SMCHD1 regulates a limited set of gene clusters on autosomal chromosomes
Abstract Background Facioscapulohumeral muscular dystrophy (FSHD) is in most cases caused by a contraction of the D4Z4 macrosatellite repeat on chromosome 4 (FSHD1) or by mutations in the SMCHD1 or DNMT3B gene (FSHD2). Both situations result in the incomplete epigenetic repression of the D4Z4-encode...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2017-06-01
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| Series: | Skeletal Muscle |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13395-017-0129-7 |
| _version_ | 1818483943795589120 |
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| author | Amanda G. Mason Roderick C. Slieker Judit Balog Richard J. L. F. Lemmers Chao-Jen Wong Zizhen Yao Jong-Won Lim Galina N. Filippova Enrico Ne Rabi Tawil Bas T. Heijmans Stephen J. Tapscott Silvère M. van der Maarel |
| author_facet | Amanda G. Mason Roderick C. Slieker Judit Balog Richard J. L. F. Lemmers Chao-Jen Wong Zizhen Yao Jong-Won Lim Galina N. Filippova Enrico Ne Rabi Tawil Bas T. Heijmans Stephen J. Tapscott Silvère M. van der Maarel |
| author_sort | Amanda G. Mason |
| collection | DOAJ |
| description | Abstract Background Facioscapulohumeral muscular dystrophy (FSHD) is in most cases caused by a contraction of the D4Z4 macrosatellite repeat on chromosome 4 (FSHD1) or by mutations in the SMCHD1 or DNMT3B gene (FSHD2). Both situations result in the incomplete epigenetic repression of the D4Z4-encoded retrogene DUX4 in somatic cells, leading to the aberrant expression of DUX4 in the skeletal muscle. In mice, Smchd1 regulates chromatin repression at different loci, having a role in CpG methylation establishment and/or maintenance. Methods To investigate the global effects of harboring heterozygous SMCHD1 mutations on DNA methylation in humans, we combined 450k methylation analysis on mononuclear monocytes from female heterozygous SMCHD1 mutation carriers and unaffected controls with reduced representation bisulfite sequencing (RRBS) on FSHD2 and control myoblast cell lines. Candidate loci were then evaluated for SMCHD1 binding using ChIP-qPCR and expression was evaluated using RT-qPCR. Results We identified a limited number of clustered autosomal loci with CpG hypomethylation in SMCHD1 mutation carriers: the protocadherin (PCDH) cluster on chromosome 5, the transfer RNA (tRNA) and 5S rRNA clusters on chromosome 1, the HOXB and HOXD clusters on chromosomes 17 and 2, respectively, and the D4Z4 repeats on chromosomes 4 and 10. Furthermore, minor increases in RNA expression were seen in FSHD2 myoblasts for some of the PCDHβ cluster isoforms, tRNA isoforms, and a HOXB isoform in comparison to controls, in addition to the previously reported effects on DUX4 expression. SMCHD1 was bound at DNAseI hypersensitivity sites known to regulate the PCDHβ cluster and at the chromosome 1 tRNA cluster, with decreased binding in SMCHD1 mutation carriers at the PCDHβ cluster sites. Conclusions Our study is the first to investigate the global methylation effects in humans resulting from heterozygous mutations in SMCHD1. Our results suggest that SMCHD1 acts as a repressor on a limited set of autosomal gene clusters, as an observed reduction in methylation associates with a loss of SMCHD1 binding and increased expression for some of the loci. |
| first_indexed | 2024-12-10T15:48:41Z |
| format | Article |
| id | doaj.art-7d4343f6468f4c0481a4b6f8b2902983 |
| institution | Directory Open Access Journal |
| issn | 2044-5040 |
| language | English |
| last_indexed | 2024-12-10T15:48:41Z |
| publishDate | 2017-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Skeletal Muscle |
