Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Methylation: Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.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: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.Sp1 Transcription Factor: Promoter-specific RNA polymerase II transcription factor that binds to the GC box, one of the upstream promoter elements, in mammalian cells. The binding of Sp1 is necessary for the initiation of transcription in the promoters of a variety of cellular and viral GENES.CpG Islands: 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.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.RNA, Messenger: 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.Transcriptional Activation: Processes that stimulate the GENETIC TRANSCRIPTION of a gene or set of genes.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.Trans-Activators: Diffusible gene products that act on homologous or heterologous molecules of viral or cellular DNA to regulate the expression of proteins.Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.DNA: 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).Cell Line: Established cell cultures that have the potential to propagate indefinitely.Repressor Proteins: Proteins which maintain the transcriptional quiescence of specific GENES or OPERONS. Classical repressor proteins are DNA-binding proteins that are normally bound to the OPERATOR REGION of an operon, or the ENHANCER SEQUENCES of a gene until a signal occurs that causes their release.Basic Helix-Loop-Helix Transcription Factors: A family of DNA-binding transcription factors that contain a basic HELIX-LOOP-HELIX MOTIF.Transcription Factor AP-1: A multiprotein complex composed of the products of c-jun and c-fos proto-oncogenes. These proteins must dimerize in order to bind to the AP-1 recognition site, also known as the TPA-responsive element (TRE). AP-1 controls both basal and inducible transcription of several genes.Homeodomain Proteins: Proteins encoded by homeobox genes (GENES, HOMEOBOX) that exhibit structural similarity to certain prokaryotic and eukaryotic DNA-binding proteins. Homeodomain proteins are involved in the control of gene expression during morphogenesis and development (GENE EXPRESSION REGULATION, DEVELOPMENTAL).Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Epigenesis, Genetic: 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.Oligonucleotide Array Sequence Analysis: Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Signal Transduction: 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.Forkhead Transcription Factors: A subclass of winged helix DNA-binding proteins that share homology with their founding member fork head protein, Drosophila.Chromatin Immunoprecipitation: 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.Histones: Small chromosomal proteins (approx 12-20 kD) possessing an open, unfolded structure and attached to the DNA in cell nuclei by ionic linkages. Classification into the various types (designated histone I, histone II, etc.) is based on the relative amounts of arginine and lysine in each.Cell Differentiation: Progressive restriction of the developmental potential and increasing specialization of function that leads to the formation of specialized cells, tissues, and organs.Cell Nucleus: 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)Basic-Leucine Zipper Transcription Factors: A large superfamily of transcription factors that contain a region rich in BASIC AMINO ACID residues followed by a LEUCINE ZIPPER domain.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Transcription Factor AP-2: A family of DNA binding proteins that regulate expression of a variety of GENES during CELL DIFFERENTIATION and APOPTOSIS. Family members contain a highly conserved carboxy-terminal basic HELIX-TURN-HELIX MOTIF involved in dimerization and sequence-specific DNA binding.Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Kruppel-Like Transcription Factors: A family of zinc finger transcription factors that share homology with Kruppel protein, Drosophila. They contain a highly conserved seven amino acid spacer sequence in between their ZINC FINGER MOTIFS.Gene Silencing: Interruption or suppression of the expression of a gene at transcriptional or translational levels.HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Genes, Reporter: Genes whose expression is easily detectable and therefore used to study promoter activity at many positions in a target genome. In recombinant DNA technology, these genes may be attached to a promoter region of interest.Transcription Factors, TFII: The so-called general transcription factors that bind to RNA POLYMERASE II and that are required to initiate transcription. They include TFIIA; TFIIB; TFIID; TFIIE; TFIIF; TFIIH; TFII-I; and TFIIJ. In vivo they apparently bind in an ordered multi-step process and/or may form a large preinitiation complex called RNA polymerase II holoenzyme.Cell Line, Tumor: A cell line derived from cultured tumor cells.Transcription Initiation Site: The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript.Chromatin: The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.YY1 Transcription Factor: A ubiquitously expressed zinc finger-containing protein that acts both as a repressor and activator of transcription. It interacts with key regulatory proteins such as TATA-BINDING PROTEIN; TFIIB; and ADENOVIRUS E1A PROTEINS.GATA4 Transcription Factor: A GATA transcription factor that is expressed in the MYOCARDIUM of developing heart and has been implicated in the differentiation of CARDIAC MYOCYTES. GATA4 is activated by PHOSPHORYLATION and regulates transcription of cardiac-specific genes.STAT3 Transcription Factor: A signal transducer and activator of transcription that mediates cellular responses to INTERLEUKIN-6 family members. STAT3 is constitutively activated in a variety of TUMORS and is a major downstream transducer for the CYTOKINE RECEPTOR GP130.DNA (Cytosine-5-)-Methyltransferase: An enzyme that catalyzes the transfer of a methyl group from S-ADENOSYLMETHIONINE to the 5-position of CYTOSINE residues in DNA.Transcription Factor TFIID: The major sequence-specific DNA-binding component involved in the activation of transcription of RNA POLYMERASE II. It was originally described as a complex of TATA-BOX BINDING PROTEIN and TATA-BINDING PROTEIN ASSOCIATED FACTORS. It is now know that TATA BOX BINDING PROTEIN-LIKE PROTEINS may take the place of TATA-box binding protein in the complex.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Zinc Fingers: 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.NFATC Transcription Factors: A family of transcription factors characterized by the presence of highly conserved calcineurin- and DNA-binding domains. NFAT proteins are activated in the CYTOPLASM by the calcium-dependent phosphatase CALCINEURIN. They transduce calcium signals to the nucleus where they can interact with TRANSCRIPTION FACTOR AP-1 or NF-KAPPA B and initiate GENETIC TRANSCRIPTION of GENES involved in CELL DIFFERENTIATION and development. NFAT proteins stimulate T-CELL activation through the induction of IMMEDIATE-EARLY GENES such as INTERLEUKIN-2.Activating Transcription Factor 3: An activating transcription factor that plays a key role in cellular responses to GENOTOXIC STRESS and OXIDATIVE STRESS.Sp3 Transcription Factor: A specificity protein transcription factor that regulates expression of a variety of genes including VASCULAR ENDOTHELIAL GROWTH FACTOR and CYCLIN-DEPENDENT KINASE INHIBITOR P27.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.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Enhancer Elements, Genetic: Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter.NF-kappa B: Ubiquitous, inducible, nuclear transcriptional activator that binds to enhancer elements in many different cell types and is activated by pathogenic stimuli. The NF-kappa B complex is a heterodimer composed of two DNA-binding subunits: NF-kappa B1 and relA.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Paired Box Transcription Factors: A family of transcription factors that control EMBRYONIC DEVELOPMENT within a variety of cell lineages. They are characterized by a highly conserved paired DNA-binding domain that was first identified in DROSOPHILA segmentation genes.Gene Expression Regulation, Neoplastic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in neoplastic tissue.RNA Polymerase II: A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 220.127.116.11.Activating Transcription Factor 2: An activating transcription factor that regulates expression of a variety of GENES including C-JUN GENES; CYCLIN A; CYCLIN D1; and ACTIVATING TRANSCRIPTION FACTOR 3.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Transcription Factor TFIIB: An RNA POLYMERASE II specific transcription factor. It plays a role in assembly of the pol II transcriptional preinitiation complex and has been implicated as a target of gene-specific transcriptional activators.E2F1 Transcription Factor: An E2F transcription factor that interacts directly with RETINOBLASTOMA PROTEIN and CYCLIN A and activates GENETIC TRANSCRIPTION required for CELL CYCLE entry and DNA synthesis. E2F1 is involved in DNA REPAIR and APOPTOSIS.Sulfites: Inorganic salts of sulfurous acid.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Azacitidine: A pyrimidine analogue that inhibits DNA methyltransferase, impairing DNA methylation. It is also an antimetabolite of cytidine, incorporated primarily into RNA. Azacytidine has been used as an antineoplastic agent.Basic Helix-Loop-Helix Leucine Zipper Transcription Factors: A family of transcription factors that contain regions rich in basic residues, LEUCINE ZIPPER domains, and HELIX-LOOP-HELIX MOTIFS.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.Gene Expression Regulation, Fungal: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in fungi.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.MEF2 Transcription Factors: Activating transcription factors of the MADS family which bind a specific sequence element (MEF2 element) in many muscle-specific genes and are involved in skeletal and cardiac myogenesis, neuronal differentiation and survival/apoptosis.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Cytosine: A pyrimidine base that is a fundamental unit of nucleic acids.GATA3 Transcription Factor: A GATA transcription factor that is found predominately in LYMPHOID CELL precursors and has been implicated in the CELL DIFFERENTIATION of HELPER T-CELLS. Haploinsufficiency of GATA3 is associated with HYPOPARATHYROIDISM; SENSORINEURAL HEARING LOSS; and renal anomalies syndrome.Luciferases: Enzymes that oxidize certain LUMINESCENT AGENTS to emit light (PHYSICAL LUMINESCENCE). The luciferases from different organisms have evolved differently so have different structures and substrates.Models, Biological: Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.GATA1 Transcription Factor: A GATA transcription factor that is specifically expressed in hematopoietic lineages and plays an important role in the CELL DIFFERENTIATION of ERYTHROID CELLS and MEGAKARYOCYTES.GATA2 Transcription Factor: An essential GATA transcription factor that is expressed primarily in HEMATOPOIETIC STEM CELLS.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.TCF Transcription Factors: A family of DNA-binding proteins that are primarily expressed in T-LYMPHOCYTES. They interact with BETA CATENIN and serve as transcriptional activators and repressors in a variety of developmental processes.Tumor Cells, Cultured: Cells grown in vitro from neoplastic tissue. If they can be established as a TUMOR CELL LINE, they can be propagated in cell culture indefinitely.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.GATA Transcription Factors: A family of transcription factors that contain two ZINC FINGER MOTIFS and bind to the DNA sequence (A/T)GATA(A/G).Methyltransferases: A subclass of enzymes of the transferase class that catalyze the transfer of a methyl group from one compound to another. (Dorland, 28th ed) EC 2.1.1.Down-Regulation: A negative regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.Microphthalmia-Associated Transcription Factor: A basic helix-loop-helix leucine zipper transcription factor that regulates the CELL DIFFERENTIATION and development of a variety of cell types including MELANOCYTES; OSTEOCLASTS; and RETINAL PIGMENT EPITHELIUM. Mutations in MITF protein have been associated with OSTEOPETROSIS and WAARDENBURG SYNDROME.Activating Transcription Factors: Activating transcription factors were originally identified as DNA-BINDING PROTEINS that interact with early promoters from ADENOVIRUSES. They are a family of basic leucine zipper transcription factors that bind to the consensus site TGACGTCA of the cyclic AMP response element, and are closely related to CYCLIC AMP-RESPONSIVE DNA-BINDING PROTEIN.Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.STAT1 Transcription Factor: A signal transducer and activator of transcription that mediates cellular responses to INTERFERONS. Stat1 interacts with P53 TUMOR SUPPRESSOR PROTEIN and regulates expression of GENES involved in growth control and APOPTOSIS.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Transcription Factor RelA: A subunit of NF-kappa B that is primarily responsible for its transactivation function. It contains a C-terminal transactivation domain and an N-terminal domain with homology to PROTO-ONCOGENE PROTEINS C-REL.Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.E2F Transcription Factors: A family of basic helix-loop-helix transcription factors that control expression of a variety of GENES involved in CELL CYCLE regulation. E2F transcription factors typically form heterodimeric complexes with TRANSCRIPTION FACTOR DP1 or transcription factor DP2, and they have N-terminal DNA binding and dimerization domains. E2F transcription factors can act as mediators of transcriptional repression or transcriptional activation.Proto-Oncogene Proteins: Products of proto-oncogenes. Normally they do not have oncogenic or transforming properties, but are involved in the regulation or differentiation of cell growth. They often have protein kinase activity.Mice, Inbred C57BLHelix-Loop-Helix Motifs: Recurring supersecondary structures characterized by 20 amino acids folding into two alpha helices connected by a non-helical "loop" segment. They are found in many sequence-specific DNA-BINDING PROTEINS and in CALCIUM-BINDING PROTEINS.Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.Sequence Alignment: 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.Mice, Knockout: Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.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.Cyclic AMP Response Element-Binding Protein: A protein that has been shown to function as a calcium-regulated transcription factor as well as a substrate for depolarization-activated CALCIUM-CALMODULIN-DEPENDENT PROTEIN KINASES. This protein functions to integrate both calcium and cAMP signals.GATA6 Transcription Factor: A GATA transcription factor that is expressed predominately in SMOOTH MUSCLE CELLS and regulates vascular smooth muscle CELL DIFFERENTIATION.Up-Regulation: A positive regulatory effect on physiological processes at the molecular, cellular, or systemic level. At the molecular level, the major regulatory sites include membrane receptors, genes (GENE EXPRESSION REGULATION), mRNAs (RNA, MESSENGER), and proteins.Activating Transcription Factor 1: An activating transcription factor that regulates expression of a variety of genes including C-JUN GENES and TRANSFORMING GROWTH FACTOR BETA2.Acetylation: Formation of an acetyl derivative. (Stedman, 25th ed)Transcription Factor 7-Like 1 Protein: A transcription factor that takes part in WNT signaling pathway where it may play a role in the differentiation of KERATINOCYTES. The transcriptional activity of this protein is regulated via its interaction with BETA CATENIN.Histone-Lysine N-Methyltransferase: An enzyme that catalyzes the methylation of the epsilon-amino group of lysine residues in proteins to yield epsilon mono-, di-, and trimethyllysine. EC 18.104.22.168.Mice, Transgenic: Laboratory mice that have been produced from a genetically manipulated EGG or EMBRYO, MAMMALIAN.Activating Transcription Factor 4: An activating transcription factor that regulates the expression of a variety of GENES involved in amino acid metabolism and transport. It also interacts with HTLV-I transactivator protein.Transcription Factor TFIIIA: One of several general transcription factors that are specific for RNA POLYMERASE III. It is a zinc finger (ZINC FINGERS) protein and is required for transcription of 5S ribosomal genes.Drosophila Proteins: Proteins that originate from insect species belonging to the genus DROSOPHILA. The proteins from the most intensely studied species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest in the area of MORPHOGENESIS and development.TATA Box: A conserved A-T rich sequence which is contained in promoters for RNA polymerase II. The segment is seven base pairs long and the nucleotides most commonly found are TATAAAA.NFI Transcription Factors: Transcription factors that were originally identified as site-specific DNA-binding proteins essential for DNA REPLICATION by ADENOVIRUSES. They play important roles in MAMMARY GLAND function and development.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Epigenomics: The systematic study of the global gene expression changes due to EPIGENETIC PROCESSES and not due to DNA base sequence changes.Gene Expression Regulation, Enzymologic: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in enzyme synthesis.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.Consensus Sequence: 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.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).Genomic Imprinting: The variable phenotypic expression of a GENE depending on whether it is of paternal or maternal origin, which is a function of the DNA METHYLATION pattern. Imprinted regions are observed to be more methylated and less transcriptionally active. (Segen, Dictionary of Modern Medicine, 1992)Proto-Oncogene Proteins c-ets: A family of transcription factors that share a unique DNA-binding domain. The name derives from viral oncogene-derived protein oncogene protein v-ets of the AVIAN ERYTHROBLASTOSIS VIRUS.CCAAT-Enhancer-Binding Proteins: 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.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.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.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Recombinant Proteins: Proteins prepared by recombinant DNA technology.SOX9 Transcription Factor: A SOXE transcription factor that plays a critical role in regulating CHONDROGENESIS; OSTEOGENESIS; and male sex determination. Loss of function of the SOX9 transcription factor due to genetic mutations is a cause of CAMPOMELIC DYSPLASIA.RNA Interference: A gene silencing phenomenon whereby specific dsRNAs (RNA, DOUBLE-STRANDED) trigger the degradation of homologous mRNA (RNA, MESSENGER). The specific dsRNAs are processed into SMALL INTERFERING RNA (siRNA) which serves as a guide for cleavage of the homologous mRNA in the RNA-INDUCED SILENCING COMPLEX. DNA METHYLATION may also be triggered during this process.DNA Footprinting: 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)5-Methylcytosine: A methylated nucleotide base found in eukaryotic DNA. In ANIMALS, the DNA METHYLATION of CYTOSINE to form 5-methylcytosine is found primarily in the palindromic sequence CpG. In PLANTS, the methylated sequence is CpNpGp, where N can be any base.In Situ Hybridization: A technique that localizes specific nucleic acid sequences within intact chromosomes, eukaryotic cells, or bacterial cells through the use of specific nucleic acid-labeled probes.Fungal Proteins: Proteins found in any species of fungus.Transcription Factor TFIIH: A general transcription factor that is involved in basal GENETIC TRANSCRIPTION and NUCLEOTIDE EXCISION REPAIR. It consists of nine subunits including ATP-DEPENDENT DNA HELICASES; CYCLIN H; and XERODERMA PIGMENTOSUM GROUP D PROTEIN.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Transcription Factor TFIIA: An RNA POLYMERASE II specific transcription factor. It may play a role in transcriptional activation of gene expression by interacting with the TATA-BOX BINDING PROTEIN component of TRANSCRIPTION FACTOR TFIID.RNA: 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)Lysine: An essential amino acid. It is often added to animal feed.Escherichia coli: 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.Bacterial Proteins: Proteins found in any species of bacterium.STAT5 Transcription Factor: A signal transducer and activator of transcription that mediates cellular responses to a variety of CYTOKINES. Stat5 activation is associated with transcription of CELL CYCLE regulators such as CYCLIN KINASE INHIBITOR P21 and anti-apoptotic genes such as BCL-2 GENES. Stat5 is constitutively activated in many patients with acute MYELOID LEUKEMIA.Cell Proliferation: All of the processes involved in increasing CELL NUMBER including CELL DIVISION.Regulatory Elements, Transcriptional: Nucleotide sequences of a gene that are involved in the regulation of GENETIC TRANSCRIPTION.T-Box Domain Proteins: Proteins containing a region of conserved sequence, about 200 amino acids long, which encodes a particular sequence specific DNA binding domain (the T-box domain). These proteins are transcription factors that control developmental pathways. The prototype of this family is the mouse Brachyury (or T) gene product.Transcription Factor DP1: A transcription factor that possesses DNA-binding and E2F-binding domains but lacks a transcriptional activation domain. It is a binding partner for E2F TRANSCRIPTION FACTORS and enhances the DNA binding and transactivation function of the DP-E2F complex.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Cell Lineage: The developmental history of specific differentiated cell types as traced back to the original STEM CELLS in the embryo.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Drosophila: A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.Blotting, Northern: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Octamer Transcription Factor-1: A ubiquitously expressed octamer transcription factor that regulates GENETIC TRANSCRIPTION of SMALL NUCLEAR RNA; IMMUNOGLOBULIN GENES; and HISTONE H2B genes.Leucine Zippers: DNA-binding motifs formed from two alpha-helixes which intertwine for about eight turns into a coiled coil and then bifurcate to form Y shaped structures. Leucines occurring in heptad repeats end up on the same sides of the helixes and are adjacent to each other in the stem of the Y (the "zipper" region). The DNA-binding residues are located in the bifurcated region of the Y.Gene Regulatory Networks: Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations.Two-Hybrid System Techniques: Screening techniques first developed in yeast to identify genes encoding interacting proteins. Variations are used to evaluate interplay between proteins and other molecules. Two-hybrid techniques refer to analysis for protein-protein interactions, one-hybrid for DNA-protein interactions, three-hybrid interactions for RNA-protein interactions or ligand-based interactions. Reverse n-hybrid techniques refer to analysis for mutations or other small molecules that dissociate known interactions.Deoxyribonuclease I: 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.Embryo, Mammalian: The entity of a developing mammal (MAMMALS), generally from the cleavage of a ZYGOTE to the end of embryonic differentiation of basic structures. For the human embryo, this represents the first two months of intrauterine development preceding the stages of the FETUS.Long Interspersed Nucleotide Elements: Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.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.Protein Methyltransferases: Enzymes that catalyze the methylation of amino acids after their incorporation into a polypeptide chain. S-Adenosyl-L-methionine acts as the methylating agent. EC 2.1.1.Time Factors: Elements of limited time intervals, contributing to particular results or situations.Erythroid-Specific DNA-Binding Factors: A group of transcription factors that were originally described as being specific to ERYTHROID CELLS.Apoptosis: One of the mechanisms by which CELL DEATH occurs (compare with NECROSIS and AUTOPHAGOCYTOSIS). Apoptosis is the mechanism responsible for the physiological deletion of cells and appears to be intrinsically programmed. It is characterized by distinctive morphologic changes in the nucleus and cytoplasm, chromatin cleavage at regularly spaced sites, and the endonucleolytic cleavage of genomic DNA; (DNA FRAGMENTATION); at internucleosomal sites. This mode of cell death serves as a balance to mitosis in regulating the size of animal tissues and in mediating pathologic processes associated with tumor growth.Nerve Tissue ProteinsGA-Binding Protein Transcription Factor: A heterotetrameric transcription factor composed of two distinct proteins. Its name refers to the fact it binds to DNA sequences rich in GUANINE and ADENINE. GA-binding protein integrates a variety of SIGNAL TRANSDUCTION PATHWAYS and regulates expression of GENES involved in CELL CYCLE control, PROTEIN BIOSYNTHESIS, and cellular METABOLISM.Tumor Suppressor Proteins: Proteins that are normally involved in holding cellular growth in check. Deficiencies or abnormalities in these proteins may lead to unregulated cell growth and tumor development.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Early Growth Response Protein 1: An early growth response transcription factor that has been implicated in regulation of CELL PROLIFERATION and APOPTOSIS.Immunohistochemistry: Histochemical localization of immunoreactive substances using labeled antibodies as reagents.Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Multigene Family: 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)DNA-Cytosine Methylases: Methylases that are specific for CYTOSINE residues found on DNA.Cell Cycle Proteins: Proteins that control the CELL DIVISION CYCLE. This family of proteins includes a wide variety of classes, including CYCLIN-DEPENDENT KINASES, mitogen-activated kinases, CYCLINS, and PHOSPHOPROTEIN PHOSPHATASES as well as their putative substrates such as chromatin-associated proteins, CYTOSKELETAL PROTEINS, and TRANSCRIPTION FACTORS.Transcription Factors, TFIII: Factors that bind to RNA POLYMERASE III and aid in transcription. They include the assembly factors TFIIIA and TFIIIC and the initiation factor TFIIIB. All combine to form a preinitiation complex at the promotor that directs the binding of RNA POLYMERASE III.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Cell Cycle: The complex series of phenomena, occurring between the end of one CELL DIVISION and the end of the next, by which cellular material is duplicated and then divided between two daughter cells. The cell cycle includes INTERPHASE, which includes G0 PHASE; G1 PHASE; S PHASE; and G2 PHASE, and CELL DIVISION PHASE.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Gene Expression Regulation, Viral: Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.High Mobility Group Proteins: A family of low-molecular weight, non-histone proteins found in chromatin.Twist Transcription Factor: A basic helix-loop-helix transcription factor that was originally identified in DROSOPHILA as essential for proper gastrulation and MESODERM formation. It plays an important role in EMBRYONIC DEVELOPMENT and CELL DIFFERENTIATION of MUSCLE CELLS, and is found in a wide variety of organisms.Chloramphenicol O-Acetyltransferase: 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 22.214.171.124.Histone Deacetylases: 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.Proto-Oncogene Protein c-ets-1: An ets proto-oncogene expressed primarily in adult LYMPHOID TISSUE; BRAIN; and VASCULAR ENDOTHELIAL CELLS.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Transcription Factor 7-Like 2 Protein: A transcription factor that takes part in WNT signaling pathway. The activity of the protein is regulated via its interaction with BETA CATENIN. Transcription factor 7-like 2 protein plays an important role in the embryogenesis of the PANCREAS and ISLET CELLS.Nucleosomes: The repeating structural units of chromatin, each consisting of approximately 200 base pairs of DNA wound around a protein core. This core is composed of the histones H2A, H2B, H3, and H4.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Neoplasm Proteins: 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.
