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Setdb1 regulates Cohesin at H3K9me3-independent topological domains [ChIP-Seq]

ABSTRACT: Identification of SMC1a and Setdb1 bound-loci in E14 mESCs.

ORGANISM(S): Mus musculus

PROVIDER: GSE123244 | GEO | 2020/12/01

REPOSITORIES: GEO

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Setdb1 regulates Cohesin at H3K9me3-independent topological domains [RNA-Seq]

Project description:Identification of SMC1a and Setdb1 bound-loci in E14 mESCs.

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Setdb1 regulates Cohesin at H3K9me3-independent topological domains [Hi-C]

Project description:Hi-C experiments were performed on E14 cells knocked down with shEV, shSetdb1, and shSmc1a. Please note that the GSM6037819 - GSM6037836 samples were generated with higher resolution to supplement the previous data (GSM5689250-GSM5689252) with low resolution.

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Setdb1 regulates Cohesin at H3K9me3-independent topological domains

Project description:Setdb1 regulates Cohesin at H3K9me3-independent topological domains

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Setdb1 regulates Cohesin at H3K9me3-independent topological domains

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

2020-12-01 | GSE123245 | GEO

Setdb1 regulates Cohesin at H3K9me3-independent topological domains [RNA-Seq]

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Setdb1 regulates Cohesin at H3K9me3-independent topological domains [Hi-C]

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DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements and chimaeric transcripts in mouse ES cells

Project description:DNA methylation and histone H3 lysine 9 trimethylation (H3K9me3) play important roles in silencing of genes and retroelements. However, a comprehensive comparison of genes and repetitive elements repressed by these pathways has not been reported. Here we show that in mouse embryonic stem cells (mESCs), the genes up-regulated following deletion of the H3K9 methyltransferase Setdb1 are distinct from those de-repressed in mESC deficient in the DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b, with the exception of a small number of primarily germline-specific genes. Numerous endogenous retroviruses (ERVs) lose H3K9me3 and are concomitantly de-repressed exclusively in SETDB1 knockout mESCs. Strikingly, ~15% of up-regulated genes are induced in association with de-repression of promoter proximal ERVs, half in the context of "chimaeric" transcripts that initiate within these retroelements and splice to genic exons. Thus, SETDB1 plays a previously unappreciated yet critical role in inhibiting aberrant gene transcription by suppressing the expression of proximal ERVs. NChIP-seq and mRNA-seq of WT, SETDB1 KO and DMNT1 TKO mESCs

2011-05-21 | E-GEOD-29413 | biostudies-arrayexpress

DNA methylation and SETDB1/H3K9me3 regulate predominantly distinct sets of genes, retroelements and chimaeric transcripts in mouse ES cells

2011-05-21 | GSE29413 | GEO

H3K14ac is linked to methylation of H3K9 by the Tudor domains of SETDB1

Project description:Mononucleosomes were isolated from murine ES cells and precipitated with the recombinant SETDB1 Triple Tudor Domain (3TD), recombinant SETDB1 Triple Tudor domain Y268A mutant, anti-H3K9me2 (Abcam, ab1220), or anti-H3K9me1 (Abcam, ab8896, Lot GR185298-1) antibodies.

2018-07-30 | E-MTAB-4982 | biostudies-arrayexpress

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