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Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation

ABSTRACT: Molecular definition of an RNA-mediated mechanism that stabilizes association of the Suv39h enzymes at mouse heterochromatin.

ORGANISM(S): Mus musculus

PROVIDER: GSE100222 | GEO | 2017/08/03

SECONDARY ACCESSION(S): PRJNA391075

REPOSITORIES: GEO

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Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation.

Project description: Not available

| S-EPMC5538826 | biostudies-literature

RNA quality control factors nucleate Clr4/SUV39H and trigger constitutive heterochromatin assembly

Project description:In eukaryotes, the Suv39 family of proteins tri-methylate lysine 9 of histone H3 (H3K9me) to form constitutive heterochromatin. However, how Suv39 proteins are nucleated at heterochromatin is not fully described. In the fission yeast, current models posit that Argonaute1-associated small RNAs (sRNAs) nucleate the sole H3K9 methyltransferase, Clr4/SUV39H, to centromeres. Here, we show that in the absence of all sRNAs and H3K9me, the Mtl1 and Red1 core (MTREC)/PAXT complex nucleates Clr4/SUV39H at a heterochromatic long noncoding RNA (lncRNA) at which the two H3K9 deacetylases, Sir2 and Clr3, also accumulate by distinct mechanisms. Iterative cycles of H3K9 deacetylation and methylation spread Clr4/SUV39H from the nucleation center in an sRNA-independent manner, generating a basal H3K9me state. This is acted upon by the RNAi machinery to augment and amplify the Clr4/H3K9me signal at centromeres to establish heterochromatin. Overall, our data reveal that lncRNAs and RNA quality control factors can nucleate heterochromatin and function as epigenetic silencers in eukaryotes.

2024-05-16 | PXD039519 | Pride

Suv39h-dependent H3K9me3 represses intact retrotransposons in mouse embryonic stem cells

Project description:Heterochromatin is required to restrict aberrant expression of retrotransposons, but it remains poorly defined due to the underlying repeat-rich sequences. We dissected Suv39h-dependent histone H3 lysine 9 trimethylation (H3K9me3) by genome-wide ChIP-sequencing in mouse embryonic stem cells (ESCs). Refined bioinformatic analyses of repeat subfamilies indicated selective accumulation of Suv39h-dependent H3K9me3 at interspersed repetitive elements that cover ~ 5% of the ESC epigenome. The majority of the ~ 8,150 intact long interspersed nuclear elements (LINEs) and endogenous retroviruses (ERVs), but only a minor fraction of the > 1.8 million degenerate and truncated LINEs/ERVs, are enriched for Suv39h-dependent H3K9me3. Transcriptional repression of these intact LINEs and ERVs is differentially regulated by Suv39h and other chromatin modifiers in ESCs but governed by DNA methylation in committed cells. These data provide a novel function for Suv39h-dependent H3K9me3 chromatin to specifically repress intact retrotransposon elements in the ESC epigenome. ChIP-seq and RNA-seq in mouse ES cells, Neural precursors and MEFs wild type and Suv39h double KO. The input for ES cells is accessioned as GSM1251941. A link to this sample can be found below.

2014-06-26 | E-GEOD-57092 | biostudies-arrayexpress

Suv39h-dependent H3K9me3 represses intact retrotransposons in mouse embryonic stem cells

2014-06-26 | GSE57092 | GEO

m6A RNA methylation of major satellite repeat transcripts facilitates chromatin association and RNA:DNA hybrid formation in mouse heterochromatin.

Project description: Not available

| S-EPMC8191757 | biostudies-literature

FAN1 controls mismatch repair complex assembly via MLH1 retention to stabilize CAG repeat expansion in Huntington's disease.

Project description: Not available

| S-EPMC8424649 | biostudies-literature

Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer.

Project description: Not available

| S-EPMC4679016 | biostudies-literature

RNA quality control factors nucleate Clr4/SUV39H and trigger constitutive heterochromatin assembly

Project description:RNA surveillance (MTREC) and degradation (exosome) complexes nucleate Clr4/SUV39H at a heterochromatic long noncoding RNA, at which the two deacetylases, Sir2 and Clr3, also amass by distinct mechanisms. Iterative cycles of H3K9 deacetylation and methylation spread Clr4 from the nucleation center which with the help from RNAi establish heterochromatin. (this is like the abstract for the paper) To identify nuclear Sir2-interacting proteins, a protocol was adopted by which frozen intact nuclei suitable for biochemical purifications were released by low pressure, semi-automated cryogrinding of frozen yeast pellets after which the nuclei were isolated by differential centrifugation. From these nuclear extracts, FLAG-tagged Sir2 was purified and analyzed by nanoscale micro-capillary tandem mass spectrometry.

2024-02-25 | MSV000094160 | MassIVE

m6A RNA methylation of major satellite repeat transcripts facilitates chromatin association and RNA:DNA hybrid formation in mouse heterochromatin

Project description:m6A RNA methylation of major satellite repeat transcripts facilitates chromatin association and RNA:DNA hybrid formation in mouse heterochromatin

2021-04-21 | GSE156481 | GEO

Survival in quiescence requires the euchromatic deployment of Clr4/SUV39H by Argonaute-associated small RNAs [RNA-Seq]

Project description:Cellular quiescence (G0) is a ubiquitous stress response through which cells enter a state of reversible dormancy, acquiring distinct properties including reduced metabolism, resistance to stress and long life. G0 entry involves dramatic changes to the chromatin landscape and transcriptional program of cells, but the mechanisms coordinating these processes remain poorly understood. Using the fission yeast, here we track the G0-associated chromatin and transcriptional changes temporally. We show that as cells enter G0, their survival and global gene expression programs become increasingly dependent on Clr4/SUV39H, the sole histone H3 lysine 9 (H3K9) methyltransferase, and RNA interference (RNAi) proteins. Notably, G0 entry results in RNAi-dependent H3K9 methylation of several euchromatic regions, prior to which Argonaute 1-associated small RNAs from these regions emerge. Overall our data reveal a new function for constitutive heterochromatin proteins in establishing the global G0 transcriptional program and suggest that stress-induced alterations in Argonaute-associated sRNAs can specify the deployment of transcriptional regulatory proteins to unique sites in eukaryotic genomes.

2016-12-05 | GSE89145 | GEO

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