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Mus musculus

ABSTRACT: Replication-independent histone turnover confers regulatory genome for adult heart homeostasis [Mnase-Seq]

PROVIDER: PRJNA404043 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6025024_1.fastq.gz	Fastqsanger.gz
	SRR6025024_2.fastq.gz	Fastqsanger.gz
	SRR6025025_1.fastq.gz	Fastqsanger.gz
	SRR6025025_2.fastq.gz	Fastqsanger.gz
	SRR6025026_1.fastq.gz	Fastqsanger.gz

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Replication-independent histone turnover confers regulatory genome for adult heart homeostasis

Project description:Replication-independent histone turnover confers regulatory genome for adult heart homeostasis

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Project description:Replication-independent histone turnover confers regulatory genome for adult heart homeostasis [ChIP-Seq]

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Mus musculus

Project description:Replication-independent nucleosome turnover confers the functional basis of cis-regulatory elements in adult heart

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Replication-independent histone turnover confers regulatory genome for adult heart homeostasis [Mnase-Seq]

Project description:Disruption and replacement of nucleosomal histone (histone turnover, HT) take place during transcription and cell division. Here we examined the functional roles for replication-independent HT in directing precise regulatory genome in terminally differentiated cardiomyocytes (CMs) of adult heart. Surprisingly, histone H2B pausing and chasing assay revealed the histone halftime ~2.5 weeks in non-replicating CMs, in sharp contrast to the longer halftime of CMs, despite in the abscence of replication-dependent passive dilution of labeled histones. Regions of high HT identified enhancers of important heart function. Co-occupancy of mutiple cardiac transcription factors in part accounted for enhancers on sites lacking nucleosome eviction by passage of RNA polymerase II. Unexpectedly, both polycomb EED and HDACs augmented HT rate in bufferring poised enhancer activition without alteration of nucleosome occupancy. Thus, our results suggest replication-indenpendent HT as an additional layer of chromatin-based regulation of functional homeostasis.

2019-06-14 | GSE103680 | GEO

Replication-independent histone turnover confers regulatory genome for adult heart homeostasis [ChIP-Seq]

2019-06-14 | GSE103679 | GEO

Dynamics of replication-independent histone turnover in budding yeast

Project description:Dynamics of replication-independent histone turnover in budding yeast

| PRJNA99055 | ENA

Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3

Project description:We developed a system to study the DNA replication-independent turnover nucleosomes containing the histone variant H3.3 in mammalian cells. By measuring the genome-wide incorporation of H3.3 at different time points following epitope-tagged H3.3 expression, we find three categories of H3.3-nucleosome turnover in vivo: rapid turnover, intermediate turnover and, specifically at telomeres, slow turnover. Our data indicate that H3.3-containing nucleosomes at enhancers and promoters undergo a rapid turnover that is associated with active histone modification marks including H3K4me1, H3K4me3, H3K9ac, H3K27ac and the histone variant H2A.Z. The rate of turnover is negatively correlated with H3K27me3 at regulatory regions and with H3K36me3 at gene bodies. Examination of incorporation dynamics of histone variant H3.3

2013-10-23 | E-GEOD-51505 | biostudies-arrayexpress

Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3

2013-10-23 | GSE51505 | GEO

Histone turnover during DNA replication

Project description:Histone turnover during DNA replication

| PRJNA794181 | ENA

Replication-independent nucleosome turnover confers the functional basis of cis-regulatory elements in adult heart

Project description:Through integrated H2BGFP ChIP-seq data over multiple conditions and time points, as well as other related ChIP-seq and RNA-seq data in adult mouse heart. We observed genomewide and locus-specific H2B turnover in non-proliferating adult cardiomyocytes (Cms), and a majority of genomic regions with rapid turnover rates distributes on cis-regulatory elements, as well as these regions are associated with heart function, regulatory factors binding and their activities. Moreover, H2B turnover rate is always positively correlated with gene transcription level on enhancers, promoters and exons. The rapid turnover rates at cis-regulatory elements can be partially explained by the binding and co-binding of RNAP II and various transcription factors (TFs). Our further analysis revealed that not only rapid H2B turnover at cis-regulatory elements responses to heart disease, but also slow turnover at H3K27me3 sites functionally responses to heart disease with a different manner. More generally, we indicate that the binding and co-binding of DNA-binding proteins, such as TFs and epigenetic enzymes, all of them coupled with H2B turnover to modulate gene transcription and chromatin state.

2020-04-17 | GSE97876 | GEO

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