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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE201331 | GEO | 2024/10/02

REPOSITORIES: GEO

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

2024-10-02 | GSE201375 | GEO

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

2024-10-02 | GSE201374 | GEO

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

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.

2024-10-02 | GSE267571 | GEO

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

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

Project description:PICKLE-mediated nucleosome condensing drives H3K27me3 spreading for the inheritance of Polycomb memory during differentiation

| PRJNA831312 | ENA

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

Project description:PICKLE-mediated nucleosome condensing drives H3K27me3 spreading for the inheritance of Polycomb memory during differentiation [Mnase-Seq]

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

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

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

Project description:PICKLE-mediated nucleosome condensing drives H3K27me3 spreading for the inheritance of Polycomb memory during differentiation [RNA-Seq]

| PRJNA1111876 | ENA

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

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

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Replication stress affects the fidelity of nucleosome-mediated epigenetic inheritance.

Project description:The fidelity of epigenetic inheritance or, the precision by which epigenetic information is passed along, is an essential parameter for measuring the effectiveness of the process. How the precision of the process is achieved or modulated, however, remains largely elusive. We have performed quantitative measurement of epigenetic fidelity, using position effect variegation (PEV) in Schizosaccharomyces pombe as readout, to explore whether replication perturbation affects nucleosome-mediated epigenetic inheritance. We show that replication stresses, due to either hydroxyurea treatment or various forms of genetic lesions of the replication machinery, reduce the inheritance accuracy of CENP-A/Cnp1 nucleosome positioning within centromere. Mechanistically, we demonstrate that excessive formation of single-stranded DNA, a common molecular abnormality under these conditions, might have correlation with the reduction in fidelity of centromeric chromatin duplication. Furthermore, we show that replication stress broadly changes chromatin structure at various loci in the genome, such as telomere heterochromatin expanding and mating type locus heterochromatin spreading out of the boundaries. Interestingly, the levels of inheritable expanding at sub-telomeric heterochromatin regions are highly variable among independent cell populations. Finally, we show that HU treatment of the multi-cellular organisms C. elegans and D. melanogaster affects epigenetically programmed development and PEV, illustrating the evolutionary conservation of the phenomenon. Replication stress, in addition to its demonstrated role in genetic instability, promotes variable epigenetic instability throughout the epigenome.

| S-EPMC5549764 | biostudies-literature

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