Transcriptomic regulation and methylation of the Lysine4 of Histone H3 during meiosis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA107085 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE10836: Meiotic time course of Histone H3 occupancy GSE10837: Meiotic time course of the trimethylation of the Lysine 4 of Histone H3 (H3K4me3) in a mutant Spo11F GSE10838: Meiotic time course of Histone H3 occupancy in a mutant Spo11F GSE10839: Meiotic time course of the trimethylation of the Lysine 4 of Histone H3 (H3K4me3) in a mutant clb5Delta-clb6Delta GSE10840: Meiotic time course of the trimethylation of the Lysine 4 of Histone H3 (H3K4me3) GSE10944: Transcriptomic regulation during meiosis GSE10947: Transcriptomic regulation during meiosis (Spo11Y135F mutant) GSE10948: Transcriptomic regulation during meiosis (Clb5Delta-Clb6Delta mutant) GSE12879: Meiotic DNA double strand breaks in wild-type and set1 cells Keywords: SuperSeries Refer to individual Series
2008-10-31 | E-GEOD-11004 | biostudies-arrayexpress
Project description:Histone H3 Lysine4 Acetylation-Methylation Dynamics Define Breast Cancer Subtypes
| PRJNA302664 | ENA
Project description:Histone modifications are associated with meiotic recombination hotspots, discrete sites with augmented recombination frequency. For example, trimethylation of histone H3 lysine4 (H3K4me3) marks most hotspots in budding yeast and mouse. Modified histones are known to regulate meiotic recombination partly by promoting DNA double strand break (DSB) formation, but the role and precise landscape of histone modifications at hotspots remain unclear. Here, we studied hotspot-associated modifications in fission yeast and found general features: acetylation of H3 lysine9 (H3K9ac) is strikingly elevated, and H3K4me3 is not significantly enriched. Remarkably, elimination of H3K9ac reduced binding of the DSB-inducing enzyme Rec12 and DSB at hotspots. We also found that the H3K4 metyltransferase Set1 promotes DSB formation at some loci, but it restricts Rec12 binding to hotspots. These results suggest that H3K9ac rather than H3K4me3 is a hotspot-associated mark involved in meiotic DSB formation in fission yeast. S.pombe cells in a pat1-114 background were induced to enter meiosis by the haploid meiosis system, and harvested one hour after the induction. ChIP were performed using anti-H3Cter, H3K9ac, -H3K14ac and -H3K4me3 antibodies. pat1-114 rad50S rec12+-FLAG cells in a wild type, H3K9A or set1+ deletion background were induced to enter meiosis by the haploid meiosis system, and harvested five hours after the induction. ChIP were performed using anti-FLAG antibodies.
2013-03-07 | E-GEOD-31648 | biostudies-arrayexpress
Project description:ChIP-on-chip analysis of histone H3 and histone H3 lysine 4 trimethylation in cells induced to undergo synchronous meiosis after growth in nitrogen-rich conditions or after nitrogen depletion.
2014-02-20 | GSE53878 | GEO
Project description:ChIP-on-chip analysis of histone H3 and histone H3 lysine 4 trimethylation in cells induced to undergo synchronous meiosis after growth in nitrogen-rich conditions or after nitrogen depletion. Comparison of H3 and H3k4Me3 in diploid pat1-114 cells grown in -N and +N conditions.
2014-02-20 | E-GEOD-53878 | biostudies-arrayexpress
Project description:Histone H3 K36me3 and RNA pol II were localized by ChIP before and after inhibition of splicing by spliceostatin for 12 hr. Total matched reads for the control and SSA treated Hela samples were 11.6 and 8.2 million for anti-H3K36me3 and 6.6 and 5.0 million for anti-pol II. ChIP-seq of histone H3 K36me3 and RNA pol II in Hela cells before and after spliceosotatin treatment
2011-09-05 | E-GEOD-30895 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2008-11-01 | GSE11004 | GEO
Project description:We used ChIP-seq to determine the whole-genome enrichment of histone H3 threonine 11 phosphorylation (H3 T11ph) during Saccharomyces cerevisiae meiosis. S. cerevisiae SK1 cells were synchronized for meiotic entry and 3 and 4 hour meiotic samples were obtained. As H3 T11ph is dependent on the formation of meiotic double strand breaks (DSBs), a negative control ChIP-seq sample was obtained from a strain lacking DSBs (spo11-yf). Concurrently, ChIP-seq was carried out for histone H3 as a control for comparision.
2017-06-28 | GSE100564 | GEO
Project description:Chromatin structure and function is maintained by dynamic protein-protein and protein-nucleic acid interactions. Histones are a family of proteins that are abundant chromatin constituents and that carry numerous post-translational modifications (PTMs). Histone PTMs mediate a variety of biological activities, including recruitment of enzymatic readers, writers and erasers that modulate protein activities, DNA replication, transcription and repair. Individual histone molecules contain multiple co-existing PTMs some of which exhibit crosstalk, i.e. coordinated or mutually exclusive activities. We here present an integrated experimental and computational approach for systems level molecular characterization of PTMs and PTM crosstalk. Using wildtype and engineered mouse embryonic stem cells with perturbations in the Polycomb Repressive Complex 1 (PRC1, suz12-/-), PRC2 (Ring1A/b-/-) and DNA methyltransferases (Dnmt1/3a/3b-/-) we performed comprehensive PTM analysis of histone H3 tails. We identified unique histone H3 PTM features of each of the four cell lines and we detected common combinatorial PTM features across cell lines. Using quantitative middle-down proteomics combined with probabilistic and statistical data analysis we extracted histone H3 PTM profiles for all four mESC systems. PTM crosstalk emerged as mutually exclusive histone PTMs or coordinately regulated PTMs independent of histone peptide abundance in the four model systems. We detected positive crosstalk between adjacent mono-methylated marks but strong negative crosstalk among most of the seven characterized di- and tri-methylations on lysines. We report novel features of PTM interplay involving hitherto poorly characterized arginine methylation and lysine methylation sites in histone H3, including H3R2me, H3R8me and H3K37me, which exhibited specific PTM codes suggesting a particular role in chromatin. All histone H3 PTM data is available in our publicly available CrossTalkDB repository at http://crosstalkdb.bmb.sdu.dk
2016-06-16 | PXD002560 | Pride
Project description:Histones modulate gene expression by chromatin compaction, regulating numerous processes such as differentiation. However, the mechanisms underlying histone degradation remain elusive. When compared with their differentiated counterparts, immortal human embryonic stem cells (hESCs) have a unique chromatin architecture and low levels of trimethylated histone H3 at lysine 9 (H3K9me3), a heterochromatin-associated modification. Here we assess a link between the intrinsic epigenetic landscape and ubiquitin-proteasome system of hESCs. We find that hESCs exhibit high expression of UBE2K, a ubiquitin-conjugating enzyme. Loss of UBE2K increases the levels of H3K9 trimethyltransferase SETDB1, resulting in H3K9 trimethylation and repression of neurogenic genes during differentiation. Concomitantly, loss of UBE2K impairs the ability of hESCs to differentiate into neural progenitors with neurogenic properties. Besides H3K9 trimethylation, we find that UBE2K binds histone H3 to induce its polyubiquitination and degradation by the proteasome. Notably, ubc-20, the worm orthologue of UBE2K, also regulates both histone H3 levels and H3K9 trimethylation in C. elegans germline. Thus, our results indicate that UBE2K crosses evolutionary boundaries to promote histone H3 degradation and reduce H3K9me3 repressive marks in immortal cells.
2020-06-01 | PXD018621 | Pride