ABI Solid Sequencing
Methylation immunoprecipitation (MeDIP) can also be performed and also on arrays. The ability to learn more about methylation ... Chromatin immunoprecipitation (ChIP) is a method for determining transcription factor binding sites and DNA-protein ... It has in the past been combined with array technology (ChIP-chip) with some success. Next gen sequencing can also be applied ... Microarrays was once the mainstay of the transcriptomics the last ten years and array based technology has subsequently ...
Each transcription factor binds to one particular set of DNA sequences and activates or inhibits the transcription of genes ... The average level of methylation varies between organisms - the worm Caenorhabditis elegans lacks cytosine methylation, while ... These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that make up ... The transcription factors do this in two ways. Firstly, they can bind the RNA polymerase responsible for transcription, either ...
The TALE protein itself may even compete with transcription factors if they are targeted to the same sequence. In addition, DNA ... Although DNA methylation typically correlates with gene repression, methylation has also been shown to play a role in gene ... Epigenetic editing using an inducible mechanism offers a wide array of potential use to study epigenetic effects in various ... The Transcription Activator-Like Effector (TALE) protein recognizes specific DNA sequences based on the composition of its DNA ...
This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene ... HOXA9 itself regulates a vast array of genes, such as Flt3, Erg, Myb and Lmo2, all of which exhibit the characteristic ... UTX, MLL and WHSC1 code for protein methylation and demethylation activity, specifically for the histone methyltransferase ... In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C ...
DBD database of predicted transcription factors Uses a curated set of DNA-binding domains to predict transcription factors in ... These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that form ... Chemical modifications of these basic amino acid residues include methylation, phosphorylation and acetylation. These chemical ... Each transcription factor binds to one specific set of DNA sequences and activates or inhibits the transcription of genes that ...
George M. Church
... of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors". Nucleic ... "RNA expression analysis using a 30 base pair resolution Escherichia coli genome array". Nature Biotechnology. 18 (12): 1262-8. ... "Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells". Nature Biotechnology. 27 (4): ... "Assessing computational tools for the discovery of transcription factor binding sites". Nature Biotechnology (Submitted ...
Epigenetics of diabetes Type 2
... may also involve epigenetic control as a contributing factor. Promoter methylation of the mitochondrial transcription factor A( ... Epigenetics may play a role in a wide array of vascular complications and in diabetes. The epigenetic variations involved with ... A subsequent study shows that under high glucose conditions, islet-specific transcription factor Pdx1 was shown to stimulate ... This happens because miR-9 down-regulated the transcription factor Onecut2 (OC2) that controls the expression of Rab27a ...
ChIP-chip experiments have been able to identify binding sites of transcription factors across the genome in yeast, drosophila ... Tiling array studies have generated high-resolution methylation maps for the Arabidopsis genome to generate the first " ... Earlier studies on chromosome 21 and 22 showed the power of tiling arrays for identifying transcription units. The authors used ... Tiling arrays have allowed researchers to apply the technique on a genome-wide scale. Array-based CGH is a technique often used ...
Polycomb Group Proteins and Cancer
The Hox genes encode transcription factors that give a specific identity to each segment along the body axis of the animal. ... These epigenetic changes include both genome-wide losses and regional gains of DNA methylation, as well as altered patterns of ... These showed that PRC1 was able to transform arrays of nucleosomes into highly compact chromatin structures in which the ... Siddique, HR; Saleem, M (2012). "Role of BMI1, a stem cell fac- tor, in cancer recurrence and chemoresistance: preclinical and ...
Facioscapulohumeral muscular dystrophy
DUX4 protein is identified as a transcription factor, and evidence suggests overexpression of DUX4 is linked to an increase in ... Higher levels of DUX4-s (vs DUX4-fl) are shown to correlate with a greater degree of DUX-4 H3K9me3-methylation. 2012 Some, but ... Transgenic mice carrying D4Z4 arrays from an FSHD1 allele (with 2.5 D4Z4 units), although lacking an obvious FSHD-like skeletal ... encoding a double-homeobox transcription factor, in skeletal muscle." In more lay terms, the D4Z4 repeats (most people have ...
Methylated DNA immunoprecipitation
... but methylation at either of these sites can repress gene expression by either interfering with the binding of transcription ... Array-based identification of MeDIP sequences are limited to the array design. As a result, the resolution is restricted to the ... Limitations to take note when using MeDIP are typical experimental factors. This includes the quality and cross-reactivity of ... Particularly for array-based procedures, as mentioned above, sequences being analyzed are limited to the specific array design ...
Molecular and epigenetic mechanisms of alcoholism
Shaywitz, A.J. and Greenberg, M.E. (1999). CREB: a stimulus-induced transcription factor activated by a diverse array of ... These mechanisms include DNA methylation, histone acetylation and methylation, and (microRNA miRNA) action. Methylation of the ... CREB is a transcription factor known to influence CNS functioning. This protein is activated by phosphorylation via the kinase ... Pandey, S.C., Zhang, D., Mittal, N., Nayyar, D. (1999). Potential role of the gene transcription factor cyclic AMP-responsive ...
Ostra białaczka szpikowa, wolna encyklopedia
Deregulated transcription factors in leukemia. „Int J Hematol". 94 (2), s. 134-41, Aug 2011. DOI: 10.1007/s12185-011-0905-9. ... Array-based genomic resequencing of human leukemia.. „Oncogene". 29 (25), s. 3723-31, Jun 2010. DOI: 10.1038/onc.2010.117. PMID ... DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. „Cancer Cell". 17 (1), s. 13-27, ... caudal-type homeobox transcription factor 2), który jest związany z określeniem osi przód-tył podczas rozwoju embrionalnego ...
In transcription factors these domains are often found in arrays (usually separated by short linker sequences) and adjacent ... such as methylation. Many proteins involved in the regulation of gene expression contain DNA-binding domains. For example, ... DBD database of predicted transcription factors Kummerfeld SK, Teichmann SA (January 2006). "DBD: a transcription factor ... proteins that regulate transcription by binding DNA are called transcription factors. The final output of most cellular ...
Histone deacetylase 5
McKinsey TA, Zhang CL, Olson EN (2001). "Activation of the myocyte enhancer factor-2 transcription factor by calcium/calmodulin ... potential role for histone methylation in control of muscle differentiation". Mol. Cell. Biol. 22 (20): 7302-12. doi:10.1128/ ... "Validation of RNAi Silencing Efficiency Using Gene Array Data shows 18.5% Failure Rate across 429 Independent Experiments". ... and MEF2-interacting transcription repressor (MITR) contributes to transcriptional repression of the MEF2 transcription factor ...
Epigenetics in stem-cell differentiation
DNA methylation can modulate the binding affinities of transcription factors by recruiting repressors such as MeCP2 which ... Recent studies have revealed that there is an array of different pathways that cooperates with one another in order to bestow ... Okamoto K, Okazawa H, Okuda A, Sakai M, Murmatsu M, Hamada H (1990). "A novel octamer binding transcription factor is ... It is demonstrated from these studies that both H3K9 di-and tri-methylation correlate with the DNA methylation and gene ...
Regulation of gene expression
Artificial transcription factors (small molecules that mimic transcription factor protein) Cellular model Conserved non-coding ... Alternative splicing can be analysed with a splicing array or with a tiling array (see DNA microarray). All in vivo RNA is ... allowing transcription to proceed. Often, DNA methylation and histone deacetylation work together in gene silencing. The ... Regulation of transcription thus controls when transcription occurs and how much RNA is created. Transcription of a gene by RNA ...
... and tumor suppressors using a custom PCR array. Analysis of DNA methylation showed methylation differences in CpG sites of the ... In the pancreas, IUGR caused a reduction in the expression of the promoter of the gene encoding a critical transcription factor ... DNA methylation is the addition of methyl groups to the DNA. When DNA is methylated in mammals, the transcription of the gene ... Therefore, higher methylation rates in H19 ICR repress transcription and prevent the lncRNA from regulating body weight. ...
Mathematical modeling suggests for a broad array of network topologies that a combination of enzymes and transcription factors ... The acetylation and methylation of histones recruits more acetyltransferases and methyltransferases that results in a positive ... An example of this is seen in the transcription of certain eukaryotic genes in which non-cooperative transcription factor ... Figure 1 in their article illustrates how an active transcription factor can be sequestered by an inhibitor into the inactive ...
Secreted frizzled-related protein 1
GLI are transcription factors that activate the transcription of Hedgehog target genes. The GLI-binding site was identified ... SFRP1 methylation has been shown to be an independent risk factor for OS. Veeck and colleagues demonstrate, via Kaplan-Meier ... More specifically, the deregulation of the Wnt signaling pathway has been implicated in a wide array of cancers that is mainly ... This demonstrates that methylation detection of SFRP1 is both feasible and reliable and that the urine methylation score (M ...
A Stimulus-Induced Transcription Factor Activated by A Diverse Array of Extracellular Signals". Annual Review of Biochemistry. ... However, the majority of these sites remain unbound due to cytosine methylation which physically obstructs protein binding. A ... The phosphorylated CREB recognizes the cAMP Response Element and serves as a transcription factor for Per1 and Per2, two genes ... CREB (cAMP response element-binding protein) is a cellular transcription factor. It binds to certain DNA sequences called cAMP ...
... is found in the brain early in development due to the two achaete-scute complex homologue transcription factor binding ... 2006). "Cell array-based intracellular localization screening reveals novel functional features of human chromosome 21 proteins ... Several post-translational modifications have been found by mass spectroscopy: five phosphorylation sites, one methylation site ... 2007). "Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE ...
... identified the rapid evolution of transcription factors in humans. Further related work looked at the expression level changes ... Maksimovic, J; Gordon, L; Oshlack, A (2012). "SWAN: Subset-quantile within array normalization for illumina infinium ... comparative analysis of RNAseq data and normalisation of methylation patterns in human DNA beadchip data. Oshlack's methodology ... "Expression profiling in primates reveals a rapid evolution of human transcription factors". Nature. 440 (7081): 242-245. ...
Head and neck cancer
Cdk4 avoiding pRb phosphorylation and thereby prevents release of E2F is a transcription factor required for activation of ... Distinct host genome methylation and expression patterns, produced even when virus isn't integrated into the host genome. ... the selection of appropriate treatment for a specific cancer depends on a complex array of variables, including tumor site, ... There are a wide variety of factors which can put someone at a heightened risk for throat cancer. Such factors include smoking ...
