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Histone H3 lysine 4 methylation recruits DNA demethylases to enforce gene expression in Arabidopsis

ABSTRACT: Histone H3 lysine 4 methylation recruits DNA demethylases to enforce gene expression in Arabidopsis

PROVIDER: PRJNA1030744 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26457600_1.fastq.gz	Fastqsanger.gz
	SRR26457600_2.fastq.gz	Fastqsanger.gz
	SRR26457800_1.fastq.gz	Fastqsanger.gz
	SRR26457800_2.fastq.gz	Fastqsanger.gz
	SRR26457601_1.fastq.gz	Fastqsanger.gz

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Histone H3 lysine 4 methylation recruits DNA demethylases to enforce gene expression in Arabidopsis.

Project description:Patterning of DNA methylation in eukaryotic genomes is controlled by de novo methylation, maintenance mechanisms and demethylation pathways. In Arabidopsis thaliana, DNA demethylation enzymes are clearly important for shaping methylation patterns, but how they are regulated is poorly understood. Here we show that the targeting of histone H3 lysine four trimethylation (H3K4me3) with the catalytic domain of the SDG2 histone methyltransferase potently erased DNA methylation and gene silencing at FWA and also erased CG DNA methylation in many other regions of the Arabidopsis genome. This methylation erasure was completely blocked in the ros1 dml2 dml3 triple mutant lacking DNA demethylation enzymes, showing that H3K4me3 promotes the active removal of DNA methylation. Conversely, we found that the targeted removal of H3K4me3 increased the efficiency of targeted DNA methylation. These results highlight H3K4me3 as a potent anti-DNA methylation mark and also pave the way for development of more powerful epigenome engineering tools.

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The anti-DNA methylation mark histone H3 lysine 4 methylation recruits DNA demethylases in Arabidopsis [ChIP-seq]

Project description:The anti-DNA methylation mark histone H3 lysine 4 methylation recruits DNA demethylases in Arabidopsis [ChIP-seq]

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The anti-DNA methylation mark histone H3 lysine 4 methylation recruits DNA demethylases in Arabidopsis [RNA-seq]

Project description:The anti-DNA methylation mark histone H3 lysine 4 methylation recruits DNA demethylases in Arabidopsis [RNA-seq]

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The anti-DNA methylation mark histone H3 lysine 4 methylation recruits DNA demethylases in Arabidopsis [WGBS, BS-PCR-seq]

Project description:The anti-DNA methylation mark histone H3 lysine 4 methylation recruits DNA demethylases in Arabidopsis [WGBS, BS-PCR-seq]

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Histone H3 lysine 4 methylation recruits DNA demethylases to enforce gene expression in Arabidopsis

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

2025-01-13 | GSE245961 | GEO

Impact of Jmjd3 and Utx histone demethylases on Histone H3 lysine 27 trimethylation (H3K27Me3) in mature CD4 SP thymocytes

2015-09-02 | GSE70795 | GEO

Impact of Jmjd3 and Utx histone demethylases on Histone H3 lysine 27 trimethylation (H3K27Me3) in mature CD4 SP thymocytes

Project description:While histone H3 lysine 27 trimethylation (H3K27Me3) is associated with gene silencing, whether H3K27Me3 demethylation affects transcription and cell differentiation in vivo has remained elusive. To investigate this, we conditionally inactivated the two H3K27Me3 demethylases, Jmjd3 and Utx, in non-dividing intrathymic CD4+ T cell precursors. We show that both enzymes redundantly promote H3K27Me3 removal at, and expression of, a specific subset of genes involved in terminal thymocyte differentiation, especially S1pr1, encoding a sphingosine-phosphate receptor required for thymocyte egress. Floxed alleles of the genes encoding Utx and Jmjd3 (Kdm6a and Kdm6b, respectively) were deleted in double positive (DP) thymocytes carrying a CD4 Cre transgene. Genome-wide H3K27Me3 ChipSeq was performed on (i) pre-selection (CD69lo) DP thymocytes from wild-type mice carrying an endogenous polyclonal TCR repertoire, (ii) mature (TCRhi CD24lo) CD4 SP thymocytes from wild type (Wt), Jmjd3KO, UtxKO and dKO mice carrying an endogenous polyclonal TCR repertoire and (iii) mature (Va2hi CD24lo) CD4 SP thymocytes from wild type and dKO mice carrying the OTII TCR transgene.

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The anti-DNA methylation mark histone H3 lysine 4 methylation recruits DNA demethylases in Arabidopsis [ChIP-seq]

Project description:Patterning of DNA methylation in eukaryotic genomes is shaped by de novo methylation, maintenance mechanisms, and demethylation pathways, but how these processes interface with epigenetic modification of histones is poorly understood. We found that the targeting of histone H3 lysine four trimethylation (H3K4me3) with the catalytic domain of the SDG2 histone methyltransferase potently erased DNA methylation and gene silencing at FWA and other genes, and also erased CG DNA methylation in the transcribed region of genes. This methylation erasure was completely blocked in the ros1 dml2 dml3 triple mutant which eliminates DNA demethylation enzymes, showing that H3K4me3 promotes the active removal of DNA methylation rather than preventing CG methylation maintenance. We also found that targeting the removal of H3K4me3 with the novel protein TRBIP1, which acts in part by recruiting the H3K4me3 demethylase JMJ14, causes potent gene silencing. Furthermore, using a CRISPR-based system to simultaneously target both TRBIP1 and a CG specific DNA methyltransferase, we observed more potent establishment of DNA methylation and gene silencing than targeting the DNA methyltransferase by itself. These results highlight H3K4me3 as a potent anti-DNA methylation mark, and reveal potent and specific tools for epigenome engineering.

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