Genome-wide maps of histone variant H3.3 occupancy in zebrafish cardiomyocytes
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ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE81893 | GEO | 2017/03/07
SECONDARY ACCESSION(S): PRJNA323351
REPOSITORIES: GEO
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2017-03-07 | GSE81865 | GEO
Project description:We report high-throughput profiling of acetylation of lysine 27 on histone H3 from whole zebrafish ventricles. The H3K27Ac mark has been shown to be present at active enhancer elements and including regions of active chromatin. We profile H3K27Ac in uninjured cardiomyocytes and those undergoing regeneration 14 days after genetic ablation. This study provides a framework for understanding chromatin transitions during adult models of regeneration.
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Project description:We report high-throughput profiling of transgenic histone H3.3 in zebrafish cardiomyocytes. The replacement histone H3.3 is deposited at sites of nucleosome turnover including regions of active chromatin. We profile H3.3 in uninjured cardiomyocytes, those undergoing regeneration 14 days after genetic ablation and those proliferating 7 days after Nrg1 stimulated hyperplasia. This study provides a framework for understanding chromatin transitions during adult models of regeneration.
2017-03-07 | GSE81862 | GEO
Project description:Genome-wide maps of histone variant H3.3 occupancy in zebrafish cardiomyocytes
| PRJNA323351 | ENA
Project description:BackgroundNucleosomes are present throughout the genome and must be dynamically regulated to accommodate binding of transcription factors and RNA polymerase machineries by various mechanisms. Despite the development of protocols and techniques that have enabled us to map nucleosome occupancy genome-wide, the dynamic properties of nucleosomes remain poorly understood, particularly in mammalian cells. The histone variant H3.3 is incorporated into chromatin independently of DNA replication and requires displacement of existing nucleosomes for its deposition. Here, we measure H3.3 turnover at high resolution in the mammalian genome in order to present a genome-wide characterization of replication-independent H3.3-nucleosome dynamics.ResultsWe developed a system to study the DNA replication-independent turnover of 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 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.ConclusionsWe have established a reliable approach to measure turnover rates of H3.3-containing nucleosomes on a genome-wide level in mammalian cells. Our results suggest that distinct mechanisms control the dynamics of H3.3 incorporation at functionally different genomic regions.
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Project description:Linker histones are involved in the formation of higher-order chromatin structure and the regulation of specific genes, yet it remains unclear what their principal binding determinants are. We generated a genome-wide high-resolution binding map for linker histone H1 in Drosophila cells, using DamID. H1 binds at similar levels across much of the genome, both in classic euchromatin and heterochromatin. Strikingly, there are pronounced dips of low H1 occupancy around transcription start sites for active genes and at many distant cis-regulatory sites. H1 dips are not due to lack of nucleosomes; rather, all regions with low binding of H1 show enrichment of the histone variant H3.3. Knockdown of H3.3 causes H1 levels to increase at these sites, with a concomitant increase in nucleosome repeat length. These changes are independent of transcriptional changes. Our results show that the H3.3 protein counteracts association of H1, providing a mechanism to keep diverse genomic sites in an open chromatin conformation.
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Project description:Nucleosomes package eukaryotic DNA and are composed of four different histone proteins, designated H3, H4, H2A, and H2B. Histone H3 has two main variants, H3.1 and H3.3, which show different genomic localization patterns in animals. We profiled H3.1 and H3.3 variants in the genome of the plant Arabidopsis thaliana and found that the localization of these variants shows broad similarity in plants and animals, along with some unique features. H3.1 was enriched in silent areas of the genome, including regions containing the repressive chromatin modifications H3 lysine 27 methylation, H3 lysine 9 methylation, and DNA methylation. In contrast, H3.3 was enriched in actively transcribed genes, especially peaking at the 3' end of genes, and correlated with histone modifications associated with gene activation, such as histone H3 lysine 4 methylation and H2B ubiquitylation, as well as RNA Pol II occupancy. Surprisingly, both H3.1 and H3.3 were enriched on defined origins of replication, as was overall nucleosome density, suggesting a novel characteristic of plant origins. Our results are broadly consistent with the hypothesis that H3.1 acts as the canonical histone that is incorporated during DNA replication, whereas H3.3 acts as the replacement histone that can be incorporated outside of S-phase during chromatin-disrupting processes like transcription.
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Project description:Histone proteins wrap DNA to form nucleosome particles that compact eukaryotic genomes while still allowing access for cellular processes such as transcription, replication and DNA repair. Histones exist as different variants that have evolved crucial roles in specialized functions in addition to their fundamental role in packaging DNA. H3.3--a conserved histone variant that is structurally very close to the canonical histone H3--has been associated with active transcription. Furthermore, its role in histone replacement at active genes and promoters is highly conserved and has been proposed to participate in the epigenetic transmission of active chromatin states. Unexpectedly, recent data have revealed accumulation of this specific variant at silent loci in pericentric heterochromatin and telomeres, raising questions concerning the actual function of H3.3. In this review, we describe the known properties of H3.3 and the current view concerning its incorporation modes involving particular histone chaperones. Finally, we discuss the functional significance of the use of this H3 variant, in particular during germline formation and early development in different species.
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Project description:Regulatory information stored in modified histones is functionally translated by effector proteins ('readers'), which identify the histone mark to determine the specificity of the response. A recent study identifying the tumor suppressor protein ZMYND11 as an exclusive reader of methylated histone variant H3.3, throws light on the role of transcription regulation in suppressing tumors.
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Project description:This SuperSeries is composed of the SubSeries listed below.
2009-10-15 | GSE16885 | GEO