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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

ABSTRACT: 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

PROVIDER: PRJNA632032 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11780909.fastq.gz	Fastqsanger.gz
	SRR11780910.fastq.gz	Fastqsanger.gz
	SRR11780911.fastq.gz	Fastqsanger.gz
	SRR11780912.fastq.gz	Fastqsanger.gz
	SRR11780913.fastq.gz	Fastqsanger.gz

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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

RNA-seq for WT and ddm1(-/-) to evaluate transposon expression in ddm1 1st generation

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Direct recruitment of TONSOKU by the N-terminal tails of histone variants H2A.X and H2A.W coordinates DNA repair

Project description:Histone variants play crucial roles in DNA replication and DNA damage repair. Plant TONSOKU (TSK) specifically recognizes unmethylated histone H3.1 to bind post-replicative chromatin for DNA repair, but the precise mechanisms of TSK recruitment to double-stranded break (DSB) sites remain unclear. Here, we discovered that the leucine-rich repeats (LRR) domain of TSK recognizes the N-terminal tail of the histone variant H2A.X, the phosphorylated form of which (also known as γ-H2A.X) is a critical marker of DSBs at both replication forks and euchromatin. Additionally, the LRR domain of TSK recognizes the N-terminal tail of the plant-specific histone H2A variant H2A.W, which is essential for DSB repair in heterochromatin, but not H2A.Z, which primarily regulates gene expression. A motif containing multiple basic and acidic residues (BAR motif), unique to H2A.Z, prevents TSK from binding. Notably, mutations that abolish TSK-H2A.X/W binding interfere with TSK-mediated DNA repair and root development. Genetic analyses indicate that H2A.X and H2A.W are redundantly required for DNA damage repair in vivo, with the N-terminus of H2A.X being particularly indispensable. This study reveals a novel H2A.X/W-dependent mechanism for recruiting the DNA repair protein TSK, highlighting the critical role of their previously uncharacterized N-terminal tails in plants.

2025-11-18 | GSE293950 | GEO

RNA-seq for Col-0 WT, ddm1(-/-) and Col-0 X ddm1 (F1) to evaluate transposon expression in F1 Col-0Xddm1 and ddm1

2021-02-10 | GSE150435 | GEO

RNA-seq for WT and ddm1(-/-) to evaluate transposon expression in ddm1 1st generation

Project description:RNA-seq for WT and ddm1(-/-) to evaluate transposon expression in ddm1 1st generation

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ChIP-seq for Histone variants and Histone modifictaions in WT and ddm1(-/-) in 1st generation Leaves.

Project description:How histone intrinsic sequence variation or regulatory modifications regulate nucleosome interactions with transcription remain unclear. To clarify this question, we examined how histone variants and histone modifications assemble in the Arabidopsis thaliana genome, identifying a limited number of chromatin states that divide euchromatin and heterochromatin in biologically significant subdomains. We showed that histone variants were as significant as histone modifications to determine the composition of chromatin states. The loss of function of the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) prevented the exchange between the histone variants H2A.Z and H2A.W over transposons resulting in their enrichment in chromatin states found only on proteins coding genes in the wild type. Hence, the dynamics of histone H2A variants exchange impacted the definition and distribution of chromatin states. We propose that dynamics of histone variants control the organization of histone modifications into chromatin states to achieve landmarks that signify the ability for transcription. Chromatin immunoprecipitation sequencing (ChIP-seq) for histone H2A variants and histone modifications in Col0 and ddm1(-/-) .

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The chromatin remodeler DDM1 silences transposons through deposition of the histone variant H2A.W

Project description:The chromatin remodeler DDM1 silences transposons through deposition of the histone variant H2A.W

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MNase-seq of seedlings in Arabidopsis thaliana Col and h2a.w mutants

Project description:10-day-old seedlings from Col and h2a.w mutants (h2a.w.6, h2a.w.7, h2a.w.6,7, h2a.w.6,7,12) were harvested. Nuclei extracted using Honda buffer was fragmented with mirococcal nuclease (MNase, NEB M0247S). The fragmented DNA was purified by phenol/chloroform/isoamyl alcohol (24:24:1) extraction, followed by ethanol precipitation and 2% agarose gel separation and gel extraction of ~145-150 bp DNA. Purified DNA sent to BGI (Hong Kong) for library preparation and sequencing.

2025-01-03 | E-MTAB-14674 | biostudies-arrayexpress

Crosslinking mass spectrometry of DDM1 complexed with the nucleosome

Project description:DECREASE IN DNA METHYLATION 1 (DDM1) is the chromatin remodeling factor that has been genetically identified in Arabidopsis thaliana as a factor involved in the maintenance of repressive epigenomic modifications over transposons. In this study, we performed crosslinking mass spectrometry and biochemical analysis using reconstituted nucleosome to understand the chromatin remodeling activity of DDM1. We found that the unique C-terminal tail of heterochromain-specific H2A.W variant binds to DDM1. This result suggest that DDM1 functions with specific histone variants for the maintenance of repressive modifications and epigenetic regulation of transposon activity.

2024-05-31 | PXD043417 | JPOST Repository

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

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