to the palindromic target sequence of c-jun. Mutation of the hXBP-1 DNA target sequence decreased DR alpha promoter activity in vivo. These studies suggest that the hXBP-1 protein acts as a transcription factor in B cells. ...
Evogene and IMAmt Sign Collaboration for Genomic Promoter Discovery and Validation in Cotton
REHOVOT, Israel and CUIABÁ, Brazil, Oct. 19, 2016-- Evogene Ltd., a leading biotechnology company for the improvement of crop productivity, and Instituto Mato-grossense do Algodão, a leading developer and marketer of cotton seeds, announced today a collaboration for the discovery and validation of novel genomic promoters to support IMAmts product...
A comparison of exogenous promoter activity at the ROSA26 locus using a PhiC31 integrase mediated cassette exchange approach in...
Modulation of promoter occupancy by cooperative DNA binding and activation-domain function is a major determinant of...
Binding of transcriptional activators to a promoter is a prerequisite process in transcriptional activation. It is well established that the efficiency of activator binding to a promoter is determined by the affinity of direct interactions between the DNA-binding domain of an activator and its specific target sequences. However, I describe here that activator binding to a promoter is augmented in vivo by the effects of two other determinants that have not been generally appreciated: (i) the number of activator binding sites present in a promoter and (ii) the potency of activation domains of activators. Multiple sites within a promoter can cooperatively recruit cognate factors regardless of whether they contain an effective activation domain. This cooperativity can result in the synergistic activation of transcription. The second effect is the enhancement of activator binding to a promoter by the presence of activation domains. In this case, activation domains are not simply tethered to the ...
Fig. 4. Analysis of the 5′ region of FEZ1 gene. A, primer extension analysis of the transcriptional start site of human FEZ1 gene. Poly(A)+ RNAs from human brain (Lane 1) and breast (Lane 2) were reverse-transcribed with a 5′-radiolabeled, gene-specific primer corresponding with the 1524-1499-bp upstream region from the first translatable methionine. Arrow, TSS, which is 69 bp upstream from the 3′-end of the primer. B, analysis of the human FEZ1 gene 5′ region. Bold bar at the top of the figure indicates the FEZ1 gene locus, in which exons are depicted in boxes. Cross-hatched boxes, deletion mutants used for the luciferase reporter assay. The 5′-end positions of the deleted promoter are indicated as nucleotide numbers from the TSS. C, luciferase reporter assay of the deleted FEZ1 promoter regions. Luciferase reporter plasmids were transfected into Fez1-positive 293 cells to identify the positive regulatory region for FEZ1 transcription. Left, 5′-end positions of the deleted promoter ...
Gene transcriptions/Distal promoters - Wikiversity
A promoter is a region of DNA that facilitates the transcription of a particular gene. Promoters can be about 100-1000 [nucleotides] long.. A promoter is on the template strand for the gene and near the gene in numbers of nucleotides (nts) along the DNA template strand. Usually, the promoter lies within the string of nucleotides between genes. Some promoters are called constitutive as they are active in all circumstances in the cell, while others are regulated becoming active in response to specific stimuli. These specific stimuli for a gene find a receptive portion within that genes promoter. In the case of genes that are used to produce proteins, the RNA polymerase II holoenzyme that actually performs the transcription from the template strand needs to find chemical cues for attachment to the DNA and where to begin transcription. Preceding this are chemical cues for which DNA strand is the template strand and in what direction transcription is to be performed. A promoter contains cues for ...
Gene transcriptions/Distal promoters - Wikiversity
A promoter is a region of DNA that facilitates the transcription of a particular gene. Promoters can be about 100-1000 [nucleotides] long.. A promoter is on the template strand for the gene and near the gene in numbers of nucleotides (nts) along the DNA template strand. Usually, the promoter lies within the string of nucleotides between genes. Some promoters are called constitutive as they are active in all circumstances in the cell, while others are regulated becoming active in response to specific stimuli. These specific stimuli for a gene find a receptive portion within that genes promoter. In the case of genes that are used to produce proteins, the RNA polymerase II holoenzyme that actually performs the transcription from the template strand needs to find chemical cues for attachment to the DNA and where to begin transcription. Preceding this are chemical cues for which DNA strand is the template strand and in what direction transcription is to be performed. A promoter contains cues for ...
Patent US7074590 - Chimeric promoters - Google Patents
This invention provides novel chimeric promoter/enhancers. The chimeric promoter/enhancers are particularly suitable for directing gene expression in mammalian cells.
An opportunistic promoter sharing regulatory sequences with either a muscle-specific or a ubiquitous promoter in the human...
The human aldolase A gene is transcribed from three different promoters, pN, pM, and pH, all of which are clustered within a small 1.6-kbp DNA domain. pM, which is highly specific to adult skeletal muscle, lies in between pN and pH, which are ubiquitous but particularly active in heart and skeletal muscle. A ubiquitous enhancer, located just upstream of pH start sites, is necessary for the activity of both pH and pN in transient transfection assays. Using transgenic mice, we studied the sequence controlling the muscle-specific promoter pM and the relations between the three promoters and the ubiquitous enhancer. A 4.3-kbp fragment containing the three promoters and the ubiquitous enhancer showed an expression pattern consistent with that known in humans. In addition, while pH was active in both fast and slow skeletal muscles, pM was active only in fast muscle. pM activity was unaltered by the deletion of a 1.8-kbp region containing the ubiquitous enhancer and the pH promoter, whereas pN remained ...
The functionality of a 3422-base pair promoter fragment from the mouse α1B-adrenergic receptor (α1BAR) gene was examined. This fragment, cloned from a mouse genomic library, was found to have significant sequence homology to the known human and rat α1BAR promoters. However, the consensus motif of several key cis-acting elements is not conserved among the rat, human, and mouse genes, suggesting species specificity. Confirming fidelity of the murine promoter, robust in vitro expression of a chloramphenicol acetyltransferase (CAT) reporter was detected in known α1BAR-expressing BC3H1, NB41A3, and DDT1MF-2 cells transiently transfected with a promoter-CAT construct. Conversely, minimal CAT expression was detected in known α1BAR-negative RAT-1 and R3T3 cells. These findings were extended by transfecting the same promoter-CAT construct into various primary cell types. In support of the hypothesis that α1ARs are differentially expressed in the smooth muscle of the vasculature, primary cultures of ...
Structural Feature of Prokaryotic Promoters and their Role in Gene Expression
Transcription initiation is an important step in the process of gene regulation in prokaryotes. Promoters are stretches of DNA sequence that are present in the upstream region of transcription start sites (TSSs), where RNA polymerase and other transcription factors bind to initiate transcription. Recent advancement in sequencing technologies has resulted in huge amount of raw data in the form of whole genome sequences. This sequence data has to be annotated, in order to identify coding, non-coding and regulatory regions. Computational tools are useful for a quick and fairly reliable annotation of many genome sequences. Promoter prediction is an important step in genome annotation process which is needed, not only for the validation of predicted genes, but also for the identiﬁcation of novel genes, especially those coding for non-coding RNA, which are missed by gene prediction programs. DNA sequence dependent structural properties such as DNA duplex stability, bendability and intrinsic ...
Links between core promoter and basic gene features influence gene expression | BMC Genomics | Full Text
Diversity in rates of gene expression is essential for basic cell functions and is controlled by a variety of intricate mechanisms. Revealing general mechanisms that control gene expression is important for understanding normal and pathological cell functions and for improving the design of expression systems. Here we analyzed the relationship between general features of genes and their contribution to expression levels. Genes were divided into four groups according to their core promoter type and their characteristics analyzed statistically. Surprisingly we found that small variations in the TATA box are linked to large differences in gene length. Genes containing canonical TATA are generally short whereas long genes are associated with either non-canonical TATA or TATA-less promoters. These differences in gene length are primarily determined by the size and number of introns. Generally, gene expression was found to be tightly correlated with the strength of the TATA-box. However significant reduction
Promoter Gene software free downloads. Promoter Gene shareware, freeware, demos: Gene Inspector by Textco BioSoftware Inc, Page Promoter by NetPromoter, Meta Tag Promoter by NetPromoter etc...
I am currently studying the regulation of several mammalian (mouse and human) promoters. Of obvious interest are known transcription factor binding sites. Since I wouldnt know an AP-1 site from an EcoRI site, I was hoping there might be a computer program on the net that would analyze a submitted sequence for consensus recognition sites. Does anyone out there have any advice? At this point, even a simple list of known consensus sites would be better than nothing. Thanks in advance, Benjamin S. Braun UCLA ...
PCR Real time Mismatch Amplification Mutation Assay (MAMA Real Time PCR) for evaluation of TNF-α promoter gene polymorphism ...
RESULTS: A percentage of 36.17% controls and 38.6% patients were heterozygosis, considering Amplification-refractory mutation system (ARMS)-PCR assay while 23% and 22.85% were heterozygosis using Mismatch Amplification Mutation Assay (MAMA)-PCR. On the contrary, 1.3% and 1.4% were homozygosis A, while 75.7% and 75.75% presented homozygosis G, taking into account the MAMA-PCR results. The two assays were significantly different (P=0.0004 at χ2 Test), but MAMA-PCR showed a better performance for TNF-α -308 G/A gene polymorphism investigation ...
Determining significance of pairwise co-occurrences of events in bursty sequences | BMC Bioinformatics | Full Text
Potential binding sites of transcription factors are an example of biological event sequences where co-occurrence patterns and burstiness occur. We applied our techniques on 10 Mbp regions from human chromosomes 1-10  (NCBI 36 assembly), where we identified potential binding sites as matches to known transcription factor binding motifs. The regions 30 - 40 Mbp were used for chromosomes 1-9, and 20 - 30 Mbp for chromosome 10, to avoid the centromere region. This dataset contains genome regions with different characteristics (e.g., C+G and gene densities), while being compact enough to be efficiently studied with several null models and window sizes. The motifs we consider are from the Jaspar collection  (Jaspar Core), all 138 motifs in the 2008 build. In these sequences we identified all matches for each Jaspar transcription factor (TF) matrix by the PoSSuMsearch program . The threshold for a match was set with p ≤ 10-5, yielding approximately 30000 matches for each 10 Mbp sequence. ...
Promoter elements Database????
In article ,310FF66A.A0A at ulam.generes.ca,, kalch ,kalch at ulam.generes.ca, wrote: , Hi, , we are trying to map promoter elements from known DNA sequence. , However, we find that the DNA analysis programs we have in the lab , (MacVector and GeneWorks) are not suitable for this analysis. Could , someone please post (or respond to me directly) where I can send (or , download) a program that will search for promoter elements (e.g. , Sp1, ERE, AP1, AP2, etc)? , , Thanks, , , Michael MacVector does do this (Im not saying that it does it well, but it has the ability). I think that the newer versions ship with a transcription factor subsequence file that has over 600 sites bound by proteins in promoter regions. You just have to do a nucleic acid subsequence search. I ran a test against the junD promoter and it found all the sites that had been mapped by Shaul etal when they cloned it (except the TATA box. Im not sure why it didnt find that as one of the subsequences is exactly the same sequence ...
Generation of mutant mice. In the strategy of IMCT (Kobayashi et al., 1995), transgenic (Tg) mice are generated that express the human interleukin-2 receptor α-subunit (IL-2Rα) under the control of a cell type-specific promoter. These mice are then treated with a recombinant immunotoxin (IT), which is composed of the variable regions of the anti-IL-2Rα monoclonal antibody and a bacterial exotoxin fragment. The transgene construct contained a 10 kb DNA fragment encoding the 5′-flanking region of the mouse neuropsin (NP) gene (Hirata et al., 2001), the second intron of the rabbit β-globin gene (Kobayashi et al., 1992), the gene cassette encoding IL-2Rα fused to green fluorescent protein (IL-2Rα/GFP) (Watanabe et al., 1998), and the polyadenylation signals of the rabbit β-globin gene and simian virus 40 early gene (Kobayashi et al., 1992). The construct was microinjected into fertilized mouse eggs, which were then implanted into pseudopregnant females. Tg mice were identified by Southern ...
PPT - Promoters PowerPoint Presentation - ID:5386988
Promoters. Oriane Broustal BIO 535. Promoters. About promoters ( structure, function,…) Two types of human promoters based on CG content Bidirectional promoters in human genome. Questions:. What are the differences between eukaryotic and prokaryotic promoters? Slideshow 5386988 by ivana
Promoter elements play important roles in isoform and cell type-specific expression. We surveyed the epigenomic promoter landscape of gastric adenocarcinoma, analyzing 110 chromatin profiles (H3K4me3, H3K4me1, H3K27ac) of primary gastric cancers, gastric cancer lines, and nonmalignant gastric tissues. We identified nearly 2,000 promoter alterations (somatic promoters), many deregulated in various epithelial malignancies and mapping frequently to alternative promoters within the same gene, generating potential pro-oncogenic isoforms (RASA3). Somatic promoter-associated N-terminal peptides displaying relative depletion in tumors exhibited high-affinity MHC binding predictions and elicited potent T-cell responses in vitro, suggesting a mechanism for reducing tumor antigenicity. In multiple patient cohorts, gastric cancers with high somatic promoter usage also displayed reduced T-cell cytolytic marker expression. Somatic promoters are enriched in PRC2 occupancy, display sensitivity to EZH2 ...
Team:NRP-UEA-Norwich/NOSensing - 2012.igem.org
Parts produced from this project: Bacterial-Mammalian/B-M (PyeaR-CArG) Hybrid Promoter -- Mammalian-Bacterial/M-B (CArG-PyeaR) Hybrid Promoter -- B-M + eCFP -- B-M + RFP -- M-B + eCFP -- M-B + RFP Our main project has resulted in the production of a hybrid bacterial and mammalian promoter optimised for induction by nitric oxide, nitrates and nitrites. We have ligated PyeaR, a known bacterial promoter and Part BBa_K216005 (Cambridge 2009) in the parts registry, with its mammalian counterpart, CArG. The resulting hybrid promoter has been synthesised in two orientations; PyeaR (bacterial, B) upstream of CArG (mammalian, M), nicknamed (B-M); and CArG upstream of PyeaR (M-B). These orientations were submitted to the parts registry as our first two biobricks. Each orientation of the promoter was ligated to enhanced cyan fluorescent protein (eCFP) and red fluorescent protein (RFP) to produce four new biobricks which have been submitted to the parts registry. These promoter + fluorescent protein ...
The proximal and distal regulatory regions encode regulatory elements required for promoter activity in cultured keratinocytes ...
The hINV basal promoter, which encodes forty one nucleotides upstream of the transcription commence web site and no AP1 web sites, is not controlled by TAM67
EPD The Eukaryotic Promoter Database
Use this page to investigate EPDnew promoters for their chromatin status or motifs enrichment/distribution with our tools. If you want to restrict the analysis to a subset of promoters please use the promoter selection tool page. ...
Identification of a novel temperature sensitive promoter in cho cells | BMC Biotechnology | Full Text
The double truncation constructs, P3 and P4, are both lacking 449 nts immediately upstream the ATG translation start codon. The absence of this region does not seem to be critical for promoter functionality, since the activity was comparable to the full-length construct (Sps1) and other mutants (Sps2-Sps6) all of which include these initial 449 upstream nts at their 3 end. As concluded from P3, the removal of nts upstream 1167 from the 5 end did not reduce activity. Therefore a series of 5-truncations were made to narrow the critical promoter region. Up to construct Sps6 which includes nts 1-763 no significant reduction was observed whereas a dramatic loss near almost background levels was noticed for the shorter constructs Sps7 to Sps11. Since construct Sps5, containing 910 nts, exhibits full activity, this 5 end was considered critical and additional constructs were designed by successively truncating 3 nts (ds13-ds17). The four long constructs dS13 - dS16 showed fairly high promoter ...
Biology-Online • View topic - Primer design in the promoter region
I want to do a ChIP assay with an antibody against acetylated histone h3. I did a cDNA microarray before and now I want to check if the genes I found there are really regulated by histone acetylation. Thats why I want to do quantitative realtime PCR after the ChIP. The problem is (correct me if I am wrong) that I now have to design primer in the promoter region. And I have no idea how I can do this. Actually I do not even know how to search for the promoter region ...
Progesterone Receptor Isoform-Specific Promoter Methylation: Association of PRA Promoter Methylation with Worse Outcome in...
PR is a classical estrogen-regulated gene (1, 2) and is frequently used as a surrogate marker for functional ERα activity. PR exists in 2 isoforms, PRA and PRB, which are the result of transcription from 2 alternative promoters, and initiation of translation at 2 different AUG codons (3). Structurally, PRB differs from PRA only in that the B receptor contains an additional 164 amino acids at the N-terminus of the protein (4). Despite structural similarities, PRA and PRB possess different functional activities. PRB has been found to be a stronger transcriptional activator than PRA, due in part to a third activation domain (AF-3) within the N-terminal 164 amino acids (5). On the other hand, PRA has been shown to act as a repressor which can inhibit other receptors, including ER and PRB (6). PRA and PRB regulate different sets of genes-of 94 progesterone-regulated genes, 65 were uniquely regulated by PRB, 4 uniquely by PRA, and only 25 by both (7). Moreover, the unliganded PR can regulate gene ...
Phosphorylation of the Gal4 DNA-binding domain is essential for activator mono-ubiquitylation and efficient promoter occupancy
Recent analysis of a Gal4 mutant (Gap71) carrying three point mutations (S22D, K23Q and K25F) in its DNA-binding domain (DBD), has demonstrated that it cannot occupy GAL promoters efficiently in cells and that it is not mono-ubiquitylated, suggesting a functional link between this modification and stable DNA binding in cells. The mechanistic underpinning of this phenotype is that this protein is hypersensitive to a newly discovered activity of the proteasomal ATPases--their ability to actively dissociate transcription factor-DNA complexes after direct interaction with the activation domain. In this paper, we examine the roles of each of the three point mutations contained in Gap71 individually. These experiments have revealed that serine 22 is a site of phosphorylation in the Gal4 DBD and that lysine 23 is essential for S22 phosphorylation, possibly acting as part of the kinase recognition site. Mutation of either residue blocks Gal4 DBD phosphorylation, its subsequent ubiquitylation and ...
