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.
journal_name
Genome Resjournal_title
Genome researchauthors
Khil PP,Smagulova F,Brick KM,Camerini-Otero RD,Petukhova GVdoi
10.1101/gr.130583.111subject
Has Abstractpub_date
2012-05-01 00:00:00pages
957-65issue
5eissn
1088-9051issn
1549-5469pii
gr.130583.111journal_volume
22pub_type
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