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Series GSE222845 Query DataSets for GSE222845
Status Public on Mar 18, 2023
Title H3K4me2/3 modulate the stability of RNA polymerase II pausing (ChIP-Seq)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Modifications of histones are intricately linked with the regulation of gene expression, with demonstrated roles in various physiological processes and disease pathogenesis. Methylation of histone H3 lysine 4 (H3K4), implemented by the COMPASS family, is enriched at promoters and associated cis-regulatory elements, with H3K4 trimethylation (H3K4me3) considered a hallmark of active gene promoters. However, the relative roles of deposition and removal of H3K4 methylation, as well as the extent to which these events contribute to transcriptional regulation have so far remained unclear. Here, through rapid depletion of either of two shared subunits of COMPASS family members, we reveal a dynamic turnover of H3K4me2 and H3K4me3 mediated by the KDM5 family of histone demethylases. Loss of H3K4me2 and H3K4me3 following COMPASS disruption does not impair the recruitment of TFIID and initiating RNA polymerase II (Pol II). Instead, their loss leads to reductions in the paused form of Pol II on chromatin while inducing the relative enrichment of the Integrator-PP2A (INTAC) termination complex, leading to reduced levels of elongating polymerases, thus revealing how H3K4me2 and H3K4me3 dynamics can regulate Pol II pausing to sustain or attenuate transcription.
 
Overall design We performed ChIP-seq, PRO-seq, or RNA-seq to investigate the role of methylation of histone H3 lysine 4 (H3K4) in regulating transcription. In this study, samples for each condition were collected in biological duplicates. Cells were treated with dTAG13 for 6, 12,or 24 hours, the corresponding control cells were treated for the same duration with vehicle only (DMSO) at the same vol/vol dilution.
 
Contributor(s) Hu S, Song A, Peng L, Chen FX
Citation(s) 36922644
Submission date Jan 13, 2023
Last update date Mar 20, 2023
Contact name Aixia Song
Organization name Fudan University
Street address Dong'an Road
City Shanghai
ZIP/Postal code 200032
Country China
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (127)
GSM6933991 ChIP_H3K4me3_DMSO-24h_mRBBP5-dTAG_ES_Rep1
GSM6933992 ChIP_H3K4me3_DMSO-24h_mRBBP5-dTAG_ES_Rep2
GSM6933993 ChIP_H3K4me3_dTAG-12h_mRBBP5-dTAG_ES_Rep1
This SubSeries is part of SuperSeries:
GSE222848 H3K4me2/3 modulate the stability of RNA polymerase II pausing
Relations
BioProject PRJNA923650

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE222845_RAW.tar 23.6 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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