Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis

ABSTRACT: Histone variants play crucial roles in gene expression, genome integrity and chromosome segregation. However, to what extent histone variants control chromatin architecture remains largely unknown. Here, we show that the previously uncharacterized histone variant H2A.W plays a crucial role in condensation of heterochromatin. Genome-wide profiling of all four types of H2A variants in Arabidopsis shows that H2A.W specifically associates with heterochromatin. H2A.W recruitment is independent of heterochromatic marks H3K9me2 and DNA methylation. Genetic interactions show that H2A.W acts in synergy with CMT3 mediated methylation to maintain genome integrity. In vitro, H2A.W enhances chromatin condensation through a higher propensity to make fiber-to-fiber interactions via its conserved C-terminal motif. In vivo, elimination of H2A.W causes decondensation of heterochromatin and conversely, ectopic expression of H2A.W promotes heterochromatin condensation. These results demonstrate that H2A.W plays critical roles in heterochromatin by promoting higher order chromatin condensation. Since similar H2A.W C-terminal motifs are present in other variant found in mammals and other organisms our findings impact our understanding of heterochromatin condensation in a wide variety of eukaryotic organisms.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE50942 | GEO | 2014/07/05

SECONDARY ACCESSION(S): PRJNA219442

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis

Project description:Histone variants play crucial roles in gene expression, genome integrity and chromosome segregation. However, to what extent histone variants control chromatin architecture remains largely unknown. Here, we show that the previously uncharacterized histone variant H2A.W plays a crucial role in condensation of heterochromatin. Genome-wide profiling of all four types of H2A variants in Arabidopsis shows that H2A.W specifically associates with heterochromatin. H2A.W recruitment is independent of heterochromatic marks H3K9me2 and DNA methylation. Genetic interactions show that H2A.W acts in synergy with CMT3 mediated methylation to maintain genome integrity. In vitro, H2A.W enhances chromatin condensation through a higher propensity to make fiber-to-fiber interactions via its conserved C-terminal motif. In vivo, elimination of H2A.W causes decondensation of heterochromatin and conversely, ectopic expression of H2A.W promotes heterochromatin condensation. These results demonstrate that H2A.W plays critical roles in heterochromatin by promoting higher order chromatin condensation. Since similar H2A.W C-terminal motifs are present in other variant found in mammals and other organisms our findings impact our understanding of heterochromatin condensation in a wide variety of eukaryotic organisms. Two mRNA-seq samples, two bisulfite-seq samples, six ChIP-seq samples.

2014-07-05 | E-GEOD-50942 | biostudies-arrayexpress

Evolution of the histone variant H2A.W reconstituted in fission yeast [ATAC-seq]

Project description:Diversification of histone variants is marked by the acquisition of distinct motifs and features through convergent evolution. H2A variants tend to be associated with defined domains of the genome. Specific features distinguish H2A variants in eukaryotes but whether evolution of these features predated the evolution of deposition mechanisms or vice-versa has remained unclear.In flowering plants, the variant H2A.W is tightly associated with heterochromatin. H2A.W evolved in land plants through acquisition of an extended C-terminal tail enriched with basic residues and a KSPK motif. Here, we used a synthetic approach in fission yeast, which lacks H2A.W and its dedicated deposition mechanism, to recapitulate the evolutionary steps that led to H2A.W and to assess the impact of the KSPK motif on heterochromatin composition and its properties. In conclusion, the acquisition of the KSPK motif in yeast promotes chromatin properties that are comparable to the properties and function of H2A.W in plant heterochromatin. Hence, the KSPK motif could have been selected before the evolution of direct heterochromatin deposition mechanisms. We propose that the acquisition of functional histone variant motifs can confer properties which affect only specific chromatin states, thereby driving the evolution of specific deposition mechanisms.

2020-08-23 | GSE152081 | GEO

Evolution of the histone variant H2A.W reconstituted in fission yeast [RNA-seq]

2020-08-23 | GSE152085 | GEO

Evolution of the histone variant H2A.W reconstituted in fission yeast [ChIP-seq]

2020-08-23 | GSE152083 | GEO

The histone variant H2A.W and linker histone H1 co-regulate heterochromatin accessibility and DNA methylation

Project description:In flowering plants, heterochromatin is demarcated by the histone variant H2A.W, elevated levels of the linker histone H1, and specific epigenetic modifications, such as high levels of DNA methylation at both CG and non-CG sites. How H2A.W regulates heterochromatin organization and interacts with other heterochromatic features is unclear. Here, we create an h2a.w null mutant via CRISPR-Cas9, h2a.w-2, to analyze the in vivo function of H2A.W. We find that H2A.W antagonizes deposition of H1 at heterochromatin and that non-CG methylation and accessibility are moderately decreased in h2a.w-2 heterochromatin. Compared to H1 loss alone, combined loss of H1 and H2A.W greatly increases accessibility and facilitates non-CG DNA methylation in heterochromatin, suggesting co-regulation of heterochromatic features by H2A.W and H1. Our results suggest that H2A.W helps maintain optimal heterochromatin accessibility and DNA methylation by promoting chromatin compaction together with H1, while also inhibiting excessive H1 incorporation.

