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Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo [ATAC]

ABSTRACT: Here, we developed mouse models expressing inducible lysine to methionine mutants of histone H3, which function as dominant negative inhibitors of methylation at their respective sites. Upon induction of H3K9M or H3K36M, we observed potent differentiation defects in stem cells and regenerative tissues. This work covers RNA-seq and ATAC-seq in this model system.

ORGANISM(S): Mus musculus

PROVIDER: GSE126825 | GEO | 2019/05/20

REPOSITORIES: GEO

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Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo

Project description:Here, we developed mouse models expressing inducible lysine to methionine mutants of histone H3, which function as dominant negative inhibitors of methylation at their respective sites. Upon induction of H3K9M or H3K36M, we observed potent differentiation defects in stem cells and regenerative tissues. This work covers ChIP-seq in this model system for H3K9me3, H3K36me3, and H3K27me3.

2019-10-07 | GSE125703 | GEO

Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo [RNA]

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RNA-seq data for lineage negative, Sca1 positive, and cKit positive hematopoietic stem/progenitor cells from H3.3K36M, H3.3K9M, or rtTA control mice

Project description:We analyzed gene expression patterns in LKS cells using RNA-seq after one week of mutant histone induction. We chose this time point to minimize secondary effects and because methylation at both H3K9 and H3K36 is maximally depleted by that time. Compared to rtTA control, 150 and 364 genes were differentially expressed in H3K9M and H3K36M expressing LKS cells, respectively. Principal component analysis indicated that biological replicates were highly consistent and expression profiles for H3K9M, H3K36M, and rtTA control were distinct. In general, gene expression changes following H3K9M induction were subtle, while induction of H3K36M led to more robust differences in expression patterns.

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Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo

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

2019-05-20 | GSE126829 | GEO

Histone H3 lysine-to-methionine mutants as a paradigm to study chromatin signaling

Project description:Histone H3 lysine27-to-methionine (H3K27M) gain-of-function mutations occur in highly aggressive pediatric gliomas. Here, we establish a Drosophila animal model for the pathogenic histone H3K27M mutation and show that its overexpression resembles Polycomb repressive complex 2 (PRC2) loss-of-function phenotypes, causing de-repression of PRC2 target genes and developmental perturbations. Similarly, a H3K9M mutant depletes H3K9 methylation levels and suppresses position-effect variegation in various Drosophila tissues. The histone H3K9 demethylase KDM3B/JHDM2 associates with H3K9M nucleosomes and its overexpression in Drosophila results in loss of H3K9 methylation levels and heterochromatic silencing defects. Here we establish histone lysine-to-methionine mutants as robust in vivo tools for inhibiting methylation pathways that also function as biochemical reagents for capturing site-specific histone-modifying enzymes, thus providing molecular insight into chromatin-signaling pathways. RNA-seq of wing imaginal discs expressing either H3.3WT-FLAG-HA or H3.3K27M-FLAG-HA.

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Mechanism for the selective sequestration of a histone H3K9 methyltransferase at heterochromatin by the H3K9M mutation

Project description:Oncogenic histone lysine-to-methionine mutations block the methylation of their corresponding lysine residues on wild type histones, but the mechanisms by which these mutations function are highly controversial. We have previously shown that in fission yeast, H3K9M containing nucleosomes sequesters the H3K9 methyltransferase Clr4 to block H3K9 methylation{Shan, 2016 #119}. Using ChIP-sequencing, here we show that even though H3K9M containing nucleosomes are broadly distributed across the genome, Clr4 is mainly sequestered at pericentric repeats. The selective sequestration of Clr4 depends not only on H3K9M, but also on H3K14 ubiquitylation (H3K14ub), a modification deposited by a Clr4 associated E3 ubiquitin ligase complex. In vitro, H3K14ub enhances the interaction between H3K9M and Clr4 and potentiates the inhibitory effects of H3K9M on Clr4 enzymatic activity. Using bio-layer interferometry, we show that the H3K9M mutation reduced association rates (kon) of Clr4 with histone tails, suggesting that Clr4 intrinsically disfavors H3K9M. More importantly, H3K9M reduced the dissociation rate (koff) of Clr4 with histone tails, demonstrating that H3K9M slows down the turnover of Clr4 once it is bound. Finally, we generated mutations on Clr4 that specifically disrupt its interaction with H3K14ub and show that they reduce the inhibitory effects of H3K9MK14ub on Clr4 enzymatic activity in vitro and relieve the sequestration of Clr4 at pericentric repeats in vivo. Therefore, the selective sequestration of Clr4 at pericentric repeats by H3K9M is due to the presence of H3K14ub at these regions, which overcomes Clr4’s aversion of H3K9M and reduces the dissociation of Clr4.

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Histone H3 lysine-to-methionine mutants as a paradigm to study chromatin signaling

2014-09-02 | GSE59891 | GEO

Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo

Project description:Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo

| PRJNA523397 | ENA

Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo

Project description:Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo

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Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo [RNA]

Project description:Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo [RNA]

| PRJNA523405 | ENA

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