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SMCHD1 activates the expression of genes required for the expansion of human myoblasts (RNA-seq)

ABSTRACT: SMCHD1 activates the expression of genes required for the expansion of human myoblasts (RNA-seq)

PROVIDER: PRJNA788536 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17222129_1.fastq.gz	Fastqsanger.gz
	SRR17222129_2.fastq.gz	Fastqsanger.gz
	SRR17222130_1.fastq.gz	Fastqsanger.gz
	SRR17222130_2.fastq.gz	Fastqsanger.gz
	SRR17222131_1.fastq.gz	Fastqsanger.gz

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SMCHD1 activates the expression of genes required for the expansion of human myoblasts

Project description:SMCHD1 activates the expression of genes required for the expansion of human myoblasts

| PRJNA788533 | ENA

SMCHD1 activates the expression of genes required for the expansion of human myoblasts (ChIP-seq)

Project description:In human muscle, SMCHD1 mutations are associated with the onset of FSHD2, but the mechanism driving the disease onset remains unclear. A commonly accepted explanation is the loss of SMCHD1 binding to the D4Z4 locus activates the expression of DUX4 in FSHD2 muscle. In this study, we used human myoblasts having DUX4 non-permissive 4qB alleles as a model to study DUX4-independent functions of SMCHD1 on myoblast cell growth. Surprisingly, depletion of SMCHD1 in these cells resulted in a cell proliferation defect. Despite the absence of DUX4 target genes’ activation, these cells showed a repression of PAX7 target genes (a hallmark of FSHD) and similar changes in expression profile compared to FSHD myoblasts. Interestingly, downregulation of cell proliferation-related genes and dysregulation of fibroblasts-specific genes were observed in SMCHD1 knockdown myoblasts and FSHD2 myoblasts but not FSHD1 myoblasts. Additionally, we identified LAP2 as direct targets of SMCHD1. Depletion of LAP2 leads to cell proliferation defect similar to the effect after SMCHD1 knockdown. These data imply that DUX4 is not the only driver for the onset of FSHD, and SMCHD1 has DUX4-independent functions in muscle growth and development.

2024-06-25 | GSE190829 | GEO

SMCHD1 activates the expression of genes required for the expansion of human myoblasts (RNA-seq)

2024-06-25 | GSE190828 | GEO

SMCHD1 activates the expression of genes required for the expansion of human myoblasts (ChIP-seq)

Project description:SMCHD1 activates the expression of genes required for the expansion of human myoblasts (ChIP-seq)

| PRJNA788535 | ENA

SMCHD1 activates the expression of genes required for the expansion of human myoblasts

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

2024-06-25 | GSE190830 | GEO

polyA RNA-seq of SMCHD1 and LRIF1 knock-out immortalized myoblasts

Project description:polyA RNA-seq was performed on different SMCHD1 and LRIF1 knock-out myoblast clones to assess the role of SMCHD1 and LRIF1 in transcriptioanl regulation in somatic cells

2023-01-31 | GSE185511 | GEO

polyA RNA-seq of SMCHD1 and LRIF1 knock-out immortalized myoblasts

Project description:polyA RNA-seq of SMCHD1 and LRIF1 knock-out immortalized myoblasts

| PRJNA769400 | ENA

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.

2021-12-15 | PXD023993 | Pride

DUX4 expression activates JNK and p38 MAP kinases in myoblasts

Project description:DUX4 expression activates JNK and p38 MAP kinases in myoblasts

| PRJNA844998 | ENA

Smchd1 dependent and independent pathways determine developmental dynamics of CpG island methylation on the inactive X chromosome.

Project description:X chromosome inactivation involves multiple levels of chromatin modification, established progressively and in a stepwise manner during early development. The chromosomal protein Smchd1 has recently been shown to play an important role in DNA methylation of CpG islands (CGIs), a late step in the X inactivation pathway required for long-term stability of gene silencing. Here we show that inactive X chromosome (Xi) CGI methylation can occur via either Smchd1 dependent or independent pathways. Smchd1 dependent CGI methylation, the primary pathway, is acquired gradually over an extended period, whereas Smchd1 independent CGI methylation occurs rapidly after the onset of X inactivation. The de novo methyltransferase Dnmt3b is required for methylation of both classes of CGI, whereas Dnmt3a and Dnmt3L are dispensable. Xi CGIs methylated by these distinct pathways differ in respect to their sequence characteristics and immediate chromosomal environment. We discuss the implications of these results for understanding CGI methylation during development. Examination of CpG methylated DNA from wild type and smchd1 null male and female somatic cells and female ES cells differentiated for either 7 or 10 days. Duplicate samples of each type were generated.

2012-10-15 | E-GEOD-37333 | biostudies-arrayexpress

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