• Rapid immunoprecipitation mass spectrometry of endogenous protein (RIME) is a method that allows the study of protein complexes, in particular chromatin and transcription factor complexes, in a rapid and robust manner by mass spectrometry (MS). The method can be used in parallel with chromatin immunoprecipitation-sequencing (ChIP-seq) experiments to provide information on both the cistrome and interactome for a given protein. (nature.com)
  • The Mammalian Promoter Database (MPromDb) is a curated database of gene promoters identified from ChIP-seq. (wikipedia.org)
  • Chromatin immunoprecipitation, or ChIP, is an antibody-based technology used to selectively enrich specific DNA-binding proteins along with their DNA targets. (cellsignal.com)
  • ChIP is used to investigate a particular protein-DNA interaction, several protein-DNA interactions, or interactions across the whole genome or a subset of genes. (cellsignal.com)
  • ChIP utilizes antibodies that selectively recognize and bind proteins, including histones, histone modifications, transcription factors, and cofactors, to provide information about chromatin states and gene transcription. (cellsignal.com)
  • A combination of proteomic analysis and molecular biology techniques used in ChIP allow for the ability to understand gene expression and regulation in cells or tissues of interest. (cellsignal.com)
  • ChIP can be used to answer a multitude of scientific questions involving the interaction of proteins and chromatin. (cellsignal.com)
  • For example, ChIP can be used to compare the presence of certain proteins at various loci, map the various proteins across a genomic region of interest, or quantify protein binding to an inducible gene in response to a stimulus over time. (cellsignal.com)
  • The principle behind ChIP is relatively straightforward and relies on the use of an antibody to isolate, or precipitate, a certain protein, histone, transcription factor, or cofactor and its bound chromatin from a protein mixture that was extracted from cells or tissues. (cellsignal.com)
  • In N-ChIP, no fixing agent is used to crosslink proteins to the chromatin. (cellsignal.com)
  • In X-ChIP, chemical fixatives such as formaldehyde are used to crosslink the protein of interest to the DNA and fragmentation of chromatin is achieved through sonication or nuclease digestion. (cellsignal.com)
  • X-ChIP also minimizes the chances of chromatin protein loss during extraction, allowing for the detection of transient protein interactions. (cellsignal.com)
  • The most common methods for single gene analysis and whole genome analysis are qPCR and ChIP-seq, respectively. (cellsignal.com)
  • We used chromatin immunoprecipitation, exonuclease digestion, and DNA sequencing (ChIP-exo/seq) to define this architecture in Saccharomyces cerevisiae ," the authors wrote. (genengnews.com)
  • Huh7 cells that overexpress USF1 were used with whole transcriptome profiling through RNA sequencing and chromatin immunoprecipitation (ChIP) sequencing methods to investigate the downstream targets of USF1. (spandidos-publications.com)
  • Furthermore, by conjoint analysis of longissimus dorsi data (tissue-specific expression, muscle module and DE-lncRNAs) and ChIP-PCR revealed NONSUSG002145.1 (adjusted p -values = 0.044), which is coexpressed with the IGF2 gene and binding with ZBED6, may play important roles in ZBED6 KO pig skeletal muscle development. (biomedcentral.com)
  • The Imprint Ultra Chromatin IP Kit is Sigma′s second generation chromatin immunoprecipitation (ChIP) kit developed for maximum sensitivity and optimum next-generation sequencing results. (sigmaaldrich.com)
  • It is optimized for ChIP reactions with chromatin from 10 6 cells (up to ~50 μg DNA), and can also be scaled up (or several preparations pooled) to accommodate 10 8 cells for genome-wide binding studies in ChIP-chip and ChIP-Seq applications. (sigmaaldrich.com)
  • Employs DNA-Blocked 'Staph-Seq' for IP (immunoprecipitation), minimizing contaminating Staph A DNA in downstream ChIP-Seq applications. (sigmaaldrich.com)
  • As ChIP-seq cannot establish physical co-occurrence of two marks on the same allele, admixture of cells that either express (green) or do not express (red) the gene in focus could explain the occurrence of both marks as well as the low expression level in the overall population. (researchgate.net)
  • Here, we present whole-genome chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) analyses of a wide variety of histone markers in the brain, heart, and liver of early human embryos shortly after their formation. (researchgate.net)
