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H3K4me3 instructs transcription at intergenic active regulatory elements [TT-TimeLapse-seq]

ABSTRACT: H3K4me3 instructs transcription at intergenic active regulatory elements [TT-TimeLapse-seq]

PROVIDER: PRJNA1226132 | ENA |

REPOSITORIES: ENA

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H3K4me3 instructs transcription at intergenic active regulatory elements [TT-TimeLapse-seq]

Project description:Tri-methylation of lysine 4 on histone H3 (H3K4me3) is a deeply conserved and functionally important histone modification enriched at transcriptionally active promoters. H3K4me3 can facilitate RNA polymerase activity in a context-dependent manner. Here, we generated an epigenetic editing tool, dCas9-PRDM9, that efficiently deposits H3K4me3 at specific target loci, and used it to interrogate the genomic and chromatin contexts required for H3K4me3 to facilitate transcription in human cells. We found that H3K4me3 deposition is sufficient to increase transcription at active candidate cis-regulatory elements (cCREs), and that this effect was independent of cCRE identity or distance from gene promoters, unrelated to transcript levels of putative target genes, and dependent on the presence of active chromatin features. We conclude that H3K4me3 is sufficient to instruct RNA polymerase activity but requires pre-existing features of transcriptionally active chromatin. These findings suggest that disease-associated dysfunction in H3K4me3 deposition or removal can disrupt the cell’s transcriptional state.

2025-07-17 | GSE290060 | GEO

H3K4me3 instructs transcription at intergenic active regulatory elements [RNA-seq]

Project description:H3K4me3 instructs transcription at intergenic active regulatory elements [RNA-seq]

| PRJNA1226133 | ENA

H3K4me3 instructs transcription at intergenic active regulatory elements [ChIP-seq]

Project description:H3K4me3 instructs transcription at intergenic active regulatory elements [ChIP-seq]

| PRJNA1226113 | ENA

H3K4me3 instructs transcription at intergenic active regulatory elements [ATAC-seq]

Project description:H3K4me3 instructs transcription at intergenic active regulatory elements [ATAC-seq]

| PRJNA1226130 | ENA

H3K4me3 instructs transcription at intergenic active regulatory elements [ATAC-seq]

2025-07-17 | GSE290056 | GEO

H3K4me3 instructs transcription at intergenic active regulatory elements [ChIP-seq]

2025-07-17 | GSE290054 | GEO

H3K4me3 instructs transcription at intergenic active regulatory elements [RNA-seq]

2025-07-17 | GSE290058 | GEO

H3K4me3 amplifies transcription at intergenic active regulatory elements

Project description:H3K4me3 amplifies transcription at intergenic active regulatory elements

| PRJNA1226122 | ENA

TT-TL-seq reveals transcriptional profiles that accompany DoG induction after hyperosmotic stress.

Project description:TT-TimeLapse-seq was used to investigate the nascent transcription profiles that accompany the induction of downstream-of-gene (DoG) containing transcripts in human cell lines. Data from HEK-293T cells exposed to hyperosmotic stress and cells transfected with siRNAs against Integrator subunit 11 are included.

2021-01-04 | GSE152059 | GEO

TT-Seq captures the human transient transcriptome

Project description:A large portion of the genome is transcribed but many of the resulting RNAs live only transiently and can generally not be mapped. Here we develop transient transcriptome sequencing (TT-Seq), a protocol that maps transcriptionally active regions in a nearly uniform manner and allows for unbiased monitoring of cellular RNA synthesis activity. Application of TT-Seq to human K562 cells recovers stable mRNAs and long intergenic non-coding RNAs, and additionally maps over 10,000 transient RNAs including enhancer RNAs, antisense RNAs, promoter-associated upstream antisense and convergent RNAs. TT-Seq also provides RNA half-lives, and reveals that transient RNAs are short and lack U1 motifs and secondary structure. TT-Seq further uncovers transcription termination sites and reveals a universal DNA motif for RNA polymerase II release.

2016-06-03 | GSE75792 | GEO

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