Histone modifications in activated and quiescent mouse muscle stem cells by ChIP-seq
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE129749 | GEO | 2020/12/08
REPOSITORIES: GEO
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Project description:We report the application of ChIPmentation on examination of H3K27ac histone mark in cultured satellite cells with siRNA treatment targeting LncMyoD. We observed no difference of H3K27ac mark around transcription start sites (TSS) after LncMyoD KD.
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Project description:Background: Bivalent chromatin refers to overlapping regions containing activating histone H3 Lys4 trimethylation (H3K4me3) and inactivating H3K27me3 marks. Existence of such bivalent marks on the same nucleosome has only recently been suggested. Previous genome-wide efforts to characterize bivalent chromatin have focused primarily on individual marks to define overlapping zones of bivalency rather than mapping positions of truly bivalent mononucleosomes. Results: Here, we developed an efficacious sequential ChIP technique for examining global positioning of individual bivalent nucleosomes. Using next generation sequencing approaches we show that although individual H3K4me3 and H3K27me3 marks overlap in broad zones, bivalent nucleosomes are focally enriched in the vicinity of the transcription start site (TSS). These seem to occupy the H2A.Z nucleosome positions previously described as salt-labile nucleosomes, and are correlated with low gene expression. Although the enrichment profiles of bivalent nucleosomes show a clear dependency on CpG island content, they demonstrate a stark anti-correlation with methylation status. Conclusions: We show that regional overlap of H3K4me3 and H3K27me3 chromatin tend to be upstream to the TSS, while bivalent nucleosomes with both marks are mainly promoter proximal near the TSS of CpG island-containing genes with poised/low expression. We discuss the implications of the focal enrichment of bivalent nucleosomes around the TSS on the poised chromatin state of promoters in stem cells.
2016-09-13 | GSE86838 | GEO
Project description:By comparing ATAC-seq from freshly isolated satellite cells (QSC), satellite cells isolated 2.5 days post-injury (ASC), and satellite cells cultured for differentiation, we observed a gradual opening of satellite cell chromatin structure during activation and differentiation process. We used ATAC-seq to study the functional role of LncMyod during satellite cell differentiation and identified genes that exhibited decrease of accessibilities to their transcription start sites (TSS). The majority of the regions are myogenesis-related genes, suggesting LncMyod plays a critical role in establishing permissive chromatin environment for myogenic progression.
2020-12-08 | GSE129745 | GEO
Project description:Post-translational modifications on histone tails are closely correlated to transcriptional states. One such modification is monomethylation on lysine 4 of histone 3(H3K4me1), a mark that has been linked to enhancers. Identifying regions enriched for H3K4me1 and depleted in H3K4me3, or regions enriched for both H3K4me1 and H3K27ac, has proven to be a feasible enhancer discovery method. At the same time, not all H3K4me1-enriched regions correspond to enhancers. H3K4me1 marks also exist at promoters, which implies that the H3K4me1 modification may have a context-dependent role in regulating transcription. We report distinct patterns of H3K4me1 that predict transcriptional regulatory states at promoters in germ cells and ESCs. We examined ChIP-seq data for H3K4me1, H3K4me3, H3K27me3, and H3K27ac in mouse and human male germ cells, and found that H3K4me1 peak density around the transcription start sites (TSS) exhibits either a broad bimodal profile or a narrower unimodal profile centered at the TSS. We then examined the position of the H3K4me1 marks relative to H3K4me3, and found that unimodal H3K4me1 directly at the TSS predicts a poised (H3K4me1/H3K27me3 bivalent) state of chromatin, while bimodal H3K4me1 flanking the TSS predicts an active state. We conclude that unimodal H3K4me1 centered on the TSS is a characteristic feature of the poised epigenetic state in ESCs and germ cells. Note: H3K4me1 and H3K27ac data are included in this GEO accession; H3K4me3 and H3K27me3 were released in GSE68507.
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2019-09-09 | PXD009794 | Pride
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2011-03-21 | E-GEOD-27969 | biostudies-arrayexpress
Project description:Purpose: The aim of this study is to explore histone modification in four basal cell populations defined by Lgr5 and Tspan8 expression taken from adult mouse mammary glands using chromatin immunoprecipitation sequencing (ChIP-seq). Methods: The ChIP DNA samples were prepared and indexed for Ilumina sequencing using the TruSeq DNA sample Prep Kit (Ilumina) as per manufacturer's instruction. The library was quantified using the Agilent Tapestation and the Qubit's RNA assay kit for Qubit 2.0 Fluorometer (Life Technologies). The indexed libraries were then prepared for paired-end 75bp sequencing on a NextSeq500 instrument using the 150 cycle kit v2 chemistry (Ilumina) as per manufacturer's instructions. Reads were aligned to the mouse genome (mm10) using the subread algorithm by Liao et al. (2013) and counted into bins associated with Entrez gene identifiers (27080 genes in total) using featureCounts in two different ways. Genebody counts summarised the number of reads overlapping anywhere between the first and last base of a given gene while promoter counts summarized the number of reads overlapping a region 3000 bases upstream to 2000 bases downstream of the TSS of each gene. For downstream analysis, genebody counts were used for the H3K27me3 marks and promoter counts were used for the H3K4me3 marks.
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2013-07-14 | E-GEOD-42522 | biostudies-arrayexpress
Project description:Transcriptional control is dependent on a vast network of epigenetic modifications. One epigenetic mark of particular interest is tri-methylation of lysine 27 on histone H3 (H3K27me3), which is catalyzed and maintained by the Polycomb Repressor Complex (PRC2). Although this histone mark is studied widely, the precise relationship between its local pattern of enrichment and regulation of gene expression is currently unclear. We have used ChIP-seq to generate genome wide maps of H3K27me3 enrichment, and have identified three enrichment profiles with distinct regulatory consequences. First, a broad domain of H3K27me3 enrichment across the body of genes corresponds to the canonical view of H3K27me3 as inhibitory to transcription. Second, a peak of enrichment around the transcription start site is commonly associated with â??bivalentâ?? genes, where H3K4me3 also marks the TSS. Finally and most surprisingly, we identified an enrichment profile with a peak in the promoter of genes that is associated with active transcription. Genes with each of these three profiles were found in different proportions in each of the cell types studied. The data analysis techniques developed here will be useful for the identification of common enrichment profiles for other histone modifications that have important consequences for transcriptional regulation. Genomic DNA was extracted from ES cells and G1ME cells in mouse. ChIP-seq with antibodies for H3K27me3, RNApol-II were run for both cell types. As a control, whole cell extract or Input DNA was also sequenced for both cell types without the inclusion of an antibody.
2011-03-21 | E-GEOD-27967 | biostudies-arrayexpress