  • We demonstrate by electromobility shift assays (EMSA) and chromatin immunoprecipitation (ChIP) that HNF1 binds to this element both in vitro and in vivo. (duke.edu)
  • Scholars@Duke publication: Identification of E2A target genes in B lymphocyte development by using a gene tagging-based chromatin immunoprecipitation system. (duke.edu)
  • The transcription factors encoded by the E2A gene are known to be essential for B lymphocyte development, and ectopic expression or gene inactivation studies have revealed several potential lineage-specific E2A target genes. (duke.edu)
  • However, it remains unknown whether these target genes are directly regulated by E2A at the transcriptional level. (duke.edu)
  • We therefore generated mice carrying an affinity-tagged E2A knock-in allele to provide a system for the direct elucidation of E2A target genes based on E2A binding to target regulatory regions. (duke.edu)
  • This technique has been used to find the target genes of TFs in mammalian systems. (wikipedia.org)
  • In a whole genome screen for direct LXRα target genes, we identified an LXRα occupancy site within the second intron of the Seladin-1/DHCR24 gene. (aspetjournals.org)
  • As a TF, USF1 has a bidirectional regulatory function, being able to regulate gene expression by activating or suppressing the promoter region of target genes ( 5 , 6 ). (spandidos-publications.com)
  • Luciferase assays showed that T471C and C862T could significantly increase the expression efficiency of downstream target genes. (jcancer.org)
  • RIViT-seq technology could speed up associating transcription factors with their target genes. (doe.gov)
  • More recently, increased expression of NOTCH pathway genes was implicated in some DIPGs and NOTCH path inhibition contributed to reduced tumor growth in culture 14 , but the specificity of these treatments for H3.3 mutant cells remains unclear. (nature.com)
  • Moreover, genome instability was attributed to impaired autophagy and several autophagy genes with tumor suppressor functions (e.g. (hindawi.com)
  • This gene is regarded as a potential tumor suppressor gene. (cancerindex.org)
  • OBJECTIVE- We identified lipocalin 2 ( Lcn2 ) as a gene induced by dexamethasone and tumor necrosis factor-α in cultured adipocytes. (diabetesjournals.org)
  • MYC overexpression thus counters tumor growth inhibition by a Stimulator of Interferon Genes (STING) agonist via suppressing induction of interferon signalling. (nki.nl)
  • On the other hand, the increasing availability of high-throughput gene sequencers that are affordable and fit on a desktop or workbench is one powerful-and much-discussed force that encourages decentralization of gene sequencing. (darkdaily.com)
  • Here, we develop a high-throughput indexed Chromatin ImmunoPrecipitation (iChIP) method coupled to massively parallel sequencing to systematically map protein-DNA interactions. (nih.gov)
  • Histone modifications and chromatin-associated protein complexes are crucially involved in the control of gene expression, supervising cell fate decisions and differentiation. (researchgate.net)
  • Background: Bivalent chromatin domains consisting of the activating histone 3 lysine 4 trimethylation (H3K4me3) and repressive histone 3 lysine 27 trimethylation (H3K27me3) histone modifications are enriched at developmental genes that are repressed in embryonic stem cells but active during differentiation. (researchgate.net)
  • The constantly-improving capabilities of these systems means that rapid gene sequencing and whole human genome sequencing will soon take their place in clinical laboratories and anatomic pathology groups. (darkdaily.com)
  • Findings from the new study-published recently in Nature through an article titled, " A high-resolution protein architecture of the budding yeast genome "-mapped precise binding sites of more than 400 different chromosomal proteins in the yeast genome, most of which regulate the expression of genes. (genengnews.com)
  • Enrichment of modifications in each metabolic domain, relative to all the genes in the genome, revealed both shared and diverse patterns. (biorxiv.org)
  • We apply iChIP to reconstruct the physical regulatory landscape of a mammalian cell, by building genome-wide binding maps for 29 transcription factors (TFs) and chromatin marks at four time points following stimulation of primary dendritic cells (DCs) with pathogen components. (nih.gov)