Human Endogenous Retrovirus-W
... which resulted in less transcription A contrasting study performed a micro-array to analyze HERV transcription in human brains ... In fact by doing a Chip-seq analysis of HERV-W LTR's it was found that ¼ of HERV-W LTR's can be bound by transcription factor ... Final putative mechanisms of control of ERVWE-1 are by CpG promoter methylation and histone modification. Overexpression of ... They found through a CHIP assay that TNFa (a cytokine) causes the p65 transcription factor to bind to the promoter. This was ...
Cryptic unstable transcript
Kaplan C, Laprade L, Winston F (2003). "Transcription Elongation Factors Repress Transcription Initiation from Cryptic Sites". ... Transcription. 2: 145-154. doi:10.4161/trns.2.3.16298. Carrozza M; et al. (2005). "Histone H3 Methylation by Set2 Directs ... Regions of non-coding RNA were mapped in several early experiments examining S. cerevisiae using a tiling array approach, which ... In the absence of the transcription elongation factors Spt6 and Spt16, nucleosomes distribute incorrectly across DNA, allowing ...
"The parkin mutant phenotype in the fly is largely rescued by metal-responsive transcription factor (MTF-1)". Mol Cell Biol. 31 ... Wang L, Xie L, Wang J, Shen J, Liu B (2013). "Correlation between the methylation of SULF2 and WRN promoter and the irinotecan ... Synthetic genetic array (SGA), synthetic lethality by microarray (SLAM), and genetic interaction mapping (GIM) are three high- ... SREBP1 regulates the transcription of BCAT2 which mediates BCAA catabolism and glutamine synthesis, which is critical for de ...
It is a genome-wide strategy for finding de novo long-range interactions between DNA elements bound by protein factors. The ... This will help identify alternative transcription start sites and polyadenylation sites of genes. RNA-PET could also be used to ... High-resolution profiling of histone methylations in the human genome. Cell. 129:823-837. Johnson DS, Mortazavi A, Myers RM, ... The advantage over chip hybridization (ChIP-Chip) is that hybridization tiling arrays do not have the statistical sensitivity ...
Kos, R; Reedy MV; Johnson RL; Erickson CA (2001). "The winged-helix transcription factor FoxD3 is important for establishing ... Morcos, PA; Li YF; Jiang S (2008). "Vivo-Morpholinos: A non-peptide transporter delivers Morpholinos into a wide array of mouse ... Morpholinos are not known to modify DNA methylation. Up to 18% of Morpholinos appear to induce nontarget-related phenotypes ... ribosome usually starts by binding to one end of the mRNA and is joined there by various other eukaryotic initiation factors, ...
The idea that modifications act as docking modules for related factors is borne out by histone methylation as well. Methylation ... In Alphaproteobacteria, methylation of adenine regulates the cell cycle and couples gene transcription to DNA replication. In ... Synthetic genetic array. References. *^ Dupont C, Armant DR, Brenner CA (September 2009). "Epigenetics: definition, ... "Epigenetic factors in cancer risk: effect of chemical carcinogens on global DNA methylation pattern in human TK6 cells". PLoS ...
Single cell sequencing
Single-cell analysis of the several transcription factors by scRNA-seq revealed heterogeneity across the population. These ... Single-cell DNA methylome sequencing quantifies DNA methylation. There are several known types of methylation that occur in ... and other types of microbiomes in order to address a wide array of questions related to microbial ecology, evolution, public ... Other methods to detect DNA methylation include methylation-sensitive restriction enzymes. Restriction enzymes also enable the ...
... including transcription factors as well as F-box proteins. In many organisms, including humans, miRNAs are linked to the ... Heritability comes from methylation of promoters targeted by RNAi; the new methylation pattern is copied in each new generation ... In a recent study validation of RNAi silencing efficiency using gene array data showed 18.5% failure rate across 429 ... the majority of genes regulated by miRNAs are transcription factors; thus miRNA activity is particularly wide-ranging and ...
The Gal4 transcription factor gene produces a two-domain protein (BD and AD) essential for transcription of the reporter gene ( ... Protein array, a chip-based method for detecting protein-protein interactions. *Synthetic genetic array analysis, a yeast based ... It may be of note that the methylation activity of certain E. coli DNA methyltransferase proteins may interfere with some DNA- ... This means that even though the transcription factor is split into two fragments, it can still activate transcription when the ...
"BRCA1 augments transcription by the NF-kappaB transcription factor by binding to the Rel domain of the p65/RelA subunit". J. ... positive regulation of transcription from RNA polymerase II promoter. • positive regulation of histone H4-K20 methylation. • ... by multi-capillary electrophoresis or also dedicated oligonucleotides array based on comparative genomic hybridization (array- ... regulation of transcription from RNA polymerase II promoter. • negative regulation of G0 to G1 transition. • transcription from ...
Laird PW (March 2010). "Principles and challenges of genomewide DNA methylation analysis". Nature Reviews. Genetics. 11 (3): ... Functional genomics focuses on the dynamic aspects such as gene transcription, translation, and protein-protein interactions, ... First, the genome must be selected, which involves several factors including cost and relevance. Second, the sequence is ... allowing for very large arrays of DNA colonies to be captured by sequential images taken from a single camera. Decoupling the ...
Long non-coding RNA
NcRNAs also target general transcription factors required for the RNAP II transcription of all genes. These general factors ... June 2003). "Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease ... tiling array data shows more than 40% of transcripts are non-polyadenylated). However, unambiguously identifying ncRNAs within ... Many of the ncRNAs that interact with general transcription factors or RNAP II itself (including 7SK, Alu and B1 and B2 RNAs) ...
"Genome-wide analysis in the mouse embryo reveals the importance of DNA methylation for transcription integrity". Nature ... LINE1 (L1) TEs that land on the human Factor VIII have been shown to cause haemophilia ... Walter M (2016). Transposon regulation upon dynamic loss of DNA methylation (Thesis). Université Pierre et Marie Curie. doi: ... The reverse transcription step is catalyzed by a reverse transcriptase, which is often encoded by the TE itself. The ...
Somatic evolution in cancer
These methylation patterns are copied to the new chromosomes when cells replicate their genomes and so methylation alterations ... System instability is a major contributing factor for genetic heterogeneity. For the majority of cancers, genome ... In cancers, loss of expression of genes occurs about 10 times more frequently by transcription silencing (caused by somatically ... and array CGH,) and karyotypic variations including chromosome structural aberrations and aneuploidy. ...
The idea that modifications act as docking modules for related factors is borne out by histone methylation as well. Methylation ... In Alphaproteobacteria, methylation of adenine regulates the cell cycle and couples gene transcription to DNA replication. In ... DNA methylation patterns are known to be established and modified in response to environmental factors by a complex interplay ... About 50% of miRNA genes are associated with CpG islands, that may be repressed by epigenetic methylation. Transcription ...
NF-κB - by reducing a disulfide bond in NF-κB, Trx1 promotes binding of this transcription factor to DNA. ... This suggests that Trx1 may also play an role in protein methylation via regulating SMYD1 expression, which is independent of ... that reside in different cell compartments and function in an array of processes. In 2010 it was discovered for the first time ... regulation of transcription, DNA-templated. • cell-cell signaling. • negative regulation of transcription from RNA polymerase ...
Regulation of gene expression
Transcription of a gene by RNA polymerase can be regulated by several mechanisms. Specificity factors alter the specificity of ... Alternative splicing can be analysed with a splicing array or with a tiling array (see DNA microarray). ... These are (1) histone acetylations and histone methylations, (2) DNA methylation at CpG sites, and (3) epigenetic ... General transcription factors position RNA polymerase at the start of a protein-coding sequence and then release the polymerase ...
... custom arrays, and arrays with larger spots on porous membranes (macroarrays). There can be anywhere from 100 spots to more ... Molecular biology is the study of the molecular underpinnings of the processes of replication, transcription, translation, and ... Also, one can measure what genes are expressed and how that expression changes with time or with other factors. There are many ... Arrays can also be made with molecules other than DNA. ...
When DNA methylation occurs at promoter regions, the sites of transcription initiation, it has the effect of repressing gene ... And, while DNA binding transcription factors provide a mechanism for specific control of cellular responses, a model where DNA ... Adaptation of next generation sequencing to DNA methylation assay provides several advantages over array hybridization. ... However instead of isolating a DNA-binding transcription factor or enhancer protein through chromatin immunoprecipitation, the ...
... a transcription factor that activates a series of transcription events in the nucleus accumbens that ultimately result in ... Leukemia can be caused by the insertion of a viral genome next to the 17-92 array of microRNAs, leading to increased expression ... In 29-66% of glioblastomas, DNA repair is deficient due to epigenetic methylation of the MGMT gene, which reduces protein ... targeting the transcription factor brain-derived neurotrophic factor (BDNF) and ultimately reducing its expression. BDNF plays ...
"Biochemical analysis of the arginine methylation of high molecular weight fibroblast growth factor-2". J. Biol. Chem. 275 (5): ... "Arginine methylation of STAT1 modulates IFNalpha/beta-induced transcription". Cell. 104 (5): 731-41. doi:10.1016/S0092-8674(01) ... Lee J, Bedford MT (2002). "PABP1 identified as an arginine methyltransferase substrate using high-density protein arrays". EMBO ... Kim S, Park GH, Paik WK (1999). "Recent advances in protein methylation: enzymatic methylation of nucleic acid binding proteins ...
Hope BT (May 1998). "Cocaine and the AP-1 transcription factor complex". Annals of the New York Academy of Sciences. 844: 1-6. ... It can also cause a wide array of kidney diseases and kidney failure. Cocaine use leads to an increased risk of hemorrhagic and ... A SAM-dependent N-methylation of putrescine gives the N-methylputrescine product, which then undergoes oxidative deamination by ... "Expression of the transcription factor deltaFosB in the brain controls sensitivity to cocaine". Nature. 401 (6750): 272-6. doi: ...
Nuclear receptor coregulators
The yeast two-hybrid protein-protein interaction assay led to the identification of an array of receptor-interacting factors in ... Histone acetylase coactivators increase the rate of acetylation, opening the nucleosome to transcription factors; histone ... Targeted, reversible enzymatic modifications such as acetylation, methylation phosphorylation and terminal modifications such ... reporter genes when fused to DNA-binding domains of heterologous transcription factors, suggesting that specific cellular ...
Zinc finger chimera
Engineered zinc finger arrays can then be used in numerous applications such as artificial transcription factors, zinc finger ... The effector domain may be a transcriptional activator (A) or repressor (R), a methylation domain (M) or a nuclease (N). ... Artificial transcription factors with engineered zinc finger arrays have been used in numerous scientific studies, and an ... The majority of engineered zinc finger arrays are based on the zinc finger domain of the murine transcription factor Zif268, ...
Methylation Arrays | Interrogate methylation sites across the genome
... quantitative interrogation of methylation sites across the genome at single-nucleotide resolution. ... ENCODE transcription factor binding sites. *miRNA promoter regions. *Assay reproducibility *98% for technical replicates ... Methylation Array Data Analysis Tips from Experts. Experts describe their approaches to analyzing Illumina methylation array ... Methylation Field Guide. Explore a variety of methods used to detect cytosine modifications, including methylation arrays, and ...
Epigenetic alterations affecting transcription factors and signaling pathways in stromal cells of endometriosis: Genome-wide...
