ChIP-seq for H3K4me3, H3K27me3, H3K79me2 in MCF10A cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE109721 | GEO | 2018/02/01
REPOSITORIES: GEO
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Project description:ChIP-seq for H3K4me3, H3K27me3, H3K79me2 in MCF10A cells
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Project description:We studied the role of the histone methyltransferase DOT1L in T cell development and differentiation. H3K79me2 and H3K4me3 ChIP-sequencing data was generated from sorted CD8 single positive thymocytes, naïve CD8 splenocytes and memory CD8 splenocytes. This was compared to RNA-sequencing data from WT and Dot1L KO mice in order to study the link between H3K79me2 and transcription.
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2011-12-08 | E-MEXP-3217 | biostudies-arrayexpress
Project description:This study describes the changes in epigenetic chromatin modifications during murine hematopoietic stem cell differentiation in vivo using a modified miniChIP-chip technology. We have addressed issues including bivalent (H3K4me3/H3K27me3) modifications, lineage priming hypothesis, and stem cell chromatin properties in our study described in Weishaupt et al., 2009 (Blood)
2009-11-09 | GSE18734 | GEO
Project description:This study describes the changes in epigenetic chromatin modifications during murine hematopoietic stem cell differentiation in vivo using a modified miniChIP-chip technology. We have addressed issues including bivalent (H3K4me3/H3K27me3) modifications, lineage priming hypothesis, and stem cell chromatin properties in our study described in Weishaupt et al., 2009 (Blood) Comparison of 4 murine hematopoietic stem, progenitor and mature cell types directly isolated from primary tissues using FACS. HSCs are phenotypically identified in bone marrow as lineage-, cKit+, Sca1+, CD150+, Flk2/Flt3- (LSKCD150+ cells). MPPs are phenotypically identified in bone marrow as lineage-, cKit+, Sca1+, CD150-, Flk2/Flt3+ (LSKCD150- cells). PreMegEs are phenotypically identified in bone marrow as lineage-, cKit+, Sca1-, CD150+, CD105-, FcgRI/IIlo and CD41- cells as described in Pronk et al., 2007. Splenic-derived CD4+ T cells are phentypically identified as CD4+, CD8-, B220-, Nk1.1- cells as described in Rolf et al., 2008.
2009-11-08 | E-GEOD-18734 | biostudies-arrayexpress
Project description:Bivalency, the paradoxical juxtaposition of transcriptionally activating trimethylation of histone H3 lysine 4 (H3K4me3) and the repressive trimethylation of histone H3 lysine 27 (H3K27me3), has been proposed to decorate developmental genes poised for gene expression regulation. Here, we report development of sequential internally calibrated chromatin immunoprecipitation (Re-ICeChIP-seq), capable of measuring absolute quantities of nucleosomal patterns of histone marks in a genome-wide fashion, combined with in situ control of antibody specificity. Re-ICeChIP-seq of H3K4me3/H3K27me3 in mESC reveals that bivalent genes can be delineated into two classes, distinguished by the nucleosomal ratio of H3K4me3 to H3K27me3. Consistent with the canonical role of bivalency, H3K27me3-rich bivalent nucleosomes demarcate promoters of poorly expressed developmental genes that may be poised for activation or repression. Yet our measurements reveal surprisingly widespread presence of bivalency at promoters of highly-expressed housekeeping genes, characterized by H3K4me3-rich bivalent nucleosomes. Moreover, the ratio of H3K4me3 to H3K27me3 at transcription start sites better correlates with gene expression than H3K4me3 or H3K27me3 alone, suggesting cooperation between opposing marks to fine-tune gene expression. Finally, we report that major H3K4 methyltransferases exhibit wide acceptance of various H3K27me3 substrates.
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Project description:Cotton is an excellent model for studying heterosis, crop domestication and bioengineering improvement. Chromatin profiling helps to reveal how histone modifications are involved in controlling differential gene expression between A and D subgenome in allotetraploid cotton. However, the detailed profiling and functional characterization of H3K27me3 and H3K4me3/H3K27me3 bivalent mark are still understudied in cotton. In this study, we conducted H3K4me3 and H3K27me3-related ChIP-seq followed by comprehensively characterizing their roles in regulating gene transcription in cotton. We found that H3K4me3 and H3K27me3 exhibited active and repressive roles in regulating expression of genes between A and D subgenome, respectively. Expression of H3K4me3-H3K27me3 bivalent genes was regulated by combinatorial actions of both marks and may be dominantly controlled by H3K4me3. More importantly, H3K4me3 exhibited enrichment levels, positioning and distance-related effects on expression levels of related genes. In addition, H3K4me3, H3K27me3 and bivalent mark can indirectly influence gene expression through TF-mediated regulatory networks. Thus, our study provides insights in functions of H3K4me3 and H3K27me3 in regulating differential gene expression between A and D subgenome in cotton.
2021-11-29 | GSE165244 | GEO
Project description:Cotton is an excellent model for studying heterosis, crop domestication and bioengineering improvement. Chromatin profiling helps to reveal how histone modifications are involved in controlling differential gene expression between A and D subgenome in allotetraploid cotton. However, the detailed profiling and functional characterization of H3K27me3 and H3K4me3/H3K27me3 bivalent mark are still understudied in cotton. In this study, we conducted H3K4me3 and H3K27me3-related ChIP-seq followed by comprehensively characterizing their roles in regulating gene transcription in cotton. We found that H3K4me3 and H3K27me3 exhibited active and repressive roles in regulating expression of genes between A and D subgenome, respectively. Expression of H3K4me3-H3K27me3 bivalent genes was regulated by combinatorial actions of both marks and may be dominantly controlled by H3K4me3. More importantly, H3K4me3 exhibited enrichment levels, positioning and distance-related effects on expression levels of related genes. In addition, H3K4me3, H3K27me3 and bivalent mark can indirectly influence gene expression through TF-mediated regulatory networks. Thus, our study provides insights in functions of H3K4me3 and H3K27me3 in regulating differential gene expression between A and D subgenome in cotton.
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Project description:Multicellular organism requires concise gene regulation during ontogeny and epigenetic modifications, such as DNA methylation and histone modification, facilitate the concise regulation. The conservative reprogramming patterns of DNA methylation in vertebrates have been well described but knowledge of how histone modifications are passed on to zygote from gametes are limited and conservations of histone modifications are not clear.We profiled H3K4me3/H3K27me3 modifications in gametes and early embryos in zebrafish and find out that patterns in gene promoter regions have been largely set to either bivalent or active states in gametes and then passed on to zygote. Bivalent states are partially maintained and active states are restored to match sperm’s pattern. But repressive H3K27me3 modifications as well as stage specific modifications in promoter regions are discarded. Prior to zygotic genome activation, patterns of genes that initialize ZGA have been converted to non-repressive states to coordinate gene expression. Histone modification in hyper methylated promoter peaks are erased independent of DNA methylome reprogramming. Comparative analysis revealed that functions of bivalent and active genes passed on from gametes are conserved in vertebrates and gene age preferences by bivalent and active histone modifications are also confirmed in vertebrates.
2019-04-17 | GSE110663 | GEO