  • My research involves identifying gene regulatory elements across the genome to help us understand how chromatin structure dictates cell function and fate. (duke.edu)
  • Chromatin immunoprecipitation assays identified SOX2-binding sites on COL1A1 and COL1A2, indicating SOX2 as a transcription factor in collagen synthesis. (cdc.gov)
  • In summary, our studies have provided evidence that E2A is directly involved in the transcriptional regulation of a number of early B-lineage genes. (duke.edu)
  • The rat HMGCS2 gene contains elements that control its multihormonal regulation and tissue specificity ( 11 - 14 ). (aacrjournals.org)
  • The research teams describe in a new study an extensive and high-resolution map of chromosome architecture and gene regulation in Saccharomyces cerevisiae -an effort they say is a major step toward improving understanding of development, evolution, and environmental responses in higher organisms. (genengnews.com)
  • The study revealed two distinct gene regulatory architectures, expanding the traditional model of gene regulation. (genengnews.com)
  • The traditional model of gene regulation involves transcription factors, which bind to specific DNA sequences to control the expression of a nearby gene. (genengnews.com)
  • Various levels of regulation, including epigenetic modifications and transcription factors, play important roles in coordinating the expression of genes. (biorxiv.org)
  • To date, our understanding of mammalian gene regulation has been hampered by the difficulty of directly measuring in vivo binding of large numbers of transcription factors to DNA. (nih.gov)
  • The epigenetic regulation of spatiotemporal gene expression is crucial for human development. (researchgate.net)
  • the presence of HDAC7 blocked the induction of key genes for macrophage function, such as immune, inflammatory, and defense response, cellular response to infections, positive regulation of cytokines production, and phagocytosis. (eur.nl)
  • These data provide the first insight into the three- dimensional (3D) structure of the CFTR locus and confirm the contribution of intronic cis-acting elements to the regulation of CFTR gene expression. (duke.edu)
  • Significant E2A binding was detected at the promoters and enhancers of several essential B-lineage genes, including the Igkappa intronic and 3' enhancers, lambda5 and VpreB surrogate light chain promoters, the EBF locus promoter region, and the mb-1 (Igalpha) promoter. (duke.edu)
  • We used RNA sequencing coupled with chromatin immunoprecipitation sequencing to analyze primed microglial inflammatory gene expression and modifications to histone H3 lysine 4 trimethylation (H3K4me3) at the promoters of primed genes. (frontiersin.org)
  • Chromatin-immunoprecipitation-sequencing reveals that MYC, together with its co-repressor MIZ1, directly binds promoters of multiple interferon-signalling genes, resulting in their downregulation. (nki.nl)
  • Results: Data addressing the function of vectors harbouring genes specifically encoding ricin, saporin, lunasin , linamarase, and tomato thymidine kinase 1 under the control of different promoters are summarised here. (weeksmd.com)
  • Bivalent promoters are defined by the presence of both activating (H3K4me3) and repressive (H3K27me3) chromatin marks. (researchgate.net)
  • Experimental work will integrate dynamic cell and single molecule imaging, quantitative proteomics, chromatin immunoprecipitation analysis (for the dynamics of NF-κB binding to target promoters) and RT-PCR and DNA microarray analysis (for measurement of endogenous gene expression). (warwick.ac.uk)
  • We found that HDAC7 specifically interacted with the transcription factor MEF2C in pre-B cells and was recruited to MEF2 binding sites located at the promoters of genes critical for macrophage function. (eur.nl)
  • For the last 30 years, mapping chromatin accessible sites has been the gold standard method to identify the location of active regulatory elements, including promoters, enhancers, silencers, and locus control regions. (duke.edu)
  • Histone post-translational modifications near the expanded repeats are consistent with heterochromatin formation and consequent FXN gene silencing. (frontiersin.org)
  • Surprisingly, specialized metabolic genes, often involved in defense, were predominantly regulated by two modifications that have opposite effects on gene expression, H3K27me3 (repression) and H3K18ac (activation). (biorxiv.org)
  • Using camalexin biosynthesis genes as an example, we confirmed that these two modifications were co-localized to form bivalent chromatin. (biorxiv.org)