Genome-wide DNA methylation data (array) ... Ets-domain transcription factor Ets21c and nuclear receptor Ftz ... Epigenetic alterations affecting transcription factors and signaling pathwa.... RNA degradation in proliferating and ... Epigenetic alterations affecting transcription factors and signaling pathways in stromal cells of endometriosis: ... Alternate exon switching establishes a tissue-specific transcription factor.... ...
ABI Solid Sequencing - Wikipedia
Methylation immunoprecipitation (MeDIP) can also be performed and also on arrays. The ability to learn more about methylation ... Chromatin immunoprecipitation (ChIP) is a method for determining transcription factor binding sites and DNA-protein ... It has in the past been combined with array technology (ChIP-chip) with some success. Next gen sequencing can also be applied ... Microarrays was once the mainstay of the transcriptomics the last ten years and array based technology has subsequently ...
A differential proteome screening system for post-translational modification-dependent transcription factor interactions |...
Here we describe array peptide screening (APS), a systematic and differential approach to detect PTM-dependent interactions in ... We have previously used this method to investigate the effect of arginine methylation of C/EBPβ peptides. The method enables ... For example, members of the C/EBP transcription factor family are extensively methylated on arginine and lysine residues in ... Peptides with and without a modified residue are applied in parallel to bacterial expression libraries in an arrayed format. ...
Quantification and accurate normalisation of small RNAs through new custom RT-qPCR arrays demonstrates Salmonella -induced...
The introduced arrays are furthermore suited for customised quantification of any class of small non-coding RNAs as exemplified ... We have developed custom RT-qPCR arrays allowing for accurate quantification of 31 small RNAs in triplicate using a 96 well ... The application of these arrays revealed microRNAs that may mediate monocyte host defence mechanisms by regulating the TGF-β ... We have successfully employed such arrays to study microRNA regulation during human monocyte differentiation as well as ...
The BRAF(V600E) causes widespread alterations in gene methylation in the genome of melanoma cells
Here, we investigated the role of BRAF(V600E) signaling in altering gene methylation in the genome of melanoma … ... Transcription Factors * DNA (Cytosine-5-)-Methyltransferase 1 * DNA (Cytosine-5-)-Methyltransferases * EZH2 protein, human ... Oligonucleotide Array Sequence Analysis * Polycomb Repressive Complex 2 * Proto-Oncogene Proteins B-raf / genetics* ... The BRAF(V600E) causes widespread alterations in gene methylation in the genome of melanoma cells Cell Cycle. 2012 Jan 15;11(2 ...
Figures and data in The transcription factors Runx3 and ThPOK cross-regulate acquisition of cytotoxic function by human Th1...
... by human CD4 T cells is an integral part of the T helper 1 differentiation pathway and is limited by the transcription factor ... a) Methylation profiles of 450,000 CpG sites were measured in T cell subsets with Infinium arrays. The figure shows the ... cells and co-expression with transcription factors in the Th1 lineage.. The expression of PRF1 and transcription factors (TF) ... Methylation profiles of 450,000 CpG sites were measured in T cell subsets with Infinium arrays in five CMV-seropositive healthy ...
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
... analysis of methylation patterns, and identification of transcription factor binding sites. Here, we describe an application of ... analysis of methylation patterns, and identification of transcription factor binding sites. Here, we describe an application of ... RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays Genome Res. 2008 Sep;18(9):1509- ... and compared the sequencing data to results obtained from Affymetrix arrays using the same RNA samples. We find that the ...
Charles R. Vinson, Ph.D. | Center for Cancer Research - National Cancer Institute
... focusing on the C/EBP family of transcription factors (TF) that bind sequence-specific DNA containing methylated cytosines (5mC ... 1) transcription factors 2) coiled-coil 3) CG methylation 4)DNA binding ... We can methylate the arrays and examine the consequences on DNA binding. ... transcription factors. These dominant-negatives contain the dimerization domain of the transcription factor and an acidic ...
DAPK2 | Cancer Genetics Web
METHODS: Human GICs were cultured in agarose and treated with inhibitors of RTKs, non-receptor kinases or transcription factors ... RESULTS: The estimated prevalence of P16 methylation was 43%, DAPK methylation was 39.7% and MGMT methylation was 39.8%. ... Reverse phase protein array analysis of the synergistic treatment indicated involvement of not only MEK and PI3K signaling ... The methylation of DAPK gene promoter region was examined by methylation-specific PCR (MSP). The expressions of DAPK protein ...
Pesquisa | Portal Regional da BVS
... factor mapping identified several potential transcription factors implicated in the link between differential methylation, ... Promoter-wide methylation was profiled with EPIC array. Whole-genome sequencing data were included for genetic and methylation ... A transcription factor dataset was integrated to identify transcription factors coordinating respective expression. In total, ... BACKGROUND: ZNF322A is an oncogenic transcription factor that belongs to the Cys2His2-type zinc-finger protein family. ...
DNA methylation presents distinct binding sites for human transcription factors | eLife
A comprehensive study of human transcription factors reveals that a greater number of these proteins bind to methylated DNA ... Third, because we do not have any TF heterodimers on our arrays, it may also generate false negatives. For example, a recent ... This can occur directly if methylation disrupts interactions between the DNA and the transcription factors, or indirectly if ... Thank you for sending your work entitled "DNA methylation presents distinct binding sites for human transcription factors" for ...
"Promoter array" studies identify cohorts of genes directly regulated by methylation, copy number change, or transcription ... ATAD2 is a physiologic target of pRB/E2F and functions as a coactivator for the transcription factors ERα, AR, and c-myc by ... A, schematic of enriched Histone-DNA methylation probes with respect to transcription start site (TSS) of each gene. A1 marks ... C, methylation status of the six genes in TCGA methylation database (75 tumor and 10 normal samples;*, P , 0.05). ...
Frontiers | DNA methylation dynamics in muscle development and disease | Frontiers in Aging Neuroscience
Traditionally, DNA methylation has been considered as a permanent repressive epigenetic mark. However, the application of ... Traditionally, DNA methylation has been considered as a permanent repressive epigenetic mark. However, the application of ... This review outlines the published data regarding DNA methylation changes along the skeletal muscle program, in both ... This review outlines the published data regarding DNA methylation changes along the skeletal muscle program, in both ...
Transcription Factors - QIAGEN
The Human Stem Cell Transcription Factors EpiTect Methyl II Signature PCR Array profiles the promoter methylation status of a ... Transcription Factors RT2 Profiler PCR Array The Human Transcription Factors RT² Profiler PCR Array profiles the expression of ... Transcription Factors RT2 Profiler PCR Array The Mouse Transcription Factors RT² Profiler PCR Array profiles the expression of ... Transcription Factors RT2 Profiler PCR Array The Rat Transcription Factors RT² Profiler PCR Array profiles the expression of 84 ...
The Maize Unstable factor for orange1 Is a Dominant Epigenetic Modifier of a Tissue Specifically Silent Allele of pericarp...
A bent arrow in the methylation map diagram represents transcription start site. (D and E) Methylation maps of P1-wr and P1-wr ... Ufo1 induces P1-wr transcription: The P1-wr locus contains six highly similar gene copies in a tandem direct array (Chopraet al ... 2001 Tissue-specific patterns of a maize Myb transcription factor are epigenetically regulated. Plant J. 27: 467-478. ... Thus, presence of the Ufo1 factor increases P1-wr transcription in pericarp. However, because p1 steady-state transcript levels ...
Infrastructure SRP Diabetes | Strategic Research Programme in Diabetes | Karolinska Institutet
Abstract 4451: Different patterns of SIRT1, KLF4, DAPK1 and SPG20 methylation in B lymphocytes correlate with the clinical...
ARID and PPARG transcription factors). Follicular hyperplasias display higher methylation levels (52.88%) than FL (38.36%) and ... By Methyl II array qPCR, we show that BCL6 methylation does not vary among samples. KLF4, DAPK1 and SPG20, show statistically ... Quantitative CpG promoter methylation analysis was performed by pyrosequencing after bisulfite conversion or by Methyl II array ... Poster Presentations - DNA Methylation 2. *. Abstract LB-281: Meta analysis of gene transcripts from fatty livers and liver ...
DNA - New World Encyclopedia
The transcription factors do this in two ways. Firstly, they can bind the RNA polymerase responsible for transcription, either ... correlate with the methylation of cytosine. For example, cytosine methylation, to produce 5-methylcytosine, is important for X- ... These proteins are important in bending arrays of nucleosomes and arranging them into more complex chromatin structures. ... making the DNA more or less accessible to transcription factors and changing the rate of transcription. Other non-specific ...
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines | Genome Biology | Full Text
Here we measured methylation levels at 22,290 CpG dinucleotides in lymphoblastoid cell lines from 77 HapMap Yoruba individuals ... Association analyses of methylation levels with more than three million common single nucleotide polymorphisms (SNPs) ... Finally, there was a significant overlap of SNPs that were associated with both methylation and gene expression levels. Our ... Furthermore, there was an enrichment of SNPs that affect both methylation and gene expression, providing evidence for shared ...
DNA-Protein Microarrays | Grace Bio-Labs, Oregon
A recent study exploited the high-throughput power of protein microarrays to examine a large repertoire of human transcription ... This large study used 154 methylated DNA sequences to probe individual arrays of over 1500 transcription factors and associated ... et al., DNA methylation presents distinct binding sites for human transcription factors, 2013. eLife; 2:e00726. ... oligonucleotides are used to probe a protein array of potential transcription factors. The protein-DNA interactions were ...
DNA Methylation Restricts Lineage-specific Functions of Transcription Factor Gata4 during Embryonic Stem Cell Differentiation |...
... cRNA probe was prepared using a two-cycle target-labeling assay and hybridized to Affymetrix MOE430v2 oligonucleotide arrays as ... Transcription factor and co-factor networks regulate cell-specific gene programs, allowing a given transcription factor to be ... In these cases, DNA methylation suppresses a limited number of gatekeeper transcription factors. The loss of DNA methylation de ... Transcription factors and epigenetic mechanisms coordinately regulate these processes , . Transcription factors play ...
Microarrays:Tiling Salt Lake City, Utah
... transcription factors, polymerases, modified histones, etc.), mapping of DNA modifications (methylation), mapping of coding and ... For two color arrays, there is no need to have a matching input control on every chip. You can treat the different colors ... Tiling arrays are being used for a variety of purposes including the mapping of binding sites for DNA binding proteins ( ... Tiling microarrays represent an extension of expression arrays. They are designed to interrogate both coding and non-coding ...
Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication
Dysregulation of a transcription factor (e.g. cMyc) can be a cause for human diseases including cancer. Newly-identified ... DNA methylation, and histone mappings (Cawely et al., 2004; Kim et al., 2005; Sun et al., 2003). The ChIP-chip approach has ... Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of ... tiling array-based ChIP-chip technique has been utilized for a whole genome-wide localization of transcription factor binding ...
Regulation of Drosophila intestinal stem cell maintenance and differentiation by the transcription factor Escargot | The EMBO...
... genome tiling arrays (Roche) at the FlyChip facility (www.flychip.org.uk). Original data are deposited in NCBIs Gene ... which led to the methylation of DNA surrounding Esg binding sites in vivo. Genomic DNA was then extracted from midguts, and the ... Nieto MA (2002) The snail superfamily of zinc‐finger transcription factors. Nat Rev Mol Cell Biol 3: 155-166. ... The escargot (esg) gene encodes a transcription factor that is expressed in stem cells in multiple tissues in Drosophila ...
