The cell biology of disease: FSHD: copy number variations on the theme of muscular dystrophy

Abstract

In humans, copy number variations (CNVs) are a common source of phenotypic diversity and disease susceptibility. Facioscapulohumeral muscular dystrophy (FSHD) is an important genetic disease caused by CNVs. It is an autosomal-dominant myopathy caused by a reduction in the copy number of the D4Z4 macrosatellite repeat located at chromosome 4q35. Interestingly, the reduction of D4Z4 copy number is not sufficient by itself to cause FSHD. A number of epigenetic events appear to affect the severity of the disease, its rate of progression, and the distribution of muscle weakness. Indeed, recent findings suggest that virtually all levels of epigenetic regulation, from DNA methylation to higher order chromosomal architecture, are altered at the disease locus, causing the de-regulation of 4q35 gene expression and ultimately FSHD.

Figure 1.

CNVs and their possible effects on gene expression. CNVs can generate different outcomes based on the nature of the affected element. If a CNV encompasses an entire gene(s) locus, the dosage of the gene may be altered, leading to gene amplification or deletion. Alternatively, the affected region can encompass only part of a gene. In this case, if the CNV includes an exon, it can result in the production of an aberrant protein isoform. When a CNV localizes to a nonprotein coding region of the gene it may generate imbalances at the level of splicing or noncoding RNA (ncRNA) production. In addition, extragenic CNVs can give rise to altered gene expression when affecting cis regulatory regions.

Figure 2.

FSHD is caused by a reduction in the copy number of D4Z4 repeats. (A) Healthy individuals carry 11–150 units of D4Z4. (B) FSHD patients have less than 11 repeats. (C) At least one copy of D4Z4 is required for FSHD development, as individuals completely lacking D4Z4 are healthy. (D) Patients having a large deletion encompassing FRG2 and DUX4c have been described, indicating that these genes are not necessary for FSHD. Dotted lines indicate that distances are not to scale.

Figure 3.

SNPs and sequence variants at 4q35. 18 different 4q haplotypes have been described. FSHD patients carry D4Z4 deletions in 4qA161, 4qA159, and 4qA168 backgrounds. These genetic contexts represent a permissive condition for the disease rather than a cause given that asymptomatic carriers have been described. SSLP, simple sequence length polymorphism; TEL, telomere.

Figure 4.

Epigenetic features at 4q35 in healthy subjects and FSHD patients. In control individuals, the D4Z4 repeat array is characterized by markers of chromatin repression, such as high levels of DNA methylation, SUV39H1-mediated H3K9me3, and EZH2-mediated H3K27me3. In contrast, FSHD patients display hypomethylation, loss of H3K9me3, and corresponding loss of HP1γ and cohesin binding. In healthy subjects, D4Z4 is specifically bound by EZH2 and a repressor complex composed of YY1, HMGB2, and nucleolin. It is still to be determined whether binding of these factors is altered in FSHD patients. The human 4q is perinuclear in both control and FSHD individuals. This localization depends on a region that is proximal to D4Z4 in healthy subjects but is D4Z4-specific and CTCF-mediated in FSHD patients. A MAR located upstream of the repeat array was found to be weakened in FSHD, altering the 3D chromosomal architecture of the region.