  • Mutants defective in H3K27m3 and H3K18ac modifications showed that both modifications are required to determine the normal transcriptional kinetics of these genes upon stress stimuli. (biorxiv.org)
  • To see if there are any interactions between epigenetic modifications across metabolic genes, we computed pairwise Pearson's correlation coefficients between the 16 epigenetic modifications based on their relative abundance at each metabolic gene region. (biorxiv.org)
  • Groups I and II included mainly the epigenetic modifications that activate gene expression. (biorxiv.org)
  • The enrichment patterns of epigenetic modifications were consistent with expression levels of genes involved in each domain under healthy conditions (Fig. S1A). (biorxiv.org)
  • The phytochemical 3,3'-diindolylmethane decreases expression of AR-controlled DNA damage repair genes through repressive chromatin modifications and is associated with DNA damage in prostate cancer cells. (oregonstate.edu)
  • Both genes are involved in transcriptional repression and we speculate their involvement in FXN gene silencing. (frontiersin.org)
  • Based on these findings, we propose that ketogenesis is an undesirable metabolic characteristic of the proliferating cell, which is down-regulated through c-Myc-mediated repression of the key metabolic gene HMGCS2 . (aacrjournals.org)
  • In contrast, metabolic genes involved in specialized and hormone metabolic domains, which are generally involved in interactions with biotic and abiotic environmental stimuli, showed distinct patterns with the enrichment of a repression mark H3K27me3 and an activation mark H3K18ac ( Fig. 1B ). (biorxiv.org)
  • Here we addressed the molecular mechanism behind repression of non-lymphoid genes in B cells. (eur.nl)
  • To gain insight into the molecular mechanisms mediating HDAC7 repression in pre-B cells, we undertook co-immunoprecipitation and chromatin immunoprecipitation experimental approaches. (eur.nl)
  • Eukaryotic expression vectors containing genes encoding plant proteins for killing of cancer cells. (weeksmd.com)
  • consequently, genes encoding some of these proteins are being used to design constructs for the inhibition of multiplying cancer cells. (weeksmd.com)
  • The computational methods that we've developed to analyze this data could serve as a jumping-off point for further development for gene regulatory studies in more complex organisms. (genengnews.com)
  • We characterized a novel LXR response element within the second intron of this gene that is able to confer LXR-specific ligand responsiveness to reporter gene in both HepG2 and human embryonic kidney 293 cells. (aspetjournals.org)
  • Here we show that bivalent domains and chromosome architecture for bivalent genes are dynamically regulated during the cell cycle in human pluripotent cells. (researchgate.net)
  • Forkhead box protein M1 (FOXM1) is a key transcription factor (TF) that regulates a common set of genes related to the cell cycle in various cell types. (mdpi.com)
  • Gene sequencing is the hot technology in both the biotech and clinical laboratory testing industries. (darkdaily.com)
  • That is because the cost of rapid gene sequencing systems is falling rapidly, even as the speed and accuracy of these latest-generation gene sequencers improves significantly. (darkdaily.com)
  • In recent years, the steady stream of technology innovations in gene sequencing have greatly improved the accuracy and the speed of automated gene sequencing systems, while greatly reducing the cost of sequencing a base pair. (darkdaily.com)
  • Thus, smaller laboratories may achieve lower costs and higher quality if they were to outsource their gene sequencing work to an emerging group of service providers. (darkdaily.com)
  • Even more important are the less-discussed user needs that drive the broader demand for smaller, load-and-walk-away gene sequencing systems. (darkdaily.com)
  • Some examples of clinical applications for these smaller gene sequencing systems include panels of tests for oncology, genetic disease, and infectious diseases. (darkdaily.com)
  • The authors observe that technical improvements to second-generation gene sequencers directly contribute to the de-commoditization of other instruments, consumables, software, IT infrastructure, and expertise used in the overall gene sequencing workflow. (darkdaily.com)
  • The effects of this trend can be seen in the noteworthy shift that is occurring in the allocation of spending on gene sequencing components. (darkdaily.com)
