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Digenic inheritance of an SMCHD1 mutation and an FSHD-permissive D4Z4 allele causes facioscapulohumeral muscular dystrophy type 2

Nature Genetics volume 44, pages 1370–1374 (2012)Cite this article

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Abstract

Facioscapulohumeral dystrophy (FSHD) is characterized by chromatin relaxation of the D4Z4 macrosatellite array on chromosome 4 and expression of the D4Z4-encoded DUX4 gene in skeletal muscle. The more common form, autosomal dominant FSHD1, is caused by contraction of the D4Z4 array, whereas the genetic determinants and inheritance of D4Z4 array contraction–independent FSHD2 are unclear. Here, we show that mutations in SMCHD1 (encoding structural maintenance of chromosomes flexible hinge domain containing 1) on chromosome 18 reduce SMCHD1 protein levels and segregate with genome-wide D4Z4 CpG hypomethylation in human kindreds. FSHD2 occurs in individuals who inherited both the SMCHD1 mutation and a normal-sized D4Z4 array on a chromosome 4 haplotype permissive for DUX4 expression. Reducing SMCHD1 levels in skeletal muscle results in D4Z4 contraction–independent DUX4 expression. Our study identifies SMCHD1 as an epigenetic modifier of the D4Z4 metastable epiallele and as a causal genetic determinant of FSHD2 and possibly other human diseases subject to epigenetic regulation.

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Figure 1: D4Z4 methylation test and families with FSHD2.
Figure 2: Families with FSHD2 with SMCHD1 mutations.
Figure 3: SMCHD1 haploinsufficiency results in DUX4 expression in normal human myoblasts.

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NCBI Reference Sequence

References

  1. Statland, J.M. & Tawil, R. Facioscapulohumeral muscular dystrophy: molecular pathological advances and future directions. Curr. Opin. Neurol. 24, 423–428 (2011).

    Article  CAS  Google Scholar 

  2. Balog, J. et al. Correlation analysis of clinical parameters with epigenetic modifications in the DUX4 promoter in FSHD. Epigenetics 7, 579–584 (2012).

    Article  CAS  Google Scholar 

  3. Bodega, B. et al. Remodeling of the chromatin structure of the facioscapulohumeral muscular dystrophy (FSHD) locus and upregulation of FSHD-related gene 1 (FRG1) expression during human myogenic differentiation. BMC Biol. 7, 41 (2009).

    Article  Google Scholar 

  4. Cabianca, D.S. et al. A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell 149, 819–831 (2012).

    Article  CAS  Google Scholar 

  5. de Greef, J.C. et al. Common epigenetic changes of D4Z4 in contraction-dependent and contraction-independent FSHD. Hum. Mutat. 30, 1449–1459 (2009).

    Article  CAS  Google Scholar 

  6. Jiang, G. et al. Testing the position-effect variegation hypothesis for facioscapulohumeral muscular dystrophy by analysis of histone modification and gene expression in subtelomeric 4q. Hum. Mol. Genet. 12, 2909–2921 (2003).

    Article  CAS  Google Scholar 

  7. van Overveld, P.G. et al. Hypomethylation of D4Z4 in 4q-linked and non-4q–linked facioscapulohumeral muscular dystrophy. Nat. Genet. 35, 315–317 (2003).

    Article  CAS  Google Scholar 

  8. Zeng, W. et al. Specific loss of histone H3 lysine 9 trimethylation and HP1γ/cohesin binding at D4Z4 repeats is associated with facioscapulohumeral dystrophy (FSHD). PLoS Genet. 5, e1000559 (2009).

    Article  Google Scholar 

  9. Gabriëls, J. et al. Nucleotide sequence of the partially deleted D4Z4 locus in a patient with FSHD identifies a putative gene within each 3.3 kb element. Gene 236, 25–32 (1999).

    Article  Google Scholar 

  10. Hewitt, J.E. et al. Analysis of the tandem repeat locus D4Z4 associated with facioscapulohumeral muscular dystrophy. Hum. Mol. Genet. 3, 1287–1295 (1994).

    Article  CAS  Google Scholar 

  11. Lyle, R., Wright, T.J., Clark, L.N. & Hewitt, J.E. The FSHD-associated repeat, D4Z4, is a member of a dispersed family of homeobox-containing repeats, subsets of which are clustered on the short arms of the acrocentric chromosomes. Genomics 28, 389–397 (1995).

