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H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination [ChIP-seq]

ABSTRACT: H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination [ChIP-seq]

PROVIDER: PRJNA667469 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12774906_1.fastq.gz	Fastqsanger.gz
	SRR12774906_2.fastq.gz	Fastqsanger.gz
	SRR12774907_1.fastq.gz	Fastqsanger.gz
	SRR12774907_2.fastq.gz	Fastqsanger.gz
	SRR12774908_1.fastq.gz	Fastqsanger.gz

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H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination [Bisulfite-seq]

Project description:DNA methylation and histone lysine tri-methylation at H3K27 (H3K27me3) are the two primary epigenetic marks for transcriptional silencing essential for cell fate determination and cell lineage commitment during development1, 2. These two marks are mutually exclusive and target distinct sets of genes in the mammalian genome3. However, whether and how H3K27me3 shapes the DNA methylome remains unknown. Here, we report that the loss of H3K27me3 modification leads to increased DNA methylation at previously marked H3K27me3 sites, revealing that H3K27me3 negatively regulates DNA methylation. Genome-wide analysis of H3 ubiquitination, essential for recruitment and activation of DNA methyltransferase DNMT14, reveals the absence of H3 ubiquitination at H3K27me3 marked nucleosomes. Moreover, loss of H3K27me3 modification induces an increase in H3K18 ubiquitination at the corresponding hypermethylated loci. Importantly, we show that H3K27me3 directly inhibits UHRF1-mediated H3 ubiquitination toward nucleosomes in a defined biochemical assay. Furthermore, UHRF1 is required for the increase in DNA methylation at previously marked H3K27me3 sites in cells with abolished H3K27me3 modification. Taken together, our findings reveal a general mechanism for H3K27me3-mediated shaping of the mammalian DNA methylome via modulation of H3 ubiquitination.

2022-06-27 | GSE159040 | GEO

H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination [RNA-seq]

2022-06-27 | GSE159041 | GEO

H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination [ChIP-seq]

2022-06-27 | GSE159042 | GEO

H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination

Project description:H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination

| PRJNA667466 | ENA

H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination [RNA-seq]

Project description:H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination [RNA-seq]

| PRJNA667471 | ENA

H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination [Bisulfite-seq]

Project description:H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination [Bisulfite-seq]

| PRJNA667470 | ENA

H3K27me3 shapes DNA methylome by inhibiting UHRF1-mediated H3 ubiquitination

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

2022-06-27 | GSE159043 | GEO

Hemi-methylated DNA regulates DNA methylation inheritance through allosteric control of H3 ubiquitylation by UHRF1

Project description:DNA methylation is a heritable chromatin modification essential to mammalian development that functions with histone post-translational modifications to regulate chromatin structure and gene expression programs. The epigenetic inheritance of DNA methylation requires the combined actions of DNMT1 and UHRF1, a histone- and DNA-binding RING E3 ubiquitin ligase that facilitates DNMT1 recruitment to sites of newly replicated DNA through the ubiquitylation of histone H3. UHRF1 binds DNA with modest selectivity towards hemi-methylated CpG dinucleotides (HeDNA); however, the contribution of HeDNA sensing to UHRF1 function remains elusive. Here, we reveal that the interaction of UHRF1 with HeDNA is required for DNA methylation inheritance but is dispensable for chromatin interaction, which is governed by reciprocal positive cooperativity between the UHRF1 histone- and DNA-binding domains. We further show that HeDNA functions as an allosteric regulator of UHRF1 ubiquitin ligase activity, directing ubiquitylation towards multiple lysines on the H3 tail adjacent to the UHRF1 histone-binding site. Collectively, our studies define a highly orchestrated epigenetic control mechanism involving modifications both to histones and DNA that facilitate UHRF1 chromatin targeting, H3 ubiquitylation, and DNA methylation inheritance.

2016-08-25 | PXD003983 | Pride

H3 ubiquitination by NEDD4 regulates H3 acetylation and

Project description:genome wide occupancy related to H3 ubiquitination at K23/36/37

2017-06-12 | GSE90119 | GEO

Histone ubiquitination-methylation crosstalk involving UHRF1 and SUV39H1/2 reinforces heterochromatin states in response to DNA hypomethylation

Project description:Histone H3 mono-ubiquitination, catalyzed by the RING E3 ubiquitin ligase UHRF1, is appreciated as a docking site for DNMT1 during DNA replication to facilitate DNA methylation maintenance. Its functions beyond this are unknown. Here, we identify simultaneous increases in UHRF1-dependent H3K18ub and SUV39H1/2-dependent H3K9me3 as prominent epigenetic alterations accompanying DNA hypomethylation induced by DNMT1 inhibition. Integrative epigenomics analyses reveal that transient accumulation of hemi-methylated DNA, resulting from incomplete DNA methylation maintenance, stimulates UHRF1-dependent H3K18ub at CpG islands that nucleates new domains of H3K9me3 and impedes PRC2 activity in these genomic regions. Notably, H3K18ub enhances the methyltransferase activity of SUV39H1/2, leading to increased H3K9me3 at these CpG island promoters. Blocking H3K18ub-dependent SUV39H1/2 activity enhances the efficacy of DNMT1 inhibitors. Collectively, these findings reveal a novel histone ubiquitination-methylation crosstalk mechanism that reinforces heterochromatin states in the absence of DNA methylation and proposes new strategies for improving cancer epigenetic therapy.

2024-12-02 | PXD049993 | Pride

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