2021-03-26 | GSE146948 | GEO

H2A.W is essential for silencing of whole genome heterochromatin in Arabidopsis

Project description:Heterochromatin of flowering plants is occupied by histone variant H2A.W and marked by DNA and H3K9 methylation. The relative impact of these heterochromatic features on activity of Transposable Elements (TEs) remains largely unknown. We obtained mutants deficient for H2A.W and key components controlling each of the key heterochromatic pathway in Arabidopsis and observed that knock out of individual pathway does not affect in a major manner TEs activity. However, when we combine the loss of H2A.W with any of the other heterochromatin controller we observe synergistic effects on heterochromatin compaction as well TEs activity. H2A.W appears to control expression of all TEs while each other heterochromatin controller target distinct subsets of TEs. We also observe an impact of linker histone H1. We propose that H2A.W acts together with several components of heterochromatin to prevents activity of distinct sets of TEs activity and chromatin architecture. Synergistic action with H2A.W is more prominent specifically in pathways controlled by the plant specific DNA chromomethyltransferases, CMT2 and CMT3.

2022-12-31 | GSE116643 | GEO

ChIP-seq for Histone Variant H2A.W, H2A.X, H1 and H3K9me2 in WT and ddm1(-/-) to quantify loss of H2A.W in ddm1 1st generation

Project description:Silencing of transposons by the chromatin remodeler DDM1 is mediated by the deposition of heterochromatic H2A variants. Transposon mobility and silencing participates in genome evolution but also threaten genome integrity. DECREASED DNA METHYLATION 1 (DDM1) belongs to a conserved family of chromatin remodelers that are required to silence transposons, yet the underlying molecular mechanism has remained unknown. Here we show that DDM1 binds the histone variant H2A.W through two conserved domains that are required to deposit H2A.W and maintain transposon silencing. The mechanism of transcriptional silencing described here is likely shared among chromatin remodelers of the DDM1 family and heterochromatic H2A variants that have evolved in mammals.

2021-02-10 | GSE150434 | GEO

ChIP-seq of histone marks (H3K27me1, H3K27me3, H3K9me2) and of the H2A.W histone variant in Arabidopsis pol2a mutants.

Project description:DNA replication requires the faithful propagation of both genetic and epigenetic information. There is evidence that DNA polymerases play a role in transcriptional silencing, but the extent of their contribution and how it relates to heterochromatin maintenance is unclear. Analyzing a new hypomorphic pol2a mutant allele, we find that POL2A, the catalytic subunit of the DNA polymerase epsilon, maintains heterochromatin silencing and nuclear organization. We also found that POL2A inhibits DNA methylation. Using ChIP-seq in wild-type and pol2a mutants, we analyzed how this related to changes in heterochromatic histone modifications (H3K27me1, H3K27me3, H3K9me2) and H2A.W heterochromatic histone variant.

2020-10-18 | E-MTAB-9046 | biostudies-arrayexpress

Compartmentalization of DNA damage response between heterochromatin and euchromatin is mediated by distinct H2A histone variants

Project description:DNA double strand break (DSB) repair depends on the ataxia telangiectasia mutated (ATM) kinase that phosphorylates the conserved C-terminal SQ motif present in the histone variant H2A.X [1-7]. In constitutive heterochromatin of mammals, DSB repair is delayed and relies on phosphorylation of the proteins HP1 and KAP1 by ATM [2, 8-14]. However, KAP1 is not conserved in plants and the HP1 related protein Like-HP1 (LHP1) is not localized at constitutive heterochromatin [15], suggesting that in plants, alternative mechanisms could be responsible for repair of DSBs in heterochromatin. In Arabidopsis, constitutive heterochromatin is marked by H3K9 methylation, and the plant-specific histone variants H2A.W which are distinguished by their C-terminal motif KSPKK and required for heterochromatin compaction [16-18]. We report that the Arabidopsis histone variant H2A.W.7 is confined to heterochromatin and carries a SQ motif that is phosphorylated by ATM. In response to DNA damage, phosphorylation of H2A.W.7 takes place in heterochromatin while H2A.X phosphorylation takes place primarily in euchromatin. We propose that H2A.W.7 evolved in addition to H2A.X to facilitate DNA damage response in highly condensed heterochromatin, thus playing a role similar to KAP1 and HP1 phosphorylation in mammals. These data support the idea of the functional diversification of histone variants and their role in spatial compartmentalization of chromatin related functions in eukaryotes.

2017-03-02 | GSE95557 | GEO

Arabidopsis thaliana

Project description:The Histone Variant H2A.W Defines Heterochromatin and Promotes Chromatin Condensation in Arabidopsis

| PRJNA219442 | ENA