Small noncoding RNAs in FSHD2 muscle cells reveal both DUX4- and SMCHD1-specific signatures
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ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE113133
PROVIDER: PRJNA450097 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7001330.fastq.gz | Fastqsanger.gz | |||
| SRR7001331.fastq.gz | Fastqsanger.gz | |||
| SRR7001332.fastq.gz | Fastqsanger.gz | |||
| SRR7001333.fastq.gz | Fastqsanger.gz | |||
| SRR7001334.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Facioscapulohumeral muscular dystrophy (FSHD) is caused by insufficient epigenetic repression of D4Z4 macrosatellite repeat where DUX4, an FSHD causing gene is embedded. There are two forms of FSHD, FSHD1 with contraction of D4Z4 repeat and FSHD2 with chromatin compaction defects mostly due to SMCHD1 mutation. Previous reports showed DUX4-induced gene expression changes as well as changes in microRNA expression in FSHD muscle cells. However, a genome wide analysis of small noncoding RNAs that might be regulated by DUX4 or by mutations in SMCHD1 has not been reported yet. Here, we identified several types of small noncoding RNAs including known microRNAs that are differentially expressed in FSHD2 muscle cells compared to control. Although fewer small RNAs were differentially expressed during muscle differentiation in FSHD2 cells compared to controls, most of the known myogenic microRNAs, such as miR1, miR133a, and miR206 were induced in both FSHD2 and control muscle cells during differentiation. Our small RNA sequencing data analysis also revealed both DUX4- and SMCHD1-specific changes in FSHD2 muscle cells. Six FSHD2 microRNAs were affected by DUX4 overexpression in control myoblasts, whereas increased expression of tRNAs and 5S rRNAs in FSHD2 muscle cells was largely recapitulated in SMCHD1-depleted control myoblasts. Altogether, our studies suggest that the small noncoding RNA transcriptome changes in FSHD2 might be different from those in FSHD1 and that these differences may provide new diagnostic and therapeutic tools specific to FSHD2.
2018-05-29 | GSE113133 | GEO
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
Project description:Structural Maintenance of Chromosomes Flexible Hinge Domain Containing 1 (SMCHD1) is a non-canonical member of the structural maintenance of chromosomes (SMC) protein family involved in the regulation of chromatin structure, epigenetic regulation and transcription. Mutations in SMCHD1 cause facioscapulohumeral muscular dystrophy type 2 (FSHD2), a rare genetic disorder characterized by progressive muscle weakness and wasting, believed to be caused by aberrant expression of DUX4 in muscle cells. Here we suggest a new role for SMCHD1 as a regulator of alternative splicing, and demonstrate how splicing alteration caused by SMCHD1 mutations lead to DUX4 expression and FSHD pathogenesis. Analyzing RNA-seq data from muscle biopsies of FSHD2 patients and FSHD2 mouse model found that hundreds of genes were alternatively spliced upon SMCHD1 mutation. At least 20% of alternatively spliced genes were associated with abnormalities of the musculature. Moreover, we show that alternatively spliced exons tend to be bound by SMCHD1, and SMCHD1 bound exons demonstrate slower elongation rate, suggesting SMCHD1 binding promotes exon exclusion by slowing RNAPII. Specifically, we discovered that SMCHD1 mutations promotes the splicing of the DNMT3B1 isoform of DNMT3B, which leads to hypomethylation of the D4Z4 region and DUX4 expression. These results suggest that alternative splicing regulated by SMCHD1 may play a major role in FSHD2 pathogenesis by promoting alternative splicing of different targets including DNMT3B, and highlight the potential for targeting alternative splicing as a therapeutic strategy for this disorder.
2024-04-13 | GSE223039 | GEO
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
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 | GSE190828 | GEO
Project description:Facioscapulohumeral muscular dystrophy (FSHD) is caused by insufficient epigenetic repression of D4Z4 macrosatellite repeat where DUX4, an FSHD causing gene is embedded. There are two forms of FSHD, FSHD1 with contraction of D4Z4 repeat and FSHD2 with chromatin compaction defects mostly due to SMCHD1 mutation. Previous reports showed DUX4-induced gene expression changes as well as changes in microRNA expression in FSHD muscle cells. However, a genome wide analysis of small noncoding RNAs that might be regulated by DUX4 or by mutations in SMCHD1 has not been reported yet. Here, we identified several types of small noncoding RNAs including known microRNAs that are differentially expressed in FSHD2 muscle cells compared to control. Although fewer small RNAs were differentially expressed during muscle differentiation in FSHD2 cells compared to controls, most of the known myogenic microRNAs, such as miR1, miR133a and miR206 were induced in both FSHD2 and control muscle cells during differentiation. Our small RNA sequencing data analysis also revealed both DUX4- and SMCHD1-specific changes in FSHD2 muscle cells. Six FSHD2 microRNAs were affected by DUX4 overexpression in control myoblasts, whereas increased expression of tRNAs and 5S rRNAs in FSHD2 muscle cells was largely recapitulated in SMCHD1-depleted control myoblasts. Altogether, our studies suggest that the small noncoding RNA transcriptome changes in FSHD2 might be different from those in FSHD1 and that these differences may provide new diagnostic and therapeutic tools specific to FSHD2.
