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  • expression
  • Expression of clock gene products in the suprachiasmatic nucleus in relation to circadian behaviour. (semanticscholar.org)
  • While gene expression noise has been shown to drive dramatic phenotypic variations, the molecular basis for this variability in mammalian systems is not well understood. (embopress.org)
  • Gene expression has been shown to be regulated by promoter architecture and the associated chromatin environment. (embopress.org)
  • Furthermore, we showed that this independence could be explained by the orthogonal control of mean expression by the transcript burst size and noise by the burst frequency. (embopress.org)
  • Analyses of the molecular basis of gene expression noise by smFISH and flow cytometry show that in mammalian cells, mean expression and noise are uncorrelated across genomic locations and are affected by the local chromatin environment. (embopress.org)
  • Using a dual‐reporter lentiviral system, the influence of the promoter sequence is deconvolved to systematically study how the chromatin environment regulates gene expression noise. (embopress.org)
  • The exposure of cell lines to 5-aza-CdR or TSA resulted in the up regulation of DLC-1 gene expression. (bmj.com)
  • I've kept up with the basic ideas in eukaryotic gene expression in order to teach undergraduate courses on that topic and in order to write appropriate information in my textbook. (blogspot.com)
  • Nuclear reprogramming describes a switch in gene expression of one kind of cell to that of another unrelated cell type. (sciencemag.org)
  • Subsequent procedures included mammalian somatic cell nuclear transfer, cell fusion, induction of pluripotency by ectopic gene expression, and direct reprogramming. (sciencemag.org)
  • They entail nuclear reprogramming, a term that describes a switch in nuclear gene expression of one kind of cell to that of an embryo or other cell type. (sciencemag.org)
  • First, identifying how reprogramming takes place can help us understand how cell differentiation and specialized gene expression are normally maintained. (sciencemag.org)
  • it involves changes in nuclear gene expression but not in gene content. (sciencemag.org)
  • Complementary approaches to assaying global gene expression are needed to assess gene expression in regions that are poorly assayed by current methodologies. (biomedcentral.com)
  • A key component of nearly all gene expression assays is the reverse transcription of transcribed sequences that has traditionally been performed by priming the poly-A tails on many of the transcribed genes in eukaryotes with oligo-dT, or by priming RNA indiscriminately with random hexamers. (biomedcentral.com)
  • Priming with multi-targeted primers in addition to oligo-dT resulted in higher sensitivity, a larger number of well-measured genes and greater power to detect differences in gene expression. (biomedcentral.com)
  • Furthermore, our multi-targeting priming methodology for genome-wide gene expression assays provides selective targeting of multiple sequences and counter-selection against undesirable sequences, facilitating a more complete and precise assay of the transcribed sequences within the genome. (biomedcentral.com)
  • To test these possibilities, we have constructed a series of expression cassettes in which the gene encoding the enhanced green fluorescent protein ( EGFP ) is under the control of DNA fragments containing single and multiple HSs of the LCR. (asm.org)
  • The LCR is marked by several hypersensitive sites (HSs) in erythroid chromatin ( 18 , 45 ) and is required for high-level expression of genes within the HBBC in erythroid cells (reviewed in references 6 and 19 ). (asm.org)
  • HS3 can also enhance expression of globin genes, with its major function seen after integration. (asm.org)
  • HS1 appears to be dispensable, since a naturally occurring deletion encompassing it does not affect β-globin gene expression ( 28 ). (asm.org)
  • Steady state to nuclear runoff ratios are used to determine gene and mRNA structure function relations that leads to gene expression and mRNA stability, predict structural determinants for mRNA stability and predict regulatory motifs for transcription rates. (google.com)
  • Steady state message levels reflect the balance of gene expression (as transcription rate) to mRNA decay rate. (google.com)
  • Expression of the immediate-early gene c- fos has been extensively used as a marker of neural activation, particularly in neuroendocrine systems (for review, see Ref. 25 ). (physiology.org)