Lund University Publications
Genome Wide Array Based Methylation Profiling Reveals Preferential Methylation of Homeobox Transcription Factor Genes In Mantle ... Array-based genomic screening at diagnosis and during follow-up in chronic lymphocytic leukemia Gunnarsson, Rebeqa LU ; ... Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays ... Mantle cell lymphoma displays a homogenous methylation profile: A comparative analysis with chronic lymphocytic leukemia ...
Insights into the Dichotomous Regulation of SOD2 in Cancer. - PubMed - NCBI
a) Transcription factors that activate SOD2 transcription are shown in green, while repressors are represented in red. The ... the proximal promoter to Intron 2 and confirmed DNA methylation marks from bisulfite sequencing and methylation bead arrays. ... including downregulation by epigenetics and activation by stress response transcription factors, further research is required ... b) Red arrows show areas of demonstrated DNA methylation. Corresponding University of California Santa Cruz (UCSC) Genome ...
Microarray Evidences the Role of Pathologic Adipose Tissue in Insulin Resistance and Their Clinical Implications
... transcription factors, and mitochondrial maintenance. However, insulin treatment altered the transcription of 29 additional ... Sixth, the assessment of adipose tissue transcription control by study of genomewide gene methylation studies and microRNA by ... is a powerful technique of assessment of gene function by measuring transcription of large number of genes in an array. This ... They find activating transcription factor (ATF) 3 (a member of the ATF/cAMP response element-binding protein family of basic ...
Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff (Phylloscopus collybita...
... transcription factors, RNA processing, and methylation), but there was a diverse array of other functions in this class of ... The genes were mainly involved in functions related to ion transport, expression regulation (transcription factors, histone ... transcription factors, histone binding, and phosphorylation), muscle development, learning (ARF4), sensory perception of sound ... and these genes have functions related to gene expression regulation via histone methylation (KDM4C), microtubule activity, and ...
DNA - Wikipedia
Each transcription factor binds to one particular set of DNA sequences and activates or inhibits the transcription of genes ... The average level of methylation varies between organisms - the worm Caenorhabditis elegans lacks cytosine methylation, while ... These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that make up ... The transcription factors do this in two ways. Firstly, they can bind the RNA polymerase responsible for transcription, either ...
Genome-wide DNA methylationTranscriptionalDifferentialProteinsLoss of DNA methylationAcetylationSignificant difference of methylation levelsLysine methylationEpigeneticsCytosineVariabilityModificationsDistinctBisulfiteTumorPhosphorylationIncrease in DNA methylationAssociations of DNA methylationConclusionsGeneticPatterns of methylationVariation in methylationExpression and methylationGenomic regionsCpGsDemethylationPromoter RegionsArginine methylationGene methylationHypo-methylationNovo methylationHistone methylationEnhancerMammalsChromosomeEssential epigeneticModificationTumorsComparative genomic hybriPromotersTissueMutationEnhancersAnalysisMicroarrays
Genome-wide DNA methylation5
- To investigate possible contributions of DNA methylation to the aetiology of rheumatoid arthritis with minimum confounding genetic heterogeneity, we investigated genome-wide DNA methylation in disease-discordant monozygotic twin pairs. (biomedcentral.com)
- Genome-wide DNA methylation was assessed in 79 monozygotic twin pairs discordant for rheumatoid arthritis using the HumanMethylation450 BeadChip array (Illumina). (biomedcentral.com)
- Mark E. Pepin et al, Genome-wide DNA methylation encodes cardiac transcriptional reprogramming in human ischemic heart failure, Laboratory Investigation (2018). (medicalxpress.com)
- The aim of this study was to evaluate genome-wide DNA methylation and gene expression in the livers of newborn rats exposed to maternal protein restriction. (plos.org)
- Recent studies, using Illumina Infinium beadarrays, have demonstrated that genome-wide DNA methylation patterns change with age [ 1 - 6 ]. (prolekare.cz)
- Furthermore, the transcriptional regulatory activity of these methylation-dependent TF-DNA interactions has not been explored. (elifesciences.org)
- Since then, the importance of DNA methylation in modulating transcriptional programs during development and differentiation processes has been strongly supported by many studies. (frontiersin.org)
- Transcription factors are also regulated by cofactors, forming complexes that can activate or inhibit transcriptional activity. (qiagen.com)
- While much is known about the transcriptional regulation of the SOD2 gene, including downregulation by epigenetics and activation by stress response transcription factors, further research is required to understand the post-translational modifications that regulate SOD2 activity in cancer cells. (nih.gov)
- Probable helicase-like transcription factor involved in transcriptional gene silencing. (mybiosource.com)
- Associates with SUVR2 and contributes to transcriptional gene silencing at RNA-directed DNA methylation (RdDM) target loci but also at RdDM-independent target loci. (mybiosource.com)
- DNA methylation and demethylation processes together with histone modification affect chromatin condensation and accessibility of transcription factor binding sites, thus either blocking or enabling transcriptional activation. (biomedcentral.com)
- Here we consider the effects on E-cad expression of eight potential regulatory factors: E-cad promoter DNA methylation, the transcript levels of six transcriptional repressors (SNAI1, SNAI2, TCF3, TCF8, TWIST1, and ZFHX1B), and E-cad DNA copy number. (aacrjournals.org)
- That might, in principle, be achieved through the use of agents that reverse promoter region methylation or by knocking down relevant transcriptional repressors. (aacrjournals.org)
- Distinct histone lysine methylation marks are involved in transcriptional repression linked to the formation and maintenance of facultative heterochromatin, although the underlying mechanisms remain unclear. (uniprot.org)
- Major progress has identified key transcriptional and signaling regulators of self-renewal and lymphomyeloid potential ( 1 - 3 ), organized their activity into defined modules ( 4 - 7 ), and resolved how shared transcription factors govern distinct lineage fate programs depending on timing and context of expression ( 8 ). (jimmunol.org)
- Adaptation to hypoxia is mediated through a coordinated transcriptional response driven largely by hypoxia-inducible factor 1 (HIF-1). (pnas.org)
- This transcriptional program is mediated, at least in part, by activation of the heterodimeric transcription factors hypoxia-inducible factor 1 and 2 (HIF-1 and HIF-2). (pnas.org)
- Transcriptional inactivation by CpG island promoter hypermethylation is a well-established mechanism for gene silencing in cancer including bladder cancer ( 8-18 ), and aberrant methylation is associated with stage, grade of the tumors as well as recurrence rate and progression ( 19-24 ). (aacrjournals.org)
- Generally, the process of gene transcription by RNA polymerase II can be described by three stages: 1) initiation, which involves the assembly of the transcriptional machinery at the gene promoters, 2) elongation of the nascent transcript, and finally, (3) termination, with release of the full-length transcript that is processed to yield mature mRNA (15, 16). (schoolbag.info)
- We used two different types of Affymetrix DNA-microarrays (430 2.0 arrays and ST 1.0 exon arrays) to characterize the global PU.1-regulated transcriptional program underlying the early processes of macrophage differentiation. (omicsdi.org)
- We validated and extended the Beadchip data using bisulfite sequencing (bis-seq), and analyzed differential methylation (DM) at the CpG-level and by an element-level classification for groups of CpGs in chromatin domains. (datamed.org)
- Here we describe array peptide screening (APS), a systematic and differential approach to detect PTM-dependent interactions in the human proteome using chemically synthesized, biotinylated peptides coupled to fluorophore-labeled streptavidin. (nature.com)
- Figure 1: Differential proteomic array peptide screening (APS). (nature.com)
- Figure 2: Result of a differential proteomic array screening using nonmodified and asymmetrical R3me2-modified C/EBPβ peptide baits. (nature.com)
- These changes occur at a genome-wide level and are distinct from genetic variants that impact DNA methylation variability in targeted genomic regions, for example, genetic polymorphisms associated with differential methylation in the H19/IGF2 locus [ 9 ]. (biomedcentral.com)
- This method uses the Illumina Infinium HumanMethylation450K Beadchip CpG methylation array data from paired lung cancer and adjacent normal tissues in The Cancer Genome Atlas (TCGA) and histone modification marker CHIP-Seq data from the ENCODE project, to predict the differential expression of RNA-Seq data in TCGA lung cancers. (biomedcentral.com)
- Discordant twins were tested for both differential DNA methylation and methylation variability between rheumatoid arthritis and healthy twins. (biomedcentral.com)
- Through genome-wide analysis of DNA methylation in disease-discordant monozygotic twins, we have identified a differentially variable DNA methylation signature, in the absence of differential methylation in rheumatoid arthritis. (biomedcentral.com)
- To our knowledge, all studies of DNA methylation in relation to RA have focussed on the identification of DMPs or DMRs, which describe differential DNA methylation levels at a particular CpG site or closely spaced group of CpG sites, respectively. (biomedcentral.com)
- Differential activation of IFN regulatory factor (IRF)-3 and IRF-5 transcription factors during viral infection. (springer.com)
- The data showed that maternal protein restriction is associated with widespread differential gene expression and DNA methylation across the genome, and that folic acid is able to reset both molecular signatures. (plos.org)
- Assessment of serum cfDNA methylation of OPCML and HOXD9 as differential biomarkers of CCA and other biliary diseases showed the area under curve (AUC) of 0.850 (0.759-0.941) for OPCML which sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy were 80.00%, 90.00%, 88.88%, 81.81%, and 85.00%, respectively. (biomedcentral.com)
- Our findings suggest the application of serum cfDNA methylation of OPCML and HOXD9 for differential diagnosis of CCA and other biliary diseases due to its less invasiveness and clinically practical method which may benefit the patients by preventing the misdiagnosis of CCA and avoiding unnecessary surgical intervention. (biomedcentral.com)
- Cancer epigenome studies have demonstrated that cancer-associated DNA methylation changes exhibit differential patterns at different length scales, with local hypermethylation at CpG islands (CGIs) often immersed within large-megabase scale blocks of widespread hypomethylation [ 17 , 18 ]. (prolekare.cz)
- You could take a look at the limma package, as it handles differential methylation (similar to gene expression). (biostars.org)
- In mammals, the methylation of CpG sites-which consist of a cytosine base next to a guanine base-is typically thought to reduce gene expression by preventing proteins called transcription factors from binding to regions of DNA called promoters. (elifesciences.org)
- This can occur directly if methylation disrupts interactions between the DNA and the transcription factors, or indirectly if other proteins that bind to the methylated DNA compete with the transcription factors for binding sites. (elifesciences.org)
- have screened the entire family of roughly 1300 human transcription factors and 210 co-factors (proteins that interact with transcription factors) for their ability to bind to some 150 different stretches of methylated DNA. (elifesciences.org)
- KLF4, DAPK1 and SPG20, show statistically significant methylation increases in FL and DLBCL compared to follicular hyperplasias, indicating a possible role of these proteins in lymphoma pathogenesis. (aacrjournals.org)
- Tiling arrays are being used for a variety of purposes including the mapping of binding sites for DNA binding proteins (transcription factors, polymerases, modified histones, etc.), mapping of DNA modifications (methylation), mapping of coding and non-coding RNA transcripts (transcriptomics), and identifying sequence gain and loss (aCGH). (utah.edu)
- These modifications control the accessibility of DNA and the recruitment of transcription factors and other proteins through their specialized targeting domains. (frontiersin.org)
- Both proteins are closely related to distinct components of budding yeast Paf1C, a transcription factor that assists in establishment and maintenance of transcription-promotive chromatin modifications such as ubiquitination of H2B by Bre1/Rad6 and methylation of histone H3 lysine-4 by the trithorax-related histone methylase Set1. (plantcell.org)
