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H3K4me1 distribution at promoters predicts the poised epigenetic state

ABSTRACT: H3K4me1 distribution at promoters predicts the poised epigenetic state

PROVIDER: PRJNA606462 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11077432.fastq.gz	Fastqsanger.gz
	SRR11077433.fastq.gz	Fastqsanger.gz
	SRR11077434.fastq.gz	Fastqsanger.gz
	SRR11077435.fastq.gz	Fastqsanger.gz
	SRR11077436.fastq.gz	Fastqsanger.gz

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H3K4me1 distribution at promoters predicts the poised epigenetic state

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.

2020-04-05 | GSE145225 | GEO

H3K4me1 Distribution Predicts Transcription State and Poising at Promoters.

Project description:Monomethylation on lysine 4 of histone H3 (H3K4me1) is commonly associated with distal enhancers, but H3K4me1 is also present at promoter regions proximal to transcription start sites. To assess a possible role for H3K4me1 in dictating gene regulatory states at promoters, we examined H3K4me1 peak density around promoters in human and mouse germ cells using an analytic strategy that allowed us to assess relationships between different epigenetic marks on a promoter-by-promoter basis. We found that H3K4me1 exhibits either a bimodal pattern at active promoters, where it flanks H3K4me3, or a unimodal pattern at poised promoters, where it coincides with both H3K4me3 and H3K27me3. This pattern is correlated with gene expression level, but is more strongly linked to a poised chromatin state, defined by the simultaneous presence of H3K4me3 and H3K27me3, than to transcriptional activity. The pattern is especially prominent in germ cells, but is also present in other cell types, including embryonic stem cells and differentiated somatic cells. We propose that H3K4me1 is a key feature of the poised epigenetic state, and suggest possible roles for this mark in epigenetic memory.

| S-EPMC7214686 | biostudies-literature

Histone H3K27ac separates active from poised enhancers and predicts developmental state

Project description:This SuperSeries is composed of the following subset Series: GSE23907: Histone H3K27ac separates active from poised enhancers and predicts developmental state (gene expression data) GSE24164: ChIP-Seq of chromatin marks at distal enhancers in Mouse Embryonic Stem Cells and adult tissues. Refer to individual Series

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Genome-wide distribution of AR, Sp1, H3K27Ac, H3K4me1 in E16.5 embryonic external genitalia (eExG)

Project description:ChIP-seq analysis of AR, Sp1, H3K27Ac, and H3K4me1; The genime-wide distribution of AR, Sp1, H3K27Ac, and H3K4me1 druing murine embryonic external genitalia (eExG) sex differentiation was shown.

2021-05-18 | GSE158279 | GEO

H3K27me3-H3K4me1 transition at bivalent promoters instructs lineage specification in development.

Project description:H3K27me3-H3K4me1 transition at bivalent promoters instructs lineage specification in development.

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An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters [RNA-Seq]

Project description:Genome-wide, little is understood about how proteins organize at inducible promoters before and after in-duction, and to what extent inducible and constitutive architectures depend on cofactors. We report that se-quence-specific transcription factors and their tethered cofactors (e.g., SAGA, Mediator, TUP, NuA4, SWI/SNF, RPD3-L) are already bound to promoters prior to induction (“poised”), rather than recruited upon induction, whereas induction recruits the pre-initiation complex (PIC). Through depletion and/or deletion ex-periments we show that SAGA does not function at constitutive promoters, although a SAGA-independent Gcn5 does acetylate +1 nucleosomes there. At poised promoters, SAGA catalyzes +1 nucleosome acetylation but not PIC assembly. At induced promoters, SAGA catalyzes acetylation, deubiquitylation, and PIC assembly. Surprisingly, SAGA mediates induction by creating a PIC that allows TFIID to stably associate, rather than creating a TFIID-independent PIC, as is generally thought. These findings suggest that inducible systems, where present, evolved on top of constitutive systems.

2022-10-27 | GSE212653 | GEO

An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters [ChIP-Exo]

2022-10-27 | GSE212654 | GEO

Genome-wide distribution of MLL4, H3K4me1 and H3K4me3 in MEF cells

Project description:Genome-wide distribution of MLL4, H3K4me1 and H3K4me3 in MEF cells

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Replicational dilution of H3K27me3 in mammalian cells and the role of poised promoters

Project description:Replicational dilution of H3K27me3 in mammalian cells and the role of poised promoters

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An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters

Project description:An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters

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