A hallmark of balancing selection is present at the promoter region of interleukin 10 : Sussex Research Online
As an anti-inflammatory mediator IL10 is beneficial in certain contexts and deleterious in others. As increased production of IL10 favours protection against inflammatory disease, whereas low production promotes elimination of foreign pathogens by the host, we investigated the possible influence of balancing selection at this locus. We began by resequencing 48 European and 48 African chromosomes across 2.2 kb of the IL10 promoter region, and compared this with four neighbouring gene regions: MK2, IL19, IL20 and IL24. Analysis of nucleotide diversity showed a positive Tajimas D-test for IL10 in Europeans, of borderline statistical significance (1.89, P=0.05). Analysis of F(st) values showed significant population divergence at MK2, IL19, IL20 and IL24 (P,0.01) but not at IL10. Taken together, these findings are consistent with the hypothesis that balancing selection has played a role in the evolution of polymorphisms in the IL10 promoter region.. ...
September | 2014 | agc kinase
This interaction may be competed off with unlabelled oligo and supershifted making use of the YB one antibody. To further dissect YB one binding inside the 2a area we developed biotin labelled oligonucleotides during which the YB one responsive aspects had been mutated at 968, 940 or both web sites. Dropping either in the YREs resulted in significantly less YB 1 binding com pared with the wild form EGFR promoter sequence. These data verify that the 968 and 940 binding web sites are bona fide YREs. With each other these data demonstrate that YB 1 is ready to bind on the initial 1 kb with the EGFR promoter, and this leads to transactivation inside a phosphorylation dependent method. Offered on-line material 9 five R61 Figure five Y box binding protein 1 binds to distinct web pages inside the epidermal development aspect receptor promoter.. AVL292 Sequence of your EGFR2a oligonucleotide used in the gel shift assays. Highlighted sequences will be the possible YB 1 binding websites. The substitutions ...
Figure 1. Promoter activity varies across several human and rodent cell lines. Cells were plated at a density of 50,000 cells per well in a 24-well plate and transduced at MOI = 15 with SMARTvector Empty Vector Control Particles expressing TurboGFP. Promoter activity was assessed at 72 hours post-transduction by the fluorescence intensity of TurboGFP.. If you are uncertain of relative promoter activity in your cells, the Dharmacon SMARTchoice Promoter Selection Plate and the SMARTchoice Inducible Non-targeting Control 4-pack allow straightforward identification of the optimal promoter in your cells of interest.. ...
Patterns of gene promoter methylation in squamous cell cancer of the head and neck<...
TY - JOUR. T1 - Patterns of gene promoter methylation in squamous cell cancer of the head and neck. AU - Hasegawa, Masayuki. AU - Nelson, Heather H.. AU - Peters, Edward. AU - Ringstrom, Elin. AU - Posner, Marshall. AU - Kelsey, Karl T.. N1 - Funding Information: Supported by: CA78609, ES08357, ES00002 and 1P01-DE12467-05.. PY - 2002/6/20. Y1 - 2002/6/20. N2 - Promoter methylation is an important pathway in transcriptional silencing of known and candidate tumor suppressor genes in Head and Neck Squamous Cell Carcinoma (HNSCC). In order to study the association of tumor suppressor gene promoter methylation in HNSCC with patient clinical characteristics, especially alcohol consumption and tobacco smoking, we examined promoter methylation of the p16INK4a, DAP-kinase, E-Cadherin, and RASSF1A genes using methylation-specific PCR (MSP) in 80 patients. The prevalence of p16INK4a, DAP-kinase, E-Cadherin, and RASSF1A promoter methylation was 26/80 (32.5%), 19/80 (23.8%), 29/80 (36.3%), 6/80 (7.5%) ...
ApoE -491A/T promoter polymorphism is not an independent risk factor, but associated with the ε4 allele in Hungarian Alzheimer...
TY - JOUR. T1 - ApoE -491A/T promoter polymorphism is not an independent risk factor, but associated with the ε4 allele in Hungarian Alzheimers dementia population. AU - Juhász, Anna. AU - Palotás, András. AU - Janka, Zoltán. AU - Rimanóczy, Ágnes. AU - Palotás, Miklós. AU - Bódi, Nikoletta. AU - Boda, Krisztina. AU - Zana, Marianna. AU - Vincze, Gábor. AU - Kálmán, János. PY - 2005/5/1. Y1 - 2005/5/1. N2 - Apolipoprotein E gene (Apoε) has three common alleles (ε2, ε3, and ε4), of which ε4 has been shown to be associated with an increased risk for Alzheimers disease (AD). Possible additional genetic factors, like the -491A variant of ApoE promoter may modify the development of AD, independently of the ApoE allele status. The objective of this study was to investigate whether A/T allelic polymorphism at site-491 of the ApoE promoter is associated with AD in a Hungarian population. The genomic DNA isolated from peripheral blood lymphocytes of 52 late-onset AD and 53 control ...
BTG3 tumor suppressor gene promoter demethylation, histone modification and cell cycle arrest by genistein in renal cancer |...
BTG3/ANA/APRO4 has been reported to be a tumor suppressor gene in some malignancies. It constitutes important negative regulatory mechanism for Src-mediated signaling, a negative regulator of the cell cycle and inhibits transcription factor E2F1. We report that BTG3 is downregulated in renal cancer and that the mechanism of inactivation is through promoter hypermethylation. Quantitative real-time polymerase chain reaction (PCR) showed that BTG3 was downregulated in cancer tissues and cells. Genistein and 5-aza-2-deoxycytidine (5Aza-C) induced BTG3 messenger RNA (mRNA) expression in A498, ACHN and HEK-293 renal cell carcinoma (RCC) cell lines. Bisulfite-modified PCR and DNA sequencing results showed complete methylation of BTG3 promoter in tumor samples and cancer cell lines. Genistein and 5Aza-C treatment significantly decreased promoter methylation, reactivating BTG3 expression. Chromatin immunoprecipitation assay revealed that genistein and 5Aza-C increased levels of acetylated histones 3, 4, ...
Assessment of gene promoter hypermethylation for detection of cervical neoplasia<...
TY - JOUR. T1 - Assessment of gene promoter hypermethylation for detection of cervical neoplasia. AU - Wisman, G. Bea A.. AU - Nijhuis, Esther R.. AU - Hoque, Mohammad O.. AU - Reesink-Peters, Nathalie. AU - Koning, Alice J.. AU - Volders, Haukeline H.. AU - Buikema, Henk J.. AU - Boezen, H. Marike. AU - Hollema, Harry. AU - Schuuring, Ed. AU - Sidransky, David. AU - Van Der Zee, Ate G.J.. PY - 2006/10/15. Y1 - 2006/10/15. N2 - Current cervical cancer screening is based on morphological assessment of Pap smears and associated with significant false negative and false positive results. Previously, we have shown that detection of hypermethylated genes in cervical scrapings using quantitative methylation-specific PCR (QMSP) is a promising tool for identification of squamous cell cervical cancer. Aim of the present pilot-study was to evaluate presence of hypermethylated genes in cervical carcinogenesis, both in squamous cell as well as adenocarcinomas. Cervical scrapings were obtained from 30 ...
Exendin-4 as a stimulator of rat insulin I gene promoter activity via bZIP/CRE interactions sensitive to serine/threonine...
TY - JOUR. T1 - Exendin-4 as a stimulator of rat insulin I gene promoter activity via bZIP/CRE interactions sensitive to serine/threonine protein kinase inhibitor Ro 31-8220. AU - Chepurny, Oleg G.. AU - Hussain, Mehboob A.. AU - Holz, George G.. PY - 2002. Y1 - 2002. N2 - Signal transduction properties of exendin-4 (Ex-4) underlying its ability to stimulate rat insulin I gene promoter (RIP1) activity were assessed in the pancreatic β-cell line INS-1. Ex-4 acted via glucagon-like peptide-1 receptors to stimulate RIP1 in a glucose-dependent manner, as measured in cells transfected with a -410-bp RIP1-luciferase construct (RIP1-Luc). The action of Ex-4 was independent of cAMP and PKA because it was not blocked by cotransfection with dominant-negative Gαs, was unaffected by pretreatment with the membrane-permeant cAMP antagonist 8-Br-Rp-cAMPS, and remained apparent after treatment with PKA inhibitors H-89 or KT 5720. Similarly, cotransfection with a dominant-negative isoform of the type-2 ...
The small subunit of the vaccinia virus early transcription factor contacts the transcription promoter DNA. | Journal of...
The vaccinia virus early transcription factor (VETF), in addition to the viral RNA polymerase, is required for efficient transcription of early genes in vitro. VETF is a heterodimeric protein that binds specifically to early gene promoters. In order to localize the VETF DNA binding domain, we have used photoreactive oligonucleotide probes with the sequence of the vaccinia virus growth factor promoter. The probes consisted of double-stranded oligonucleotides incorporating radiolabeled dAMP and 5-bromo-dUMP into sequences of the promoter known to contact VETF. Irradiation of a DNA probe having these nucleotides located upstream of the transcription start site in the presence of VETF resulted in the transfer of label to a polypeptide that comigrated with the small subunit of VETF. The label transfer reaction was shown to occur with the recombinant VETF small subunit in the absence of the large subunit. These results indicate that the small subunit comprises at least part of the VETF DNA binding ...
TFIIA has activator-dependent and core promoter functions in vivo. - Semantic Scholar
The physiological role of TFIIA was investigated by analyzing transcription in a yeast strain that contains a TATA-binding protein (TBP) mutant (N2-1) defective for interacting with TFIIA. In cells containing N2-1, transcription from a set of artificial his3 promoters dependent on different activators is generally reduced by a similar extent, indicating that TFIIA function is largely nonselective for activators. In addition, TATA element utilization, a core promoter function, is altered at his3 promoters dependent on weak activators. Genomic expression analysis reveals that 3% of the genes are preferentially affected by a factor of 4 or more. Chimeras of affected promoters indicate that the sensitivity to the TFIIA-TBP interaction can map either to the upstream or core promoter region. Unlike wild-type TBP or TFIIA, the N2-1 derivative does not activate transcription when artificially recruited to the promoter via a heterologous DNA binding domain, indicating that TFIIA is important for transcription
HKU Scholars Hub: Two Inr elements are important for mediating the activity of the proximal promoter of the human gonadotropin...
Differential usage of several transcription start sites in the human GnRH receptor gene was evident in human brain and pituitary. To locate the promoter responsible for a cluster of the 3′ CAP sites from -635 to -578 (relative to ATG) found in the pituitary, a proximal promoter element was identified at -677/-558 by 5′ and 3′ deletion mutant analysis. The promoter element drove a 13.1 ± 0.6-fold increase in reporter gene activity in an orientation-dependent manner in the mouse gonadotrope-derived αT3-1 cells. Within the core promoter element, two functional AT-rich Inr motifs, interacting with the same protein factor with different affinities, were identified. By Southwestern blot analysis and competitive gel mobility shift assays, multiple nuclear factors (36-150 kDa) were found to interact specifically with the core promoter element. Interestingly, these nuclear proteins also interacted with a previously identified distal promoter of the human GnRH receptor gene. Taken together, our ...
Single Or Dual Luciferase Assay - World of Odes
Lab Reagents Human IgG antibody Laboratories manufactures the single or dual luciferase assay reagents distributed by Genprice. The Single Or Dual Luciferase Assay reagent is RUO (Research Use Only) to test human serum or cell culture lab samples. To purchase these products, for the MSDS, Data Sheet, protocol, storage conditions/temperature or for the concentration, please contact luciferase assay. Other Single products are available in stock. Specificity: Single Category: Or Group: Dual Luciferase. Dual Luciferase information ...
YUHSpace: RANTES gene promoter polymorphisms are associated with bronchial hyperresponsiveness in Korean children with asthma
title: RANTES gene promoter polymorphisms are associated with bronchial hyperresponsiveness in Korean children with asthma, doi: 10.1007/s00408-007-9049-3, category: Article
Four promoters subject to regulation by ExoR and PhoB direct transcription of the Sinorhizobium meliloti exoYFQ operon involved...
Succinoglycan (EPS I), the main acidic exopolysaccharide of Sinorhizobium meliloti, is required for the initiation and elongation of infection threads during nodulation of the host plant alfalfa. The gene products of the exoYFQ operon are involved in the first step of succinoglycan biosynthesis as well as in the polymerisation of subunits to the high-molecular-mass form of this exopolysaccharide. One promoter region that directs transcription of exoX and two promoter regions that drive transcription of exoY were mapped in the exoX-exoY intergenic region. The distal exoY promoter region containing three putative -10 promoter elements was active under standard growth conditions and was subject to ExoR-dependent regulation. Although this promoter region was stimulated in a phoB mutant, no PHO box-like sequences were found, suggesting an indirect regulatory effect of PhoB. The proximal promoter contains a PHO box-like sequence in the putative - 35 region and was affected by low and high phosphate ...
Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch<...
TY - JOUR. T1 - Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch. AU - Liu, Nan. AU - Hargreaves, Victoria V.. AU - Zhu, Qian. AU - Kurland, Jesse V.. AU - Hong, Jiyoung. AU - Kim, Woojin. AU - Sher, Falak. AU - Macias-Trevino, Claudio. AU - Rogers, Julia M.. AU - Kurita, Ryo. AU - Nakamura, Yukio. AU - Yuan, Guo Cheng. AU - Bauer, Daniel E.. AU - Xu, Jian. AU - Bulyk, Martha L.. AU - Orkin, Stuart H.. N1 - Funding Information: We thank Peter Skene and Steven Henikoff for advice on protocols for CUT&RUN, Birgit Knoechel for assistance with DNA sequencing, and Paul Bruno for improvements in protein purification. We appreciate the generosity of Merlin Crossley for sharing findings during the evolution of these studies. Fluorescence polarization experiments were performed at the Institute for Chemistry and Cell Biology-Longwood Screening Facility at HMS. Octet experiments were performed at the Center for Macromolecular Interactions in the Department of Biological ...
FKH1 - Fork head protein homolog 1 - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) - FKH1 gene & protein
cytosol, nucleus, centromeric DNA binding, chromatin binding, DNA replication origin binding, RNA polymerase II core promoter proximal region sequence-specific DNA binding, sequence-specific DNA binding, transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding, transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding, anatomical structure morphogenesis
Early promoter-binding factor from vaccinia virions - Enlighten: Publications
A factor, present in transcriptionally active extracts prepared from purified vaccinia virus particles, binds to vaccinia early promoter sequences. The specificity of binding was demonstrated by electrophoretic mobility shift assays using the 5-terminal segments of two early genes and related and unrelated competitor DNA fragments. DNase I footprint analysis indicated that the factor formed a complex with promoter regions of both genes and protected sequences of 10-15 nucleotides centered 21-24 nucleotides upstream of the RNA start sites. The lack of protection of a late regulatory sequence and of an early promoter with transcriptionally inactivating single-nucleotide substitutions suggested that the protein is an early transcription factor. When subjected to glycerol gradient centrifugation, the DNA-binding factor was resolved from RNA polymerase and sedimented as a 7.5S species with an estimated molecular weight of 130,000. ...
LATS2 promoter hypermethylation and its effect on gene expression in human breast cancer
Tumor‑specific promoter hypermethylation of large tumor suppressor, homolog 2 (LATS2), a tumor suppressor gene, has been investigated using methylation‑specific polymerase chain reaction (MSP) assays in different types of human cancer producing conflicting results. The aim of the present study was to evaluate the methylation status of the LATS2 promoter region using bisulfite sequencing with a next generation sequencer for breast cancer. In the 11 patients enrolled in the present study, the LATS2 promoter methylation index (MI) was uniformly high in tumor and normal tissues of the breast (median, 84.0 and 87.4%, respectively). The presence of LATS2 promoter hypermethylation was confirmed in isolated tumor cells and normal epithelial cells using the magnetic‑activated cell sorting method. In situ hybridization for LATS2 messenger RNA (mRNA) revealed that the mRNA expression of LATS2 was higher in normal epithelial cells, compared with tumor cells, however, it was not significantly ...
Identification of a Novel Strong and Ubiquitous Promoter/Enhancer in the Silkworm Bombyx mori | G3: Genes | Genomes | Genetics
Transgenic techniques offer a valuable tool for determining gene functions. Although various promoters are available for use in gene overexpression, gene knockdown, and identification of transgenic individuals, there is nevertheless a lack of versatile promoters for such studies, and this dearth acts as a bottleneck, especially with regard to nonmodel organisms. Here, we succeeded in identifying a novel strong and ubiquitous promoter/enhancer in the silkworm. We identified a unique silkworm strain whose reporter gene showed strong and ubiquitous expression during the establishment of enhancer trap strains. In this strain, the transposon was inserted into the 5′UTR of hsp90, a housekeeping gene that is abundantly expressed in a range of tissues. To determine whether the promoter/enhancer of hsp90 could be used to induce strong gene expression, a 2.9-kb upstream genomic fragment of hsp90 was isolated (hsp90P2.9k), and its transcriptional activation activity was examined. Strikingly, hsp90P2.9k ...
Dual luciferase assay - proper controls? - Cell Biology - BioForum
Dual luciferase assay - proper controls? - posted in Cell Biology: Hey everyone, I am trying to perform a dual luciferase reporter assay in a cell line with promoters established from another cell line. cDNA and protein of the gene are present in both cell lines. Problem: In the new cell line, the luciferase activity for my promoters of interest is below pGL3, whereas TKpGL3 is as highly active as in the other cell line. Renilla activity was equal in all probes. So I am looking for appr...
Isolation and Characterization of Three Cassava Elongation Factor 1 Alpha (MeEF1A) Promoters | KK Genetika & Bioteknologi...
In plant genetic engineering, the identification of gene promoters leading to particular expression patterns is crucial for the development of new genetically modified plant generations. This research was conducted in order to isolate and characterize several new promoters from cassava (Manihot esculenta Crantz) elongation factor 1 alpha (EF1A) gene family. Three promoters MeEF1A3, MeEF1A4 and MeEF1A5 were successfully isolated. Sequence analyses showed that all of the promoters contain three conserved putative cis-acting elements which are located upstream of the transcription start site. These elements are included a TEF1, a TELO and TATA boxes. In addition, all of the promoters also have the 5′UTR intron but with a different lengths. These promoters were constructed translationally with gusAreporter gene (promoter::gusA fusion) in pBI-121 binary vector to build a new binary vector using Overlap Extension PCR Cloning (OEPC) technique. Transient expression assay that was done by using ...
The trmA promoter has regulatory features and sequence elements in common with the rRNA P1 promoter family of Escherichia coli....
