Common epigenetic changes of D4Z4 in contraction-dependent and contraction-independent FSHD

Abstract

Facioscapulohumeral muscular dystrophy (FSHD), caused by partial deletion of the D4Z4 macrosatellite repeat on chromosome 4q, has a complex genetic and epigenetic etiology. To develop FSHD, D4Z4 contraction needs to occur on a specific genetic background. Only contractions associated with the 4qA161 haplotype cause FSHD. In addition, contraction of the D4Z4 repeat in FSHD patients is associated with significant D4Z4 hypomethylation. To date however, the methylation status of contracted repeats on non-pathogenic haplotypes has not been studied. We have performed a detailed methylation study of the D4Z4 repeat on chromosome 4q and on a highly homologous repeat on chromosome 10q. We show that patients with a D4Z4 deletion (FSHD1) have D4Z4-restricted hypomethylation. Importantly, controls with a D4Z4 contraction on a non-pathogenic chromosome 4q haplotype or on chromosome 10q also demonstrate hypomethylation. In fifteen FSHD families without D4Z4 contractions but with at least one 4qA161 haplotype (FSHD2), we observed D4Z4-restricted hypomethylation on chromosomes 4q and 10q. This finding implies that a genetic defect resulting in D4Z4 hypomethylation underlies FSHD2. In conclusion, we describe two ways to develop FSHD; (1) contraction-dependent or (2) contraction-independent D4Z4 hypomethylation on the 4qA161 subtelomere.

Diagnostic approach for FSHD revisited: SMCHD1 mutations cause FSHD2 and act as modifiers of disease severity in FSHD1

“…In healthy individuals with a 'full length' repeat array (410 copies) of D4Z4, the transcription of DUX4 is suppressed by a condensed heterochromatin structure of the surrounding genomic region. [20][21][22] For FSHD1, the second genetic component required is a contraction of D4Z4 repeats to less than 10 units. 10 This is associated with hypomethylation of the D4Z4 repeat array and a relaxation of the chromatin structure allowing for transcription of DUX4.…”

“…10 This is associated with hypomethylation of the D4Z4 repeat array and a relaxation of the chromatin structure allowing for transcription of DUX4. 16,22 On an FSHD permissive haplotype, the most distal copy of DUX4 uses the polyadenylation signal of the adjoining pLAM region whereby this transcript is stabilized. 18 Thus, this genomic background is now permissive for the expression of DUX4.…”

“…[24][25][26] Heterozygous loss-of-function mutations in SMCHD1 are viable in the mouse model and seem to have an effect on the chromatin structure of the D4Z4 locus resulting in D4Z4 hypomethylation and somatic derepression of DUX4 transcription in FSHD2 patients. 22,24 In combination with the FSHD-permissive haplotype, haploinsufficiency of SMCHD1 results in expression of DUX4. 23 In this study, we analyzed two cohorts of patients with typical clinical FSHD phenotypes for the genetic features of FSHD2.…”

Evidence-based guideline summary: Evaluation, diagnosis, and management of facioscapulohumeral muscular dystrophy

“…11,12 Complicating matters is the existence of a genetically distinct but clinically identical FSHD type-FSHD type 2 (FSHD2)-now known to account for approximately 5% of patients with clinically defined FSHD. 13,14 Unlike the majority of patients with FSHD (i.e., FSHD1), patients with FSHD2 do not have contractions in the 4q35 D4Z4. As with FSHD1, and despite a normal number of repeats, the chromatin structure at the D4Z4 repeats is more open, and at least one 4q35 allele is an A variant.…”

DNA polymorphism and epigenetic marks modulate the affinity of a scaffold/matrix attachment region to the nuclear matrix

“…Other genetic and epigenetic abnormalities affecting the subtelomeric region of chromosome 4q have also been observed in various pathologies including the Rett and ICF syndromes, 25 as well as in several types of cancer. [26][27][28][29][30][31][32] Here, we have tested whether mechanisms controlling the association of the FR-MAR to the NM could be similar in different cell types. We have used primary myoblasts from FSHD patients and cervical carcinoma cell lines where the D4Z4 repeat array can be either strongly methylated or demethylated.…”