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Gene expression analysis upon stable SmcHD1 Knock Down

ABSTRACT: To study the role of SmcHD1 in regulating gene expression, we have stably knocked down SmcHD1 in HEK293 cells and looked at change in gene expression. shRNA3 and shRNA4 were used to target the expression of the SmcHD1 gene (Genbank Accession number NM_015295). The protein levels of SmcHD1 were knocked down in excess of 90% normal levels in 293 cells. shRNA NC5 a scrambled control shRNA and did not change SmcHD1 protein levels in 293 cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE52065 | GEO | 2014/01/31

SECONDARY ACCESSION(S): PRJNA226720

REPOSITORIES: GEO

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Gene expression analysis upon stable SmcHD1 Knock Down

Project description:To study the role of SmcHD1 in regulating gene expression, we have stably knocked down SmcHD1 in HEK293 cells and looked at change in gene expression. shRNA3 and shRNA4 were used to target the expression of the SmcHD1 gene (Genbank Accession number NM_015295). The protein levels of SmcHD1 were knocked down in excess of 90% normal levels in 293 cells. shRNA NC5 a scrambled control shRNA and did not change SmcHD1 protein levels in 293 cells. Agilent single color 28004 was used on 9 Samples.

2014-01-31 | E-GEOD-52065 | biostudies-arrayexpress

A proteomics study identifying interactors of the FSHD2 gene product SMCHD1 reveals RUVBL1-dependent DUX4 repression.

Project description:Structural Maintenance of Chromosomes Hinge Domain Containing 1 (SMCHD1) is a chromatin repressor, which is mutated in >95% of Facioscapulohumeral dystrophy (FSHD) type 2 cases. In FSHD2, SMCHD1 mutations ultimately result in the presence of the cleavage stage transcription factor DUX4 in muscle cells due to a failure in epigenetic repression of the D4Z4 macrosatellite repeat on chromosome 4q, which contains the DUX4 locus. While binding of SMCHD1 to D4Z4 and its necessity to maintain a repressive D4Z4 chromatin structure are well documented, it is unclear how SMCHD1 is recruited to D4Z4, and how it exerts its repressive properties on the chromatin. Here, we employ a quantitative proteomics approach to identify and characterize novel SMCHD1 interacting proteins, and assess their functionality in D4Z4 repression. We identify 47 robust SMCHD1 interactors, of which 19 are present in D4Z4 chromatin. We demonstrate that one of these SMCHD1 interacting proteins in D4Z4, RuvB-like 1 (RUVBL1) is indeed required for maintaining DUX4 silencing in FSHD myocytes. We also confirm the interaction of SMCHD1 with EZH inhibitory protein (EZHIP), which prevents global H3K27me3 deposition by the Polycomb repressive complex PRC2, providing novel insights into the potential function of SMCHD1 in the repression of DUX4 in the early stages of embryogenesis. The SMCHD1 interactome outlined herein can thus provide further direction into research on the potential function of SMCHD1 at genomic loci where SMCHD1 is known to act, such as D4Z4 repeats, the inactive X chromosome, autosomal gene clusters, imprinted loci and telomeres.

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ATAC-seq in Smchd1 wild-type and Smchd1 deleted neural stem cells.

Project description:We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq, chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. We additionally analysed Smchd1 binding genome-wide using ChIP-seq. Together, we find that deletion of Smchd1 alters chromosome conformation at Smchd1 target genes including the inactive X chromosome, Hox genes and imprinted loc. Smchd1 deletion results in gain in Ctcf binding and activation of enhancers. We propose Smchd1 functions by limiting Ctcf-mediated chromosome looping.

2018-06-30 | GSE111721 | GEO

RNA-seq in Smchd1 wild-type and Smchd1 deleted differentiating male ES cells.

Project description:We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq, chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. We additionally analysed Smchd1 binding genome-wide using ChIP-seq. Together, we find that deletion of Smchd1 alters chromosome conformation at Smchd1 target genes including the inactive X chromosome, Hox genes and imprinted loci. Smchd1 deletion in differentiating ES cells results in failed Hox gene silencing. Smchd1 deletion results in gain in Ctcf binding and activation of enhancers. We propose Smchd1 functions by limiting Ctcf-mediated chromosome looping.

2018-06-30 | GSE111724 | GEO

RNA-seq in Smchd1 wild-type and Smchd1 null presomitic mesoderm from E9.5 embryos

Project description:We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conformation. We used in situ Hi-C to analyse chromosome conformation changes upon deletion of the epigenetic regulator Smchd1 in female neural stem cells. In parallel, we analysed nucleosome accessibility using ATAC-seq, gene expression using RNA-seq, chromatin marks H3K27me3 and H3K27ac and Ctcf binding using ChIP-seq. We additionally analysed Smchd1 binding genome-wide using ChIP-seq. Together, we find that deletion of Smchd1 alters chromosome conformation at Smchd1 target genes including the inactive X chromosome, Hox genes and imprinted loci. Smchd1 deletion in differentiating ES cells results in failed Hox gene silencing and Smchd1 null E9.5 embryos show altered Hox gene expression.. Smchd1 deletion results in gain in Ctcf binding and activation of enhancers. We propose Smchd1 functions by limiting Ctcf-mediated chromosome looping.

2018-06-30 | GSE112041 | GEO

RRBS in Smchd1 control and Smchd1 deleted male and female neural stem cells.

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Allele-specific RNA-seq in Smchd1 control and Smchd1 deleted female neural stem cells.

2018-06-30 | GSE112043 | GEO

RNA-seq in Smchd1 control and Smchd1 deleted male and female neural stem cells.

2018-06-30 | GSE111723 | GEO

In situ Hi-C in Smchd1 wild-type and Smchd1 deleted neural stem cells.

2018-06-30 | GSE111720 | GEO

Smchd1 regulates autosomal genes subject to monoallelic expression

Project description:Analysis of the genes that escape silencing in the MommeD1 allele of Smchd1 Total RNA from E9.5 embryos compared in a two factor design - gender and Smchd1 genotype

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