  • NEIBank [ 1 , 2 ] is a project for ocular genomics that provides data resources and analytic tools for gene discovery and investigation of gene expression in the eye. (molvis.org)
  • NEIBank is a unified resource for understanding what is known about gene expression in the eye, providing tools for identifying cDNA clones for functional studies, and examining the genomics of human eye disease. (molvis.org)
  • The expression level of different TMPRSS2-ERG fusion genes is correlated to pathologic variables of aggressive prostate cancer and disease progression. (dovepress.com)
  • 4 , 5 Recent studies have found that the expression level of different TMPRSS2-ERG fusion genes is correlated to pathologic variables associated with the progression of aggressive prostate cancer. (dovepress.com)
  • known genes
  • We conclude that, while there are bona fide new intergenic transcripts, their number and abundance is generally low in comparison to known genes, and the genome is not as pervasively transcribed as previously reported. (blogspot.com)
  • This process relies on a combination of identification by sequence identity, overlap with known genes, genome position of the sequence, and quality control measures to identify and filter out erroneous or artifactual data. (molvis.org)
  • susceptibility
  • Evidence suggests that psychotic symptoms may be influenced by genetic factors, and recent studies in schizophrenia, bipolar affective disorder (BPAD) and Alzheimer's disease with psychosis (AD+P) suggest that psychosis susceptibility or modifier genes may act across diseases. (ox.ac.uk)
  • Other studies evaluating more markers, that could potentially modulate RANTES gene transcription alongside other genetic modifiers of malaria susceptibility, may provide further explanations to these less dramatic findings. (biomedcentral.com)
  • genome-wide
  • We analyzed meiotic recombination events genome-wide in mlh3 Δ, pch2 Δ, and mlh3 Δ pch2 Δ mutants to test the effect of variation in crossover frequency on obligate crossovers. (g3journal.org)
  • Although sequence variants in gene promoters and protein-coding regions provide obvious prioritization of disease-causing variants, most (88%) genome-wide association study (GWAS) loci are in non-coding DNA, suggesting regulatory functions 1 . (blogspot.com)
  • Genetics
  • 1 Biology 11 Name: Population Genetics: Changes in the Gene Pool and Gene Frequency Evolution through natural selection describes how populations change over time but it is not the only way that populations can change. (docplayer.net)
  • Saccharomyces
  • We designed an algorithm to find common sequence motifs that were present within most protein-coding genes of Saccharomyces cerevisiae and of Neurospora crassa , but that were not present within their ribosomal RNA or transfer RNA genes. (biomedcentral.com)
  • Examining the response of Saccharomyces cerevisiae to nitrogen deficiency and profiling Neurospora crassa early sexual development, we demonstrated that using multi-targeted primers in reverse transcription led to superior performance of microarray profiling and next-generation RNA tag sequencing. (biomedcentral.com)
  • eukaryotic
  • Methods for determining transcription rate of mRNA in eukaryotic cells using nuclear runoff transcription where labeled RNA molecules are hybridized against an array of at least 500 nucleic acid molecule probes representing at least part of the genome of the native eukaryotic organism to identify the quantity of nascent mRNA transcripts in said cells. (google.com)
  • This invention discloses and provides improvements in analyzing transcription of mRNA in eukaryotic cells using nuclear runoff transcription assays, including analysis of nuclear runoff transcription products by microarrays containing genes of interest, e.g. microarrays of nucleic acid molecules representing a genome of interest. (google.com)
  • phenotype
  • Changes in Phenotype and Genotype Frequency Due to Natural Selection The diagram below shows an imaginary species of beetles with 3 phenotypes determined by the amount of pigment deposited in the cuticle (exoskeleton). (docplayer.net)
  • Phenotype Black Dark Pale Genotype (alleles present) AA = homozygous dominant Aa = heterozygous Aa = homozygous recessive Notice the dark coloured beetles carry the recessive a gene. (docplayer.net)
