@article{Khil01052012,
author = {Khil, Pavel P. and Smagulova, Fatima and Brick, Kevin M. and Camerini-Otero, R. Daniel and Petukhova, Galina V.}, 
title = {Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA},
volume = {22}, 
number = {5}, 
pages = {957-965}, 
year = {2012}, 
doi = {10.1101/gr.130583.111}, 
abstract ={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.}, 
URL = {http://genome.cshlp.org/content/22/5/957.abstract}, 
eprint = {http://genome.cshlp.org/content/22/5/957.full.pdf+html}, 
journal = {Genome Research} 
}