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

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

PROVIDER: PRJNA632029 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11780903.fastq.gz	Fastqsanger.gz
	SRR11780904.fastq.gz	Fastqsanger.gz
	SRR11780905.fastq.gz	Fastqsanger.gz
	SRR11780906.fastq.gz	Fastqsanger.gz
	SRR11780907.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 Col-0 WT, ddm1(-/-) and Col-0 X ddm1 (F1) to evaluate transposon expression in F1 Col-0Xddm1 and ddm1

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

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

2021-02-10 | GSE150436 | GEO

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

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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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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.

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Project description:Eukaryotic DNA methylation is found in silent transposable elements and active genes. Nucleosome remodelers of the DDM1/Lsh family are thought to be specifically required to maintain transposon methylation, but the reason for this is unknown. Here, we find that a chromatin gradient that extends from the most heterochromatic transposons to euchromatic genes determines the requirement of DDM1 for methylation maintenance in all sequence contexts. We also show that small RNA-directed DNA methylation (RdDM) is inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. DDM1 and RdDM independently mediate nearly all transposon methylation, which is catalyzed by the methyltransferases MET1 (CG), CMT3 (CHG), DRM2 (CHH) and CMT2 (CHH), and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that the Arabidopsis genome is defined by a heterochromatic continuum that governs the access of DNA methyltransferases and potentially all DNA binding proteins. Examination of DNA methylation, transcription and nucleosomes in Arabidopsis wild-type and/or ddm1, RdDM and DNA methylase mutants.

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AGO2 silences mobile transposons in the nucleus of quiescent cells

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