Evolutionarily diverse determinants of meiotic DNA break and recombination landscapes across the genome

Abstract

Fission yeast Rec12 (Spo11 homolog) initiates meiotic recombination by forming developmentally programmed DNA double-strand breaks (DSBs). DSB distributions influence patterns of heredity and genome evolution, but the basis of the highly nonrandom choice of Rec12 cleavage sites is poorly understood, largely because available maps are of relatively low resolution and sensitivity. Here, we determined DSBs genome-wide at near-nucleotide resolution by sequencing the oligonucleotides attached to Rec12 following DNA cleavage. The single oligonucleotide size class allowed us to deeply sample all break events. We find strong evidence across the genome for differential DSB repair accounting for crossover invariance (constant cM/kb in spite of DSB hotspots). Surprisingly, about half of all crossovers occur in regions where DSBs occur at low frequency and are widely dispersed in location from cell to cell. These previously undetected, low-level DSBs thus play an outsized and crucial role in meiosis. We further find that the influence of underlying nucleotide sequence and chromosomal architecture differs in multiple ways from that in budding yeast. DSBs are not strongly restricted to nucleosome-depleted regions, as they are in budding yeast, but are nevertheless spatially influenced by chromatin structure. Our analyses demonstrate that evolutionarily fluid factors contribute to crossover initiation and regulation.

High-Resolution Global Analysis of the Influences of Bas1 and Ino4 Transcription Factors on Meiotic DNA Break Distributions in Saccharomyces cerevisiae

“…The discrepancies may arise from the use of a rad50S-like mutant background for the Southern blot determinations or may trace to measurement imprecision in either Spo11-oligo maps or Southern blot determinations. Prior studies in S. cerevisiae and S. pombe have established excellent overall quantitative agreement between Spo11 (Rec12) oligo counts and DSB frequencies measured by Southern blotting, but small differences between the methods have been noted in the past for some hotspots (Pan et al 2011;Sasaki et al 2013;Fowler et al 2014), comparable to the differences seen here. Thus, as expected, the Spo11-oligo maps in general showed excellent quantitative agreement with direct assays of DSBs and, equally important, provided excellent spatial accuracy in defining DSB positions (Pan et al 2011;Fowler et al 2014).…”

“…Even those sequence motifs and their binding factors that are clearly capable of specifying strong DSB hotspot activity in some genomic contexts work poorly or not at all in other contexts (Ponticelli and Smith 1992;Mieczkowski et al 2006; this work). Moreover, presence of a sequence motif with DSB-targeting potential is by itself a poor predictor of local DSB frequency (Mieczkowski et al 2006;Fowler et al 2014). …”

Meiotic Recombination: The Essence of Heredity

“…Local determinants of DSB location include cis-acting DNA sequences, transcription factors, histone modifications, and chromatin accessibility (Hwang and Hunter 2011;Lichten and de Massy 2011;Tischfield and Keeney 2012;Baudat et al 2013;Yamada and Ohta 2013;Fowler et al 2014). DSB formation is facilitated by factors that are components of the homolog axes (e.g., Schwacha and Kleckner 1994;Mao-Draayer et al 1996;Ellermeier and Smith 2005;Goodyer et al 2008;Kugou et al 2009;Daniel et al 2011), and the ensuing recombination complexes are visibly associated with these structures (Zickler and Kleckner 1999).…”

Local and sex-specific biases in crossover vs. noncrossover outcomes at meiotic recombination hot spots in mice

“…The fission yeast Schizosaccharomyces pombe provides a distinct example for how recombination outcome can vary dramatically from place to place in the genome (Hyppa and Smith 2010;Fowler et al 2014). In this organism, crossovers are distributed fairly uniformly-i.e., with nearly constant centimorgans per kilobase-despite highly nonuniform distribution of DSBs ("crossover invariance").…”