Competitive repair by naturally dispersed repetitive DNA during non-allelic homologous recombination - eScholarship (2011)

Competitive Repair by Naturally Dispersed Repetitive DNA during Non-Allelic Homologous Recombination Margaret L. Hoang 1,2 , Frederick J. Tan 1¤a , David C. Lai 3¤b , Sue E. Celniker 4 , Roger A. Hoskins 4 , Maitreya J. Dunham 5 , Yixian Zheng 1 , Douglas Koshland 1 * ¤a 1 Howard Hughes Medical Institute and Department of Embryology, Carnegie Institution, Baltimore, Maryland, United States of America, 2 Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America, 3 Baltimore Polytechnic Institute, Ingenuity Program, Baltimore, Maryland, United States of America, 4 Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America, 5 Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America Abstract Genome rearrangements often result from non-allelic homologous recombination (NAHR) between repetitive DNA elements dispersed throughout the genome. Here we systematically analyze NAHR between Ty retrotransposons using a genome-wide approach that exploits unique features of Saccharomyces cerevisiae purebred and Saccharomyces cerevisiae/ Saccharomyces bayanus hybrid diploids. We find that DNA double-strand breaks (DSBs) induce NAHR–dependent rearrangements using Ty elements located 12 to 48 kilobases distal to the break site. This break-distal recombination (BDR) occurs frequently, even when allelic recombination can repair the break using the homolog. Robust BDR–dependent NAHR demonstrates that sequences very distal to DSBs can effectively compete with proximal sequences for repair of the break. In addition, our analysis of NAHR partner choice between Ty repeats shows that intrachromosomal Ty partners are preferred despite the abundance of potential interchromosomal Ty partners that share higher sequence identity. This competitive advantage of intrachromosomal Tys results from the relative efficiencies of different NAHR repair pathways. Finally, NAHR generates deleterious rearrangements more frequently when DSBs occur outside rather than within a Ty repeat. These findings yield insights into mechanisms of repeat-mediated genome rearrangements associated with evolution and cancer. Citation: Hoang ML, Tan FJ, Lai DC, Celniker SE, Hoskins RA, et al. (2010) Competitive Repair by Naturally Dispersed Repetitive DNA during Non-Allelic Homologous Recombination. PLoS Genet 6(12): e1001228. doi:10.1371/journal.pgen.1001228 Editor: Gregory P. Copenhaver, The University of North Carolina at Chapel Hill, United States of America Received August 27, 2010; Accepted October 29, 2010; Published December 2, 2010 Copyright: s 2010 Hoang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was funded by HHMI to DK and YZ. Sequencing of chromosome III Ty clusters was also supported by NIH grant HG00747 to Gary H. Karpen. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: koshland@berkeley.edu ¤a Current address: Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America ¤b Current address: University of Maryland, College Park, Maryland, United States of America homologous recombination (HR) defines four fundamental parameters for NAHR that we address here. The first parameter is the position of a DSB relative to repetitive and unique sequences. DNA resection starts from the DSB ends and is thought to activate break-proximal sequences before break-distal sequences [7]. Based on this model, break-proximal recipients (sequences at or near the break site) direct homology searches before break-distal recipients (sequences distal from the break site). Therefore, a DSB near or in a repetitive element should activate that repeat as a recipient, which may search for a non-allelic donor repeat to promote NAHR. Alternatively, a DSB in a large track of unique sequences should preferentially activate break-proximal unique sequences as recipients. In a diploid, these break-proximal recipients can repair efficiently using allelic donors on the sister chromatid or homolog. Therefore it has been assumed, but never tested directly, that a DSB in unique sequences in a diploid will rarely induce NAHR. However, a few studies in haploid yeast have observed a preference for recombination using more distal sequences over break-proximal recipients, suggesting that break- distal recipients can participate in homology searches [8–10]. The second important parameter of NAHR is the percent and length of identity shared between a recipient and potential donors. Introduction Human structural variation contributes to phenotypic differ- ences and susceptibility to disease [1]. Recent studies suggest that many structural variants are mediated by non-allelic homologous recombination (NAHR) between dispersed repetitive DNA elements [2–5]. While the importance of NAHR in shaping genome structure is becoming more apparent, the mechanism of NAHR remains poorly understood. NAHR (also known as ectopic recombination) utilizes the molecular pathways that mediate allelic homologous recombina- tion (AHR) between sister chromatids or homologs. AHR and NAHR are both initiated by a double-strand break (DSB) that is processed by 59-39 DNA resection to generate 39-OH tailed single- stranded DNA (ssDNA) intermediates [6]. The resected ssDNA, called the recipient, is activated to search for homologous sequences, called the donor, to be used as a template for repair. If the recipient is unique DNA, then the donor will be the homolog or sister chromatid, and AHR ensues. However, if the recipient is repetitive DNA, it may choose a non-allelic repeat as a donor, leading to NAHR and potentially a chromosome rearrangement. The establishment of this basic recipient-donor partnership during PLoS Genetics | www.plosgenetics.org December 2010 | Volume 6 | Issue 12 | e1001228