Early Replication Fragile Sites May Underlie Gene Rearrangements

DNA replication stress caused by oncogene activation or replication fork stalling can induce spontaneous double-strand breaks, particularly at genomic loci known to be inherently unstable, such as late-replicating common fragile sites (CFS). However, in yeast, replication fork collapse can also preferentially affect early-replicating genomic regions, prompting Barlow and colleagues to investigate whether fragility at early-replicating sites can similarly contribute to mammalian genomic instability using activated murine B lymphocytes, which are particularly prone to genomic instability due to their rapid proliferation and DNA damage–dependent immunoglobulin gene rearrangement. Potential loci were found by treating cells synchronized in early S phase with hydroxyurea, an inhibitor of DNA replication, and identifying regions of newly synthesized DNA commonly bound by DNA repair proteins and replication protein A, which binds single-stranded DNA at stalled replication forks. These loci, termed early replication fragile sites (ERFS), were distinct from known CFSs, prone to DNA breakage, and enriched at repetitive elements, GC-rich DNA, and transcriptionally active regions. Of note, some of the most fragile ERFSs were within genes involved in recurrent translocations in lymphomas, suggesting that the inherent instability of this class of fragile sites may contribute to human disease. To evaluate this possibility, the murine ERFS coordinates were mapped to syntenic regions of the human genome and compared with copy number abnormalities observed in patients with diffuse large B-cell lymphoma (DLBCL). Strikingly, 51.6% of DLBCL copy number changes overlapped with syntenic ERFS regions, and ERFSs were over 80% more likely to be deleted or amplified in DLBCL than CFSs. An additional analysis of genes homozygously deleted in cancer genomes revealed that approximately 40% fall within ERFSs. These findings suggest that ERFSs may represent a source of DNA breaks that lead to common genomic rearrangements observed in human cancer.

Barlow JH, Faryabi RB, Callén E, Wong N, Malhowski A, Chen HT, et al. Identification of early replicating fragile sites that contribute to genome stability. Cell 2013 Jan 24 [Epub ahead of print].

• ©2013 American Association for Cancer Research.