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The histone H3 lysine 36 demethylases KDM2A and KDM2B restrict DNMT3A-mediated de novo DNA methylation in oocytes to support embryonic development

ABSTRACT: The histone H3 lysine 36 demethylases KDM2A and KDM2B restrict DNMT3A-mediated de novo DNA methylation in oocytes to support embryonic development

PROVIDER: PRJNA983810 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24923900.fastq.gz	Fastqsanger.gz
	SRR24924000.fastq.gz	Fastqsanger.gz
	SRR24924100.fastq.gz	Fastqsanger.gz
	SRR24924200.fastq.gz	Fastqsanger.gz
	SRR24924300.fastq.gz	Fastqsanger.gz

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The histone H3 lysine 36 demethylases KDM2A and KDM2B restrict DNMT3A-mediated de novo DNA methylation in oocytes to support embryonic development [WGBS]

Project description:DNA methylation (DNAme) controls gene expression, genome stability and cell identity in many mammalian organisms. Genomes of most somatic cells and spermatozoa are largely methylated, apart from CpG-dense sequences including gene promoters1. In mouse oocytes, DNAme is mostly limited to transcribed regions2,3. The mechanisms restricting global DNAme acquisition in developing oocytes and the relevance thereof for regulating gene expression and embryo development after fertilization are unknown. Here we show that the histone H3 lysine 36 dimethyl (H3K36me2) demethylases KDM2A and KDM2B redundantly execute multiple chromatin functions during oocyte development, which are vital to pre- and post-implantation development. Firstly, by serving as recruitment factors of variant Polycomb Repressive Complex 1 (vPRC1), they control genome-wide H2A mono-ubiquitination deposition (H2AK119u1) and PRC1-dependent gene repression4. Secondly, as demethylases, KDM2A/KDM2B prevent global H3K36me2 accumulation, thereby impeding DNMT3A-catalyzed de novo DNAme within PRC1-controlled promoter, genic, and intergenic regions, and even at non-PRC1-controlled CpG-dense gene promoters5. Decisively, we demonstrate that aberrant Dnmt3a-dependent DNAme established in Kdm2a/Kdm2b double mutant oocytes represses transcription from maternal loci in two-cell embryos and impairs pre-implantation development. Hence, KDM2A/KDM2B are essential for defining the appropriate oocyte DNA methylome which in turn conveys competence for early embryonic development. Our research implies that the reprogramming capacity eminent to early embryos is insufficient to erase aberrant DNAme from maternal chromatin. Lastly, our work shows that early development is vulnerable to gene dosage haplo-insufficiency effects, possibly in a parental-specific manner.

2025-03-27 | GSE234966 | GEO

The histone H3 lysine 36 demethylases KDM2A and KDM2B restrict DNMT3A-mediated de novo DNA methylation in oocytes to support embryonic development [Cut&Run]

2025-03-27 | GSE234967 | GEO

The histone H3 lysine 36 demethylases KDM2A and KDM2B restrict DNMT3A-mediated de novo DNA methylation in oocytes to support embryonic development [RNA-seq]

2025-03-27 | GSE234965 | GEO

The histone H3 lysine 36 demethylases KDM2A and KDM2B restrict DNMT3A-mediated de novo DNA methylation in oocytes to support embryonic development [WGBS]

Project description:The histone H3 lysine 36 demethylases KDM2A and KDM2B restrict DNMT3A-mediated de novo DNA methylation in oocytes to support embryonic development [WGBS]

| PRJNA983818 | ENA

The histone H3 lysine 36 demethylases KDM2A and KDM2B restrict DNMT3A-mediated de novo DNA methylation in oocytes to support embryonic development [RNA-seq]

Project description:The histone H3 lysine 36 demethylases KDM2A and KDM2B restrict DNMT3A-mediated de novo DNA methylation in oocytes to support embryonic development [RNA-seq]

| PRJNA983814 | ENA

The histone H3 lysine 36 demethylases KDM2A and KDM2B restrict DNMT3A-mediated de novo DNA methylation in oocytes to support embryonic development [Cut&Run]

