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Epigenetic modifier Smchd1 maintains a normal pool of long-term repopulating hematopoietic stem cells in mice II

ABSTRACT: Epigenetic modifier Smchd1 maintains a normal pool of long-term repopulating hematopoietic stem cells in mice II

PROVIDER: PRJNA779954 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16929141_1.fastq.gz	Fastqsanger.gz
	SRR16929141_2.fastq.gz	Fastqsanger.gz
	SRR16929142_1.fastq.gz	Fastqsanger.gz
	SRR16929142_2.fastq.gz	Fastqsanger.gz
	SRR16929143_1.fastq.gz	Fastqsanger.gz

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Epigenetic modifier Smchd1 maintains a normal pool of long-term repopulating hematopoietic stem cells in mice

Project description:Epigenetic modifier Smchd1 maintains a normal pool of long-term repopulating hematopoietic stem cells in mice

| PRJNA779937 | ENA

Epigenetic modifier Smchd1 maintains a normal pool of long-term repopulating hematopoietic stem cells in mice I

Project description:Epigenetic modifier Smchd1 maintains a normal pool of long-term repopulating hematopoietic stem cells in mice I

| PRJNA779245 | ENA

Epigenetic modifier Smchd1 maintains a normal pool of long-term repopulating hematopoietic stem cells in mice II

Project description:We have used a conditional mouse model to investigate the role of Smchd1 specifically in hematopoiesis. We found that Smchd1-deleted mice have an altered hematopoietic stem and progenitor cell (HSPC) compartment with reduced repopulating capacity in competitive bone marrow transplantation assays and the gradual loss of adult hematopoietic stem cells (HSCs) with age, suggesting a role for Smchd1 in the maintenance of long-term adult HSCs. The phenotype was more pronounced in female Smchd1-deleted mice, which showed a more severe reduction in HSCs with age, as well as depleted numbers of B cell lymphocytes. Gene expression profiling of Smchd1 deficient HSCs and B cells revealed several known and novel Smchd1-sensitive genes, a significant disruption to X-linked gene expression, although this was not widespread upregulation of X-linked genes in female cells. These data show Smchd1 as a new regulator of long-term HSCs whose effects are more profound in females.

2022-06-20 | GSE188685 | GEO

Epigenetic modifier Smchd1 maintains a normal pool of long-term repopulating hematopoietic stem cells in mice I

2022-06-20 | GSE188517 | GEO

Epigenetic modifier SMCHD1 maintains a normal pool of long-term hematopoietic stem cells.

Project description:SMCHD1 (structural maintenance of chromosomes hinge domain containing 1) is a noncanonical SMC protein that mediates long-range repressive chromatin structures. SMCHD1 is required for X chromosome inactivation in female cells and repression of imprinted and clustered autosomal genes, with SMCHD1 mutations linked to human diseases facioscapulohumeral muscular dystrophy (FSHD) and bosma arhinia and micropthalmia syndrome (BAMS). We used a conditional mouse model to investigate SMCHD1 in hematopoiesis. Smchd1-deleted mice maintained steady-state hematopoiesis despite showing an impaired reconstitution capacity in competitive bone marrow transplantations and age-related hematopoietic stem cell (HSC) loss. This phenotype was more pronounced in Smchd1-deleted females, which showed a loss of quiescent HSCs and fewer B cells. Gene expression profiling of Smchd1-deficient HSCs and B cells revealed known and cell-type-specific SMCHD1-sensitive genes and significant disruption to X-linked gene expression in female cells. These data show SMCHD1 is a regulator of HSCs whose effects are more profound in females.

| S-EPMC9287190 | biostudies-literature

Epigenetic modifier Smchd1 maintains a normal pool of long-term repopulating hematopoietic stem cells in mice

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

2022-06-20 | GSE188686 | GEO

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

Changes in gene expression in SMCHD1 knockout clones of HCT116

Project description:Development of effective therapies for complex Mendelian disorders such as Facioscapulohumeral muscular dystrophy necessitates a clear understanding of the pathology of this disease. The inappropriate expression of DUX4-fl is believed to be responsible for the disease phenotype. We sought to understand the role of SMCHD1, an epigenetic modifier of the D4Z4 array, in DUX4-fl expression, by a TALEN mediated knockout of the gene in a model cell line HCT116. Analysis of SMCHD1 and DNMT knockouts of HCT116, along with patient cell lines highlighted the importance of epigenetic determinants of the disease and revealed a novel DUX4 isoform. We show that while SMCHD1 loss sensitizes cells to DUX4 expression by increasing transcription of unspliced product from D4Z4, splicing of the transcripts to generate disease associated DUX4-fl can only be induced by CpG hypomethylation and loss of heterochromatic histone marker H3K9me3. Additionally, telomere shortening has an effect similar to SMCHD1 loss, suggesting involvement of a telomere position effect in maintaining DUX4 repression. In light of our observations, we have developed a model for expression of DUX4-fl through a simultaneous loss of heterochromatin at D4Z4 and at the telomere, otherwise maintained by SMCHD1 that acts as a bridge between these two regions.

2022-06-20 | GSE58796 | GEO

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

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

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