  • We evaluated the CpG island methylator phenotype pathway characterized by concordant methylation of gene promoters that often silences transcription of the genes, the microsatellite instability pathway, and K- ras and p53 gene status in 247 colorectal carcinomas from the three selected Middle Eastern countries of Egypt, Jordan, and Turkey. (aacrjournals.org)
  • overexpression
  • Western diet characterized by high calories, fat, refined carbohydrates, and animal proteins is associated with p53 mutation and overexpression of the gene product ( 13 , 16 , 17 ). (aacrjournals.org)
  • Fifty percent of patients with positive prostate-specific antigen tests show overexpression of fusion genes of transmembrane protease serine 2 (TMPRSS2) and erythroblastosis virus E26 transformation-specific (ETS) transcription factor family, such as TMPRSS2-ERG (v-ets erythroblastosis virus E26 oncogene homology) 3 , 4 ( Figure 1A ). (dovepress.com)
  • Moran
  • It shows the DNA binding sites of various restriction enzymes on Drosophila melanogaster DNA clones containing hsp70 heat shock genes (Moran et al. (blogspot.com)
  • organisms
  • Methods of constructing recombinant organisms with enhanced stability for mRNA expressed from a gene of interest comprise introducing into the genome of an organism a gene containing one or more sequence elements that confer structural stability on mRNA transcribed from said gene. (google.com)
  • We consider the problem of biological complexity via a projection of protein-coding genes of complex organisms onto the functional space of the proteome. (biomedcentral.com)
  • lineage transcription
  • We hypothesised that oligodendrocyte lineage transcription factor 2 (OLIG2), a regulator of white matter development and a candidate gene for schizophrenia, may also be associated with psychotic symptoms in AD. (ox.ac.uk)
  • polymerase
  • Reverse transcription-polymerase chain reaction (RT-PCR) was used to detect DLC-1 transcripts in RPMI 8226, U266, OPM-2 and XG-2 cell lines. (bmj.com)
  • The postings listed below describe the various steps of transcription and the structure of RNA polymerase. (blogspot.com)
  • It describes the locations of the human genes for RNA polymerase subunits. (blogspot.com)
  • According to our understanding of transcription, it is expected that RNA polymerase will bind accidentally at thousands of sites in the gnome and the probability of initiating the occasional transcript is significant [ How RNA Polymerase Binds to DNA ]. (blogspot.com)
  • State-of-the-art methods for detection of TMPRSS2-ERG fusion genes include reverse transcription polymerase chain reaction (RT-PCR) with a detection limit of 1 fmol at urinary condition. (dovepress.com)
  • factors
  • Transcription factors bind to thousands of sites on the Drosophila genome. (blogspot.com)
  • Here, we show that FoxO transcription factors serve to promote AKT phosphorylation at Ser473 in response to NVP-BEZ235 treatment in renal cancer cells. (aacrjournals.org)
  • I could have done the same experiment using transcription factors. (blogspot.com)
  • If I had several dozen transcription factors from human cells, I could have mapped their binding sites on my Drosophila DNA and made a figure just like the one shown above. (blogspot.com)
  • What they did was to map the sites in human DNA that bind human transcription factors. (blogspot.com)
  • Recent studies have described important roles for lineage-determining transcription factors (LDTFs), also referred to as pioneer factors or master regulators, in selecting cell-type-specific enhancers 12,13,14,15 , but the sequence determinants that guide their binding are poorly understood. (blogspot.com)
  • First, thymocytes that are reprogrammed by the SCL and LMO1 oncogenic transcription factors into self-renewing pre-leukemic stem cells (pre-LSCs) remain non-malignant, as evidenced by their capacities to generate functional T cells. (nih.gov)
  • immunity
  • Previous studies show that variations in the RANTES gene affect RANTES protein production, hence altering host immunity. (biomedcentral.com)
  • abnormal
  • 2 Therefore, a method to determine and differentiate types of fusion genes in patient samples is required to understand the function of abnormal genes in cancer. (dovepress.com)
  • specific gene
  • Finally, we show that specific gene families transposed at specific points in evolutionary time, particularly after whole-genome duplication events in the Brassicales, and suggest that genes in mobile gene families are under different selection pressure than syntenic genes. (plantcell.org)