  • Gene expression variability, variations within the variety of mRNA per cell throughout a inhabitants of cells, is ubiquitous throughout various organisms with broad impacts on mobile phenotypes. (chipready.com)
  • Mutations in this gene cause various glaucoma phenotypes including primary congenital glaucoma, autosomal dominant iridogoniodysgenesis anomaly, and Axenfeld-Rieger anomaly. (cancerindex.org)
  • In summary, the results demonstrated that USF1 binds to the promoter region of thousands of genes and affects a large part of DEGs indirectly. (spandidos-publications.com)
  • As a proangiogenic response effecter, the interaction of Sema4D with plexin-B1 is dependent on the COOH-terminal PDZ-binding motif of plexin-B1, which binds two guanine nucleotide exchange factors (GEFs) for Rho and is mediated by the activation of Rho-initiated (Ras homolog gene family) pathways ( 4 - 8 ). (jcancer.org)
  • The K27M and G34R mutations induced several of the same pathways suggesting key shared oncogenic mechanisms including activation of neurogenesis and NOTCH pathway genes. (nature.com)
  • What pathways are this gene/protein implicaed in? (cancerindex.org)
  • Yeast cells provide a simple model system with 6,000 genes, most of which are found in other organisms, including humans, making them excellent candidates for studying fundamental genetics and complex biological pathways. (genengnews.com)
  • The upregulated DEGs were primarily protein‑coding genes enriched in immune and inflammation response pathways, while the downregulated DEGs were mainly coding long non‑coding (lnc)RNAs, indicating the regulatory function of USF1. (spandidos-publications.com)
  • Metabolism underpins development and physiology, but little is known about how metabolic genes and pathways are regulated, especially in multicellular organisms. (biorxiv.org)
  • orthogonal exPeriMental changes and pathways induced by EGE investigated the impact of aSSeSSMent of ePigenetic environmental factors in cancer causation, both current H. pylori infection and driver geneS and their link to underpinning studies of etiology e , pigenetic memory of past (eradicated) environMental carcinogenS carcinogen evaluation, and prevention. (who.int)
  • HMGCS2 , the gene that regulates ketone body production, is expressed in liver and several extrahepatic tissues, such as the colon. (aacrjournals.org)
  • The results showed that USF1 significantly regulates 350 differentially expressed genes (DEGs). (spandidos-publications.com)
  • More recently we have demonstrated that C/EBPβ regulates the expression of several genes involved in inflammatory processes and brain injury [ 14 ] and mice lacking C/EBPβ showed a reduced inflammatory response after kainic acid injection and exhibited a dramatic reduction in pyramidal cell loss in the CA1 and CA3 subfields of the hippocampus [ 15 ]. (biomedcentral.com)
  • A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter. (duke.edu)
  • Ionizing radiation together with ERalpha knock down results in additive effect on transcription of endogenous p53-target gene p21 (CDKN1) in human breast cancer cells. (nih.gov)
  • A. Correlation analysis reveals four groups of epigenetic marks, activating (red) and repressing (blue), based on their relative abundance on metabolic genes. (biorxiv.org)
  • Genomic location of these long noncoding RNA is disproportionately enriched near CAD-related TFs (transcription factors), genetic loci, and gene regulators of SMC identity, suggesting the importance of their function in disease. (stanford.edu)
  • We develop a computational model for the hematopoietic erythroid-myeloid lineage decision, which is determined by a genetic switch involving the genes PU.1 and GATA-1. (lu.se)
  • Thus, in B cells HDAC7 is a transcriptional repressor of undesirable genes. (eur.nl)
  • We, therefore, tested the hypothesis that hypoxia would enhance or "prime" microglial pro-inflammatory gene expression in response to a later inflammatory challenge without programmatically increasing basal levels of pro-inflammatory cytokine expression. (frontiersin.org)
  • However, prior to commitment, it has been cells, it is evident that GATA-1 and PU.1 are able to specify observed that many genes are expressed at intermediate or basal erythroid and myeloid cell fates (see [16] and references therein). (lu.se)
  • These ATG genes are highly conserved in mammalian cells, allowing to study their functions also in higher eukaryotes [ 1 - 4 ]. (hindawi.com)
