Monitoring homology search during DNA double-strand break repair in vivo

Mol Cell. 2013 Apr 25;50(2):261-72. doi: 10.1016/j.molcel.2013.02.020. Epub 2013 Mar 21.


Homologous recombination (HR) is crucial for genetic exchange and accurate repair of DNA double-strand breaks and is pivotal for genome integrity. HR uses homologous sequences for repair, but how homology search, the exploration of the genome for homologous DNA sequences, is conducted in the nucleus remains poorly understood. Here, we use time-resolved chromatin immunoprecipitations of repair proteins to monitor homology search in vivo. We found that homology search proceeds by a probing mechanism, which commences around the break and samples preferentially on the broken chromosome. However, elements thought to instruct chromosome loops mediate homology search shortcuts, and centromeres, which cluster within the nucleus, may facilitate homology search on other chromosomes. Our study thus reveals crucial parameters for homology search in vivo and emphasizes the importance of linear distance, chromosome architecture, and proximity for recombination efficiency.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Nucleus / metabolism
  • Chromosomes, Fungal / metabolism
  • DNA Breaks, Double-Stranded*
  • DNA Helicases / metabolism
  • DNA Repair Enzymes / metabolism
  • DNA, Single-Stranded / genetics
  • DNA, Single-Stranded / metabolism
  • Genes, Mating Type, Fungal
  • Histones / metabolism
  • Protein Binding
  • Rad51 Recombinase / metabolism
  • Recombinational DNA Repair*
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Saccharomyces cerevisiae Proteins / metabolism
  • Sequence Homology, Nucleic Acid


  • DNA, Single-Stranded
  • Histones
  • Saccharomyces cerevisiae Proteins
  • RAD51 protein, S cerevisiae
  • Rad51 Recombinase
  • RAD54 protein, S cerevisiae
  • DNA Helicases
  • DNA Repair Enzymes

Associated data

  • GEO/GSE44844