The tRNA(m5U54)methyltransferase, whose structural gene is designated trmA, catalyzes the formation of 5-methyluridine in position 54 of all tRNA species in Escherichia coli. The synthesis of this enzyme has previously been shown to be both growth rate dependent and stringently regulated, suggesting regulatory features similar to those of rRNA. We have determined the complete nucleotide sequence of the trmA operon in E. coli and the sequence of the trmA promoter region in Salmonella typhimurium and also analyzed the transcriptional regulation of the gene. The trmA and the btuB (encoding the vitamin B12 outer membrane receptor protein) promoters are divergent promoters separated by 102 bp between the transcriptional start sites. The trmA promoters of both E. coli and S. typhimurium share promoter elements with the rRNA P1 promoter. The sequence downstream from the -10 region of the trmA promoter is homologous to the discriminatory region found in stringently regulated promoters. Next to and ...
Epigenetic alteration: new insights moving from tissue to plasma - the example of PCDH10 promoter methylation in colorectal...
Background:Tumour-released DNA in blood represents a promising biomarker for cancer detection. Although epigenetic alterations such as aberrant promoter methylation represent an appealing perspective, the discordance existing between frequencies of alterations found in DNA extracted from tumour tissue and cell-free DNA (cfDNA) has challenged their practical clinical application. With the aim to explain this bias of agreement, we investigated whether protocadherin 10 (PCDH10) promoter methylation in tissue was associated with methylation pattern in matched cfDNA isolated from plasma of patients with colorectal cancer (CRC), and whether the strength of concordance may depend on levels of cfDNA, integrity index, as well as on different clinical-pathological features.Methods:A quantitative methylation-specific PCR was used to analyse a selected CpG site in the PCDH10 promoter of 67 tumour tissues, paired normal mucosae, and matched plasma samples. The cfDNA integrity index and cfDNA concentration ...
Identification of a novel beta-cell glucokinase (GCK) promoter mutation (-71G|C) that modulates GCK gene expression through...
OBJECTIVE: Inactivating mutations in glucokinase (GCK) cause mild fasting hyperglycemia. Identification of a GCK mutation has implications for treatment and prognosis; therefore, it is important to identify these individuals. A significant number of patients have a phenotype suggesting a defect in glucokinase but no abnormality of GCK. We hypothesized that the GCK beta-cell promoter region, which currently is not routinely screened, could contain pathogenic mutations; therefore, we sequenced this region in 60 such probands. RESEARCH DESIGN AND METHODS: The beta-cell GCK promoter was sequenced in patient DNA. The effect of the identified novel mutation on GCK promoter activity was assessed using a luciferase reporter gene expression system. Electrophoretic mobility shift assays (EMSAs) were used to determine the impact of the mutation on Sp1 binding. RESULTS: A novel -71G|C mutation was identified in a nonconserved region of the human promoter sequence in six apparently unrelated probands. Family testing
Importance of cAMP-response element-binding protein in regulation of expression of the murine cyclic nucleotide...
Incubation of 3T3-L1 preadipocytes with isobutylmethylxanthine (IBMX), dexamethasone, and insulin, alone or in combination, demonstrated that IBMX, which increased cAMP-response element-binding protein (CREB) phosphorylation, was the predominant regulator of Pde3b expression. Real time PCR and immunoblotting indicated that in 3T3-L1 preadipocytes, IBMX-stimulated induction of Pde3b mRNA and protein was markedly inhibited by dominant-negative CREB proteins. By transfecting preadipocytes, differentiating preadipocytes, and HEK293A cells with luciferase reporter vectors containing different fragments of the 5- flanking region of the Pde3b gene, we identified a distal promoter that contained canonical cis-acting cAMP-response elements (CRE) and a proximal, GC-rich promoter region, which contained atypical CRE. Mutation of the CRE sequences dramatically reduced distal promoter activity; H89 inhibited IBMX-stimulated CREB phosphorylation and proximal and distal promoter activities. Distal promoter ...
A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription...
Conventional wisdom holds that, owing to the dominance of features such as chromatin level control, the expression of a gene cannot be readily predicted from knowledge of promoter architecture. This is reflected, for example, in a weak or absent correlation between promoter divergence and expression divergence between paralogs. However, an inability to predict may reflect an inability to accurately measure or employment of the wrong parameters. Here we address this issue through integration of two exceptional resources: ENCODE data on transcription factor binding and the FANTOM5 high-resolution expression atlas. Consistent with the notion that in eukaryotes most transcription factors are activating, the number of transcription factors binding a promoter is a strong predictor of expression breadth. In addition, evolutionarily young duplicates have fewer transcription factor binders and narrower expression. Nonetheless, we find several binders and cooperative sets that are disproportionately associated
A simple metric of promoter architecture robustly predicts expression breadth of human genes suggesting that most transcription...
Background: Conventional wisdom holds that, owing to the dominance of features such as chromatin level control, the expression of a gene cannot be readily predicted from knowledge of promoter architecture. This is reflected, for example, in a weak or absent correlation between promoter divergence and expression divergence between paralogs. However, an inability to predict may reflect an inability to accurately measure or employment of the wrong parameters. Here we address this issue through integration of two exceptional resources: ENCODE data on transcription factor binding and the FANTOM5 high-resolution expression atlas. Results: Consistent with the notion that in eukaryotes most transcription factors are activating, the number of transcription factors binding a promoter is a strong predictor of expression breadth. In addition, evolutionarily young duplicates have fewer transcription factor binders and narrower expression. Nonetheless, we find several binders and cooperative sets that are ...
Microbiology Society Journals | Functional interaction of Oct transcription factors with the family of repeats in Epstein-Barr...
The family of repeats (FR) is a major upstream enhancer of the Epstein-Barr virus (EBV) latent C promoter (Cp) that controls transcription of six different latent nuclear proteins following interaction with the EBV nuclear protein EBNA1. Here, it was shown that Cp could also be activated by octamer-binding factor (Oct) proteins. Physical binding to the FR by the cellular transcription factors Oct-1 and Oct-2 was demonstrated by using an electrophoretic mobility-shift assay. Furthermore, Oct-1 in combination with co-regulator Bob.1, or Oct-2 alone, could drive transcription of a heterologous thymidine kinase promoter linked to the FR in both B cells and epithelial cells. Cp controlled by the FR was also activated by binding of Oct-2 to the FR. This may have direct implications for B cell-specific regulation of Cp.
TERT promoter mutations and their association with BRAF V600E mutation and aggressive clinicopathological characteristics of...
In this large cohort, we found TERT promoter mutations to be common, particularly in FTC and BRAF mutation-positive PTC, and associated with aggressive clinicopathological characteristics.
Gene transcriptions/Boxes/AGCs/Laboratory - Wikiversity
The upstream regions of the human CYP11A and bovine CYP11B genes [have] a distal promoter in each gene. The distal promoters are located at −1.8 to −1.5 kb in the upstream region of the CYP11A gene and −1.5 to −1.1 kb in the upstream region of the CYP11B gene. Using cloned chicken βA-globin genes, either individually or within the natural chromosomal locus, enhancer-dependent transcription is achieved in vitro at a distance of 2 kb with developmentally staged erythroid extracts. This occurs by promoter derepression and is critically dependent upon DNA topology. In the presence of the enhancer, genes must exist in a supercoiled conformation to be actively transcribed, whereas relaxed or linear templates are inactive. Distal protein-protein interactions in vitro may be favored on supercoiled DNA because of topological constraints. Distal promoter regions may be a relatively small number of nucleotides, fairly close to the TSS such as (-253 to -54) or several regions of ...
The Pem homeobox gene. Androgen-dependent and -independent promoters and tissue-specific alternative RNA splicing. - Semantic...
The Pem gene encodes an atypical homeodomain protein, distantly related to Prd/Pax family members, that we demonstrate is regulated in a complex transcriptional and post-transcriptional manner. We show that the rat Pem genomic structure includes three 5-untranslated (5-UT) exons and four coding exons, three of which encode the homeodomain. Several alternatively spliced transcripts were identified, including one that skips an internal coding exon, enabling this mRNA to express a novel form of the Pem protein. Other alternatively spliced mRNAs were characterized that possess different 5-UT regions, including a muscle-specific transcript. The different 5-UT termini present in Pem transcripts conferred different levels of translatability in vitro. Two promoters containing multiple transcription initiation sites were identified: a distal promoter (Pd) in the first 5-UT exon and a proximal promoter (Pp) located in the intron upstream of the first coding exon. The Pd was active in placenta, ovary, tumor
A novel Saa3-promoter reporter distinguishes inflammatory subtypes in experimental arthritis and human synovial fibroblasts |...
Results In vivo, the Saa3-promoter reporter activity was strongly upregulated at 1 and 2 days after the first and second SCW challenge. The Saa3-promoter activities during acute inflammation correlated with Tc uptake measurements but were more sensitive and able to respond to the ongoing synovitis in the chronic phase of SCW arthritis. Molecular stratification defined two inflammatory SF subtypes, unrelated to disease classification. Relative Saa3-promoter responses to interleukin 1β, tumour necrosis factor α and TLR4 agonist were significantly increased in OA/RA SF with a high compared to a low inflammatory profile subtype. Serum stimulation of the Saa3-promoter reporter cell-line could distinguish between healthy and RA patients.. ...
The BioBricks Foundation:Standards/Technical/E.coli promoter standard - OpenWetWare
Naively, promoter strength is a function of 3 variables: holoenzyme affinity for promoter, equilibrium between closed and open complex and efficiency/frequency of promoter escape (this includes all events between opening of DNA helix and clearance of the promoter - in particular initiating synthesis of the first phosphodiester bond, idling/stuttering leading to the generation of nonproductive RNA oligos and finally clearance of the promoter). In the absence of activation/repression, the -40 to +15 region controls all 3 of these variables (-35,-10 define binding, -10-+4 define DNA opening, +1-+20 define promoter escape) - I think this is the absolute minimum we should use to define a promoter. More realistically, we should probably include back to -100 and forward to +20 as the vast majority of both repressors and activators act in this region (see a sampling of ~200 coli promoters below). ...
Differential and Opposing Regulation of PAI-1 Promoter Activity by Estrogen Receptor α and Estrogen Receptor β in Endothelial...
ERα and ERβ exert differential effects on the transcriptional activity of the human PAI-1 promoter in transient transfection studies using cultured endothelial cells. Our experiments demonstrate that ERα increases the promoter activity of PAI-1 promoter fragments in response to estrogen. ERα interacts with at least 1 ERE located at position −422 in the proximal PAI-1 promoter to elicit this estrogen-dependent activation of the PAI-1 promoter. In contrast, ERβ fails to induce, and in fact may suppress, the activity of PAI-1 promoter constructs tested in BAECs through an estrogen-independent mechanism. Furthermore, ERβ exerts a dominant-negative effect on ERα to blunt the estrogen-dependent activation of the PAI-1 promoter in BAECs. Based on these findings, we speculate that the balance of ERα and ERβ in vascular tissue modulates vascular PAI-1 production via estrogen-dependent and estrogen-independent mechanisms.. The observations reported here are consistent with recent studies that ...
2544 | Stanford Health Care
We have isolated the 5 region of the ecto-5-nucleotidase (low K(m) 5-NT) gene and established that a 969-base pair (bp) fragment confers cell-specific expression of a CAT reporter gene that correlates with the expression of endogenous ecto-5-NT mRNA and enzymatic activity. A 768-bp upstream negative regulatory region has been identified that conferred lymphocyte-specific negative regulation in a heterologous system with a 244-bp deoxycytidine kinase core promoter. DNase I footprinting identified several protected areas including Sp1, Sp1/AP-2, and cAMP response element (CRE) binding sites within the 201-bp core promoter region and Sp1, NRE-2a, TCF-1/LEF-1, and Sp1/NF-AT binding sites in the upstream regulatory region. Whereas the CRE site was essential in mediating the negative activity of the upstream regulatory region in Jurkat but not in HeLa cells, mutation of the Sp1/AP-2 site decreased promoter activity in both cell lines. Electrophoretic mobility shift assay analysis of proteins ...
Identification of a cell type-specific silencer in the first exon of the His-1 gene - CaltechAUTHORS
The His-1 gene is developmentally expressed in the murine choroid plexus but is silenced in the adult brain. To test the hypothesis that the gene contains cis-acting elements that contribute to this repression, we have analyzed segments of the proximal promoter for negative regulatory sequences by transient transfection analysis. The activity of the proximal promoter was moderately influenced by positively and negatively acting sequences located from 2335 to 2168 and 2617 to 2335, respectively. A strong His-1-positive regulatory element (HPRE, 118 to 129) was essential for maximal promoter activity and could also enhance the activity of the heterologous SV40 promoter in an orientation-dependent manner. The HPRE contains homology to the neuronal restrictive silencer element (NRSE) but interacted with nuclear proteins that were distinct from the NRSE-binding factor (NRSF). By contrast, a potent negative regulatory sequence (HNRE) was identified in the first exon that repressed either the His-1 or ...
Oncogenic activation of ras results in changes in the transcription of several genes leading to uncontrolled cell growth. In this paper, we demonstrate that transformation of fibroblast cells by the ras oncogene leads to transcriptional repression of the smooth muscle α-actin promoter. Transient transfection analysis of plasmids containing the 5′ upstream region of the human α-actin gene fused to human growth hormone or bacterial chloramphenicol acetyltransferase coding sequences into Rat-2 and ras-transformed Rat-2 (HO6) cells indicates that α-actin promoter is repressed in ras-transformed cells. In addition, stable rat fibroblast cell lines expressing human growth hormone or β-galactosidase under the control of α-actin promoter exhibit repressed reporter gene activity following transformation by the ras oncogene. α-Actin promoter-driven β-galactosidase activity is derepressed in revertants of ras-transformed stable cell lines. This revertant cell line expresses elevated levels of ras ...
Promoter Methylation Status of E-Cadherin, hMLH1, and p16 Gene...
Promoter Methylation Status of E-Cadherin, hMLH1, and p16 Genes in Nonneoplastic Gastric Epithelia: Silencing of tumor suppressor and tumor-related genes by hyp
Silencing and transcriptional properties of the imprinted Airn ncRNA are independent of the endogenous promoter | The EMBO...
One of the most intriguing aspects of Airn‐dependent gene silencing is the ability of Airn transcription to silence neighbouring genes in cis, although its own promoter is unaffected. In these studies, a mouse PGK promoter is able to silence Igf2r in differentiated ES cells, without being itself affected. Currently, two models have been suggested to explain the silencing activity of the Airn ncRNA. The RNA‐directed targeting model is based on parallels to X chromosome inactivation and proposes a function for the Airn ncRNA itself. This model proposes that the Airn ncRNA coats the silenced region and recruits effector proteins that induce widespread repressive epigenetic modifications (Pauler et al, 2007). Intuitively, this model implies a special ability of the Airn promoter to resist silencing as the induced epigenetic changes on the paternal allele silence Igf2r, Slc22a2 and Slc22a3, but not the Airn promoter. Our findings argue against this model, as the PGK promoter in the APD‐PGK ...
Tlx1 - T-cell leukemia homeobox protein 1 - Mus musculus (Mouse) - Tlx1 gene & protein
RNA polymerase II core promoter proximal region sequence-specific DNA binding, transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
CorpusUL: Differential binding of the transcription factors Sp1, AP-1, and NFI to the promoter of the human α5 integrin gene...
Purpose. Damage to the corneal epithelium results in the massive secretion of fibronectin (FN) shortly after injury and induces the expression of its integrin receptor α5β1. The authors reported previously that FN induces α5 expression in human corneal epithelial cells and rabbit corneal epithelial cells by altering the binding of the transcription factor (TF) Sp1 to a regulatory element from the α5 promoter that it is also flanked by binding sites for the TFs NFI and AP-1. Here, they assessed the function of NFI and AP-1 on α5 gene expression and evaluated the contribution of FN to their overall regulatory influence. Methods. TF binding to the α5 promoter was evaluated in vitro by electrophoretic mobility shift assays and in vivo by ligation-mediated PCR or chromatin immunoprecipitation. TFs expression was monitored by Western blot, whereas their influence was assessed by transfection and RNAi analyses. Results. Coexpression of Sp1, NFI, and AP-1 was demonstrated in all cell types, and ...
Enhanced expression and HIV- 1 inhition of chimeric tRNALys3-Ribozymes under dual U6 snRNA and tRNA promoters<...
TY - JOUR. T1 - Enhanced expression and HIV- 1 inhition of chimeric tRNALys3-Ribozymes under dual U6 snRNA and tRNA promoters. AU - Chang, Zongli. AU - Westaway, Shawn. AU - Li, Shirley. AU - Zaia, John A.. AU - Rossi, John J.. AU - Scherer, Lisa J.. PY - 2002/10/1. Y1 - 2002/10/1. N2 - We previously demonstrated that chimeric tRNALys3-ribozymes targeting the primer binding site of HIV produced virions with reduced infectivity. To further enhance the anti-HIV efficiency of these ribozymes by increasing their level of transcription, we designed several tRNALys3 promoter variants and compared their expression levels from the internal tRNALys3 promoters and also from an exogenous human U6 snRNA promoter. The dual U6/tRNA promoter constructs gave rise to much higher levels of expression than constructs that used only an internal tRNA promoter. The most abundant expression is produced when a U6 promoter drives a chimeric tRNALys3-ribozyme containing a mutation in the tRNA B box. As detected by ...
Promoter (genetics) - Wikipedia
Bidirectional promoters are short (,1 kbp) intergenic regions of DNA between the 5 ends of the genes in a bidirectional gene pair. A bidirectional gene pair refers to two adjacent genes coded on opposite strands, with their 5 ends oriented toward one another. The two genes are often functionally related, and modification of their shared promoter region allows them to be co-regulated and thus co-expressed. Bidirectional promoters are a common feature of mammalian genomes. About 11% of human genes are bidirectionally paired.. Bidirectionally paired genes in the Gene Ontology database shared at least one database-assigned functional category with their partners 47% of the time. Microarray analysis has shown bidirectionally paired genes to be co-expressed to a higher degree than random genes or neighboring unidirectional genes. Although co-expression does not necessarily indicate co-regulation, methylation of bidirectional promoter regions has been shown to ...
