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Methods Mol Biol. 2011;745:47-63. doi: 10.1007/978-1-61779-129-1_4.

Genome-wide detection of meiotic DNA double-strand break hotspots using single-stranded DNA.

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  • 1Whitehead Institute for Biomedical Research, Cambridge, MA, USA.


The controlled fragmentation of chromosomes by DNA double-strand breaks (DSBs) initiates meiotic recombination, which is essential for meiotic chromosome segregation in most eukaryotes. This chapter describes a straightforward microarray-based approach to measure the genome-wide distribution of meiotic DSBs by detecting the single-stranded DNA (ssDNA) that transiently accumulates at DSB sites during recombination. The protocol outlined here has been optimized to detect meiotic DSBs in Saccharomyces cerevisiae. However, because ssDNA is a universal intermediate of homologous recombination, this method can ostensibly be adapted to discover and analyze programmed or damage-induced DSB hotspots in other organisms whose genome sequence is available.

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