- These include chromatin-remodeling factors, which displace nucleosomes along the DNA, and histone-modifying enzymes, which add or remove various posttranslational modifications including small chemical groups (acetylation, phosphorylation, and methylation) and proteins (ubiquitination and SUMOylation) on nucleosomal histones. (plantcell.org)
- Although significant progress has defined the major transcription factors that regulate lineage specification, the architectural proteins that globally coordinate DNA methylation, histone modification, and changes in gene expression are poorly defined. (jimmunol.org)
- In vitro methylation assays, on the other hand, are useful biochemical assays, which are sensitive, and consistently reveal if the identified proteins are indeed PRMT substrates. (jove.com)
- The exquisite specificity with which gene networks are expressed is mediated by regulatory proteins called transcription factors. (schoolbag.info)
- The most intensively studied of these are the various transcription factors, which are proteins that regulate transcription. (blogspot.com)
- The specificity of these transcription factors' interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to "read" the DNA sequence. (blogspot.com)
- The MODified Histone Peptide Array* is a valuable research tool that can be used to screen antibodies, enzymes and proteins for cross-reactivity or binding interactions with histones and their post-translational modifications (PTM). (activemotif.com)
- Antibodies, Enzymes and Protein Domains - Active Motif offers a broad selection of histone modification antibodies , HAT , HDAC , HMT or HDM proteins and bromodomains that can be utilized in combination with the MODified Histone Peptide Array. (activemotif.com)
- The MODified Histone Peptide Array is designed to study the binding specificity of antibodies, enzymes and proteins. (activemotif.com)
- The addition of a methyl group displaces transcription factors that normally bind to the DNA and attracts methyl-binding proteins associated with gene silencing. (xtalks.com)
- Coupled with GenePix® Pro Microarray Image Analysis Software and Acuity® Microarray Informatics Software, the GenePix Systems provide powerful, flexible, and easy-to-use solutions for the acquisition and analysis of data from all types of arrays, including nucleic acids , proteins, tissues, and cells. (moleculardevices.com)
- Result The short-term effects of YY1 knockdown on the transcription of the domain Out of three siRNA constructs made to knockdown YY1, we discovered one build that consistently reduced the YY1 proteins level in transiently transfected cells of both Neuro2A (Fig.1A) and NIH3T3 TAE684 small molecule kinase inhibitor (data not shown). (bioscience2006.org)
Loss of DNA methylation2
- In cancers cells, massive global loss of DNA methylation (hypomethylation) has been observed, and such hypomethylation in promoters can activate aberrant expression of oncogenes [ 7 ]. (biomedcentral.com)
- CpG dinucleotides outside CpG islands are generally hypermethylated in normal cells and undergo a substantial loss of DNA methylation in cancers. (aacrjournals.org)
- All histones are subject to some level of methylation or acetylation, which would either open up or close the local chromatin structures to enable or repress gene expression. (biomedcentral.com)
- This pattern of silencing was reflected by increased methylation and decreased acetylation of histone H3 K9 in the transgene. (whiterose.ac.uk)
- Chemical modifications of these basic amino acid residues include methylation, phosphorylation and acetylation. (blogspot.com)
- The MODified Histone Peptide Arrays screen 59 acetylation, methylation, phosphorylation, and citrullination modifications on the N-terminal tails of histones H2A, H2B, H3 and H4. (activemotif.com)
Significant difference of methylation levels2
- Results Comparison of FSHD1, FSHD2 and Control subjects showed a highly significant difference of methylation levels in all CpGs tested. (bmj.com)
- The significant difference of methylation levels of OPCML and HOXD9 was observed in serum cfDNA of CCA compared to other biliary diseases. (biomedcentral.com)
- Conclusions These data point to the CpGs distal to the D4Z4 array as a critical region reflecting multiple factors affecting the epigenetics of FSHD. (bmj.com)
- Epigenetics is the study of heritable modifications of DNA which can alter gene expression without changing the DNA sequence and which can be influenced by environmental factors, such as smoking [ 4 ]. (biomedcentral.com)
- Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits Epigenetics Chromatin. (usc.edu)
- suggests that methylated cytosine can effectively act as a 'fifth base'-in addition to adenine, cytosine, guanine and thymine-and emphasizes the importance of DNA methylation for regulating gene expression. (elifesciences.org)
- The most widely researched type of DNA methylation in human is the cytosine methylation of CpG islands and their associated regions, such as CpG shores [ 5 ]. (biomedcentral.com)
- For instance, hydrogen peroxide acts as a nucleophile to deprotonate the cytosine molecule at the C-5 position, which accelerates the reaction of DNA with the positive-charged intermediate S-adenosyl-L-methionine in the process of DNA methylation [ 12 ]. (biomedcentral.com)
- DNA methylation is a heritable epigenetic modification process whereby CpG dinucleotides are methylated at the C5 position of cytosine. (rth.dk)
- Methylation is an epigenetic modification that involves the addition of methyl groups to cytosine residues, resulting in down regulation of gene expression. (xtalks.com)
- CpG dense regions (containing high frequency of repeated cytosine adjacent to guanine via phosphodiester bond) are hot spots for methylation and governs cellular differentiation and functioning. (xtalks.com)
- The methylation variability signature was then compared with methylation variants from studies of other autoimmune diseases and with an independent healthy population. (biomedcentral.com)
- This methylation variability signature also highlighted potential epigenetic disruption of multiple RUNX3 transcription factor binding sites as being associated with disease development. (biomedcentral.com)
- Intra-Gene DNA Methylation Variability Is a Clinically Independent Prognostic Marker in Women's Cancers. (nih.gov)
- We introduce a novel per-gene measure of intra-gene DNA methylation variability (IGV) based on the Illumina Infinium HumanMethylation450 platform, which is prognostic independently of well-known predictors of clinical outcome. (nih.gov)
- b) The intra-gene methylation variability (IGV) is calculated from the variation around the mean methylation level, i.e., from the dashed vertical lines, and is similarly calculated separately for the TSS200 and gene body genomic regions. (nih.gov)
- Functional methylomes have been mapped using next generation capture sequencing technologies to distinguish variability in methylation patterns between cell types and disease. (xtalks.com)
- Post-translational modifications (PTMs) of transcription factors alter interactions with co-regulators and epigenetic modifiers. (nature.com)
- DNA methylation is one of the best studied epigenetic modifications and one major constituent of the epigenome of a cell. (aacrjournals.org)
- Epigenetic aberrations involving DNA methylation, histone modifications, and noncoding miRNA dysregulation have been shown to be intimately linked with and play a critical role in tumour initiation, progression, and metastases. (hindawi.com)
- It also depends on the organization of the chromatin, including covalent modification of nucleotides, such as cytidine methylation, and post-translational modifications of histones, which form the core of nucleosomes around which DNA is wrapped. (frontiersin.org)
- Alteration of epigenetic enzyme activity, histone modifications and DNA-methylation is, in fact, typically associated with the ageing process. (mdpi.com)
- Several forms of epigenetic regulation exist and these include histone modifications and DNA methylation. (aacrjournals.org)
- The arrays are glass slides that contain up to four histone post-translational modifications per peptide to allow for analysis of individual histone modifications as well as the effects of neighboring modifications. (activemotif.com)
- These modifications can be stably inherited and undergo continuous changes throughout the cellular lifetime, influenced by environment and other factors. (xtalks.com)
- Grey lines indicate three regions with distinct methylation profiles. (elifesciences.org)
- Moreover, some transcription factors and co-factors bind to methylated and non-methylated DNA targets with distinct sequences. (elifesciences.org)
- Genome-wide methylation characterization by arrays in diagnostic T-ALL samples identified two distinct methylation subgroups denoted CIMP+ (CpG Island Methylator Phenotype high) and CIMP- (low). (diva-portal.org)
- Unsupervised hierarchical clustering separated the tumors into two distinct methylation groups (clusters A and B), where cluster B had higher average methylation and increased number of hypermethylated CpG sites (CpGs). (diva-portal.org)
- Overall design: Bisulfite converted DNA from 9 primary cell cultures of endometriosis stromal cells from ovarian ectopic sites (OESC) and control endometrial stromal cells (CESC) were hybridized to the Illumina Infinium 450k Human Methylation Beadchip. (datamed.org)
- Quantitative CpG promoter methylation analysis was performed by pyrosequencing after bisulfite conversion or by Methyl II array qPCR on genomic DNA. (aacrjournals.org)
- Methods We investigated, by bisulfite sequencing, the DNA methylation levels of the region distal to the D4Z4 array selectively in PAS-positive alleles. (bmj.com)
- However, we did not find that DAPK promoter methylation was associated with gender status and tumor histology. (cancerindex.org)
- Follicular hyperplasias display higher methylation levels (52.88%) than FL (38.36%) and DLBCL (32.65%) on SIRT1 promoter suggesting a possible inverse correlation between tumor aggressiveness and SIRT1 methylation. (aacrjournals.org)
- Epigenetic changes in SIRT1 methylation inversely correlate with NHL aggressiveness (decreasing in the order: follicular hyperplasias - FL - DLBCL), while KLF4, DAPK1 and SPG20 show a methylation increase that correlates with tumor aggressiveness. (aacrjournals.org)
- Since understanding the molecular dysregulation of such processes in cancer cells will lead to disentangle tumor progression, ChIP-seq, miRNA-seq and methylation arrays serve as basis for epigenetic studies. (dsmz.de)
- Signaling through interferon regulatory factor-5 sensitizes p53-deficient tumor to DNA damage-induced apoptosis and cell death. (springer.com)
- In this study, 45 tumor samples, 12 tumor-free kidney cortex tissues, and 24 peripheral blood samples from patients with clear cell RCC (ccRCC) were analyzed by genome-wide promoter-directed methylation arrays and related to clinicopathological parameters. (diva-portal.org)
- DNA methylation classification of ccRCC tumor samples at diagnosis can serve as a clinically applicable prognostic marker in ccRCC. (diva-portal.org)
Increase in DNA methylation2
- Although all classes of annotated genomic regions assessed show an increase in DNA methylation over time, probes located in intragenic regions, enhancers and low-density CpG promoters are significantly over-represented, while CpG islands and high-CpG density promoters are depleted among the most dynamic probes. (biomedcentral.com)
- Also, the promoter genomic regions showing an increase in DNA methylation at day 7 relative to day 1 are significantly enriched with a number of transcription factors binding motifs including those of Mfsd6l, Mef2c, Meis3, Tead4, and Runx1. (biomedcentral.com)
Associations of DNA methylation3
- In conclusion, we report novel associations of DNA methylation with oxidative stress, some of which also show evidence of a relation with T2D incidence. (biomedcentral.com)
- Inverse associations of DNA methylation at cg25365794 ( ALOXE3 ) and cg08862778 ( MTOR ) with 8-isoprostane levels were observed in a derivation set ( n = 1000) and validated in two independent subsets of the cohort ( n = 548 and n = 741). (biomedcentral.com)
- Multivariate regression models were used to evaluate the associations of DNA methylation at the two CpG sites with lung, colorectal, prostate, breast, and overall cancer incidence as well as CVD, cancer, and all-cause mortality. (biomedcentral.com)
- DNA and the biological processes centered on its activities (translation, transcription, replication, genetic recombination , and so forth) are amazing in their complexity and coordination. (newworldencyclopedia.org)
- Our results demonstrate a strong genetic component to inter-individual variation in DNA methylation profiles. (biomedcentral.com)
- Both lines of evidence suggest genetic variants associated with gene expression variation are located predominantly near transcription start sites. (biomedcentral.com)
