GSE40673
An allele-aware approach identifies altered nuclear associations of the contracted D4Z4 array at the FSHD locus
Facioscapulohumeral dystrophy (FSHD) is caused by a deletion in a D4Z4 macrosatellite repeat array in the 4q subtelomere that leads to somatic de-repression of the transcription factor DUX4. It is not fully understood how array contractions cause de-repression, but they alter the local chromatin structure of D4Z4, resulting in loss of heterochromatic markers. In order to determine whether pathogenic contractions also alter the nuclear organization of the FSHD locus, we designed an allele-aware, high-throughput circular chromosome conformation capture assay (4C-seq) that distinguishes the two 4q copies of the locus from each other and from a paralogous locus in the 10q subtelomere. Using a short sequence length polymorphism (SSLP) four kilobasepairs from the array as âharacterized the genomic contacts made by the four copies of the FSHD locus in muscle cell nuclei. The SSLP contacts predominate on the same chromosome arm as the bait, decaying rapidly beyond 30-40 Mb. Contacts on other chromosomes were enriched near centromeres and CTCF sites. We also found that the FSHD locus normally contacts regions adjacent to the nuclear lamina and with low overall gene expression. However, we found that the deleted locus in FSHD cells makes more contacts with regions with comparatively lower lamina adjacency and higher overall gene expression than in control cells. Furthermore, association of D4Z4 with components of the nuclear lamina was reduced in FSHD cells relative to control cells. Our results suggest that altered nuclear organization at 4q35 may be one factor in the de-repression of DUX4 in FSHD. Overall design: 5 primary cells (2 control, 1 FSHD1, 1 FSHD2, and 1 FSHD3) were used to generate 4C libraries in biological duplicate, for a total of 10 4C libraries