    Article  CAS  Google Scholar 

  12. Snider, L. et al. RNA transcripts, miRNA-sized fragments and proteins produced from D4Z4 units: new candidates for the pathophysiology of facioscapulohumeral dystrophy. Hum. Mol. Genet. 18, 2414–2430 (2009).

    Article  CAS  Google Scholar 

  13. Snider, L. et al. Facioscapulohumeral dystrophy: incomplete suppression of a retrotransposed gene. PLoS Genet. 6, e1001181 (2010).

    Article  Google Scholar 

  14. van der Maarel, S.M., Tawil, R. & Tapscott, S.J. Facioscapulohumeral muscular dystrophy and DUX4: breaking the silence. Trends Mol. Med. 17, 252–258 (2011).

    Article  CAS  Google Scholar 

  15. Geng, L.N. et al. DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy. Dev. Cell 22, 38–51 (2012).

    Article  CAS  Google Scholar 

  16. Bosnakovski, D. et al. An isogenetic myoblast expression screen identifies DUX4-mediated FSHD-associated molecular pathologies. EMBO J. 27, 2766–2779 (2008).

    Article  CAS  Google Scholar 

  17. Kowaljow, V. et al. The DUX4 gene at the FSHD1A locus encodes a pro-apoptotic protein. Neuromuscul. Disord. 17, 611–623 (2007).

    Article  Google Scholar 

  18. Vanderplanck, C. et al. The FSHD atrophic myotube phenotype is caused by DUX4 expression. PLoS ONE 6, e26820 (2011).

    Article  CAS  Google Scholar 

  19. Wallace, L.M. et al. DUX4, a candidate gene for facioscapulohumeral muscular dystrophy, causes p53-dependent myopathy in vivo. Ann. Neurol. 69, 540–552 (2011).

    Article  CAS  Google Scholar 

  20. Wuebbles, R.D., Long, S.W., Hanel, M.L. & Jones, P.L. Testing the effects of FSHD candidate gene expression in vertebrate muscle development. Int. J. Clin. Exp. Pathol. 3, 386–400 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. van Deutekom, J.C. et al. FSHD associated DNA rearrangements are due to deletions of integral copies of a 3.2 kb tandemly repeated unit. Hum. Mol. Genet. 2, 2037–2042 (1993).

    Article  CAS  Google Scholar 

  22. Wijmenga, C. et al. Chromosome 4q DNA rearrangements associated with facioscapulohumeral muscular dystrophy. Nat. Genet. 2, 26–30 (1992).

    Article  CAS  Google Scholar 

  23. Dixit, M. et al. DUX4, a candidate gene of facioscapulohumeral muscular dystrophy, encodes a transcriptional activator of PITX1. Proc. Natl. Acad. Sci. USA 104, 18157–18162 (2007).

    Article  CAS  Google Scholar 

  24. Lemmers, R.J. et al. Facioscapulohumeral muscular dystrophy is uniquely associated with one of the two variants of the 4q subtelomere. Nat. Genet. 32, 235–236 (2002).

    Article  CAS  Google Scholar 

  25. Lemmers, R.J. et al. A unifying genetic model for facioscapulohumeral muscular dystrophy. Science 329, 1650–1653 (2010).

    Article  CAS  Google Scholar 

  26. Spurlock, G., Jim, H.P. & Upadhyaya, M. Confirmation that the specific SSLP microsatellite allele 4qA161 segregates with fascioscapulohumeral muscular dystrophy (FSHD) in a cohort of multiplex and simplex FSHD families. Muscle Nerve 42, 820–821 (2010).

    Article  Google Scholar 

  27. Thomas, N.S. et al. A large patient study confirming that facioscapulohumeral muscular dystrophy (FSHD) disease expression is almost exclusively associated with an FSHD locus located on a 4qA-defined 4qter subtelomere. J. Med. Genet. 44, 215–218 (2007).

    Article  CAS  Google Scholar 

  28. Bamshad, M.J. et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nat. Rev. Genet. 12, 745–755 (2011).

    Article  CAS  Google Scholar 

  29. Bhalla, N., Biggins, S. & Murray, A.W. Mutation of YCS4, a budding yeast condensin subunit, affects mitotic and nonmitotic chromosome behavior. Mol. Biol. Cell 13, 632–645 (2002).

    Article  CAS  Google Scholar 

  30. Lieb, J.D., Capowski, E.E., Meneely, P. & Meyer, B.J. DPY-26, a link between dosage compensation and meiotic chromosome segregation in the nematode. Science 274, 1732–1736 (1996).