- To better understand the role of genetic variation in controlling DNA methylation variation, and its resulting effects on gene expression variation, we studied DNA promoter methylation across the genome in 77 human lymphoblastoid cell lines (LCLs) from the HapMap collection. (biomedcentral.com)
- Although influenced by both intrinsic and extrinsic factors, the genetic mechanisms coordinating the decision between self‐renewal and initiation of differentiation remain poorly understood. (embopress.org)
- Its precise etiology is unknown but expected to have a genetic component and is complex, that is, contributed by both hereditary and environmental factors [ 17 , 18 ]. (hindawi.com)
- Some racial groups like Pima Indians and Asian Indians have strong genetic factor in their increased susceptibility to develop diabetes [ 19 - 22 ]. (hindawi.com)
- The extent to which development- and age-associated epigenetic changes are influenced by genetic, environmental and stochastic factors remains to be discovered. (biomedcentral.com)
- C. Yang, L. Wang, S. Zhang, H. Zhao (2013) Accounting for non-genetic factors by low-rank representation and sparse regression for eQTL mapping. (yale.edu)
- Rheumatoid arthritis is a common autoimmune disorder influenced by both genetic and environmental factors. (biomedcentral.com)
- Epigenome-wide association studies can identify environmentally mediated epigenetic changes such as altered DNA methylation, which may also be influenced by genetic factors. (biomedcentral.com)
- The most widely studied epigenetic phenomenon is DNA methylation, which may act as a composite measure of numerous environmental exposures, making it an intriguing candidate for investigation of diseases that involve both genetic and environmental factors, such as RA. (biomedcentral.com)
- Disease-discordant MZ twin pairs offer an ideal study design as they are matched for many factors, including genetic variation and as such they offer a crucial advantage in epigenetic studies [ 11 ]. (biomedcentral.com)
- Genetic variants and disease-associated factors contribute to enhanced interferon regulatory factor 5 expression in blood cells of patients with systemic lupus erythematosus. (springer.com)
- It is widely considered that the primary determinants of risk of non-communicable diseases derive from a combination of environmental factors and the cumulative effects of multiple genetic variations . (plos.org)
- We integrated genome-wide genetic data to identify methylation-associated quantitative trait loci robustly associated with 16 of the 18 MVPs and found one MVP, cg00574958 at CPT1A , with a possible direct causal role in T2DM. (diabetesjournals.org)
- Diagnostic tissue samples from 115 ccRCC patients were analysed by Illumina HumanMethylation450K arrays and methylation status of 155,931 promoter associated CpGs were related to genetic aberrations, gene expression and clinicopathological parameters. (springer.com)
- Dr. Elin Grundberg has been an Assistant Professor at McGill University since 2012, where her group in the Department of Human Genetics is applying various next-generation sequencing approaches to understand genetic and epigenetic factors underlying complex disease susceptibility. (xtalks.com)
Patterns of methylation1
Variation in methylation1
Expression and methylation1
- We found that the methylome transition from day 1 to day 7 is characterized by the excess of genomic regions which gain over those that lose DNA methylation. (biomedcentral.com)
- a) The mean methylation level over a specific genomic region is calculated separately for the TSS200 (promoter) and gene body genomic regions. (nih.gov)
- In a pilot, genome-scale study of DNA from buccal epithelium, a relatively homogeneous tissue, we show that one-third of the CpGs assayed show dynamic methylation between birth and 18 months. (biomedcentral.com)
- We identified a promoter methylation classifier (PMC) panel consisting of 172 differently methylated CpGs accompanying progress of disease. (springer.com)
- Higher TNM stage was correlated to an increase in average methylation level (p = 0.003) and number of hypermethylated CpGs (p = 0.003), whereas a number of hypomethylated CpGs were mainly unchanged. (diva-portal.org)
- However, the application of genome-wide approaches has allowed the analysis of DNA methylation in different genomic contexts revealing a more dynamic regulation than originally thought, since active DNA methylation and demethylation occur during cellular differentiation and tissue specification. (frontiersin.org)
- DNA methylation, especially CpG methylation at promoter regions, has been generally considered as a potent epigenetic modification that prohibits transcription factor (TF) recruitment, resulting in transcription suppression. (elifesciences.org)
- In higher eukaryotes, methylation of CpG sites, especially at promoter regions, is generally considered as the hallmark of gene silencing ( Baylin, 2005 ). (elifesciences.org)
- In mammals, DNA methylation is mediated by DNA methyltransferases (DNMTs) that are responsible for de novo methylation and maintenance of methylation patterns during replication. (biomedcentral.com)
- Cooperates with PolIVb to facilitate RNA-directed de novo methylation and silencing of homologous DNA. (mybiosource.com)
- L3MBTL1, a histone-methylation-dependent chromatin lock. (uniprot.org)
- We found that the family of 2-oxoglutarate-dependent dioxygenases are coordinately targeted by HIF, and up-regulated expression helps maintain global levels of histone methylation under hypoxic conditions. (pnas.org)
- dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression Nucleic Acids Res. (usc.edu)
- The pattern of gene transcription depends on the dynamic interplay of numerous transcription factors, binding to promoter, enhancer, and silencer regions. (frontiersin.org)
- The pioneer factor FOXA1 has been shown to induce functional enhancer competency through chromatin openings. (harvard.edu)
- Another example is TENET, an analytical approach that associates genome-wide expression changes of transcription factors with gain or loss in enhancer activities by correlating DNA methylation levels at enhancers with the gene expression of transcription factors [ 4 ]. (biomedcentral.com)
- FSHD1 is caused by contraction of the highly polymorphic D4Z4 macrosatellite repeat array on chromosome 4q35. (bmj.com)
- DNA methylation occurs during critical normal processes like development, genomic imprinting, and X-chromosome inactivation ( 2-4 ). (aacrjournals.org)
- The file is organized by columns, containing the chromosome number, position on chromosome, and percentage of methylation for that location for each subject (15 subjects total). (biostars.org)
- The most common form of FSHD, FSHD1 (Online Mendelian Inheritance in Man [OMIM] entry 158900), is linked to contractions of a D4Z4 macrosatellite repeat array in the subtelomere of chromosome 4 at 4q35.2 ( 3 - 5 ). (asm.org)
- In the general healthy population, this repeat array varies between 11 and 100 D4Z4 repeats on both 4q chromosomes, whereas in FSHD1 patients the array is contracted to 1 to 10 repeats on one chromosome, with a requirement for at least one D4Z4 unit to develop disease. (asm.org)
- For example, members of the C/EBP transcription factor family are extensively methylated on arginine and lysine residues in short, conserved, modular domains, implying modification-dependent cofactor docking. (nature.com)
- It considers a comprehensive list of 1424 features spanning the four categories of CpG methylation, histone H3 methylation modification, nucleotide composition, and conservation. (biomedcentral.com)
- The selected features cover all four data types, with histone H3 methylation modification (32 features) and CpG methylation (15 features) being most abundant. (biomedcentral.com)
- This genome marking process includes modification of DNA by methylation at CpG sites and modification of the chromatin around which DNA is wound. (plos.org)
- MODified Histone Peptide Array - peptide arrays contain 384 unique histone modification combinations. (activemotif.com)
- Active Motif uses the Histone Peptide Array to help validate the binding specificity of our histone modification antibodies. (activemotif.com)
- We investigated the methylation in bladder cancer with respect to location in genome, consistency, variation in metachronous tumors, impact on transcripts, chromosomal location, and usefulness as urinary markers. (aacrjournals.org)
- The methylation of metachronous tumors was stable and targeted to certain pathways. (aacrjournals.org)
- However, the predicted age of the tumors based on methylation profile did not correlate with TNM stage, morphological grade, or methylation cluster. (diva-portal.org)
Comparative genomic hybri2
- It has been shown that CpG methylation tends to occur in promoters located upstream of the transcription starting site [ 6 ], and increased methylation (hypermethylation) in the promoter is negatively associated with the gene expression level[ 1 ]. (biomedcentral.com)
- CpG sites within CpG islands are usually in an unmethylated state permissive to transcription in normal cells but become hypermethylated at certain promoters in cancers. (aacrjournals.org)
- These sites extend beyond just the CpG-dense regions near promoters which current arrays tend to be bias toward (eg. (xtalks.com)
- We have expressed a dominant-negative that inhibits both the C/EBP and JUN family of transcription factors in fat tissue. (cancer.gov)
- The main advantage of using the TCGA gene expression data set is its multidimensional data, i.e., it holds gene expressions for each single sample derived from different array origin, which is normalized, annotated, and validated for the expression variation relevance with the type of tissue rather than with type of array generation. (aacrjournals.org)
- Here, we report a systematic analysis of DNA methylation profiling data from various tissue types to elucidate the mechanism underlying the derepression of the CTAs in cancer. (biomedcentral.com)
- We analyzed the methylation profiles of 501 samples including sperm, several cancer types, and their corresponding normal somatic tissue types. (biomedcentral.com)
- Selective activity of a specific set of enhancers defines tissue-specific gene transcription. (harvard.edu)
- As ALOXE3 is mainly expressed in skin tissue, the observed association might reflect the fact that both DNA methylation at the ALOXE3 gene and urinary 8-isoprostane concentrations depend on the level of OS in tissues. (biomedcentral.com)
- The comprehensive adipose-panel allows parallel assessment of tissue methylation and genotypes. (xtalks.com)
- The provided protocol for RT-qPCR arrays enables straight-forward microRNA expression analysis. (biomedcentral.com)
- Ultra-high-throughput sequencing is emerging as an attractive alternative to microarrays for genotyping, analysis of methylation patterns, and identification of transcription factor binding sites. (nih.gov)
- Clinical effect of DAPK promoter methylation in gastric cancer: A systematic meta-analysis. (cancerindex.org)
- Therefore, we performed a meta-analysis to assess the role of DAPK promoter methylation in GC. (cancerindex.org)
- Thus, the analysis of data from different array origins increases its robustness. (aacrjournals.org)
- Photostable nanoparticles arrayed on glass slides for calibration of fluorescence imaging systems and quantitative analysis. (gracebio.com)
- Additionally, methylation analysis of this region allows the establishment of a rapid and sensitive tool for FSHD diagnosis. (bmj.com)
- In the present study, we performed genome-wide promoter DNA methylation analysis at diagnosis to identify DNA methylation profiles associated with risk for progress. (springer.com)
- DNA methylation analysis at diagnosis in ccRCC has the potential to improve outcome-prediction in non-metastatic patients at diagnosis. (springer.com)
- I tried going over a few bioconductor packages for R as well as different software for methylation analysis, but found no one that can handle this kind of data. (biostars.org)
- The purpose is to run an analysis (similar to a gwsa using Plink, for exmaple) in order to find differences in methylations between the study groups. (biostars.org)
- Hi, has anybody experience in methylation analysis of data generated by Roche GS Junior system? (biostars.org)
- Hi I have a very basic question regarding the analysis of whole genome methylation sequencing dat. (biostars.org)
- Array Analyze Software - free PC compatible software program to analyze spot intensities and generate Excel-based files with raw data and graphical analysis. (activemotif.com)
- Microarrays was once the mainstay of the transcriptomics the last ten years and array based technology has subsequently branched out to other areas. (wikipedia.org)
- Tiling microarrays represent an extension of expression arrays. (utah.edu)
- To identify miRNAs regulated by estrogen signaling in breast cancer, their expression in ERα-positive breast cancer cell lines were compared before and after estrogen-activation using both the µParaflo-microfluidic microarrays and Dual Labeled Probes-low density arrays. (jove.com)