DNA Replication Timing Is Maintained Genome-Wide in Primary Human Myoblasts Independent of D4Z4 Contraction in FSH Muscular Dystrophy

Abstract

Facioscapulohumeral muscular dystrophy (FSHD) is linked to contraction of an array of tandem 3.3-kb repeats (D4Z4) at 4q35.2 from 11-100 copies to 1-10 copies. The extent to which D4Z4 contraction at 4q35.2 affects overall 4q35.2 chromatin organization remains unclear. Because DNA replication timing is highly predictive of long-range chromatin interactions, we generated genome-wide replication-timing profiles for FSHD and control myogenic precursor cells. We compared non-immortalized myoblasts from four FSHD patients and three control individuals to each other and to a variety of other human cell types. This study also represents the first genome-wide comparison of replication timing profiles in non-immortalized human cell cultures. Myoblasts from both control and FSHD individuals all shared a myoblast-specific replication profile. In contrast, male and female individuals were readily distinguished by monoallelic differences in replication timing at DXZ4 and other regions across the X chromosome affected by X inactivation. We conclude that replication timing is a robust cell-type specific feature that is unaffected by FSHD-related D4Z4 contraction.

SORBS2transcription is activated by telomere position effect–over long distance upon telomere shortening in muscle cells from patients with facioscapulohumeral dystrophy

“…By quantifying the 3D-chromatin organization of the 4q35 locus by 3C and 3D-FISH (Figs. 1C, 2), we report that the organization is similar between conditions when telomeres are long, a finding that is supported by previous replication timing experiments (Pope et al 2011). However, this chromatin organization is sensitive to telomere length in FSHD isogenic clones with short telomeres (Figs.…”

“…In FSHD1B, chromosomal looping might be modified by SMCHD1 mutation, which is implicated in chromosomal structural maintenance (Blewitt et al 2008) and/or D4Z4 hypomethylation. However, it remains unclear whether or not FSHD cells have a different 4q35 chromatin organization (Pirozhkova et al 2008;Bodega et al 2009;Pope et al 2011), and no reports have integrated the possible influence of telomere length on the chromatin structure of the 4q35 end (e.g., the last 5 Mb of Chromosome 4).…”

Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia

“…1). This extends previous results demonstrating the robust stability of replication profiles between common cell types Ryba et al 2010;Pope et al 2011). The average of all replicates from these four cell lines provides a single B-cell-derived replication-timing profile that will herein be called ''control'' in comparisons with leukemia profiles, with the given caveat that leukemic samples are arrested at various stages in lymphoblast development from immature to more mature pre-B stages (Ferrando et al 2002;Nemazee 2006;Mullighan et al 2007) as indicated by their immunophenotypes where available (Supplemental Table 1).…”

“…This raised the possibility that they represent misregulation of developmental control over replication timing, as has been described for DNA methylation changes in cancers (Hansen et al 2011;Pujadas and Feinberg 2012). To test this hypothesis, we compared the collection of leukemia fingerprints with profiles of the same genomic regions from nine cell types that we have profiled in the past (Weddington et al 2008;Pope et al 2011;Ryba et al 2011b). More than half of these aligned in register to a developmentally regulated replication domain boundary ( Fig.…”

“…Developmentally regulated changes take place in units of 400-800 kb and are associated with changes in subnuclear 3D organization of the affected domains . This replication-timing program is a highly stable epigenetic characteristic of a given cell type that is indistinguishable between the same cell types from different individuals (Pope et al 2011). This stability has allowed for the development of tools to unambiguously determine cellular identity using their specific ''replication fingerprints'' (Ryba et al 2011b).…”