Interleukin-6-174 G/C promoter gene polymorphism in nasal polyposis and asthma
Cavalcanti, Alexandre B.; Berwanger, Otavio; Suzumura, Erica A.; Amato, Marcelo B. P.; Tallo, Fernando S.; Rezende, Ederlon A. C.; Telles, Jose M. M.; Romano, Edson; Guimaraes, Helio P.; Regenga, Marisa M.; Takahashi, Luzia N.; Teixeira, Cassiano; Oliveira, Roselaine P.; Carvalho, Vitor O.; Diaz-Quijano, Fredi A.; Carvalho, Carlos R. R.; Kodama, Alessandra A.; Ribeiro, Gisele F. M.; Abreu, Matheus O.; Oliveira, Ivonaldo M.; Guyatt, Gordon; Ferguson, Niall; Walter, Stephen; Vasconcelos, Marcia O. M.; Segundo, Valerio J.; Ferraz, Iris L.; Silva, Rosicley S.; Oliveira Filho, Wilson de; Silva, Nelson B.; Heirel, Debora C. B.; Takatani, Rodrigo R.; Sousa Neto, Jefferson A.; Neto, Jeronimo C. B.; Almeida, Samara D.; Chamy, Gauco; Goncalves Neto, Graciliano J. L.; Dias, Alysson P.; Silva, Rozangela R.; Tavares, Roberta C.; Souza, Marcia L. V. D.; Decio, Janaina C.; Lima, Cyntia M. L. S.; Ferreira Neto, Fleury; Oliveira, Katia R.; Dias, Polyana P. L. C.; Brandao, Andre L. S. B.; Ramos, Joroastro E.; ...
Regulation of MAO-A and MAO-B Gene Expression | BenthamScience
Title: Regulation of MAO-A and MAO-B Gene Expression. VOLUME: 11 ISSUE: 15. Author(s):J. C. Shih and K. Chen. Affiliation:Department of Cell andNeurobiology, Keck School of Medicine, University of SouthernCalifornia, 1985 Zonal Ave. Los Angeles, California, 90033, USA. Keywords:mao a, mao b, gene regulation, promoter, sp1, protein kinase c, mapkinase, egr-1. Abstract: MAO A and B genes are made of 15 exons with identical exon-intron organization. They are located on X-chromosome organized in opposite direction, tail to tail with 24kb apart. Both promoters are GC-rich and regulated by transcription factor Sp1. However, they have distinctly different features. MAO B gene, but not MAO A gene, has TATA box. MAO B promoter contains two clusters of overlapping Sp1 sites, the CACCC repressor element. Transcription factors Sp1 and Sp4 can activate MAO B promoter activity through the proximal cluster of Sp1 sites and its activation can be repressed by the over-expression of Sp3 and a related family ...
Fibronectin transcription in liver cells: promoter occupation and function in sinusoidal endothelial cells and hepatocytes :...
Hepatocytes (Heps) and sinusoidal endothelial cells (SECs) perform different roles in normal and pathological liver functions through the differential expression of fibronectin (FN) polypeptides. Nonetheless, the molecular basis underlying cell-type specific FN expression remains unknown. Using liver cell isolation techniques followed by short-term primary culture and transient transfection, here, we compare the transcriptional regulation of the FN promoter in Heps and SEC in conditions that closely resemble in vivo physiology. Transfection experiments allowed us to reveal cell-type specific regulatory elements operating through the proximal regions of the FN promoter. To investigate this further, we examined the occupation patterns of key elements of the FN promoter such as the -170 CRE and -150 CCAAT sites. Transcriptional activity of mutagenised promoter constructs confirmed that in Heps, these two sites behave as a composite element critical for normal promoter activity. In addition, ...
Pho signal transduction network reveals direct transcriptional regulation of one two-component system by another two-component...
The PhoP binding pattern within the resA promoter is similar to other PhoP-regulated promoters(Liu, 1997; Liu and Hulett, 1997; 1998; Liu et al., 1998a, b), in that (i) both PhoP and PhoP∼P bind to these promoters; (ii) PhoP∼P extends the binding site further upstream and/or downstream, and has a higher binding affinity; and (iii) the core PhoP-binding region (region bound by PhoP and PhoP∼P) is located from about −22 to −60 in all these promoters(Liu and Hulett, 1998), including resA. A feature unique to the resA promoter among PhoP-regulated promoters is that it contains only two of the consensus PhoP binding repeats in the core binding region (Fig. 6), instead of at least four as seen in other Pho promoters studied. Ongoing expression and footprinting analyses of a site-specific mutagenized PhoP regulated promoter (S. Eder and F. M. Hulett, unpublished) indicate that PhoP binds to 6 bp repeated TT(A/T/C)ACA sequences separated by 4-5 bp, and that PhoP binding to one set of consensus ...
Cloning of a wheat puroindoline gene promoter by IPCR and analysis of promoter regions required for tissue-specific expression...
Read Cloning of a wheat puroindoline gene promoter by IPCR and analysis of promoter regions required for tissue-specific expression in transgenic riceseeds, Plant Molecular Biology on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Generation of the Mouse FasL Promoter Reporter Constructs and Motifs-Directed Mutagenesis. Mouse FasL promoter cloned in pGL3 vector was a gift from Dr. Timothy L. Ratiff (University of Iowa, Iowa City, IA). The cloning of FasL promoter and generation of luciferase reporter construct in pGL3 vector have been described previously (Crist et al., 2003).. To determine the role of NF-κB in regulation of FasL promoter in the presence of TCDD, we generated three FasL promoter constructs with or without NF-κB motifs. We designated these constructs FasL231, FasL191, and FasL324 based on the size of the respective PCR-amplified fragments. The primers used to generate various fragments of mouse FasL promoter are shown in Table 1. For directional cloning, all upstream primers included SacI restriction site and downstream primers included XhoI restriction site.. The amplified PCR fragments FasL231, FasL191, and FasL324 were first cloned into the polylinker sites of Topo PCR2.1 T/A vector and then sequenced ...
Partial promoter substitutions generating transcriptional sentinels of diverse signaling pathways in embryonic stem cells and...
We present a system by which diverse transcriptional reporter elements, downstream of different signal transduction pathways, elicit cellular fluorescence in an agonist-dependent and agonist-selective fashion in live cells and embryos. By employing the constitutively active Rosa26 gene and analyzing its upstream promoter sequences, we made successive deletions with the intention of preserving the inherent openness of the locus and its constitutive activity, while diminishing core promoter function sufficiently to provide a low background of transcription in the absence of signal pathway activity. The −228 deletion endpoint satisfied these criteria, whereas the −60 deletion retained high constitutive activity. Fortunately, we discovered that insertion of all signaling elements studied here at −60 resulted in a marked diminution of basal activity. Not unexpectedly, the different −228 and −60 constructs provided slightly different results in terms of basal and induced activity with ...
Transkripsi (genetik) bahasa Indonesia, ensiklopedia bebas
The promoter region in higher eukaryotes. ISBN 0-7167-3520-2. Diakses tanggal 2010-08-17.. Pemeliharaan CS1: Banyak nama: ... An Introduction to Genetic Analysis. University of British Columbia, University of California, Harvard University (edisi ke-7 ... Glossary - Promoter. ISBN 0-7167-3520-2. Diakses tanggal 2010-08-17.. Pemeliharaan CS1: Banyak nama: authors list (link) ... Rangsangan akan mengaktifkan bagian promoter inti, segmen gen yang berfungsi sebagai pencerap RNA polimerase yang ...
UGT1A1 is associated with a TATA box promoter region; this region most commonly contains the genetic sequence A(TA)6TAA; this ... the most common of which results from adding another dinucleotide repeat TA to the promoter region, resulting in A(TA)7TAA, ... most commonly due to a polymorphism in the promoter region of the UGT1A1 gene". Journal of Hepatology. 33 (3): 348-351. doi: ... "Genetic variation in bilirubin UPD-glucuronosyltransferase gene promoter and Gilbert's syndrome". Lancet. 347 (9001): 578-81. ...
The complex binds to the promoter region to activate transcription, enhancing the creation of sucrose phosphorylase. ... Genetic regulation of sucrose phosphorylase is also performed by metabolites. Through experimentation it is known that genes ... Reid SJ, Abratt VR (May 2005). "Sucrose utilisation in bacteria: genetic organisation and regulation". Applied Microbiology and ...
Genetic sequences involved in gene regulation are typically found in the promoter regions of the eukaryotic genome. ... promoter regions and miscellaneous regions. The bioinformatic displayed a total of 148 H-DNA or triplet DNA possible structures ... Consequently, the promoter region has displayed the ability to form H-DNA with a higher frequency. A bioinformatic analysis of ... The promoter region accounted for the higher frequency with 71 triplate structures, while the exons accounted for 57 triplate ...
The 3′ coding region of mir-433 is also the promoter of the neighbouring miRNA gene: mir-127. The two genes overlap and are ... This is a method by which genetic information can be stored in a compact and efficient way. Mir-433, along with the other ... No such association was found between mir-433 variation and Parkinson's disease despite the fact that variation in the region ... A single nucleotide polymorphism (SNP) in the 3′ untranslated region (UTR) of HDAC6 was found to segregate with the ...
A genetic variation in the Kv1.3 promoter region is associated with low insulin sensitivity and impaired glucose tolerance. ... "Topology of the pore-region of a K + channel revealed by the NMR-derived structures of scorpion toxins". Neuron. 15 (5): 1169- ... "A family of three mouse potassium channel genes with intronless coding regions". Science. 247 (4945): 973-5. doi:10.1126/ ...
Genetically modified organism
The gene is then combined with other genetic elements, including a promoter and terminator region and a selectable marker. A ... Genetic engineers must isolate the gene they wish to insert into the host organism and combine it with other genetic elements, ... It was the first plant to be altered using genetic engineering and is considered a model organism for not only genetic ... With the advent of genetic engineering, new genetic changes can easily be introduced into these bacteria. Most food-producing ...
In addition, the Isoelectric Point of FAM149A is 9.891999 The following is an analysis of the promoter region for FAM149A. It ... shows a number of transcription factor binding sites that may have strong contribution to regulating the genetic expression. ... Here is the promoter for the FAM149A gene provided by ElDorado and the sequence extracted from the information. The following ... Only the dog contains what is considered as an Evolutionary Conserved Region (ECR). Based on the graphs on the right, the ...
Genetically modified animal
The gene is then combined with other genetic elements, including a promoter and terminator region and usually a selectable ... The genetic modification is an RNA molecule that prevents the virus reproduction by mimicking the region of the flu virus ... Genetic modification of the myxoma virus has been proposed to conserve European wild rabbits in the Iberian peninsula and to ... However, the genetic material will be stored at the Canadian Agricultural Genetics Repository Program. In 2006, a pig was ...
Therefore, genetic markers that are close to the region of interest in chromosome 6q24 can be selected. Chromosome duplication ... It was discovered that a differentially methylated region (DMR) is present within the shared promoter of these genes. Generally ... Different genetic inheritance or genetic mutations can lead to different diagnosis of NDM (Permanent or Transient Neonatal ... The prognosis can be confirmed with genetic analysis to find the genetic cause of the disease. With proper management, the ...
Transgenerational stress inheritance
Stress can also result in inheritable changes DNA methylation in the promoter regions of the estrogen receptor alpha (ERα), ... Small non-coding RNAs may serve as a potential mechanism for stress-related genetic changes in offspring. Mouse models of ... These heritable epigenetic modifications include DNA methylation of the promoter regions of genes that affect sensitivity to ... Evidence of decreased complexity in the CA1 and CA3 region of the hippocampus in terms of dendritic length and spine density ...
A genetic variant in the promoter region, A-161T, has been examined with respect to personality traits and showed no major ... Nöthen MM, Erdmann J, Shimron-Abarbanell D, Propping P (Dec 1994). "Identification of genetic variation in the human serotonin ... "Genetic diversity of the human serotonin receptor 1B (HTR1B) gene". Genomics. 72 (1): 1-14. doi:10.1006/geno.2000.6411. PMID ...
He was the author of the discovery of the genetic polymorphism of the promoter region of the gene of the leukotriene C4 ... He was the promoter of fourteen doctoral dissertations. He is a member of the Polish Society of Paediatrics (since 1986), the ... synthase; and he participated in establishing the relationship between genetic overexpression caused by the presence of the ...
The SV40 promoter was conventionally used until research showed that vectors driven by the Rous Sarcoma Virus (RSV) promoter ... These "genetic adjuvants" can be administered as a: mixture of 2 plasmids, one encoding the immunogen and the other encoding ... Accessory regions pertaining to the plasmid backbone may engage in a wide range of structural instability phenomena. Well-known ... The advantages of genetic adjuvants are their low cost and simple administration, as well as avoidance of unstable recombinant ...
A promoter is a region of DNA that facilitates transcription of a particular gene when a transcription factor binds to it. ... Promoters are typically located near the genes they regulate and upstream of them. A genetic insulator is a boundary element ... Ultimately genetic, evolutionary, and biochemical approaches can all be used in a complementary way to identify regions that ... Promoters facilitate the transcription of a particular gene and are typically upstream of the coding region. Enhancer sequences ...
... have been shown to be essential for the imprinting of genes in their corresponding regions. Differentially methylated regions ... The first imprinted genetic disorders to be described in humans were the reciprocally inherited Prader-Willi syndrome and ... Indeed, methylation loss at H19 imprinted gene has been observed associated with MTHFR gene promoter hypermethylation in semen ... Those regions which when inherited from a single parent result in a discernible phenotype contain imprinted gene(s). Further ...
To date all regulatory regions (promoters) and genes that have been examined in detail at the molecular level, have TRAM ... According to Dover, TRAM is a genetic system that has features of non-mendelian inheritance Turnover, copy number and ... Molecular drive is a term coined by Gabriel Dover in 1982 to describe evolutionary processes that change the genetic ... Molecular drive operates independently of natural selection and genetic drift. The best-known such process is the concerted ...
Vesicular monoamine transporter
Specifically, the SLC18A2 promoter region for the VMAT2 gene has been identified as an area where several polymorphisms form ... Studies using a genetic rodent model to understand clinical depression in humans suggest that VMAT2 genetic or functional ... Genetic research models have shown that polymorphisms in SLC18A1 and SLC18A2, the genes that encode for VMAT1 and 2 proteins ... VMAT gene sequence analysis demonstrates that 4 aspartic acid residues in the middle region of TMD I, VI, X, and XI and one ...
There is also alternative promoter region with about 900 bp between exon 3 and 4 suggesting that the fourth isoform might be ... The protein encoded by this gene interacts with calcineurin A and inhibits calcineurin-dependent signaling pathways of genetic ... Down syndrome critical region gene 1, also known as DSCR1, is a protein that in humans is encoded by the DSCR1 gene. RCAN1 is a ... "Entrez Gene: DSCR1 Down syndrome critical region gene 1". Arron JR, Winslow MM, Polleri A, Chang CP, Wu H, Gao X, et al. (June ...
Synechocystis sp. PCC 6803
Type I promoters consists of a consensus -35 and -10 region (Pribnow box) upstream of the gene start site. Heidorn et al. 2011 ... The iGem Registry hosts these promoter sequences as part of the BioBrick initiative to create interchangeable genetic parts. ... Several popular inducible promoters in E. coli are the pBad, pTet, and pLac promoters, all of which repress gene expression by ... Several such promoters were evaluated in Synechocystis sp. PCC6803 by Peca 2007. These promoters are not ideal, as metal ions ...
TFG-TEC binds to the proximal promoter region of the ENO3 gene. Click on genes, proteins and metabolites below to link to ... Advances in genetic testing, such as exome sequencing and specific gene panels, can provide greater access to diagnoses for ... The ENO3 gene spans 6 kb and contains 12 exons, though the first exon is an untranslated region and, thus, non-coding. This ... Upstream of the first exon lies a TATA-like box and CpG-rich region, which contains recognition motifs for binding ...
At the ends of the linear chromosomes are specialized regions of DNA called telomeres. The main function of these regions is to ... Genetic engineering. Further information: Molecular biology, Nucleic acid methods, and Genetic engineering ... Genes contain an open reading frame that can be transcribed, and regulatory sequences such as promoters and enhancers, which ... known collectively as the genetic code. The genetic code consists of three-letter 'words' called codons formed from a sequence ...
Epithelial cell adhesion molecule
... end of the EpCAM gene causes epigenetic inactivation of the MSH2 gene by hypermethylating the promoter region of the MSH2 gene ... A problem in EpCAM can indirectly cause Lynch syndrome, a genetic disorder that leads to increased risk of cancer. Deletion of ... Tomita N, Yamano T, Matsubara N, Tamura K (February 2013). "[A novel genetic disorder of Lynch syndrome - EPCAM gene deletion ...
Several genetic links to shyness are current areas of research. One is the serotonin transporter promoter region polymorphism ( ... Scientists believe that they have located genetic data supporting the hypothesis that shyness is, at least, partially genetic. ... "Relation of shyness in grade school children to the genotype for the long form of the serotonin transporter promoter region ... The long version of the 5-HTT gene-linked polymorphic region (5-HTTLPR) is now postulated to be correlated with shyness, but in ...
Golden Gate Cloning
Level 0 modules are the base for MoClo system, where they contain genetic elements like a promoter, a 5' untranslated region ( ... First-tier Golden Gate assembly constructs the single-gene construct by adding in genetic elements such as promoter, open ... In this process, one needs to make sure that the introduced mutation will not affect the genetic function encoded by the ... An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules". PLOS ONE. 6 (7): e21622. Bibcode:2011PLoSO ...
Chromosome 9 open reading frame 43
The promoter region of C9orf43 predicted by Genomatix ElDorado is 1199 base pairs long and contains a CpG island and part of ... C9orf43 has no known disease associations, however the polyglutamine repeat region is similar to genetic precursors in ... The 3' untranslated region of C9orf43 contains 3 predicted stem -loop structures with 4 miRNA predicted to bind. C9orf43 has ... An increase in the length of the polyglutamine repeat region is seen in diseases such as Huntington's disease and ...
Antisocial personality disorder
... such as the 2R and 3R alleles of the promoter region, have associations with aggressive behavior in men. The ... Genetic. Research into genetic associations in antisocial personality disorder is suggestive that ASPD has some or even a ... Twin studies, which are designed to discern between genetic and environmental effects, have reported significant genetic ... Genetic associations studies have suggested that the short "S" allele is associated with impulsive antisocial behavior and ASPD ...
Genetic determination. See also: Human genetic clustering. Eye color is an inherited trait influenced by more than one gene.[13 ... The same DNA sequence in the region of the OCA2 gene among blue-eyed people suggests they may have a single common ancestor.[44 ... which is hypothesized to interact with the OCA2 gene promoter, reduced expression of OCA2 with subsequent reduction in melanin ... 2007). "Genetic determinants of hair, eye and skin pigmentation in Europeans". Nat. Genet. 39 (12): 1443-52. doi:10.1038/ng. ...