| S-EPMC6048983 | biostudies-literature
Project description:FSHD is characterized by the misexpression of DUX4 in skeletal muscle. Although DUX4 upregulation is thought to be the pathogenic cause of FSHD, DUX4 is lowly expressed in patient samples, and analysis of the consequences of DUX4 expression has largely relied on artificial overexpression. To better understand the native expression profile of DUX4 and its targets, we first performed pooled RNA-seq on a 6-day differentiation time-course in FSHD2 patient-derived primary myoblasts. We identify a set of 54 FSHD-induced genes upregulated in FSHD2 cells starting at day 2 of differentiation through the end of the time-course. Using single-cell and single-nucleus RNA-seq on FSHD2 myoblasts and day 3 and day 5 differentiated myotubes respectively, we captured, for the first time, DUX4 expressed at the single-nucleus level in a native state. We identified two populations of FSHD myotube nuclei based on low or high enrichment of DUX4 and FSHD-induced genes (FSHD-Lo and “FSHD Hi”, respectively). FSHD-Hi nuclei upregulate many cell cycle related genes with significant enrichment of E2F target genes and p53 signaling activation. In FSHD-Hi myotube nuclei, multiple DUX4 target genes are co-expressed including a set of transcription factors, such as DUXA, ZSCAN4 and LEUTX. DUXA (the DUX4 paralog) is more widely expressed than DUX4, and depletion of DUXA suppressed the expression of LEUTX and ZSCAN4 in late, but not early, differentiation. The results indicate that the DUXA can take over the role of DUX4 and maintain target gene expression. These results may provide explanation as to why it is easier to detect and monitor DUX4 target genes than DUX4 itself in patient cells and suggest a self-sustaining network of gene dysregulation that perpetuates this disease after DUX4 is no longer expressed.
2020-04-07 | GSE143452 | GEO
Project description:FSHD is characterized by the misexpression of DUX4 in skeletal muscle. Although DUX4 upregulation is thought to be the pathogenic cause of FSHD, DUX4 is lowly expressed in patient samples, and analysis of the consequences of DUX4 expression has largely relied on artificial overexpression. To better understand the native expression profile of DUX4 and its targets, we first performed pooled RNA-seq on a 6-day differentiation time-course in FSHD2 patient-derived primary myoblasts. We identify a set of 54 FSHD-induced genes upregulated in FSHD2 cells starting at day 2 of differentiation through the end of the time-course. Using single-cell and single-nucleus RNA-seq on FSHD2 myoblasts and day 3 and day 5 differentiated myotubes respectively, we captured, for the first time, DUX4 expressed at the single-nucleus level in a native state. We identified two populations of FSHD myotube nuclei based on low or high enrichment of DUX4 and FSHD-induced genes (FSHD-Lo and “FSHD Hi”, respectively). FSHD-Hi nuclei upregulate many cell cycle related genes with significant enrichment of E2F target genes and p53 signaling activation. In FSHD-Hi myotube nuclei, multiple DUX4 target genes are co-expressed including a set of transcription factors, such as DUXA, ZSCAN4 and LEUTX. DUXA (the DUX4 paralog) is more widely expressed than DUX4, and depletion of DUXA suppressed the expression of LEUTX and ZSCAN4 in late, but not early, differentiation. The results indicate that the DUXA can take over the role of DUX4 and maintain target gene expression. These results may provide explanation as to why it is easier to detect and monitor DUX4 target genes than DUX4 itself in patient cells and suggest a self-sustaining network of gene dysregulation that perpetuates this disease after DUX4 is no longer expressed.
2020-04-07 | GSE143492 | GEO
Project description:FSHD is characterized by the misexpression of DUX4 in skeletal muscle. Although DUX4 upregulation is thought to be the pathogenic cause of FSHD, DUX4 is lowly expressed in patient samples, and analysis of the consequences of DUX4 expression has largely relied on artificial overexpression. To better understand the native expression profile of DUX4 and its targets, we first performed pooled RNA-seq on a 6-day differentiation time-course in FSHD2 patient-derived primary myoblasts. We identify a set of 54 FSHD-induced genes upregulated in FSHD2 cells starting at day 2 of differentiation through the end of the time-course. Using single-cell and single-nucleus RNA-seq on FSHD2 myoblasts and day 3 and day 5 differentiated myotubes respectively, we captured, for the first time, DUX4 expressed at the single-nucleus level in a native state. We identified two populations of FSHD myotube nuclei based on low or high enrichment of DUX4 and FSHD-induced genes (FSHD-Lo and “FSHD Hi”, respectively). FSHD-Hi nuclei upregulate many cell cycle related genes with significant enrichment of E2F target genes and p53 signaling activation. In FSHD-Hi myotube nuclei, multiple DUX4 target genes are co-expressed including a set of transcription factors, such as DUXA, ZSCAN4 and LEUTX. DUXA (the DUX4 paralog) is more widely expressed than DUX4, and depletion of DUXA suppressed the expression of LEUTX and ZSCAN4 in late, but not early, differentiation. The results indicate that the DUXA can take over the role of DUX4 and maintain target gene expression. These results may provide explanation as to why it is easier to detect and monitor DUX4 target genes than DUX4 itself in patient cells and suggest a self-sustaining network of gene dysregulation that perpetuates this disease after DUX4 is no longer expressed.
2020-04-07 | GSE143453 | GEO
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