Chapter 4 Genome-Wide Detection of Meiotic DNA Double-Strand Break Hotspots Using Single-Stranded DNA

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 chap-ter 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 recombi-nation, this method can ostensibly be adapted to discover and analyze programmed or damage-induced DSB hotspots in other organisms whose genome sequence is available. Key words: ssDNA, meiosis, double-strand breaks, hotspots, microarray. 1