Somatic evolution in cancer
Cytogenetic studies localized the region to the long arm of chromosome 13, and molecular genetic studies demonstrated that ... while in most cases the loss is due to methylation of its promoter region. Similarly, when loss of expression of the DNA ... Genetic heterogeneity in neoplasms. There are multiple levels of genetic heterogeneity associated with cancer, including ... This theory predicts a unique genetic composition in each neoplasm due to the random process of mutations, genetic ...
"Mobile Genetic Elements. 3 (4): e25845. doi:10.4161/mge.25845. PMC 3812789. PMID 24195014.. ... The inverted repeat regions are highly conserved among land plants, and accumulate few mutations. Similar inverted ... The two RNA polymerases may recognize and bind to different kinds of promoters within the chloroplast genome. The ribosomes ... It further contends that only a minority of the genetic material is kept in circular chromosomes while the rest is in branched ...
RNA polymerase II core promoter proximal region sequence-specific DNA binding. • steroid hormone receptor activity. • steroid ... "Genetic variation in the progesterone receptor gene and ovarian cancer risk". American Journal of Epidemiology. 161 (5): 442- ... transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding. • metal ion ... One promoter region polymorphism, +331G/A, creates a unique transcription start site. Biochemical assays showed that the +331G/ ...
Recent research projects carried out in the Museum have included studies on genetic markers for disease, facial reconstruction ... Lothian Region buses 3,5,7,8,14,29, 30, 31,33,37, 47, 49 to Nicolson Street. ...
perinuclear region of cytoplasm. • early endosome. • synaptic vesicle. • macromolecular complex. • sarcolemma. • synapse. • ... These rare genetic variants are autosomal dominant. Cancer. In addition to its role in Alzheimer's disease, ... negative regulation of transcription from RNA polymerase II promoter. • proteolysis. • regulation of synaptic plasticity. • ... negative regulation of core promoter binding. • negative regulation of low-density lipoprotein receptor activity. • positive ...
perinuclear region of cytoplasm. • chromatin. • condensed chromosome. • nuclear chromosome, telomeric region. • nucleus. • ... Methylation of the promoter of miR-34a, resulting in under-expression of miR-34a, is observed in 79% of prostate cancers and 63 ... "Genetic unmasking of an epigenetically silenced microRNA in human cancer cells". Cancer Res. 67 (4): 1424-9. doi:10.1158/0008- ... catalyses strand transfer between a broken sequence and its undamaged homologue to allow re-synthesis of the damaged region ( ...
Gene transfer and genetic exchangeEdit. Halobacterium volcanii, an extreme halophilic archaeon, forms cytoplasmic bridges ... and in the region of soil that surrounds plant roots (the rhizosphere). ... directing the binding of the RNA polymerase to a gene's promoter. However, other archaeal transcription factors are closer ... Current knowledge on genetic diversity is fragmentary and the total number of archaeal species cannot be estimated with any ...
One study found less than 30% of 1031 potential promoter regions contain a putative TATA box motif in humans. In Drosophila, ... Genetic engineering. TATA box modification. Evolutionary changes have pushed plants to adapt to the changing ... In bacteria, promoter regions may contain a Pribnow box, which serves an analogous purpose to the eukaryotic TATA box. The ... Mutations in maize promoters affect the expression of the promoter genes in a plant-organ-specific manner. A duplication of ...
H2BK123Ub occurs throughout transcribed regions, but this mark is required for COMPASS to trimethylate H3K4 at promoters.[ ... However, it is an excellent mark of active promoters and the level of this histone modification at a gene's promoter is broadly ... Another H2A variant H2A.X is phosphorylated at S139 in regions around double-strand breaks and marks the region undergoing DNA ... This trimethylation occurs at the promoter of active genes and is performed by the COMPASS complex. ...
2003). "HADHB, HuR, and CP1 bind to the distal 3'-untranslated region of human renin mRNA and differentially modulate renin ... large-scale identification and characterization of putative alternative promoters of human genes". Genome Res. 16 (1): 55-65. ... "Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression". PLoS ONE. 5 (9): e12862. doi:10.1371/ ... untranslated region of human renin mRNA and differentially modulate renin expression". The Journal of Biological Chemistry. 278 ...
Minor genetic variations are found consistently in different geographic areas; thus, genetic analysis of JC virus samples has ... It is thought that these differences in promoter sequence contribute to the fitness of the virus in the CNS and thus to the ... no mutations were found in the VP1 coding region, however, a 143 base-pair deletion was identified in the agnogene, coding for ... JCV found in the central nervous system of PML patients almost invariably have differences in promoter sequence to the JCV ...
FOXP2 - 维基百科，自由的百科全书
第二亚族（COUP-TF（英语：Chicken ovalbumin upstream promoter-transcription factor）（I、II）、Ear-2（英语：V-erbA-related gene）、HNF4（英语： ... 4.1） Rel homology region（英语：Rel homology domain）. NF-κB（NFKB1、NFKB2、REL、RELA、RELB） · NFAT（C1、C2、C3、C4、5） ... Gene information at Genetic Home Reference. *Language and Genetics Research at the Max Planck Institute for Psycholinguistics ...
L region is an untranslated leader region that gives the signal for packaging of the genome RNA. The 3' end includes 3 regions ... Gammaretroviral and lentiviral vectors for gene therapy have been developed that mediate stable genetic modification of treated ... The promoter of the provirus DNA can also cause over expression of regulatory genes. ... The 5' end includes four regions, which are R, U5, PBS, and L. The R region is a short repeated sequence at each end of the ...
"Genetic mosaics in animals and man". pp27-129, in Stern, C. Genetic Mosaics and Other Essays. Harvard University Press, ... The FLP gene can then be induced selectively, commonly using either the heat shock promoter or the GAL4/UAS system. The ... un-methylated regions in the genome. Further, the accumulation of DNA copy errors and damage over a lifetime lead to ... What does such genetic chimerism mean for health and disease?". The Scientist. Archived from the original on 25 April 2017. ...
OPN1LW - Википедија, слободна енциклопедија
1993). „Genetic heterogeneity among blue-cone monochromats.". Am. J. Hum. Genet. 53 (5): 987-1000. PMC 1682301 . PMID 8213841. ... Arveiler B, Vincent A, Mandel JL (1989). „Toward a physical map of the Xq28 region in man: linking color vision, G6PD, and ... 1994). „The human blue opsin promoter directs transgene expression in short-wave cones and bipolar cells in the mouse retina." ... coagulation factor VIII genes to an X-Y homology region.". Genomics. 4 (4): 460-71. PMID 2501212. doi:10.1016/0888-7543(89) ...
List of atheists in science and technology
She was a pioneer in the genetic analysis of bacteriophages and contributed to the early development of molecular biology. ... and pioneer of exobiology and promoter of the SETI. Although Sagan has been identified as an atheist according to some ... in the Afar Triangle region of Hadar, Ethiopia. ... Brenner made significant contributions to work on the genetic ... Hermann Joseph Muller (1890-1967): American geneticist and educator, best known for his work on the physiological and genetic ...
Quantitative genetics focuses on genetic variance due to genetic interactions. Any two locus interactions at a particular gene ... where an enhancer from one allele acts in trans to activate transcription from the promoter of the second allele. Alternately, ... adaptation can move proteins into more precarious or rugged regions of the fitness landscape. These shifting "fitness ... In this regression, the observed two locus genetic effects are treated as dependent variables and the "pure" genetic effects ...
This region has zero dispersion. The middle windows (S and C) around 1500 nm are the most widely used. This region has the ... In the late 1990s through 2000, industry promoters, and research companies such as KMI, and RHK predicted massive increases in ... Genetic engineering *Gene therapy. *Head transplant. *Isolated brain. *Life extension *Strategies for Engineered Negligible ... losses are high in this region so this window is used primarily for short-distance communications. The current lower windows (O ...
Of special interest is the CaMV 35S promoter, which is a very strong promoter most frequently used in plant transformations. ... The RNA carries genetic information to code for the production of new infectious particles. More recently virus research has ... untranslated regions of viral mRNA. Some viruses (e.g. tobacco mosaic virus (TMV)) have RNA sequences that contain a "leaky" ... Genetic and Structural Analyses of Pea Embryo Invasion by Pea Seed-Borne Mosaic Virus". The Plant Cell. 6: 777-787. doi:10.2307 ...
Epigenetics of neurodegenerative diseases
"Functional and sequence analysis of human neuroglobin gene promoter region". primary. Biochimica et Biophysica Acta. 1809 (4-6 ... Genetic cause. Spinal muscular atrophy is linked to genetic mutations in the SMN1 (Survival of Motor Neuron 1) gene. The ... SMN1 is located in a telomeric region of human chromosome 5 and also contains SMN2 in a centromeric region. SMN1 and SMN2 are ... has been observed in promoters of presenilin 1, GSK3beta, which phosphorylates tau protein, and BACE1, an enzyme ...
... proposes several transcriptional regulators for CASS4 based on its promoter region sequence: NF-κβ, p53, LCR-F1 (NFE2-L1, ... "Genetic determinants of disease progression in Alzheimer's disease". Journal of Alzheimer's Disease. 43 (2): 649-55. doi ... Identified S305 phosphorylation by PKA/PKG in the unstructured region containing SH2-binding sites of CASS4. ... The CASS4 C-terminus has a short region of CAS family homology, but lacks obvious similarity at the level of primary amino acid ...
Insulin-like growth factor 2
... along with Differentially-methylated Region-1 (DMR1) and Matrix Attachment Region −3 (MAR3). These three DNA sequences bind to ... CTCF can no longer bind to the insulator, and so the enhancer is now free to turn on the father's IGF2 promoter. ... regulation of gene expression by genetic imprinting. • skeletal system development. • cellular protein metabolic process. • ... extracellular region. • platelet alpha granule lumen. • extracellular. Biological process. • ...
Lamb MJ, Jablonka E (2005). Evolution in four dimensions: genetic, epigenetic, behavioral, and symbolic variation in the ... Gene expression can be controlled through the action of repressor proteins that attach to silencer regions of the DNA. These ... "Double strand breaks can initiate gene silencing and SIRT1-dependent onset of DNA methylation in an exogenous promoter CpG ... These are normal genetic diseases caused by gene deletions or inactivation of the genes, but are unusually common because ...
For example, it is likely that the methylation of lysine 9 on histone H3 (H3K9me3) in the promoter region of genes prevents ... It is now generally accepted that in addition to genetic aberrations, cancer can be initiated by epigenetic changes in which ... The pre-SET region contains cysteine residues that form triangular zinc clusters, tightly binding the zinc atoms and ... The SET domain itself contains a catalytic core rich in β-strands that, in turn, make up several regions of β-sheets. Often, ...
Single cell sequencing
When RRBS is applied to bulk samples, majority of the CpG sites in gene promoters are detected, but site in gene promoters only ... Single-cell resolution can uncover the roles of genetic mosaicism or intra-tumor genetic heterogeneity in cancer development or ... A transposase inserts sequencing adapters directly into open regions of chromatin, allowing those regions to be amplified and ... Single-nucleotide polymorphisms (SNPs), which are a big part of genetic variation in the human genome, and copy number ...
سرطان پروستات - ویکیپدیا، دانشنامهٔ آزاد
... this SNP is located in the promoter region of the MSMB gene, thus affects the amount of MSMB protein synthesized and secreted ... Genetic. Genetic background may contribute to prostate cancer risk, as suggested by associations with race, family, and ... The region of prostate gland where the adenocarcinoma is most common is the peripheral zone. Initially, small clumps of cancer ... "The case of scirrhous of the prostate gland with corresponding affliction of the lymphatic glands in the lumbar region and in ...
1996). "Molecular genetic analysis of the human Lewis histo-blood group system. II. Secretor gene inactivation by a novel ... Pang H, Soejima M, Koda Y, Kimura H (2005). "A novel tetrameric short tandem repeat located in the 3' flanking region of the ... large-scale identification and characterization of putative alternative promoters of human genes". Genome Res. 16 (1): 55-65. ... 1995). "Molecular cloning of a human genomic region containing the H blood group alpha(1,2)fucosyltransferase gene and two H ...
... and their coding sequence is grouped and regulated together in a regulatory region, containing a promoter and an operator. Most ... Messenger RNA (mRNA) is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they ... Coding regionsEdit. Main article: Coding region. Coding regions are composed of codons, which are decoded and translated (in ... and three prime untranslated region (3' UTR), respectively. These regions are transcribed with the coding region and thus are ...
Histidin amonijačna lijaza
1991). "Localization of histidase to human chromosome region 12q22----q24.1 and mouse chromosome region 10C2----D1.". Cytogenet ... 2010). "New genetic associations detected in a host response study to hepatitis B vaccine.". Genes Immun. 11 (3): 232-8. PMID ... 2005). "Regulation by glucagon of the rat histidase gene promoter in cultured rat hepatocytes and human hepatoblastoma cells ...
The gene promoter region of ALOX5 contains 8 GC boxes but lacks TATA boxes or CAT boxes and thus resembles the gene promoters ... These genetic studies allow that ALOX5 along with the chemotactic factors and SPMs that they contribute to making may play ... Homozygous variants for this five repeat promoter region in a study of 624 asthmatic children in Ankara, Turkey were much more ... a GC-rich core region including the Sp1/Egr-1 sites may be critical for basal 5-LO promoter activity. ...
Category:Genetic promoter regions - Wikimedia Commons
Promoter (vi); promoter region, genetic promoter region, Promoter Regions, Genetic, Promoter (genetics) (en); مروج, Promoters, ... "Genetic promoter regions" 분류에 속하는 미디어. 다음은 이 분류에 속하는 파일 120개 가운데 120개입니다. ... Promoter (id); promotor (nn); Promotor (nb); Promoter (sh); Promotor (oc); Promoter (hu); மரபணு தொடரிகள் (ta); پڕۆمۆتەر (ckb); ... 원본 주소 "https://commons.wikimedia.org/w/index.php?title=Category:Genetic_promoter_regions&oldid=325427430" ...
Genetic polymorphisms in promoter and intronic regions of CYP1A2 gene in Roma and Hungarian population samples. - PubMed - NCBI
Association of Genetic Variation in the Promoter Region of OXTR with Differences in Social Affective Neural Processing
... we investigated the effect of variation in the common functional rs2268498 T/C polymorphism in the promoter region of OXTR on ... These results indicate the impact of this OXTR genetic variant on individual differences in social affective neural processing. ... "Association of Genetic Variation in the Promoter Region of OXTR with Differences in Social Affective Neural Processing," ... we investigated the effect of variation in the common functional rs2268498 T/C polymorphism in the promoter region of OXTR on ...
Frontiers | Genetic basis of olfactory cognition: extremely high level of DNA sequence polymorphism in promoter regions of the...
The expression level of each gene is controlled by its regulatory regions, and especially, by the promoter [a region of DNA ... by the promoter (a region of DNA about 100-1000 base pairs long located upstream of the transcription start site). We analyzed ... data from the 1000 Genomes Project and revealed an extremely high level of single nucleotide polymorphisms in promoter regions ... data from the 1000 Genomes Project and revealed an extremely high level of single nucleotide polymorphisms in promoter regions ...
Association of Genetic Variation in the Promoter Region of OXTR with Differences in Social Affective Neural Processing
... and genetic variation in OXTR  on emotion processing in the amygdala and connected social brain regions . ... we investigated the effect of variation in the common functional rs2268498 T/C polymorphism in the promoter region of OXTR on ... parietal cortex and occipital regions (Pcorr < 0.01). For fear versus neutral activated regions were restricted to the right ... Effect of OXTR genetic variation at SNP rs- 2268498 during the emotion processing task. The T/T group (n = 14) had bilaterally ...
Genetic Polymorphism in the Serotonin Transporter Promoter Region and Ecological Success in Macaques | National Institute of...
Genetic Polymorphism in the Serotonin Transporter Promoter Region and Ecological Success in Macaques. Publication Type:. ... Home » Publication » Genetic Polymorphism in the Serotonin Transporter Promoter Region and Ecological Success in Macaques ... A well-characterised sequence length polymorphism in the serotonin transporter promoter region (5-HTTLPR) influences individual ...
Promoter Regions, Genetic | REACH
"Promoter Regions, Genetic" by people in this website by year, and whether "Promoter Regions, Genetic" was a major or minor ... "Promoter Regions, Genetic" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical ... Promoter Regions, Genetic*Promoter Regions, Genetic. *Genetic Promoter Region. *Genetic Promoter Regions ... Below are the most recent publications written about "Promoter Regions, Genetic" by people in Profiles. ...
Re-sequencing of the APOAI promoter region and the genetic association of the -75G | A polymorphism with increased cholesterol...
The aim of this study was to determine the genetic association of polymorphisms in the APOAI promoter region with plasma lipid ... A 435 bp region of the APOAI promoter was analyzed by re-sequencing in 549 Kuwaiti samples. DNA was extracted from blood taken ... The target sequence included a partial segment of the promoter region, 5UTR and exon 1 located between nucleotides −141 to + ... This study is the first to report sequence analysis of the APOAI promoter in an Arab population. The unexpected positive ...
Prevalence of genetic polymorphisms in the promoter region of the alpha-1 antitrypsin ( SERPINA1 ) gene in chronic liver...
The c.-1973T , C polymorphism located in the SERPINA1 promoter region is found more frequent in A1AT deficiency patients with ... Kok, K.F., te Morsche, R.H., van Oijen, M.G. et al. Prevalence of genetic polymorphisms in the promoter region of the alpha-1 ... Prevalence of genetic polymorphisms in the promoter region of the alpha-1 antitrypsin (SERPINA1) gene in chronic liver disease ... The c.-1973T , C polymorphism located in the SERPINA1 promoter region is found more frequent in A1AT deficiency patients with ...
Overproduced p73alpha activates a minimal promoter through a mechanism independent of its transcriptional activity
We and others showed that these splicing variants have different transcriptional effects on promoters with a p53-binding cons … ... Promoter Regions, Genetic* * Protein Binding * Protein Structure, Tertiary * RNA / metabolism * RNA, Messenger / metabolism ... Overproduced p73alpha activates a minimal promoter through a mechanism independent of its transcriptional activity FEBS Lett. ... We and others showed that these splicing variants have different transcriptional effects on promoters with a p53-binding ...
Functional and genetic characterization of the promoter region of apolipoprotein H (β<sub>2</sub>...
