Abstract 1777: Genome-wide identification of replication-associated breakpoints.

Previous studies have defined sequences that are difficult to replicate and, consequently, are more vulnerable to replication-associated breaks and recombination events. However, many of these sequences have been identified through indirect and biased approaches. To identify genomic sequences that contribute to replication-associated breakpoints, we have performed genome-wide screens to determine the location, sequence, and frequency of replication perturbations within the mammalian genome. To convert these transient pause sites in S phase into longer-lived intermediates, asynchronous ATR-inhibited cells were treated with a low dose of polymerase inhibitor (0.2 μM aphidicolin) to promote selective replication fork collapse at difficult-to-replicate sequences. Affected regions were then isolated by chromatin immunoprecipitation of RPA (RPA-ChIP) and by a recently developed novel DNA breakpoint isolation method. Following deep sequencing, these sites were mapped within 1-5 kb regions and sequences at the center of these peaks were binned to quantify the overall frequency of replication fork collapse at such sites. Surprisingly, sequences that have long been thought to be among the most difficult to replicate, such as CGG repeats, were overshadowed by distinct repetitive sequences that are relatively uncharacterized. These sites were greater than 50-fold enriched over background, and were more common as replication-troubled regions than other well characterized sequences (e.g. triplet repeats, fragile sites, etc). In total, over 100 independently confirmed sites were identified, with most sequences observed in multiple locations across the genome. Notably, common fragile sites, which have been speculated to harbor such replication slow zones, were not observed to be particularly enriched in RPA-ChIP samples, consistent with recent observations that these sites are fragile for reasons other than impeded DNA replication rates. These findings and others indicating a larger role of chromatin structure in common fragile site breakage will be discussed. Citation Format: Yu-Chen Tsai, Nishita Shastri, Kevin D. Smith, Jonathan Schug, Rafael Casellas, Eric J. Brown. Genome-wide identification of replication-associated breakpoints. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1777. doi:10.1158/1538-7445.AM2013-1777 Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.