Project description:The histone H3 lysine 36 demethylases KDM2A and KDM2B restrict DNMT3A-mediated de novo DNA methylation in oocytes to support embryonic development [Cut&Run]

| PRJNA983817 | ENA

Structural basis of paralog-specific KDM2A/B nucleosome recognition

Project description:The nucleosome acidic patch is a major interaction hub for chromatin, providing a platform for enzymes to dock and orient for nucleosome-targeted activities. In order to define the molecular basis of acidic patch recognition proteome-wide, we performed an amino acid resolution acidic patch interactome screen. We discovered that the histone H3 lysine 36 (H3K36) demethylase KDM2A, but not its closely related paralog, KDM2B, requires the acidic patch for nucleosome binding. These KDM2 family JumonjiC (JmjC) domain lysine demethylases are critical to heterochromatin formation and are commonly misregulated in cancer. Despite fundamental roles in transcriptional regulation in health and disease, the molecular mechanisms governing nucleosome substrate specificity of KDM2A/B, or any other JmjC lysine demethylases, remain unclear. We used a covalent JmjC inhibitor to solve cryo-EM structures of KDM2A and KDM2B trapped in action on the nucleosome. Our structures show that KDM2-nucleosome binding is paralog-specific and facilitated by dynamic nucleosomal DNA unwrapping and histone charge shielding that mobilize the H3K36 sequence for demethylation.

2023-02-14 | PXD032791 | Pride

The histone H3 lysine 36 demethylases KDM2A and KDM2B restrict DNMT3A-mediated de novo DNA methylation in oocytes to support embryonic development

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

2025-03-27 | GSE234968 | GEO

Transcriptome analysis of histone demethylase Kdm2a knockout in mouse embryonic stem cells

Project description:H3K36 methylation plays an important role in gene regulation. The role of H3K36 demethylase Kdm2b has been well studied. However, the role of Kdm2a in embryonic stem cells are still unkonwn. To study the function of Kdm2a in embryonic stem cells. We used CRISPR-gRNA system to knockout Kdm2a. We analyzed the gene expression change and identified target genes and repeats of Kdm2a. We uncovered a novel role of Kdm2a in regulating gene expression in embryonic stem cells.

2019-08-20 | GSE117148 | GEO

KDM2B binds CpG islands and modulates recruitment of Ring1b

Project description:CpG island elements are associated with most mammalian gene promoters, yet how they contribute to gene regulation remains poorly understood. Recently it has become clear that a subset of CpG islands in embryonic stem cells can act as polycomb response elements and are recognized by the polycomb silencing systems to regulate the expression of genes involved in pluripotency and early developmental transcription programs. How CpG islands function mechanistically as nucleation sites for polycomb repressive complexes remains unknown. Here we discover that the KDM2B protein, by virtue of its ZF-CxxC DNA binding domain, specifically recognizes non-methylated DNA in CpG islands elements genome-wide. Through a physical interaction with the polycomb repressive complex 1 (PRC1), KDM2B targets PRC1 to CpG islands where it contributes to H2AK119ub1 and gene repression at a subset of polycomb targets. Unexpectedly, we also find that CpG islands are occupied by low levels of PRC1 throughout the genome, suggesting that the KDM2B-PRC1 complex may sample CpG island associated genes for susceptibility to polycomb mediated silencing. These observations demonstrate an unexpected and direct link between recognition of CpG islands by KDM2B and targeting of the polycomb repressive system. This provides the basis for a new model describing the functionality of CpG islands as mammalian PREs. ChIP-Seq to compare KDM2A vs. KDM2B genome-wide binding profiles and to understand the contribution of KDM2B to RING1B nucleation. Binding of Kdm2a and Kdm2b to the genome was examined in wildtype mESC, and Kdm2b and Ring1b in mESC where Kdm2b has been stably knocked down by shRNA.

2012-12-26 | E-GEOD-40860 | biostudies-arrayexpress

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