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SRX1160443: GSM1858317: H3K4me3_KO_rep1; Mus musculus; ChIP-Seq
1 ILLUMINA (NextSeq 500) run: 73.3M spots, 5.4G bases, 2.3Gb downloads

Submitted by: Gene Expression Omnibus (GEO)
Study: Genome-wide H2B monoubiquitination regulates gene expression by coordinating H3K4me3 and H3K27me3 [ChIP-Seq Data Set]
show Abstracthide Abstract
Gene body-associated monoubiquitination of H2B (H2Bub1) coupled with promoter-associated active histone modifications such as trimethylation H3 on lysine 4 (H3K4me3) and acetylation H3 on lysine 27 (H3K27ac) facilitate gene transcription. However, surprisingly, only a subset of genes is altered in their expression following knockdown of H2B ubiquitin-protein ligases RNF20 or RNF40 in human cells. In order to obtain a more complete genome- and transcriptome-wide understanding of the role of H2Bub1 in gene transcription, we generated tamoxifen-inducible Rnf40 knockout mouse embryonic fibroblasts (MEFs). Mapping of H2Bub1, H3K4me3, H3K27me3, and H3K27ac occupancy identified an “ascending” gene cluster including bivalent genes, which is occupied by low to moderate amounts of H2Bub1 and exhibits high variability in transcription. We provide evidence that the variation in expression is highly associated with the variations in H3K4me3, H3K27me3, and H3K27ac occupancy. Moreover, these variably marked “ascent” genes are selectively regulated in Rnf40-deficient MEFs. Consistent with previous studies, the effect of Rnf40 loss on the expression of genes within this cluster is also variable with some genes demonstrating increased while others decreased mRNA levels following Rnf40 deletion. Importantly, we identified the Ezh2 gene as an Rnf40/H2Bub1 target whose expression significantly decreased in Rnf40-deficient MEFs. Notably, we show that genes upregulated following Rnf40 deletion are enriched for H3K27me3, which is decreased following Rnf40 deletion, and these effects can be mimicked by treating with a small molecule EZH2 inhibitor. On the other hand, consistent with findings in many eukaryotic systems, genes whose expression decreases following Rnf40 deletion show an enrichment of H3K4me3 and decreased levels following deletion. Together, we provide mechanistic information by which Rnf40, presumably via H2Bub1, modulates gene expression via coordination of the active and repressive marks H3K4me3 and H3K27me3. Overall design: examination of H2Bub1, H3K4me3, H3K27me3, and H3K27ac in Rnf40+/+ and Rnf40-/- mouse embryonic fibroblasts were generated by deep sequencing
Sample: H3K4me3_KO_rep1
SAMN04003019 • SRS1041475 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: NextSeq 500
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: Cells were crosslinked with 1% Formaldehyde for 10 minutes and quenched with 1.25 M Glycine. The nuclear pellets were sonicated to the fragment range of 200-400 bp. Sonicated extracts were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose. Library preparations were done using NEBnext Ultra DNA library preparation kit according to the manufacturer’s instructions.
Experiment attributes:
GEO Accession: GSM1858317
Links:
Runs: 1 run, 73.3M spots, 5.4G bases, 2.3Gb
Run# of Spots# of BasesSizePublished
SRR217623373,259,1225.4G2.3Gb2017-01-06

ID:
1687214

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