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Proc Natl Acad Sci U S A. 2016 Jan 12;113(2):E146-54. doi: 10.1073/pnas.1523660113. Epub 2015 Dec 29.

Chromosome position determines the success of double-strand break repair.

Author information

1
Department of Biology, Brandeis University, Waltham, MA 02454-9110; Rosenstiel Center, Brandeis University, Waltham, MA 02454-9110;
2
Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115;
3
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94107;
4
Center for Bioinformatics and Molecular Biostatistics, Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94143.
5
Department of Biology, Brandeis University, Waltham, MA 02454-9110; Rosenstiel Center, Brandeis University, Waltham, MA 02454-9110; haber@brandeis.edu.

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.

KEYWORDS:

chromosome conformation; donor location; double-strand break repair; homologous recombination; homology search

PMID:
26715752
PMCID:
PMC4720327
DOI:
10.1073/pnas.1523660113
[Indexed for MEDLINE]
Free PMC Article

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