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Article Dans Une Revue Genome Research Année : 2012

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

Résumé

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.

Dates et versions

hal-00877675 , version 1 (29-10-2013)

Identifiants

Citer

Pavel P Khil, Fatima Smagulova, Kevin M Brick, R Daniel Camerini-Otero, Galina V Petukhova. Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNA.. Genome Research, 2012, 22 (5), pp.957-65. ⟨10.1101/gr.130583.111⟩. ⟨hal-00877675⟩
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