| spelling | doaj.art-7d4343f6468f4c0481a4b6f8b29029832022-12-22T01:42:52ZengBMCSkeletal Muscle2044-50402017-06-017111310.1186/s13395-017-0129-7SMCHD1 regulates a limited set of gene clusters on autosomal chromosomesAmanda G. Mason0Roderick C. Slieker1Judit Balog2Richard J. L. F. Lemmers3Chao-Jen Wong4Zizhen Yao5Jong-Won Lim6Galina N. Filippova7Enrico Ne8Rabi Tawil9Bas T. Heijmans10Stephen J. Tapscott11Silvère M. van der Maarel12Human Genetics, Leiden University Medical CenterMolecular Epidemiology, Leiden University Medical CenterHuman Genetics, Leiden University Medical CenterHuman Genetics, Leiden University Medical CenterDivision of Human Biology, Fred Hutchinson Cancer Research CenterDivision of Human Biology, Fred Hutchinson Cancer Research CenterDivision of Human Biology, Fred Hutchinson Cancer Research CenterDivision of Human Biology, Fred Hutchinson Cancer Research CenterHuman Genetics, Leiden University Medical CenterNeuromuscular Disease Unit, Department of Neurology, University of Rochester Medical CenterMolecular Epidemiology, Leiden University Medical CenterDivision of Human Biology, Fred Hutchinson Cancer Research CenterHuman Genetics, Leiden University Medical CenterAbstract Background Facioscapulohumeral muscular dystrophy (FSHD) is in most cases caused by a contraction of the D4Z4 macrosatellite repeat on chromosome 4 (FSHD1) or by mutations in the SMCHD1 or DNMT3B gene (FSHD2). Both situations result in the incomplete epigenetic repression of the D4Z4-encoded retrogene DUX4 in somatic cells, leading to the aberrant expression of DUX4 in the skeletal muscle. In mice, Smchd1 regulates chromatin repression at different loci, having a role in CpG methylation establishment and/or maintenance. Methods To investigate the global effects of harboring heterozygous SMCHD1 mutations on DNA methylation in humans, we combined 450k methylation analysis on mononuclear monocytes from female heterozygous SMCHD1 mutation carriers and unaffected controls with reduced representation bisulfite sequencing (RRBS) on FSHD2 and control myoblast cell lines. Candidate loci were then evaluated for SMCHD1 binding using ChIP-qPCR and expression was evaluated using RT-qPCR. Results We identified a limited number of clustered autosomal loci with CpG hypomethylation in SMCHD1 mutation carriers: the protocadherin (PCDH) cluster on chromosome 5, the transfer RNA (tRNA) and 5S rRNA clusters on chromosome 1, the HOXB and HOXD clusters on chromosomes 17 and 2, respectively, and the D4Z4 repeats on chromosomes 4 and 10. Furthermore, minor increases in RNA expression were seen in FSHD2 myoblasts for some of the PCDHβ cluster isoforms, tRNA isoforms, and a HOXB isoform in comparison to controls, in addition to the previously reported effects on DUX4 expression. SMCHD1 was bound at DNAseI hypersensitivity sites known to regulate the PCDHβ cluster and at the chromosome 1 tRNA cluster, with decreased binding in SMCHD1 mutation carriers at the PCDHβ cluster sites. Conclusions Our study is the first to investigate the global methylation effects in humans resulting from heterozygous mutations in SMCHD1. Our results suggest that SMCHD1 acts as a repressor on a limited set of autosomal gene clusters, as an observed reduction in methylation associates with a loss of SMCHD1 binding and increased expression for some of the loci.http://link.springer.com/article/10.1186/s13395-017-0129-7SMCHD1FSHDChromatinMethylation |
| spellingShingle | Amanda G. Mason Roderick C. Slieker Judit Balog Richard J. L. F. Lemmers Chao-Jen Wong Zizhen Yao Jong-Won Lim Galina N. Filippova Enrico Ne Rabi Tawil Bas T. Heijmans Stephen J. Tapscott Silvère M. van der Maarel SMCHD1 regulates a limited set of gene clusters on autosomal chromosomes Skeletal Muscle SMCHD1 FSHD Chromatin Methylation |
| title | SMCHD1 regulates a limited set of gene clusters on autosomal chromosomes |
| title_full | SMCHD1 regulates a limited set of gene clusters on autosomal chromosomes |
| title_fullStr | SMCHD1 regulates a limited set of gene clusters on autosomal chromosomes |
| title_full_unstemmed | SMCHD1 regulates a limited set of gene clusters on autosomal chromosomes |
| title_short | SMCHD1 regulates a limited set of gene clusters on autosomal chromosomes |
| title_sort | smchd1 regulates a limited set of gene clusters on autosomal chromosomes |
| topic | SMCHD1 FSHD Chromatin Methylation |
| url | http://link.springer.com/article/10.1186/s13395-017-0129-7 |
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