Functional and genetic characterization of the promoter region of apolipoprotein H (β2-glycoprotein I). FEBS Journal. 2010 Feb; ... Functional and genetic characterization of the promoter region of apolipoprotein H (β2-glycoprotein I). In: FEBS Journal. 2010 ... Functional and genetic characterization of the promoter region of apolipoprotein H (β2-glycoprotein I). / Suresh, Sangita; ... Functional and genetic characterization of the promoter region of apolipoprotein H (β2-glycoprotein I). ...
Induced expression of a Drosophila hsp70 promoter-fusion transgene is reduced after repeated heat shocks
... white transgene in Drosophila were measured after single and multiple heat shocks to determine whether the hsp70 promoter could ... Promoter Regions, Genetic / genetics* * Shock / genetics* Substances * Heat-Shock Proteins ... The hsp70 promoter is unsuitable for use in fusion gene constructs for long term expression studies where repeated heat shocks ... Induced expression of a Drosophila hsp70 promoter-fusion transgene is reduced after repeated heat shocks Genet Res. 1992 Jun;59 ...
For each of the following unbalanced reactions, suppose | bartleby
Promoter (genetics) - Wikipedia
Wikimedia Commons has media related to Genetic promoter regions.. *ORegAnno - Open Regulatory Annotation Database ... A promoter region is located before the -35 and -10 Consensus sequences. The closer the promoter region is to the consensus ... In genetics, a promoter is a region of DNA that initiates transcription of a particular gene. Promoters are located near the ... Although the term "bidirectional promoter" refers specifically to promoter regions of mRNA-encoding genes, luciferase assays ...
Genetic analysis of the promoter region of the GATA4 gene in patients with ventricular septal defects. - PubMed - NCBI
Genetic analysis of the promoter region of the GATA4 gene in patients with ventricular septal defects.. Wu G1, Shan J, Pang S, ... we hypothesized that the promoter region variants of the GATA4 gene may be genetic causes of VSD. In this study, we analyzed ... within the promoter region of the GATA gene were identified in 5 VSD patients, but in none of controls. One heterozygous ... our data suggest that these sequence variants within the promoter region of the GATA4 gene may contribute to the VSD etiology ...
Genetic dissection of the light-inducible carQRS promoter region of Myxococcus xanthus. - MRC Weatherall Institute of Molecular...
In order to elucidate regions with the promoter required for activity, point mutations were introduced into the carQRS promoter ... By mapping the extent of the promoter region, identifying sequences important for promoter activity, and highlighting potential ... The promoter-null point mutations and 6-bp deletion mutations implied that the carQRS promoter requires a functional gufA ... two changes enhanced promoter activity and two changes caused the mutant promoter to become constitutive and independent of ...
Plants | Free Full-Text | The Arabidopsis Plant Intracellular Ras-group LRR (PIRL) Family and the Value of Reverse Genetic...
Systematic reverse genetic analysis of this novel LRR family has therefore identified gametophytically active genes that ... otherwise would likely be missed by forward genetic screens. ... Promoter region (-272). a Mutant isolated from Wisconsin T-DNA ... Analysis of junction sites confirmed the position of the insertions in the first exon and the presumed promoter region, ... Forward genetic approaches have proven effective for identifying loci with gametophytic functions [1,2,3,4,5]. One strategy for ...
WUSCHEL is a primary target for t... preview & related info | Mendeley
... important role in ensuring proper development in higher eukaryotes by controlling accessibility of cis-regulatory DNA regions ... Promoter Regions, Genetic/genetics. *Reverse Transcriptase Polymerase Chain Reaction. *Sequence Analysis, DNA ... Using genetic and molecular analyses we have identified WUSCHEL (WUS) as a biologically important target of the SNF2-class ... We present evidence that SYD is recruited to the WUS promoter and that it is involved in regulation of the stem cell pool ...
Jun proteins modulate the ovary-specific promoter of aromatase gene in ovarian granulosa cells via a cAMP-responsive element.
Promoter Regions, Genetic*. Proto-Oncogene Proteins c-jun / genetics, metabolism*. Transcriptional Activation. ... Furthermore, chromatin immunoprecipitation indicated the presence of cJun at the proximal region of the native PII promoter. ... The Jun-mediated repression was specific to the aromatase promoter, as Jun proteins stimulated known AP1-responsive promoters ... in the PII promoter-proximal region. Alteration of the CRE-like site impaired both the cAMP-responsive transcriptional ...
A novel G-quadruplex-forming GGA repeat region in the c-myb promoter is a critical regulator of promoter activity.
The c-myb promoter contains multiple GGA repeats beginning 17 bp downstream of the transcription initiation site. GGA repeats ... Promoter Regions, Genetic*. Repressor Proteins / metabolism*. Transcription Factors / metabolism*. Trinucleotide Repeats. Grant ... Several G-quadruplex regions have been identified in promoters and shown to be critical for regulation of promoter activity. ... Deletion of GGA repeat region 1 or both regions 1 and 2 in the c-myb promoter increased relative luciferase activities by 3- to ...
Genetic polymorphisms in the locus control region and promoter of GH1 are related to serum IGF-I levels and height in patients...
Genetic polymorphisms in the locus control region and promoter of GH1 are related to serum IGF-I levels and height in patients ... and the highly polymorphic GH1 promoter. We analyzed GH1 LCR/promoter single nucleotide polymorphisms (SNPs) in patients with ... GH1 Promoter SNPs 6, 8 and 9 were associated with height and IGF-1 levels among patients, and SNPs 6 and 11 with height in ... In IGHD patients, promoter SNPs 6, 8 and 9 were associated with height and IGF-1 levels. In controls, SNPs 6 and 11 were ...
Study on the Promoter Region-149C＞T and-579G＞T Polymorphism of DNMT3B with Genetic Susceptibility to Esophageal Cancer of Han...
Study on the Promoter Region-149C＞T and-579G＞T Polymorphism of DNMT3B with Genetic Susceptibility to Esophageal Cancer of Han ... Study on the Promoter Region-149C＞T and-579G＞T Polymorphism of DNMT3B with Genetic Suscept ... promoter region single nucleo tide polymorphism (SNP)-149C？T and-579G？T with genetic susceptibility of esophageal cancer (EC) ... Conclusion The DNMT3B promoter region-149C？T and-579G？T were not associated with the genetic susceptibility of esophageal ...
Association of genetic variants in the promoter region of genes encoding p22phox (CYBA) and glutamate cysteine ligase catalytic...
Association of genetic variants in the promoter region of genes encoding p22phox (CYBA) and glutamate cysteine ligase catalytic ... at the promoter region of the CYBA and GCLC genes modulate the risk for decreased GFR in type 1 diabetes patients even after ... in the promoter region of three genes related to cellular redox balance: (1) -675 T → A in CYBA (unregistered), where the T ... Biochemical and genetic characterization of Italian subpopulation. Am Heart J. 2007, 154: 1123-1129. 10.1016/j.ahj.2007.07.029. ...
Genetic variants in the H2AFX promoter region are associated with risk of sporadic breast cancer in non-Hispanic white women...
Genetic variants in the H2AFX promoter region are associated with risk of sporadic breast cancer in non-Hispanic white women ... Genetic variants in the H2AFX promoter region are associated with risk of sporadic breast cancer in non-Hispanic white women ... in the H2AFX promoter region and 1057C , T [rs7350] in the 3 untranslated region (UTR)) in 467 patients with sporadic breast ... The histone protein family member X (H2AFX) is important in maintaining chromatin structure and genetic stability. Genetic ...
Characterization of a Novel Plant Promoter Specifically Induced by Heavy Metal and Identification of the Promoter Regions...
Genetic analysis of transgenic tobacco. Sterile T1 seeds were plated on MS medium supplemented with 200 μg/mL kanamycin. Two ... Identification of two promoter regions responsible for heavy metals. A, The sequence of the two promoter regions. Region I (− ... Two HMREs Lie in the −222/−147 Promoter Region. To test this, the 76-bp promoter fragment was subdivided into two pieces, one ... The wild-type region I, mutated region I, and region II were in the context of 35SΔ64 fused to GUS gene to construct pBMRE, ...
IL4R | Cancer Genetics Web
Genetic Predisposition. *Promoter Regions. *Linkage Disequilibrium. *Cytokines. *Case-Control Studies. *Receptors, ... BACKGROUND: Malignant B-cell clones are affected by both acquired genetic alterations and by inherited genetic variations ... Genetic determinants of UV-susceptibility in non-melanoma skin cancer.. PLoS One. 2011; 6(7):e20019 [PubMed] Free Access to ... Genetic variants in immunoregulatory genes and risk for childhood lymphomas.. Eur J Haematol. 2009; 83(4):334-42 [PubMed] ...
FLNC | Cancer Genetics Web
Hypermethylation at gene promoter regions is often associated with transcriptional silencing; however, expression of only 245 ... This pilot study was aimed to identify the genetic alteration in 100 bp upstream and downstream flanking regions in addition to ... Aberrant DNA methylation in the promoter regions of gene, which leads to inactivation of tumor suppressor and other cancer- ... PURPOSE: EBV-associated gastric carcinoma shows global CpG island methylation of the promoter region of various cancer-related ...
Comprehensive analysis of the MLH1 promoter region in 480 patients with colorectal cancer and 1150 controls reveals new...
Genetic susceptibility to non-polyposis colorectal cancer. J Med Genet 1999;36:801-18. ... MLH1 and EPM2AIP1 are bidirectionally paired genes with a shared promoter region. The core promoter region for MLH1 has been ... we searched for promoter variants in patients with CIMP tumours and controls. We sequenced the MLH1 promoter region at least up ... covering the MLH1 promoter until c.-667. With MS-MLPA kit ME011 (MRC Holland), the MLH1 promoter region from c.-659 to c.116+90 ...
Transcriptional regulation of Fcgr2b gene by polymorphic promoter region and its contribution to humoral immune responses. -...
We earlier found deletion polymorphism in the Fcgr2b promoter region among mouse strains in which systemic autoimmune disease- ... Although NZW- and BALB/c-derived segments from position -302 to +585 of Fcgr2b upstream region produced significant levels of ... Genetic contributions of nonautoimmune SWR mice toward lupus nephritis.. *Shangkui Xie, Sherman H Chang, +4 authors C. Mohan ... We earlier found deletion polymorphism in the Fcgr2b promoter region among mouse strains in which systemic autoimmune disease- ...
Analysis of the Corynebacterium diphtheriae DtxR Regulon: Identification of a Putative Siderophore Synthesis and Transport...
Any promoter activity in the intergenic regions would drive expression of the lacZ gene on plasmid pCM502. Promoter fusion ... Genetic organization of the yersiniabactin biosynthetic region and construction of avirulent mutants in Yersinia pestis. Infect ... An approximately 200-bp DNA fragment containing the tox promoter region was derived from plasmid pPOB (49), and the DNA ... Transcriptional analysis of the promoter regions in clones CD-3, CD-4, and CD7-4 indicated that they were not regulated by iron ...
GenesPolymorphismsGeneticsMethylationPolymorphismSequencesProteinsCharacterizationProximalKnown as promoter hypermethylationMutationsGenomeDeletionHypermethylationVariationNucleic AcidVariantVariants in the promoter regionNucleotideGene expressionTranscription Initiation SiteFused to the uidA reporter geneChromosomeEpigeneticMotifsMiceDownstreamHumansTissue specificityChromosomalAnalysisMolecularEnhanced promoter activityEnhancerPlasmidsAlterationFragmentsSporadicOperonBindsActivityRegulationMarkersGenetically ModifiedTranscriptional start siteRegulatoryMinimalExpressionSNPsRegulatorTATAIntergenicCharacterizeGenomic region
- We analyzed single nucleotide polymorphisms using human whole-genome data from the 1000 Genomes Project and revealed an extremely high level of single nucleotide polymorphisms in promoter regions of olfactory receptor genes and HLA genes. (frontiersin.org)
- Lactose is inhibiting the repressor, allowing the RNA polymerase to bind with the promoter and express the genes, which synthesize lactase. (wikipedia.org)
- Promoters are located near the transcription start sites of genes, on the same strand and upstream on the DNA (towards the 3' region of the anti-sense strand ). (wikipedia.org)
- Systematic reverse genetic analysis of this novel LRR family has therefore identified gametophytically active genes that otherwise would likely be missed by forward genetic screens. (mdpi.com)
- With a complete and well-annotated genome sequence and well-established genetic resources, Arabidopsis thaliana has proven a valuable model system for identifying genes with functions in gametophyte development. (mdpi.com)
- Open reading frames downstream from IRP1 and IRP6 encode homologs of ABC iron transport systems, and it was recently reported that genes downstream from the IRP6 promoter are involved in the uptake of the C. diphtheriae C7 siderophore corynebactin ( 35 ). (asm.org)
- Murine studies have linked TGF-β signaling to emphysema, and human genome-wide association studies (GWAS) studies of lung function and COPD have identified associated regions near genes in the TGF-β superfamily. (elifesciences.org)
- 2.2.12 Other genes and genetic systems in Bacillus stearothermophilus. (barnesandnoble.com)
- Transcriptional fusions to lacZ permitted the identification of three functional promoters corresponding to three transcriptional units for the structural genes and another promoter for the regulatory gene allR . (asm.org)
- For example, insertions near promoter regions, which are short segments of DNA that are used to initiate gene transcription (the synthesis of RNA from DNA), can lead to overactivity of genes. (britannica.com)
- Fur and its corepressor, Fe 2+ , inhibit the transcription of an array of genes that are crucial to iron-acquisition systems (e.g., siderophore synthesis and their uptake) by means of binding to a specific target sequence (Fur box) in their promoters. (pnas.org)
- In the cell nucleus, it seems that promoters are distributed preferentially at the edge of the chromosomal territories, likely for the co-expression of genes on different chromosomes. (wikipedia.org)
- In bread wheat ( Triticum aestivum L.), COs are mostly limited to subtelomeric regions of chromosomes, resulting in a substantial loss of breeding efficiency in the proximal regions, though these regions carry ∼60-70% of the genes. (genetics.org)
- These "islands" commonly occur in promoter regions of genes (regions where RNA polymerase binds to start transcription), which are located at the 5 ′ ("five prime") end of the genes. (encyclopedia.com)
- In fact, about 50 percent of all genes contain a CpG island in their promoter regions. (encyclopedia.com)
- They looked closely at the genomes of finch species and found that recombination was localized to the promoter regions of genes and highly conserved over millions of years. (sciencemag.org)
- Although, that numerous genes located in the SSC15 region of interest has been analysed for their effect on pig traits, this region is still highly curious. (springer.com)
- The single promoter controls the expression of both genes. (medlineplus.gov)
- The A-rich motif was preferentially associated with promoters while the CCN-repeat and the CTT-repeat motifs were preferentially associated with genes. (weizmann.ac.il)
- In a large case control study of Gambian children, a genetic variant of the TNF-[alpha] gene promoter region was found to have a relative risk of seven for death or severe neurological sequels due to severe malaria, suggesting that regulatory polymorphisms of cytokine genes affect the outcome of severe infection . (thefreelibrary.com)
- Here, we describe an algorithm, Local Distribution of Short Sequences for Prokaryotes (LDSS-P), to identify conserved short motifs located at specific positions in the promoters of co-expressed prokaryotic genes. (stanford.edu)
- Comparative population analysis suggested that genomic regions harboring energy- and reproduction-associated genes are probably under selection in cultivated citrus. (nature.com)
- We also narrowed the genetic locus responsible for citrus polyembryony, a form of apomixis, to an 80-kb region containing 11 candidate genes. (nature.com)
- Exist a possible therapeutic effect of PUFAs on the prevention and development of obesity due to their ability to reversively modify the methylation of the promoters of genes associated with lipid metabolism and to modulate the activity of certain microRNAs. (elsevier.es)
- To date, most genetic progress for quantitative traits in livestock, especially for dairy cows has been made by selection on phenotype or on estimated breeding values (EBV) derived from phenotype, without knowledge of the number of genes that affect the trait or the effects of each gene. (intechopen.com)
- Molecular genetics allows for the study the genetic make-up of individuals at the DNA level and may provide the tools to make those opportunities a reality, either by direct selection on genes that affect traits of interest major genes or quantitative trait loci (QTL) - or through selection on genetic markers linked to QTL. (intechopen.com)
- We hypothesized that common genetic variation in the proximal promoter regions of transporter genes contribute to observed variation in drug response. (mendeley.com)
- Traditional molecular techniques have been used in research in discovering the genes and enzymes that are involved in aflatoxin formation and genetic regulation. (mdpi.com)
- Genetic engineering, also called genetic modification or genetic manipulation, is the direct manipulation of an organism's genes using biotechnology. (wikipedia.org)
- It is a set of technologies used to change the genetic makeup of cells, including the transfer of genes within and across species boundaries to produce improved or novel organisms. (wikipedia.org)
- Genetic polymorphisms in promoter and intronic regions of CYP1A2 gene in Roma and Hungarian population samples. (nih.gov)
- We hypothesized that the high level of polymorphisms in olfactory receptor promoters was responsible for the diversity in regulatory mechanisms controlling the expression levels of olfactory receptor proteins. (frontiersin.org)
- The aim of this study was to determine the genetic association of polymorphisms in the APOAI promoter region with plasma lipid levels in a cohort of healthy Kuwaiti volunteers. (biomedcentral.com)
- Therefore, we believe that H2AFX promoter polymorphisms may contribute to the etiology of sporadic breast cancer in young non-Hispanic white women. (duke.edu)
- Objectives To explore the functional basis for the association between ankylosing spondylitis (AS) and single-nucleotide polymorphisms (SNPs) in the IL23R - IL12RB2 intergenic region. (bmj.com)
- Two common genetic polymorphisms have been linked to the neuroadaptive impact of Δ9-tetrahydrocannabinol (THC) exposure and to executive functions in animals: the catechol-O-methyltransferase ( COMT ) gene val158met polymorphism and the SLC6A4 gene 5-HTTLPR polymorphism. (nature.com)
- An organized collection of information is provided regarding genetic polymorphisms that have been identified to influence the risk of developing IVDD. (frontiersin.org)
- Pharmacogenetic studies on the discovery of novel human genetic polymorphisms, their functional significance and their relationship to outcome of drug therapy, susceptibility to adverse drug reactions and susceptibility to complex diseases. (ncl.ac.uk)
- This finding of the HSPB7 gene from a genetic search for idiopathic DCM using a large SNP panel underscores the influence of common polymorphisms on DCM susceptibility. (plos.org)
- A total of 579 polymorphisms were identified in the proximal promoters (-250 to +50 bp) and flanking 5' sequence of 107 transporters in the ATP Binding Cassette (ABC) and Solute Carrier (SLC) superfamilies in 272 DNA samples from ethnically diverse populations. (mendeley.com)