  • At least for abundantly expressed genes, the frequency of cDNAs from a specific gene provides an indication of the relative level of transcription of that gene. (molvis.org)
  • Regions
  • PCR was performed for regions spanning J H 4, Eμ and Cμ as shown in the scheme above, and for a region within the Cd74 gene as a loading control. (nih.gov)
  • The coding regions of the genes are shown by the solid black bars in the figure. (blogspot.com)
  • CpG islands are 0.5 to 2 kb regions rich in cytosine-guanosine dinucleotides that are present in the 5′ region of about half of all human genes. (aacrjournals.org)
  • Methods
  • Here, we mapped the transcripts produced in an S. cerevisiae strain lacking Set2, and applied rigorous statistical methods to identify sites of cryptic transcription at high resolution. (nih.gov)
  • different
  • Nature paper on transcription factor binding in different mouse strains? (blogspot.com)
  • if you don't have different genes then you don't have different traits. (discovermagazine.com)
  • It is, however, challenging to investigate in vivo mechanisms at the single-cell level because individual cells are not synchronized and are heterogeneous, receiving key signaling at different times and frequencies in the body. (rupress.org)
  • supF = 1.8, 364 transitions) cutoffs are plotted for different gene-length bins. (nih.gov)
  • We found that our assay was able to identify three different types of fusion gene with a wide detection range and detection limit of 1 fmol (almost the same level of the RT-PCR result reported). (dovepress.com)
  • assays
  • Nuclear runoff assays measure transcription rates directly. (google.com)
  • I have discovered and disclose the utility of nuclear runoff assays to generate labeled transcript mRNA hybridization probes for use with transcription profiling arrays. (google.com)
  • fusion gene
  • We also provide follow up regarding a previously published case of histiocytic sarcoma with IGH/BCL2 fusion gene in which the patient subsequently developed follicular lymphoma and, later, diffuse large B-cell lymphoma. (stanford.edu)
  • 6 , 7 The isoform of the fusion gene exon 1 of TMPRSS2 combined with exon 4 of ERG is the most common type of fusion gene in prostate cancer. (dovepress.com)
  • define
  • Back in the olden days, before DNA sequencing became cheap and easy, we used to construct restriction maps of DNA to define genes. (blogspot.com)
  • Thus
  • Thus, the projection of transcription units (TU) and alternative splice-variant (SV) forms onto proteome functional space could generate new types of relational networks (e.g. (biomedcentral.com)
  • Factor
  • What this means is that stretches of coding region contain codons AND transcription factor binding sites (duh! (blogspot.com)
  • Of course, none of those binding sites would be biologically relevant since the binding of a human transcription factor to fruit fly DNA isn't ever gong to happen in the real world. (blogspot.com)
  • For any given transcription factor, there will be about 800,000 binding sites in the human genome. (blogspot.com)
  • The "problem" that it's relatively easy to identify transcription factor binding sites but it's quite another matter to determine if they are functional. (blogspot.com)
  • carcinogenesis
  • Deleted in liver cancer-1 ( DLC-1 ) is a tumour suppressor gene that is inactive in liver carcinogenesis. (bmj.com)
  • tumor
  • Interestingly, the histiocytic tumor component has been shown to harbor BCL2 gene translocations that are identical to those found in the lymphoma. (stanford.edu)
  • ENCODE
  • Genes in the β-globin gene complex ( HBBC , containing HBE1, HBG2, HBG1, HBD , and HBB ), together with those in the α-globin gene complex ( HBZ2, HBA2 , and HBA1 ) encode the developmentally regulated, erythroid-specific family of hemoglobins in vertebrates. (asm.org)
  • mRNA
  • The catalog of genes identified by EST sequencing of an unnormalized, unsubtracted cDNA library reflects a random sample of the mRNA present in the cell. (molvis.org)
  • alleles
  • The gene controlling this trait is represented by 2 alleles (2 forms of the gene) identified as A and a. (docplayer.net)
  • This migration of individuals adds new alleles (forms of a gene) to a population. (docplayer.net)
  • If this colonizing or founder population is made up of only a few individuals, it will probably have a non-representative sample of alleles from the parent population s gene pool. (docplayer.net)