Summary The nonrandom distribution of meiotic recombination shapes patterns of inheritance and genome evolution, but chromosomal features governing this distribution are poorly understood. Formation of the DNA double-strand breaks (DSBs) that initiate recombination results in accumulation of Spo11 protein covalently bound to small DNA fragments. We show here that sequencing these fragments provides a genome-wide DSB map of unprecedented resolution and sensitivity. We use this map to explore the influence of large-scale chromosome structures, chromatin, transcription factors, and local sequence composition on DSB distributions. Our analysis supports the view that the recombination terrain is molded by combinatorial and hierarchical interaction of factors that work on widely different size scales. Mechanistic aspects of DSB formation and early processing steps are also uncovered. This map illuminates the occurrence of DSBs in repetitive DNA elements, repair of which can lead to chromosomal rearrangements. We discuss implications for evolutionary dynamics of recombination hotspots.

DNA double-strand breaks (DSBs) with protein covalently attached to 5′ strand termini are formed by Spo11 to initiate meiotic recombination 1,2 . The Spo11 protein must be removed for the DSB to be repaired, but the mechanism for removal has been unclear 3 . We show here that meiotic DSBs in budding yeast are processed by endonucleolytic cleavage that releases Spo11 attached to an oligonucleotide with a free 3′-OH. Surprisingly, two discrete Spo11-oligonucleotide complexes were found in equal amounts, differing with respect to the length of the bound DNA. We propose that these forms arise from different spacings of strand cleavages flanking the DSB, with every DSB processed asymmetrically. Thus, the ends of a single DSB may be biochemically distinct at or before the initial processing step-significantly earlier than previously thought. SPO11-oligonucleotide complexes were identified in extracts of mouse testis, indicating that this mechanism is evolutionarily conserved. Oligonucleotide-topoisomerase II complexes were also present in extracts of vegetative yeast, although not subject to the same genetic control as for generating Spo11-oligonucleotide complexes. Our findings suggest a general mechanism for repair of protein-linked DSBs.We previously proposed that Spo11 might be removed from DSB ends by either of two mechanisms: direct hydrolysis of the covalent protein-DNA linkage, or single-stranded endonucleolytic cleavage releasing Spo11 covalently attached to a short oligonucleotide (Fig. 1a) 1,4 . These mechanisms are distinguished by the presence or absence of an oligonucleotide bound to Spo11. We identified this predicted protein-DNA complex using a direct biochemical approach in S. cerevisiae. A strain expressing HA epitope-tagged Spo11 was induced to enter meiosis, denaturing extracts were prepared, then Spo11-HA was immunoprecipitated and treated with 32 P-labelled nucleotide and terminal deoxynucleotidyl transferase (TdT), which catalyzes untemplated addition of nucleotides to a free 3′-OH DNA end. A chain terminating nucleotide was used to limit incorporation to a single residue.Four radiolabelled bands were observed between ~60 and 110 kDa (Fig. 1b, lane 3). Two bands (asterisks) were non-specific because they were present when TdT and nucleotide were incubated alone (Fig. 1b, lane 1). Two bands (solid arrows) were specific for Spo11-HA because they were not seen with mock immunoprecipitation (Fig. 1b, lane 2), or untagged Spo11 (Fig.1b, lane 4). Labelling was not observed if DSBs were not formed, namely, when the catalytic tyrosine of Spo11 was mutated to phenylalanine 2 (Fig. 1b, lane 5) or in a mei4 mutant 4 (Fig. 1b, lane 6). Labelled Spo11 species were also not observed in rad50S or sae2Δ mutants (Fig. 1b, lanes 7-8), in which Spo11 remains covalently attached to DSB ends 1,5 . Thus, Spo11-oligonucleotide complexes did not arise from non-physiological disruption of covalent Spo11-DSB complexes.Correspondence and requests for materials should be addressed to S.K. (e-mail: keeneys@mskcc.or...

SUMMARY MRE11 within the MRE11-RAD50-NBS1 (MRN) complex acts in DNA double-strand break repair (DSBR), detection and signaling; yet, how its endo- and exonuclease activities regulate DSB repair by non-homologous end-joining (NHEJ) versus homologous recombination (HR) remains enigmatic. Here we employed structure-based design with a focused chemical library to discover specific MRE11 endo- or exonuclease inhibitors. With these inhibitors we examined repair pathway choice at DSBs generated in G2 following radiation exposure. Whilst endo- or exonuclease inhibition impairs radiation-induced RPA chromatin binding, suggesting diminished resection, the inhibitors surprisingly direct different repair outcomes. Endonuclease inhibition promotes NHEJ in lieu of HR, whilst exonuclease inhibition confers a repair defect. Collectively, the results describe nuclease-specific MRE11 inhibitors, define distinct nuclease roles in DSB repair, and support a mechanism whereby MRE11 endonuclease initiates resection, thereby licensing HR followed by MRE11 exo and EXO1/BLM bidirectional resection towards and away from the DNA end, which commits to HR.

Repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) requires resection of 5′-termini to generate 3′-single-strand DNA tails1. Key components of this reaction are Exonuclease 1 and the bifunctional endo/exonuclease, Mre112-4. Mre11 endonuclease activity is critical when DSB termini are blocked by bound protein—such as by the DNA end-joining complex5, topoisomerases6, or the meiotic nuclease, Spo117-13—but a specific function for the Mre11 3′-5′ exonuclease activity has remained elusive. Here, we reveal a role for the Mre11 exonuclease during the resection of Spo11-linked 5′-DNA termini in vivo. We show that the residual resection observed in Exo1-mutant cells is dependent on Mre11, and that both exonuclease activities are required for efficient DSB repair. Previous work has indicated resection to traverse unidirectionally1. Using a combination of physical assays for 5′-end-processing, our results suggest an alternative mechanism involving bidirectional resection. First, Mre11 nicks the strand to be resected up to 300 nucleotides from the 5′-terminus of the DSB—much further away than previously assumed. Second, this nick enables resection in a bidirectional manner, using Exo1 in the 5′-3′ direction away from the DSB, and Mre11 in the 3′-5′ direction towards the DSB end. Finally, Mre11 exonuclease activity confers resistance to DNA damage in cycling cells, suggesting that Mre11-catalysed resection may be a general feature of various DNA repair pathways.