- Many transporter promoters contained multiple common polymorphisms. (mendeley.com)
- To test this hypothesis, we studied genetic polymorphisms in the inflammation pathway in relation to lung cancer risk. (aacrjournals.org)
- In genetics , a promoter is a region of DNA that initiates transcription of a particular gene . (wikipedia.org)
- In genetics , a promoter is a sequence of DNA to which proteins bind that initiate transcription of a single RNA from the DNA downstream of it. (wikipedia.org)
- They neither teach molecular genetics nor provide an exhaustive review of the current state of the art of molecular and genetic cardiology relevant to arrhythmias. (ahajournals.org)
- The diagnosis value of promoter methylation of UCHL1 in the serum for progression of gastric cancer. (cancerindex.org)
- Aberrant promoter methylation has been considered as a potential molecular marker for gastric cancer (GC). (cancerindex.org)
- The promoter methylation status of UCHL1, FLNC, THBS1, and DLEC1 was assessed by quantitative methylation-specific PCR (QMSP) in the serum of 82 GC patients, 46 chronic atrophic gastritis (CAG) subjects, and 40 healthy controls. (cancerindex.org)
- The promoter methylation degree of FLNC, THBS1, UCHL1, and DLEC1 in serum could tell the existence of GC and only UCHL1 in the serum was also associated with poor prognosis of GC. (cancerindex.org)
- This abnormal MLH1 promoter methylation is not hereditary when arising de novo, whereas a stably heritable and variant-induced CEM was described for one single allele. (bmj.com)
- We searched for MLH1 promoter variants causing a germline or somatic methylation induction or transcriptional repression. (bmj.com)
- One novel, complex MLH1 variant c.-63_-58delins18 is present in a patient with CRC with CEM and his sister, both showing a complete allele-specific promoter methylation and transcriptional silencing. (bmj.com)
- The other nine promoter variants detected in 17 individuals were not associated with methylation. (bmj.com)
- 2 3 In the rare condition of a constitutional epimutation of MLH1 (CEM), an abnormal MLH1 promoter methylation in all somatic tissues epigenetically causes a functional MLH1 defect. (bmj.com)
- 4-7 In addition to germline defects, the group of patients with MSI-H tumours lacking MLH1 protein staining also includes a substantial number of sporadic CRC cases showing CpG-island methylator-phenotype (CIMP) and at least partial biallelic MLH1 promoter methylation in tumour tissue only. (bmj.com)
- Genome-wide mapping of histone modifications and mass spectrometry reveal H4 acetylation bias and H3K36 methylation at gene promoters in fission yeast. (nextbio.com)
- Tronche F, Rollier A, Bach I, Weiss MC, Yaniv M. The rat albumin promoter: cooperation with upstream elements is required when binding of APF/HNF1 to the proximal element is partially impaired by mutation or bacterial methylation. (umassmed.edu)
- While methylation in eukaryotes does not mark DNA for digestion, methylation can inactivate a promoter and thereby silence gene expression from a viral promoter. (encyclopedia.com)
- In addition to silencing gene expression from foreign DNA promoters, methylation has also been shown to prevent DNA sequences such as transposons from moving to a new site in the DNA. (encyclopedia.com)
- Impact of the genome on the epigenome is manifested in DNA methylation patterns of imprinted regions in monozygotic and dizygotic twins. (edu.au)
- In this study, we investigated the correlation between OPN mRNA and its promoter methylation changes by the 5-aza-dc treatment in fibroblast cell and promoter assay. (hindawi.com)
- Aberrant methylation of porcine OPN was frequently found in different tissues of somatic nuclear transferred cloning pigs, and bisulfite sequence data suggested that the OPN promoter region −2615 to −2239 nucleotides (nt) may be a crucial regulation DNA element. (hindawi.com)
- These data suggested that methylation in the OPN promoter plays a crucial role in the regulation of OPN expression that we found in cloned pigs genome. (hindawi.com)
- Aberrant promoter methylation is frequently observed in different types of lung cancer. (aacrjournals.org)
- We used a novel quantitative DNA methylation analysis technology to complete a large-scale cytosine methylation profiling study involving 47 gene promoter regions in 96 lung cancer patients. (aacrjournals.org)
- Hence, large-scale studies that evaluate quantitative methylation for multiple CpG sites in various gene regions and a large number of samples are rare. (aacrjournals.org)
- Promoter Methylation of p16 Gene in Cervical Cancer. (koreamed.org)
- It is an epigenetic process that involves DNA methylation and histone methylation without altering the genetic sequence. (wikipedia.org)
- Motivated by recent work, we investigated the effect of variation in the common functional rs2268498 T/C polymorphism in the promoter region of OXTR on neural responses to fear expressions. (scirp.org)
- A well-characterised sequence length polymorphism in the serotonin transporter promoter region (5-HTTLPR) influences individual behavioural traits and cognitive abilities in humans and rhesus macaques. (nias.res.in)
- C polymorphism located in the SERPINA1 promoter region is found more frequent in A1AT deficiency patients with liver disease compared to patients with pulmonary disease, but data are lacking regarding contribution to the development of liver diseases caused by other aetiologies. (biomedcentral.com)
- Objective To investigate the association of DNA methyltransfcrase 3B (DNMT3B) promoter region single nucleo tide polymorphism (SNP)-149C？T and-579G？T with genetic susceptibility of esophageal cancer (EC) of Han population in Jiangsu Suqian. (bvsalud.org)
- Genetic regulation of birth weight and fasting glucose by a common polymorphism in the islet cell promoter of the glucokinase gene. (diva-portal.org)
- Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes. (sickkids.ca)
- By mapping the extent of the promoter region, identifying sequences important for promoter activity, and highlighting potential topological effects, we provide a foundation for further analysis of the carQRS promoter. (ox.ac.uk)
- Promoters contain specific DNA sequences such as response elements that provide a secure initial binding site for RNA polymerase and for proteins called transcription factors that recruit RNA polymerase. (wikipedia.org)
- These transcription factors have specific activator or repressor sequences of corresponding nucleotides that attach to specific promoters and regulate gene expression. (wikipedia.org)
- The above consensus sequences, while conserved on average, are not found intact in most promoters. (wikipedia.org)
- Electrophoretic mobility shift assays indicated that DtxR was able to bind to DNA fragments carrying the 19-bp operator regions, and transcriptional analysis of putative promoter elements adjacent to the binding site sequences revealed that most of these regions displayed iron- and DtxR-regulated activity. (asm.org)
- analyzed the genetic sequences of TGFB2 from patients with emphysema and compared them to those from healthy individuals. (elifesciences.org)
- 2.2.8 Promoter regions and other control sequences in Thermus. (barnesandnoble.com)
- The nucleotide sequences of ryhB , its promoter (i.e., -35 and -10), and its operator (i.e. (pnas.org)
- Promoter regions are indicated by white boxes, while protein coding sequences are indicated by colored boxes. (pnas.org)
- Expression of phospholipases and promoter sequences of smase from clinical isolates and ATCC strains of B. cereus.A) 50% Ammonium sulfate precipitation fractions of the culture supernatants (1.0 mg protein) were subjected to SDS-PAGE and Western blotting using anti-Bc-SMase, -PCPLC, and -PIPLC antibodies. (nih.gov)
- B, C) The sequences of the promoter region of plc and smase from clinical isolates and ATCC strains of B. cereus were aligned by the program T-Coffee . (nih.gov)
- Identifying functional elements in promoter sequences is a major goal in computational and experimental genome biology. (stanford.edu)
- A promoter is induced in response to changes in abundance or conformation of regulatory proteins in a cell, which enable activating transcription factors to recruit RNA polymerase. (wikipedia.org)
- Jun proteins modulate the ovary-specific promoter of aromatase gene in ovarian granulosa cells via a cAMP-responsive element. (biomedsearch.com)
- Ectopic expression of the Jun proteins in a human granulosa cell line significantly inhibited an ovary-specific promoter (PII) of the aromatase gene, whereas expression of dominant-negative mutants of Jun led to increased promoter activity. (biomedsearch.com)
- The Jun-mediated repression was specific to the aromatase promoter, as Jun proteins stimulated known AP1-responsive promoters in the same cellular context. (biomedsearch.com)
- Electrophoretic gel mobility assay showed that endogenous Jun proteins bound to a functionally important cAMP-responsive element (CRE) in the PII promoter-proximal region. (biomedsearch.com)
- The third part of the article reviews the potential for a genetic approach to understanding diversity in cardiac function, focusing in particular on ion channels and gap junction proteins as the central players in normal and abnormal electrophysiology. (ahajournals.org)
- The first company to focus on genetic engineering, Genentech, was founded in 1976 and started the production of human proteins. (wikipedia.org)
- Since lipid levels may be under genetic control [ 2 , 5 ], the identification and characterization of genetic variants associated with plasma concentrations may provide some insight into the genotype-phenotype relationship [ 3 ] and allow for lifestyle adjustments to improve health. (biomedcentral.com)
- Since multiple cell types contribute to emphysema, large-scale functional annotation projects such as the Genotype-Tissue Expression Project (GTEx) ( GTEx Consortium, 2015 ) and the Encyclopedia of Regulatory Elements (ENCODE) ( ENCODE Project Consortium, 2012 ) can be integrated with GWAS signals to identify candidate regulatory regions, tissues, and cell types of interest for more detailed functional characterization. (elifesciences.org)
- Genetic characterization and evolutionary inference of TNF-[alpha] through computational analysis. (thefreelibrary.com)
- In this study, we report the characterization of the minimal promoter of the MC4R gene and the search for sequence variants in the MC4R promoter associated with human obesity. (diabetesjournals.org)
- 4 ), the lack of consistent findings emphasizes the need for comprehensive characterization of the genetic variation in and around the ADIPOQ gene. (diabetesjournals.org)
- Furthermore, chromatin immunoprecipitation indicated the presence of cJun at the proximal region of the native PII promoter. (biomedsearch.com)
- Alignment of human and mouse proximal promoter. (diabetesjournals.org)
- Genetic variation in the proximal. (mendeley.com)
- The proximal promoters of transporters that were highly expressed in the liver had greater nucleotide diversity than those that were highly expressed in the kidney consistent with greater negative selective pressure on the promoters of kidney transporters. (mendeley.com)
- Collectively, these results suggest that the proximal promoter region of membrane transporters is rich in variation and that variants in these regions may play a role in interindividual variation in drug disposition and response. (mendeley.com)
Known as promoter hypermethylation2
- In order to elucidate regions with the promoter required for activity, point mutations were introduced into the carQRS promoter between positions -151 and 6. (ox.ac.uk)
- The promoter-null point mutations and 6-bp deletion mutations implied that the carQRS promoter requires a functional gufA promoter for transcriptional activity and vice versa. (ox.ac.uk)
- Mutations in the coding region of the GATA4 gene have been identified in CHD patients, including VSD. (cdc.gov)
- As an example, if someone has genetic mutations that alter the activity of a gene called TGFB2 , their risk of developing emphysema increases. (elifesciences.org)
- However, the specific genetic mutations that modify the activity of TGFB2 were previously unknown. (elifesciences.org)
- The aim of the present study was to analyse the effect of PLCD4, PECR, FN1 and PNKD mutations on pig productive traits and tested the usefulness of targeted enrichment DNA sequencing method as tool for preselection of genetic markers. (springer.com)
- Less commonly, individuals with SDHC gene mutations or promoter hypermethylation develop only GIST or a different combination of tumors. (medlineplus.gov)
- Heterozygous mutations in the coding sequence of the serpentine melanocortin 4 receptor (MC4R) are the most frequent genetic cause of severe human obesity. (diabetesjournals.org)
- Since haploinsufficiency has been proposed as a causal mechanism of obesity associated with these mutations, reduction in gene transcription caused by mutations in the transcriptionally essential regions of the MC4R promoter may also be a cause of severe obesity in humans. (diabetesjournals.org)
- Systematic screening of 431 obese children and adults for mutations in the coding sequence and the minimal core promoter of MC4R reveals that genetic variation in the transcriptionally essential region of the MC4R promoter is not a significant cause of severe obesity in humans. (diabetesjournals.org)
- Heterozygous mutations in the coding region of the melanocortin 4 receptor ( MC4R ) gene are the cause of 1-6% of severe early-onset obesity cases ( 3 - 10 ). (diabetesjournals.org)
- Under this assumption, reduced gene transcription caused by mutations in essential regions of the MC4R promoter could also be a cause of obesity in humans. (diabetesjournals.org)
- The minimal promoter of the human MC4R has not been delineated, and the search for genetic variants associated with obesity at the MC4R locus has so far been limited to coding mutations. (diabetesjournals.org)
- The Jackson Laboratory has rigorous genetic quality control and mutant gene genotyping programs to ensure the genetic background of JAX® Mice strains as well as the genotypes of strains with identified molecular mutations. (jax.org)
- Human Genome Epidemiology:A Scientific Foundation for Using Genetic Information To Improve Health and Prevent Disease. (epa.gov)
- The whole genome sequence database in the public domain (www.ensembl.org) provides an opportunity to look for the genetic architecture of this gene. (thefreelibrary.com)
- Using a starter line selected for detailed analysis, the efficiency of tagging over a 50-kb region in the genome was examined. (plantphysiol.org)
- Deletion analysis of p73alpha revealed that the transactivation domain of p73 was not involved in this activity and the C-terminal region of p73alpha which is a specific structure of this variant was essential, suggesting that this phenomenon occurs independent of the transactivation activity of p73alpha and that the C-terminal extension of p73alpha may affect the basal level of transcription. (nih.gov)
- Deletion analysis localized the core APOH promoter to ∼ 160 bp upstream of ATG codon with the presence of critical cis-acting elements between -166 and -65. (northwestern.edu)
- deletion) within the promoter region of the GATA gene were identified in 5 VSD patients, but in none of controls. (cdc.gov)
- deletion) were increased significantly compared with the wild-type GATA4 gene promoter. (cdc.gov)
- Deletion of one or two (GGA)(4) motifs destabilizes this secondary structure and increases c-myb promoter activity, indicating that the G-quadruplexes formed in the c-myb GGA repeat region may act as a negative regulator of the c-myb promoter. (biomedsearch.com)
- Complete deletion of the c-myb GGA repeat region abolishes c-myb promoter activity, indicating dual roles of the c-myb GGA repeat element as both a transcriptional repressor and an activator. (biomedsearch.com)
- Using chromatin conformation capture, we confirmed that the region containing rs1690789 contacts the TGFB2 promoter in fibroblasts, and CRISPR/Cas-9 targeted deletion of a ~ 100 bp region containing rs1690789 resulted in decreased TGFB2 expression in primary human lung fibroblasts. (elifesciences.org)
- Hypermethylation occurs when too many small molecules called methyl groups are attached to the promoter region. (medlineplus.gov)
- A single change impairing the SDHC gene, either promoter hypermethylation or a germline mutation, increases the risk that an individual will develop a tumor. (medlineplus.gov)
- Some people with GIST inherit a germline mutation in one copy of the gene and have promoter hypermethylation affecting the other copy. (medlineplus.gov)
- Other affected individuals have promoter hypermethylation affecting both copies of the SDHC gene. (medlineplus.gov)
- These data provide novel mechanistic evidence linking genetic variation affecting the TGF-β pathway to emphysema in humans. (elifesciences.org)
- To test this hypothesis we defined the minimal promoter region of the human MC4R and evaluated the extent of genetic variation in this region compared with the coding region in two cohorts of severely obese subjects. (diabetesjournals.org)
- This relies on recombinant nucleic acid techniques to form new combinations of heritable genetic material followed by the incorporation of that material either indirectly through a vector system or directly through micro-injection, macro-injection or micro-encapsulation. (wikipedia.org)
- These results indicate the impact of this OXTR genetic variant on individual differences in social affective neural processing. (scirp.org)
- A, was found in one VSD patient, but in none of controls, which significantly inhibited the transcriptional activities of TBX20 gene promoter, suggesting that the variant may contribute to the VSD etiology. (cdc.gov)
- Conclusion We report the second promoter variant stably inducing a hereditary CEM. (bmj.com)
- This view rests on biased gene conversion, in which the broken chromosome copies genetic information from its uncut homolog and may generate an extra copy of a genetic variant ( Fig. 1A ). (sciencemag.org)
Variants in the promoter region1
- Investigation of variants in the promoter region of PIK3C3 in schizophrenia. (sigmaaldrich.com)
- Using a sliding window analysis, we observed that, on average, nucleotide diversity (pi) was lowest at approximately 300 bp upstream of the transcription start site, suggesting that this region may harbor important functional elements. (mendeley.com)
- Greater nucleotide diversity was observed in promoters with strong activity compared to promoters with weak activity, suggesting that weak promoters are under more negative selective pressure than promoters with high activity. (mendeley.com)
- As GATA4 is a dosage-sensitive regulator during development, our data suggest that these sequence variants within the promoter region of the GATA4 gene may contribute to the VSD etiology by altering its gene expression. (cdc.gov)
- Defective Fc gamma RII gene expression in macrophages of NOD mice: genetic linkage with up-regulation of IgG1 and IgG2b in serum. (semanticscholar.org)
Transcription Initiation Site1
- The c-myb promoter contains multiple GGA repeats beginning 17 bp downstream of the transcription initiation site. (biomedsearch.com)
Fused to the uidA reporter gene3
- Promoter fragments extending to −1068, −388, −210 or −124 upstream of the translation initiation ATG codon and the sequence coding for the first 13 amino acids of the puroindoline-b, were translationally fused to the uidA reporter gene encoding β-glucuronidase and transferred to rice calli via particle bombardment-mediated transformation. (deepdyve.com)
- The 1068 bp and 124 bp promoters were also transcriptionally fused to the uidA reporter gene. (deepdyve.com)
- Finally, the hybrid aspen PttRPS18 promoter was fused to the uidA reporter gene and transformed into hybrid aspen plants. (deepdyve.com)
- The target sequence included a partial segment of the promoter region, 5'UTR and exon 1 located between nucleotides −141 to +294 upstream of the APOAI gene on chromosome 11. (biomedcentral.com)