    Article  CAS  Google Scholar 

  31. Chuang, P.T., Albertson, D.G. & Meyer, B.J. DPY-27:a chromosome condensation protein homolog that regulates C. elegans dosage compensation through association with the X chromosome. Cell 79, 459–474 (1994).

    Article  CAS  Google Scholar 

  32. Dej, K.J., Ahn, C. & Orr-Weaver, T.L. Mutations in the Drosophila condensin subunit dCAP-G: defining the role of condensin for chromosome condensation in mitosis and gene expression in interphase. Genetics 168, 895–906 (2004).

    Article  CAS  Google Scholar 

  33. Kanno, T. et al. A structural-maintenance-of-chromosomes hinge domain–containing protein is required for RNA-directed DNA methylation. Nat. Genet. 40, 670–675 (2008).

    Article  CAS  Google Scholar 

  34. Blewitt, M.E. et al. An N-ethyl-N-nitrosourea screen for genes involved in variegation in the mouse. Proc. Natl. Acad. Sci. USA 102, 7629–7634 (2005).

    Article  CAS  Google Scholar 

  35. Blewitt, M.E. et al. SmcHD1, containing a structural-maintenance-of-chromosomes hinge domain, has a critical role in X inactivation. Nat. Genet. 40, 663–669 (2008).

    Article  CAS  Google Scholar 

  36. Gendrel, A.V. et al. Smchd1-dependent and -independent pathways determine developmental dynamics of CpG island methylation on the inactive X chromosome. Dev. Cell 23, 265–279 (2012).

    Article  CAS  Google Scholar 

  37. Rakyan, V.K., Blewitt, M.E., Druker, R., Preis, J.I. & Whitelaw, E. Metastable epialleles in mammals. Trends Genet. 18, 348–351 (2002).

    Article  CAS  Google Scholar 

  38. Duhl, D.M., Vrieling, H., Miller, K.A., Wolff, G.L. & Barsh, G.S. Neomorphic agouti mutations in obese yellow mice. Nat. Genet. 8, 59–65 (1994).

    Article  CAS  Google Scholar 

  39. van der Maarel, S.M., Frants, R.R. & Padberg, G.W. Facioscapulohumeral muscular dystrophy. Biochim. Biophys. Acta 1772, 186–194 (2007).

    Article  CAS  Google Scholar 

  40. Scionti, I. et al. Facioscapulohumeral muscular dystrophy: new insights from compound heterozygotes and implication for prenatal genetic counselling. J. Med. Genet. 49, 171–178 (2012).

    Article  CAS  Google Scholar 

  41. Lemmers, R.J. et al. Specific sequence variations within the 4q35 region are associated with facioscapulohumeral muscular dystrophy. Am. J. Hum. Genet. 81, 884–894 (2007).

    Article  CAS  Google Scholar 

  42. Lemmers, R.J. et al. Contractions of D4Z4 on 4qB subtelomeres do not cause facioscapulohumeral muscular dystrophy. Am. J. Hum. Genet. 75, 1124–1130 (2004).

    Article  CAS  Google Scholar 

  43. van Overveld, P.G. et al. Variable hypomethylation of D4Z4 in facioscapulohumeral muscular dystrophy. Ann. Neurol. 58, 569–576 (2005).

    Article  CAS  Google Scholar 

  44. de Greef, J.C. et al. Clinical features of facioscapulohumeral muscular dystrophy 2. Neurology 75, 1548–1554 (2010).

    Article  CAS  Google Scholar 

  45. Lemmers, R.J.L. et al. Complete allele information in the diagnosis of facioscapulohumeral muscular dystrophy by triple DNA analysis. Ann. Neurol. 50, 816–819 (2001).

    Article  CAS  Google Scholar 

  46. Lemmers, R.J.L.F. et al. Worldwide population analysis of the 4q and 10q subtelomeres identifies only four discrete duplication events in human evolution. Am. J. Hum. Genet. 86, 364–377 (2010).

    Article  CAS  Google Scholar 

  47. Pfaffl, M.W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29, e45 (2001).

    Article  CAS  Google Scholar 

  48. Nelson, J.D., Denisenko, O. & Bomsztyk, K. Protocol for the fast chromatin immunoprecipitation (ChIP) method. Nat. Protoc. 1, 179–185 (2006).

