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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE103681 | GEO | 2019/06/14

REPOSITORIES: GEO

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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

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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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

Dynamics of replication-independent histone turnover in budding yeast

Project description:This SuperSeries is composed of the following subset Series: GSE6664: Ratios for unsync cells GSE6665: Ratios for G1 arrested cells (Printed array) GSE6666: Ratios for G1 arrested cells (Agilent array) GSE6667: PolII occupancy GSE6668: Nucleosome occupancy GSE6669: H3 occupancy GSE6670: Ratios for Htz1D cells (Agilent array) Keywords: SuperSeries Refer to individual Series

2010-06-11 | E-GEOD-6680 | biostudies-arrayexpress

Dynamics of replication-independent histone turnover in budding yeast

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

2007-05-16 | GSE6680 | GEO

Dynamics of replication-independent histone turnover in budding yeast

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

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Histone turnover during DNA replication

Project description:Histone turnover during DNA replication

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Histone turnover during DNA replication

Project description:Using a recently established histone turnover sensor, we measured the genome-wide H3 turnover during S-phase in S.cerevisiae.

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Nucleosome Turnover Regulates Histone Methylation Patterns over the Genome.

Project description:Recent studies have indicated that nucleosome turnover is rapid, occurring several times per cell cycle. To access the effect of nucleosome turnover on the epigenetic landscape, we investigated H3K79 methylation, which is produced by a single methyltransferase (Dot1l) with no known demethylase. Using chemical-induced proximity (CIP), we find that the valency of H3K79 methylation (mono-, di-, and tri-) is determined by nucleosome turnover rates. Furthermore, propagation of this mark is predicted by nucleosome turnover simulations over the genome and accounts for the asymmetric distribution of H3K79me toward the transcriptional unit. More broadly, a meta-analysis of other conserved histone modifications demonstrates that nucleosome turnover models predict both valency and chromosomal propagation of methylation marks. Based on data from worms, flies, and mice, we propose that the turnover of modified nucleosomes is a general means of propagation of epigenetic marks and a determinant of methylation valence.

| S-EPMC6510544 | biostudies-literature

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