TY  - JOUR
A1  - Khil, Pavel P.
A1  - Smagulova, Fatima
A1  - Brick, Kevin M.
A1  - Camerini-Otero, R. Daniel
A1  - Petukhova, Galina V.
T1  - Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA
Y1  - 2012/05/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 957 
EP  - 965 
DO  - 10.1101/gr.130583.111 
VL  - 22 
IS  - 5 
UR  - http://genome.cshlp.org/content/22/5/957.abstract 
N2  - 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. 
ER  -