    Article  CAS  Google Scholar 

  49. Aartsma-Rus, A. Overview on AON design. Methods Mol. Biol. 867, 117–129 (2012).

    Article  CAS  Google Scholar 

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Acknowledgements

The authors thank all subjects and family members for their participation. We thank D. Nickerson and J. Shendure for excellent assistance and B. Trask for helpful discussions and critical reading of the manuscript. This work was supported by grants from the US National Institutes of Health (NIH) (National Institute of Neurological Disorders and Stroke (NINDS) P01NS069539, Clinical & Translational Science Award (CTSA) UL1RR024160, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) R01AR045203 and National Human Genome Research Institute (NHGRI) HG005608 and HG006493), a Netherlands Genomics Initiative (NGI) Horizon Valorization Project Grant (93515504), The University of Washington Center for Mendelian Genomics, the Muscular Dystrophy Association (MDA; 217596), the Fields Center for FSHD Research, the Geraldi Norton and Eklund family foundation, the FSH Society, The Friends of FSH Research, European Union Framework Programme 7 agreements 223026 (NMD-chip), 223143 (TechGene) and 2012-305121 (NEUROMICS) and the Stichting FSHD. Y.S. is supported by the China Scholarship Council.

Author information

Author notes

  1. Jessica C de Greef

    Present address: Present addresses: Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA, and Howard Hughes Medical Institute, Iowa City, Iowa, USA.,

  2. Richard J L F Lemmers and Rabi Tawil: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands

    Richard J L F Lemmers, Judit Balog, Patrick J van der Vliet, Kirsten R Straasheijm, Yvonne D Krom, Rinse Klooster, Yu Sun, Johan T den Dunnen, Jessica C de Greef, Annemieke M Aartsma-Rus, Rune R Frants & Silvère M van der Maarel

  2. Department of Neurology, Neuromuscular Disease Unit, University of Rochester Medical Center, Rochester, New York, USA

    Rabi Tawil & Colleen M Donlin-Smith

  3. Department of Pediatrics, University of Washington, Seattle, Washington, USA

    Lisa M Petek, Gregory J Block, Amanda M Amell, Michael J Bamshad & Daniel G Miller

  4. Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands

    Gijs W E Santen, Rowida Almomani, Johan T den Dunnen & Bert Bakker

  5. Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands

    Quinta Helmer

  6. Department of Neurology, Neuromuscular Centre Nijmegen, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands

    George W Padberg & Baziel G M van Engelen

  7. Department of Neurology, Academic Medical Center, Amsterdam, The Netherlands

    Marianne de Visser

  8. Centre de Référence des Maladies Neuromusculaires, Nice University Hospital, Nice, France

    Claude Desnuelle & Sabrina Sacconi

  9. Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7277, Nice University Hospital, Nice, France

    Claude Desnuelle & Sabrina Sacconi

  10. Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA

    Galina N Filippova & Stephen J Tapscott

  11. Department of Genome Sciences, University of Washington, Seattle, Washington, USA

    Michael J Bamshad & Daniel G Miller

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  1. Richard J L F Lemmers
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Contributions

R.J.L.F.L., R.T., M.J.B., S.J.T., D.G.M., R.R.F., B.B., A.M.A.-R. and S.M.v.d.M. conceived of and designed the study. D.G.M., S.J.T. and S.M.v.d.M. directed the study. G.W.E.S., Y.S., Q.H. and D.G.M. performed the bioinformatics data analysis. R.T., B.G.M.v.E., G.W.P., S.S., C.D. and M.d.V. performed assessments of the FSHD2 phenotype. R.J.L.F.L., D.G.M., L.M.P., J.B., G.J.B., A.M.A., P.J.v.d.V., R.A., K.R.S., Y.D.K., R.K. and J.C.d.G. performed experiments. R.T., J.T.d.D., C.M.D.-S., G.W.P., B.G.M.v.E., G.N.F., M.d.V., C.D. and S.S. contributed samples, reagents, data and comments on the manuscript. R.J.L.F.L., S.J.T., D.G.M. and S.M.v.d.M. analyzed and interpreted data, and wrote the manuscript with the assistance and final approval of all authors.

Corresponding authors

Correspondence to Stephen J Tapscott, Daniel G Miller or Silvère M van der Maarel.

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Lemmers, R., Tawil, R., Petek, L. et al. Digenic inheritance of an SMCHD1 mutation and an FSHD-permissive D4Z4 allele causes facioscapulohumeral muscular dystrophy type 2. Nat Genet 44, 1370–1374 (2012). https://doi.org/10.1038/ng.2454

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