-  Furthermore, in humans, promoters show certain structural features characteristic for each chromosome. (wikipedia.org)
- DNA double-strand breaks (DSBs) generated by the Spo11 protein initiate meiotic recombination, which alters genetic linkage and promotes pairing and accurate chromosome segregation ( 1 ). (sciencemag.org)
- The potential genetic markers for pig productive traits were identified by using targeted enrichment DNA sequencing of chromosome 15 region that is QTL-rich. (springer.com)
- In pigs, chromosome 15 contains a region between the microsatellites SW1683 and SW906 (79.3-89.3 cM, 127-135 Mbp) which is highly rich in QTLs associated with meat quality, fat content and growth traits. (springer.com)
- Meiotic recombination rates are highly non-uniform along the chromosome, being very low around centromeres and variable in distal chromosomal regions. (weizmann.ac.il)
- We selected for this study the A. thaliana ABI1-Rps2-Ck1 segment on chromosome 4, which, according to previous comparative genetic mapping, is structurally conserved in Brassica species ( S adowski and Q uiros 1998 ). (genetics.org)
- These mice have the Ple17-lacZ transgene targeted as a single copy "knockin" into the upstream region of the Hprt locus on the X chromosome. (jax.org)
- Methods We performed conditional analysis on genetic association data and used epigenetic data on chromatin remodelling and transcription factor (TF) binding to identify the primary AS-associated IL23R-IL12RB2 intergenic SNP. (bmj.com)
- PTEN promoter silencing and Cowden syndrome: the role of epigenetic regulation of KILLIN. (medlineplus.gov)
- Meiotic recombination occurs in the context of chromatin, therefore we investigated both genetic and epigenetic factors that affect this process. (weizmann.ac.il)
- In order to understand what are the genetic and epigenetic features that characterize a crossover event. (weizmann.ac.il)
- The resulting 5272 TF-target interactions revealed extensive changes in the pattern of promoter binding and identified damage-specific binding motifs. (nih.gov)
- Three DNA motifs enriched in crossover regions and less abundant in crossover-poor pericentric regions were identified. (weizmann.ac.il)
- The promoter region contains various transcription factor binding motifs with numerous CpG dinucleotides. (hindawi.com)
- Apes and mice have a specific gene, PRDM9 , that is associated with genomic regions with high rates of recombination, called hotspots. (sciencemag.org)
- We performed the largest GWAS of emphysema patterns to date, identifying 10 GWAS loci including an association peak spanning a 200 kb region downstream from TGFB2 . (elifesciences.org)
- derived from a portion of the promoter of the C8ORF46 gene and three downstream putative regulatory elements from the RIKEN cDNA 3110035E14 (C8ORF46) gene) upstream of a frt-flanked beta-galactosidase (lacZ) gene, an SV40 early polyA signal, and a human HPRT complementary sequence (containing exon1, intron1, exon2, and part of intron2). (jax.org)
- With this background in mind, we conducted a fine-mapping study of ADIPOQ , including regulatory regions upstream and downstream of the gene. (diabetesjournals.org)
- The dual nature of TNF-[alpha] in humans thus raises a challenge in evolutionary research to understand whether this dual nature is an intrinsic property of human TNF-[alpha] or if a similar genetic nature also occurs in related taxa. (thefreelibrary.com)
- Genetic engineering could potentially fix severe genetic disorders in humans by replacing the defective gene with a functioning one. (wikipedia.org)
- Theoretically, hotspots-favored sites of recombination initiation-either evolve rapidly toward extinction or are conserved, especially if they are chromosomal features under selective constraint, such as promoters. (sciencemag.org)
- Meiotic recombination impacts the evolution of organisms by generating a new genetic diversity through the shuffling of alleles via crossover (reciprocal exchange of large chromosomal segments) or gene conversion (Non-reciprocal exchange of small chromosomal segments). (weizmann.ac.il)
- The chromosomal regions flanking the T-DNA were cloned by plasmid rescue. (deepdyve.com)
- A 757 bp DNA fragment, originating from the rescued plasmid and covering the genomic region immediately upstream from the right-border sequence of the T-DNA, was used as a probe to isolate the corresponding chromosomal region from a wild-type hybrid aspen genomic library. (deepdyve.com)
- Comparative sequencing revealed microsyntenic changes resulting from chromosomal structural rearrangements, which are often undetectable by genetic mapping. (genetics.org)
- Adiponectin is encoded by the gene ADIPOQ located in the chromosomal region 3q27. (diabetesjournals.org)
- This study is the first to report sequence analysis of the APOAI promoter in an Arab population. (biomedcentral.com)
- Cross-species conservation analysis of the APOH promoters of seven species indicated that basic promoter elements are highly conserved across species. (northwestern.edu)
- Genetic analysis of the TBX20 gene promoter region in patients with ventricular septal defects. (cdc.gov)
- Detailed analysis of this 76-bp fragment indicated that heavy metal-responsive elements were localized in two regions (−222/−188 and −187/−147), each of which could separately confer heavy metal-responsive expression on the β -glucuronidase gene in the context of a minimal cauliflower mosaic virus 35S promoter. (plantphysiol.org)
- In particular, PL models allow the analysis of the qualitative dynamics of the network using only weak information on the ordering of parameters rather than their exact numerical values.We illustrate the use of these techniques, implemented in the computer tool Genetic Network Analyzer (GNA), in the case of the E. coli network. (springer.com)
- Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli . (springer.com)
- Symbolic reachability analysis of genetic regulatory networks using discrete abstractions. (springer.com)
- Cloning of a wheat puroindoline gene promoter by IPCR and analysis of promoter regions required. (deepdyve.com)
- Analysis of 5′ promoter deletions identified the region between −388 and −210 as essential for endosperm expression, and the region between −210 and −124 as essential for expression in the epithelium of the scutellum. (deepdyve.com)
- Northern analysis revealed that the PttRPS18 gene was expressed mainly in the cambial region. (deepdyve.com)
- Histochemical analysis of GUS activity showed that the PttRPS18promoter was expressed in the cambial region in the same manner as the luciferase reporter gene in the initial screening. (deepdyve.com)
- 5′RACE followed by functional promoter analysis in multiple cell lines indicates that an 80-bp region is essential for the transcriptional activity of the MC4R promoter. (diabetesjournals.org)
- Research topic: Genetic analysis of the nutritional source-dependent regulation of a sporulation gene, spoVG, in the Gram-positive soil bacterium, Bacillus subtilis. (cameron.edu)
- Research interest: Genetic analysis of the cholinergic nervous system in the soil nematode, Caenorhabditis elegans. (cameron.edu)
- 1991. Analysis of the upstream activating sequence and site of carbon and nitrogen source repression in the promoter of an early induced sporulation gene of Bacillus subtilis. (cameron.edu)
- Additional studies in experimental animals will deepen our understanding of the genetic basis of VSD and shed light on designing novel molecular therapies for adult VSD patients carrying these variants. (cdc.gov)
- Using genetic and molecular analyses we have identified WUSCHEL (WUS) as a biologically important target of the SNF2-class ATPase SPLAYED (SYD) in the shoot apical meristem of Arabidopsis. (mendeley.com)
- 4.5 Molecular genetic studies of acidophiles. (barnesandnoble.com)
- Abstract -Genetic approaches have succeeded in defining the molecular basis of an increasing array of heart diseases, such as hypertrophic cardiomyopathy and the long-QT syndromes, associated with serious arrhythmias. (ahajournals.org)
- The current state of the art of the molecular and genetic basis of inherited arrhythmias is first reviewed, followed by practical advice on the role of genetic testing in these and other syndromes and the way in which new findings have influenced current understanding of the molecular and biophysical basis of arrhythmogenesis. (ahajournals.org)
- The main reasons why molecular genetic information can result in greater genetic gain than phenotypic information are: a) Assuming no genotyping errors, molecular genetic information is not affected by environmental effects and, therefore, has heritability equal to 1. (intechopen.com)
- b)-Molecular genetic information can be available at an early age, in principle at the embryo stage, thereby allowing early selection and reduction of generation intervals. (intechopen.com)
- C) Molecular genetic information can be obtained on all selection candidates, which is especially beneficial for sex-limited traits, traits that are expensive or difficult to record, or traits that require slaughter of the animal (carcass traits) ( Dekkers, 2004 ). (intechopen.com)
Enhanced promoter activity1
- While most sequence changes abolished carQRS promoter activity, two changes enhanced promoter activity and two changes caused the mutant promoter to become constitutive and independent of CarQ. (ox.ac.uk)
- To circumvent this problem, a 0.7-kb fragment of the S segment was fused to Gn, and a hybrid CAG promoter/enhancer in conjunction with (or without) the WPRE (Woodchuck hepatitis virus post-transcriptional regulatory element) was used to improve the expression of fusion protein GnS0.7 in the adenoviral expression system. (curehunter.com)
- The results showed that the recombinant adenovirus with the CAG promoter/enhancer (rAd-GnS0.7-pCAG) expressed approximately 2.1-fold more GnS0.7 than the unmodified recombinant adenovirus containing GnS0.7 (rAd-GnS0.7-pShuttle). (curehunter.com)
- These results demonstrate that the CAG promoter/enhancer improved significantly the expression of the chimeric gene GnS0.7 in the adenovirus expression system. (curehunter.com)
- 2.2.6 Genetic transfer and plasmids in Thermus. (barnesandnoble.com)
- Genetic Alteration of p16INKA4A Promoter Region in Endometrial Carcinoma. (koreamed.org)
- Promoters IRP1 to IRP5 and their associated DtxR binding sites were identified by screening promoter fusion libraries for DNA fragments that contained iron- and DtxR-regulated promoter activity ( 22 , 48 ), while the IRP6 promoter was obtained by a cycle selection method ( 35 ). (asm.org)
- DNA fragments with promoters, in this case Pm sequence −98 to +10, are cloned between the EcoRI and BamHI sites in pIA12 to generate the Pm-lacZ fusions. (nih.gov)
- To date, the genetic causes for sporadic VSDs remain largely unknown. (cdc.gov)
- T [rs7350] in the 3' untranslated region (UTR)) in 467 patients with sporadic breast cancer and 488 cancer-free controls. (duke.edu)
- Here, we examine the role of common genetic variants on the sporadic form of dilated cardiomyopathy. (plos.org)
- Therefore, this study is an important step towards revealing insight in the genetic background of the sporadic form of dilated cardiomyopathy. (plos.org)
- We report the clinical and genetic studies of four sporadic BHD cases and four families with a total of 23 affected subjects. (bmj.com)
- The first gene product of the operon, CarQ, is a sigma factor belonging to the ECF family and is responsible for light-dependent initiation of transcription at the carQRS promoter. (ox.ac.uk)
- 1995. Translation of the open reading frame encoded by comS, a gene of the srf operon, is necessary for the development of genetic competence, but not surfactin biosynthesis, in Bacillus subtilis. (cameron.edu)
- There is no lactose to inhibit the repressor , so the repressor binds to the operator , which obstructs the RNA polymerase from binding to the promoter and making lactase. (wikipedia.org)
- Furthermore, we demonstrated that Myc-associated zinc finger protein (MAZ) represses c-myb promoter activity and binds to the c-myb T:H:H:T G-quadruplexes. (biomedsearch.com)
- and a region called the promoter, to which the RNA polymerase binds. (britannica.com)
- under the control of one promoter (a short segment of DNA to which the RNA polymerase binds to initiate transcription). (britannica.com)
- Mor then binds and activates transcription from the WT or mutant Pm promoter cloned in pIA12, leading to synthesis of β-galactosidase at levels proportional to Pm activity. (nih.gov)
- RNA polymerase then binds to DNA at a region called the promoter via binding to the transcription factors. (reference.com)
- In conclusion, we have characterized the functional promoter of APOH and identified functional variants that affect the transcriptional activity of the APOH promoter. (northwestern.edu)
- A novel G-quadruplex-forming GGA repeat region in the c-myb promoter is a critical regulator of promoter activity. (biomedsearch.com)
- Our findings show that the T:H:H:T G-quadruplex-forming region in the c-myb promoter is a critical cis-acting element and may repress c-myb promoter activity through MAZ interaction with G-quadruplexes in the c-myb promoter. (biomedsearch.com)
- Transformed tobacco ( Nicotiana tabacum ) seedlings expressing β -glucuronidase under control of the PvSR2 promoter region (−687/+48) showed heavy metal-specific responsive activity that depended on the type and concentration of the heavy metal and the type of organ. (plantphysiol.org)
- GUS activity was detected only in seeds, except in those having integrated the 124 bp promoter. (deepdyve.com)
- Middle promoter two-plasmid in vivo assay system for promoter activity. (nih.gov)
- The promoter is a region of DNA near the gene that controls gene activity (expression). (medlineplus.gov)
- Promoter assay data revealed that four methylated CpG sites presenting in the −2615 to −2239 nt region cause significant downregulation of OPN promoter activity. (hindawi.com)
- SOCS1 and SOCS3 possess a kinase-inhibitory region (KIR) domain that is critical for inhibition of kinase activity [ 1 ]. (hindawi.com)
- Twenty-one promoters were evaluated for activity using reporter assays. (mendeley.com)
- en] Glucocorticoids have been shown to inhibit the activity of the human prolactin (hPRL) promoter. (ac.be)
- We present evidence that SYD is recruited to the WUS promoter and that it is involved in regulation of the stem cell pool maintenance via direct transcriptional control of this master regulator. (mendeley.com)
- These findings further our understanding of the regulation of PvSR2 expression and provide a new heavy-metal-inducible promoter system in transgenic plants. (plantphysiol.org)
- Transcriptional regulation of Fcgr2b gene by polymorphic promoter region and its contribution to humoral immune responses. (semanticscholar.org)
- An organism that is generated through genetic engineering is considered to be genetically modified (GM) and the resulting entity is a genetically modified organism (GMO). (wikipedia.org)
Transcriptional start site3
- We defined the minimal carQRS promoter as a 145-bp fragment of DNA upstream of the carQRS transcriptional start site, which includes the promoter for a divergent gene, gufA. (ox.ac.uk)
- As promoters are typically immediately adjacent to the gene in question, positions in the promoter are designated relative to the transcriptional start site , where transcription of DNA begins for a particular gene (i.e., positions upstream are negative numbers counting back from -1, for example -100 is a position 100 base pairs upstream). (wikipedia.org)
- Deletions from the 5′ end revealed that a sequence between −222 and −147 relative to the transcriptional start site was sufficient for heavy metal-specific induction of the promoter region of PvSR2 . (plantphysiol.org)
- Promoters represent critical elements that can work in concert with other regulatory regions ( enhancers , silencers , boundary elements/ insulators ) to direct the level of transcription of a given gene. (wikipedia.org)
- SNF2 chromatin-remodeling ATPases play an important role in ensuring proper development in higher eukaryotes by controlling accessibility of cis-regulatory DNA regions to transcription factors and to the transcriptional machinery. (mendeley.com)
- To elucidate its heavy metal-regulatory mechanism at the transcriptional level, we isolated and characterized the promoter region (−1623/+48) of PvSR2 . (plantphysiol.org)
- Region I (−222/−188) contains a motif (metal-regulatory element-like sequence) similar to the consensus metal-regulatory element of the animal metallothionein gene, and mutation of this motif eliminated the heavy metal-inducible function of region I. Region II (−187/−147) had no similarity to previously identified cis-acting elements involved in heavy metal induction, suggesting the presence of a novel heavy metal-responsive element. (plantphysiol.org)
- Piecewise-linear models of genetic regulatory networks: Equilibria and their stability. (springer.com)
- The promoter/regulatory regions of the human C8ORF46 gene direct expression of β-galactosidase. (jax.org)
- Recent work has shown that RNA polymerase (Pol) II can be recruited to and transcribe distal regulatory regions. (cnrs.fr)
- CONCLUSIONS- Adiponectin levels are associated with SNPs in two different regulatory regions (5′ promoter and 3′UTR), whereas diabetes incidence and time-averaged fasting glucose are associated with a missense SNP of ADIPOQ . (diabetesjournals.org)
- Here we show that when transiently overexpressed, p73alpha but not p73beta activated several minimal promoters without the p53BCS, while p73gamma and p73epsilon activated them to a much lesser extent than p73alpha, and p53 suppressed the promoters without p53BCS as reported previously. (nih.gov)
- The hsp70 promoter is unsuitable for use in fusion gene constructs for long term expression studies where repeated heat shocks are required. (nih.gov)
- Forward genetic screens have also targeted mutants exhibiting abnormal gametophtye development or altered expression of gametophyte-specific reporter constructs [ 8 , 9 , 10 , 11 , 12 ]. (mdpi.com)
- Methods We analysed the MLH1 promoter sequence in five different patient groups with colorectal cancer (CRC) (n=480) composed of patients with i) CEM (n=16), ii) unsolved loss of MLH1 expression in CRC (n=37), iii) CpG-island methylator-phenotype CRC (n=102), iv) patients with LS (n=83) and v) MLH1-proficient CRC (n=242) as controls. (bmj.com)
- people with this type of genetic change have normal expression of the PTEN gene. (medlineplus.gov)
- Using transient expression experiments in rat pituitary cells, we located the sequence conferring glucocorticoid inhibition to a region which contains Pit-1 binding sites, responsible for pituitary-specific expression, but does not seem to contain a glucocorticoid receptor (GR) binding site. (ac.be)
- As TBX20 functions as a dosage-dependent regulator during the heart development, we hypothesized that the sequence variants within the promoter region of the TBX20 gene may contribute to CHD. (cdc.gov)
- As the GATA4 factor is a dosage-sensitive regulator, we hypothesized that the promoter region variants of the GATA4 gene may be genetic causes of VSD. (cdc.gov)
- Sebelum RNA polimerase dapat terikat pada promoter inti, faktor transkripsi TFIID akan membentuk kompleks dengan kotak TATA. (wikipedia.org)
- Importantly, we also identify genomic features called transcriptional initiation platforms (TIPs) that are characterized by large areas of Pol II and GTF recruitment at promoters, intergenic and intragenic regions. (cnrs.fr)
- MacAlpine and colleagues used a technique known as Repli-seq to characterize newly replicated regions of DNA with next generation sequencing. (eurekalert.org)
- One of the approaches based on next-generation sequencing (NGS) is targeted enrichment of genomic DNA (TEDNA-seq) sequencing, which allows the identification of a directly selected genomic region by using hybridization probes during DNA library preparation. (springer.com)
- This locus was later mapped to a genomic region that spans approximately 380 kb 12 . (nature.com)