title: Chromosome position determines the success of double-strand break repair.
abstract: Repair of a chromosomal double-strand break (DSB) by gene conversion depends on the ability of the broken ends to encounter a donor sequence. To understand how chromosomal location of a target sequence affects DSB repair, we took advantage of genome-wide Hi-C analysis of yeast chromosomes to create a series of strains in which an induced site-specific DSB in budding yeast is repaired by a 2-kb donor sequence inserted at different locations. The efficiency of repair, measured by cell viability or competition between each donor and a reference site, showed a strong correlation (r = 0.85 and 0.79) with the contact frequencies of each donor with the DSB repair site. Repair efficiency depends on the distance between donor and recipient rather than any intrinsic limitation of a particular donor site. These results further demonstrate that the search for homology is the rate-limiting step in DSB repair and suggest that cells often fail to repair a DSB because they cannot locate a donor before other, apparently lethal, processes arise. The repair efficiency of a donor locus can be improved by four factors: slower 5' to 3' resection of the DSB ends, increased abundance of replication protein factor A (RPA), longer shared homology, or presence of a recombination enhancer element adjacent to a donor.
authors.affiliation: Department of Biology, Brandeis University, Waltham, MA 02454-9110; Rosenstiel Center, Brandeis University, Waltham, MA 02454-9110;
authors.forename: Cheng-Sheng
authors.initials: CS
authors.lastname: Lee
authors.affiliation: Department of Biology, Brandeis University, Waltham, MA 02454-9110; Rosenstiel Center, Brandeis University, Waltham, MA 02454-9110;
authors.forename: Ruoxi W
authors.initials: RW
authors.lastname: Wang
authors.affiliation: Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115;
authors.forename: Hsiao-Han
authors.initials: HH
authors.lastname: Chang
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94107;
authors.forename: Daniel
authors.initials: D
authors.lastname: Capurso
authors.affiliation: Center for Bioinformatics and Molecular Biostatistics, Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94143.
authors.forename: Mark R
authors.initials: MR
authors.lastname: Segal
authors.affiliation: Department of Biology, Brandeis University, Waltham, MA 02454-9110; Rosenstiel Center, Brandeis University, Waltham, MA 02454-9110; haber@brandeis.edu.
authors.forename: James E
authors.initials: JE
authors.lastname: Haber
mesh_terms: D015139:Blotting, Southern; D045584:Chromosome Positioning; D015825:Chromosomes, Fungal; D053903:DNA Breaks, Double-Stranded; D004260:DNA Repair; D004261:DNA Replication; D056426:Genetic Loci; D007700:Kinetics; D050296:Microbial Viability; D011995:Recombination, Genetic; D051716:Replication Protein A / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism
chemical_list: D051716:Replication Protein A; D029701:Saccharomyces cerevisiae Proteins
keywords: chromosome conformation; donor location; double-strand break repair; homologous recombination; homology search