  • Promoter region motif analysis indicated that ETV5 has more binding motifs and genes than USF1 itself for USF1‑regulated DEGs, indicating that USF1 may indirectly modulate gene expression by regulating ETV5 expression in Huh7 cells. (spandidos-publications.com)
  • By interrogating microarray data from neuronal cells treated with inhibitors of different specificity, we selected two genes encoding histone macroH2A ( H2AFY2 ) and Polycomb group ring finger 2 ( PCGF2 ) that were specifically down-regulated by the inhibitors targeting HDACs1 and 3 versus the more selective inhibitors for further investigation. (frontiersin.org)
  • Here we report successful gene editing of H3.3K27M and G34R point mutations in human normal brain and pediatric glioma cells, generating pairs of otherwise isogenic cell lines that allowed us to define epigenetic and transcriptomic changes contributing to gliomagenesis in the native genomic context. (nature.com)
  • Taken together, our findings suggest striking overlap between putative mechanisms of K27M and G34R mutations and point to increased NOTCH signaling playing a key role in K27M-related gliomagenesis, resulting from aberrant gene derepression due to impaired H3K27me3 deposition at super-enhancers in H3.3 mutant cells. (nature.com)
  • To study the transformative effects of oncohistone mutations in human pediatric gliomas in an otherwise isogenic context, we used CRISPR-Cas9 gene editing to revert H3.3K27M mutations in glioma cells back to wild type (WT) while in parallel introducing H3.3K27M and G34R point mutations into human astrocytes and H3.3WT glioma cells (Fig. 1a ). (nature.com)
  • In CaCo-2 colonic epithelial cells, the expression of this gene increases with cell differentiation. (aacrjournals.org)
  • Atherosclerotic plaques consist mostly of smooth muscle cells (SMC), and genes that influence SMC phenotype can modulate coronary artery disease (CAD) risk. (stanford.edu)
  • The underlying mechanism responsible for the effects of lunasin on NK cells is likely due to epigenetic modulation on target gene loci. (weeksmd.com)
  • Gene therapy has attracted attention for its potential to specifically and efficiently target cancer cells with minimal toxicity to normal cells. (weeksmd.com)
  • In contrast, in the case of ''true'' bivalency, virtually all cells in the population carry both marks simultaneously at the promoter in question, leading to low, if any, expression for that gene in all cells. (researchgate.net)
  • The cystic fibrosis transmembrane conductance regulator gene (CFTR) is expressed primarily in epithelial cells. (duke.edu)
  • Chromatin immunoprecipitations in naive CD4, but not CD8, T cells, demonstrated association of the IL-4 promoter with acetylated histone. (doe.gov)
  • Strikingly, K27M and G34R induced many overlapping changes, including reduced overall H3K27me3 and induction of NOTCH pathway genes, including ASCL1 . (nature.com)
  • The factors responsible for the postnatal and starvation-associated induction of HMGCS2 gene expression have been identified and shown to involve changes in circulating hormone and fatty acid levels. (aacrjournals.org)
  • We found a significantly lower expression of key autophagy- (ATG-) related genes in primary AML as compared to healthy granulocytes, an increased autophagic activity during all- trans retinoic acid- (ATRA-) induced neutrophil differentiation, and an impaired AML differentiation upon inhibition of ATG3, ATG4D, and ATG5. (hindawi.com)
  • Furthermore, we found that Seladin-1/DHCR24 gene expression is significantly decreased in skin isolated from LXRβ-null mice. (aspetjournals.org)
  • Increased OLR1 expression, resulting either from TZD treatment or adenoviral gene delivery, significantly augments adipocyte cholesterol content and enhances fatty acid uptake. (jci.org)
  • Previous studies from our laboratory indicated that C/EBPβ is implicated in inflammatory process and brain injury, since mice lacking this gene were less susceptible to kainic acid-induced injury. (biomedcentral.com)
  • Furthermore, secondary structure prediction showed that mutations at T471C and C862T apparently lead to change of the gene structure. (jcancer.org)
  • Surprisingly, however, the majority of primed genes were not enriched for H3K4me3 acutely following hypoxia exposure. (frontiersin.org)
  • So-called constitutive genes-those that perform basic "housekeeping" functions and are nearly always active at low levels-required only a basic set of regulatory controls, whereas those activated by environmental signals, known as inducible genes, had a more specialized architecture. (genengnews.com)
