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The application of ChIP-seq to study the impact of the CXCdel mutation and SETD2 inhibition on H3K27me3 spreading.

ABSTRACT: The application of ChIP-seq to study the impact of the CXCdel mutation and SETD2 inhibition on H3K27me3 spreading.

PROVIDER: PRJNA821526 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18544762_1.fastq.gz	Fastqsanger.gz
	SRR18544762_2.fastq.gz	Fastqsanger.gz
	SRR18544763_1.fastq.gz	Fastqsanger.gz
	SRR18544763_2.fastq.gz	Fastqsanger.gz
	SRR18544764_1.fastq.gz	Fastqsanger.gz

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The application of ChIP-seq to study the impact of the CXCdel mutation and SETD2 inhibition on H3K27me3 spreading.

Project description:We conducted quantitative ChIP-seq to study the impact of the CXCdel mutation and SETD2 inhibition on H3K27me3 spreading. In addition, we performed standard ChIP-seq for EZH2 in wt and CXCdel Karpas-422 and K562 cell lines.

2023-02-08 | GSE199809 | GEO

PICKLE-mediated nucleosome condensing drives H3K27me3 spreading for the inheritance of Polycomb memory during differentiation [ChIP-Seq]

Project description:The Polycomb repressive complex 2 (PRC2) is an essential epigenetic regulator that deposits repressive H3K27me3 for transcriptional gene silencing in eukaryotes. The PRC2-mediated gene silencing process occurs in two steps: the initial H3K27me3 deposition at the nucleation region, and the subsequent spreading of H3K27me3 over the entire gene. Lack of H3K27me3 spreading gives rise to a metastable state that could lead to loss of silencing. H3K27me3 spreading is thus a key step critical for the establishment of stable long-term Polycomb silencing in both animals and plants.Here, we uncover that Arabidopsis thaliana PICKLE (PKL), a member of the conserved Chromodomain Helicase DNA-binding (CHD) family of chromatin remodeling ATPase13, is dispensable for the nucleation but especially required for the efficient spreading of H3K27me3 at thousands of Polycomb target genes. PKL localizes to the spreading regions in a non-DNA-sequence-specific manner through its SANT-SILDE domain. PKL then upregulates the chromatin density by its CHROMODOMAIN and ATPase domain , enabling the H3K27me3 methyltransferase CURLY LEAF (CLF) to deposit H3K27me3 on nucleosomes in the spreading regions to facilitate the H3K27me3 spreading.

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PICKLE-mediated nucleosome condensing drives H3K27me3 spreading for the inheritance of Polycomb memory during differentiation [ATAC-Seq]

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Project description:Our study aims to understand the H3K36me3 and H3K27me3 genome-wide alterations by analysing CHIP-seq data between setd2 wt and ko germinal center B cells, characterize the function of H3K36me3 methyltransferase setd2 in H3K36me3 itself and H3K27me3, further we aim to H3K27me3 from phf19 ,which is H3K27me3 regulator, WT and KO group to investigate the mechanism of H3K36me3 dependent H3K27me3 modification introduced by setd2.

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Project description:Nucleation and spreading of H3K27me3 are critical steps for the initiation and maintenance, respectively, of mitotically inheritable Polycomb-mediated repressive chromatin states in cell identity memory, in both animals and plants. Although a semiconservative read-and-write mechanism is proposed to play a key role in H3K27me3 propagation, the specific determinant and underlying mechanism by which the Polycomb Repressive Complex 2 (PRC2) accesses unmodified nucleosomes for propagating H3K27me3 remain enigmatic. Using Arabidopsis thaliana as a model, we show that the chromatin remodeling activity of PICKLE (PKL) has a specialized role in H3K27me3 spreading to safeguard cell identity during differentiation. PKL specifically binds to H3K27me3 spreading regions but not nucleation sites of Polycomb target genes and physically interacts with the MSI1 subunit of PRC2. Loss of PKL abolishes the occupancy of the PRC2 catalytic subunit CLF in spreading regions and leads to aberrant differentiation. Nucleosome condensing endowed by the ATPase function of PKL ensures that unmodified nucleosomes are accessible to PRC2 catalytic activity. Our findings highlight that PKL-dependent nucleosome compaction is critical for PRC2-mediated H3K27me3 read-and-write functions in H3K27me3 spreading, thus revealing a mechanism by which repressive chromatin domains are established and propagated.

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Project description:To understand the molecular basis how Setd2 loss enhances metastatic traits of PCa, we carried out RNA-seq and H3k27me3 Chip-seq using mice-derived prostatic organoid cells from 3-month-old PtenPC+/− and PtenPC+/−;Setd2PC−/− mice.To further validate Setd2 loss accelerated prostate tumorigenesis is dependent on EZH2 upregulation,we conduct high throughput sequencing of organoid cells derived from PtenPC+/− and PtenPC+/−;Setd2PC−/− mice with Ezh2 knockout.To understand the molecular basis whether the tumor suppressive function of Setd2 is depends on its methylation of EZH2 at k735, we also carried out RNA-seq using mice-derived prostatic organoid cells from 2-month-old PtenPC-/- and PtenPC-/-;Ezh2K735R mice.We integrated all the RNA-seq and chip-seq data generated from organoid cells.

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2024-08-07 | GSE196241 | GEO

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