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

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

PROVIDER: PRJNA1226113 | ENA |

REPOSITORIES: ENA

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

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

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

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H3K4me3 instructs transcription at intergenic active regulatory elements [ChIP-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 | GSE290054 | GEO

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

2025-07-17 | GSE290058 | GEO

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

2025-07-17 | GSE290056 | GEO

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

2025-07-17 | GSE290060 | GEO

H3K4me3 amplifies transcription at intergenic active regulatory elements

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-07-14 | GSE290064 | GEO

Mapping active promoters by ChIP-seq profiling of H3K4me3 in cichlid fish - a first step to uncover cis-regulatory elements in ecological model teleosts

Project description:Evolutionary alterations to cis-regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For non-model organisms with adaptive key-innovations, patterns of regulatory evolution have been predominantly limited to targeted sequence-based analyses. Chromatin-immunoprecipitation with high-throughput sequencing (ChIP-seq) is a technology that has only been used in genetic model systems and is a powerful experimental tool to screen for active cis-regulatory elements. Here, we show that it can also be used in ecological model systems and permits genome-wide functional exploration of cis-regulatory elements. As a proof of concept, we use ChIP-seq technology in adult fin tissue of the cichlid fish Oreochromis niloticus to map active promoter elements, as indicated by occupancy of trimethylated Histone H3 Lysine 4 (H3K4me3). The fact that cichlids are one of the most phenotypically diverse and species-rich families of vertebrates could make them a perfect model system for the further in-depth analysis of the evolution of transcriptional regulation. examination of H3K4me3 in adult fin tissue of the Nile tilapia (Oreochromis niloticus)

2015-07-07 | E-GEOD-62791 | biostudies-arrayexpress

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