  • However, the researchers found that "housekeeping" genes-which comprise the majority of genes in yeast-lacked a protein-DNA architecture that would allow specific transcription factors to bind, a hallmark of inducible genes. (genengnews.com)
  • In K27M lines, the decrease of H3K27me3 was especially pronounced at super-enhancers of specific gene clusters, including the NOTCH pathway genes. (nature.com)
  • Combining transcriptional data and in silico modeling along with in vitro validation, we identified CAD gene ZEB2 as a target through which these lncRNAs exert their function in SMC phenotypic transition.Expression of a large and diverse set of lncRNAs in human coronary artery SMC are highly dynamic in response to CAD-related stimuli. (stanford.edu)
  • Abelson-transformed pre-B cell lines derived from these mice were used in chromatin immunoprecipitation experiments to identify regulatory sequences bound by E2A in the context of an early B lymphocyte environment. (duke.edu)
  • The resolution and completeness of the data allowed us to identify 21 protein assemblages and also to identify the absence of specific regulatory control signals at housekeeping genes," concluded study co-author Shaun Mahony, PhD, an assistant professor of biochemistry and molecular biology at Penn State. (genengnews.com)
  • Streamlining Regulon Identification in Bacteria Regulons are a group of genes that can be turned on or off by the same regulatory protein. (doe.gov)
  • BaF3 mouse pro-B cell line treated with 10 ng/mL Recombinant Mouse IL-3 (Catalog # 403-ML ) for 1 hour was fixed using formaldehyde, resuspended in lysis buffer, and sonicated to shear chromatin. (rndsystems.com)
  • Instead, native chromatin is isolated from cell nuclei that are digested with a nuclease. (cellsignal.com)
  • Knocking down p53 and ERalpha by small interfering RNA elicits opposite effects on p53-target gene expression and cell cycle progression. (nih.gov)
  • Dynamic binding of transcription factors to DNA elements specifies gene expression and cell fate, in both normal physiology and disease. (nih.gov)
  • Functionally, the TFs are organized in a hierarchy of different types: Cell differentiation factors bind most of the genes and remain largely unchanged during the stimulation. (nih.gov)
  • Central to this is the transient increase in H3K4-trimethylation at developmental genes during G1, thereby creating a 'window of opportunity' for cell-fate specification. (researchgate.net)
  • Our findings uncover a novel role for HDAC7 in maintaining the identity of a particular cell type by silencing lineage-inappropriate genes. (eur.nl)
  • CuSO4 promotes epithelial-mesenchymal transition (EMT) as shown by increased cell migration and increased EMT marker and fibrotic gene expressions. (bvsalud.org)
  • Capsid gene delivery into the striatum of mouse brain or interskeletal muscle resulted in cell death and inflammation, likely through capsid-induced apoptosis in vivo. (cdc.gov)
  • Rat hippocampi were micro-dissected (for mRNA, microRNA, and DNA methylation analysis) or frozen whole (for chromatin immunoprecipitation). (karger.com)
  • Weighted gene coexpression network analysis (WGCNA) of 1570 DE-lncRNAs between WT and ZBED6 KO pigs was used to define the following six lncRNA modules specific to different tissues: skeletal muscle, heart, lung, spleen, kidney and liver modules. (biomedcentral.com)
  • Analysis of the mouse C3 promoter showed that it is directly regulated by C/EBPβ through a C/EBPβ consensus site located at position −616/-599 of the gene. (biomedcentral.com)
  • Studies in yeast have identified a series of autophagy- (ATG-) related genes forming the autophagy machinery. (hindawi.com)
  • Our data suggest that Seladin-1/DHCR24 is an LXR target gene and that LXR may regulate lipid raft formation. (aspetjournals.org)
  • Consistent with previous long noncoding RNA studies, these lncRNAs overall have fewer exons, are shorter in length than protein-coding genes (pcGenes), and have relatively low expression level. (stanford.edu)
  • Further, many of the TF-DNA interactions at stimulus-activated genes are established during differentiation and maintained in a poised state. (nih.gov)
  • Genes can maintain spatiotemporal expression patterns by long-range interactions between cis-acting elements. (duke.edu)
  • Dynamical models based upon known interactions between these master genes, such as mutual antagonism and autoregulation, fail to make the system bistable, a desired feature for robust lineage determination. (lu.se)