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Among them, several distinct rare genetic diseases are linked to mutations in SMCHD1 that encodes the structural maintenance of chromosomes flexible hinge domain containing 1 chromatin-associated factor. In humans, its function as well as the impact of its mutations remains poorly defined. To fill this gap, we determined the episignature associated with heterozygous SMCHD1 variants in primary cells and cell lineages derived from induced pluripotent stem cells for Bosma arhinia and microphthalmia syndrome (BAMS) and type 2 facioscapulohumeral dystrophy (FSHD2). In human tissues, SMCHD1 regulates the distribution of methylated CpGs, H3K27 trimethylation and CTCF at repressed chromatin but also at euchromatin. Based on the exploration of tissues affected either in FSHD or in BAMS, i.e. skeletal muscle fibers and neural crest stem cells, respectively, our results emphasize multiple functions for SMCHD1, in chromatin compaction, chromatin insulation and gene regulation with variable targets or phenotypical outcomes. We concluded that in rare genetic diseases, SMCHD1 variants impact gene expression in two ways: (i) by changing the chromatin context at a number of euchromatin loci or (ii) by directly regulating some loci encoding master transcription factors required for cell fate determination and tissue differentiation.<\/jats:p>","DOI":"10.1093\/nar\/gkad523","type":"journal-article","created":{"date-parts":[[2023,6,19]],"date-time":"2023-06-19T10:08:53Z","timestamp":1687169333000},"page":"7269-7287","source":"Crossref","is-referenced-by-count":11,"title":["In skeletal muscle and neural crest cells, SMCHD1 regulates biological pathways relevant for Bosma syndrome and facioscapulohumeral dystrophy phenotype"],"prefix":"10.1093","volume":"51","author":[{"given":"Camille","family":"Laberthonni\u00e8re","sequence":"first","affiliation":[{"name":"Aix Marseille Univ, INSERM, Marseille Medical Genetics , Marseille 13005, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M\u00e9gane","family":"Delourme","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, INSERM, Marseille Medical Genetics , Marseille 13005, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rapha\u00ebl","family":"Chevalier","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, INSERM, Marseille Medical Genetics , Marseille 13005, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Camille","family":"Dion","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, INSERM, Marseille Medical Genetics , Marseille 13005, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Ganne","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, INSERM, Marseille Medical Genetics , Marseille 13005, 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Marseille, Laboratory of predictive Oncology , Marseille 13009, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Max","family":"Chaffanet","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, INSERM, CNRS, Institut Paoli Calmette, Centre de Recherche en Canc\u00e9rologie de Marseille, Laboratory of predictive Oncology , Marseille 13009, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shifeng","family":"Xue","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, National University of Singapore , Singapore 117558,\u00a0 Singapore"},{"name":"Genome Institute of Singapore, A*STAR , Singapore, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karine","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Aix Marseille Univ, INSERM, Marseille Medical Genetics , Marseille 13005, France"},{"name":"D\u00e9partement de G\u00e9n\u00e9tique M\u00e9dicale, AP-HM, H\u00f4pital d\u2019enfants de la Timone , Marseille 13005, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4070-7997","authenticated-orcid":false,"given":"Bruno","family":"Reversade","sequence":"additional","affiliation":[{"name":"Genome Institute of Singapore, A*STAR , Singapore, Singapore"},{"name":"Department of Medical Genetics, Ko\u00e7 University , School of Medicine, Istanbul, Turkey"},{"name":"Department of Physiology, Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore , Singapore"},{"name":"Laboratory of Human Genetics & Therapeutics, Smart-Health Initiative, BESE , KAUST, Thuwal, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J\u00e9r\u00f4me","family":"D\u00e9jardin","sequence":"additional","affiliation":[{"name":"Institut de G\u00e9n\u00e9tique Humaine, UMR 9002, CNRS\u2013Universit\u00e9 de Montpellier , Montpellier 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