Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA

Genome Res. 2012 May;22(5):957-65. doi: 10.1101/gr.130583.111. Epub 2012 Feb 24.


Meiotic DNA double-stranded breaks (DSBs) initiate genetic recombination in discrete areas of the genome called recombination hotspots. DSBs can be directly mapped using chromatin immunoprecipitation followed by sequencing (ChIP-seq). Nevertheless, the genome-wide mapping of recombination hotspots in mammals is still a challenge due to the low frequency of recombination, high heterogeneity of the germ cell population, and the relatively low efficiency of ChIP. To overcome these limitations we have developed a novel method--single-stranded DNA (ssDNA) sequencing (SSDS)--that specifically detects protein-bound single-stranded DNA at DSB ends. SSDS comprises a computational framework for the specific detection of ssDNA-derived reads in a sequencing library and a new library preparation procedure for the enrichment of fragments originating from ssDNA. The use of our technique reduces the nonspecific double-stranded DNA (dsDNA) background >10-fold. Our method can be extended to other systems where the identification of ssDNA or DSBs is desired.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Chromatin Immunoprecipitation
  • Chromosome Mapping / methods*
  • DNA Breaks, Double-Stranded
  • DNA, Single-Stranded / genetics*
  • Gene Library
  • Inverted Repeat Sequences
  • Male
  • Meiosis / genetics
  • Mice
  • Mice, Inbred C57BL
  • Recombination, Genetic*
  • Sequence Analysis, DNA


  • DNA, Single-Stranded