Downloaded from genome.cshlp.org on October 10, 2021 - Published by Cold Spring Harbor Laboratory Press Genome-wide variability in recombination activity is associated with meiotic chromatin organization Xiaofan Jin1, Geoff Fudenberg1,2, and Katherine S. Pollard1,3,4,* 1Gladstone Institutes, San Francisco, USA 2Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA 3University of California San Francisco, San Francisco, USA 4Chan-Zuckerberg Biohub, San Francisco, USA *Corresponding author:
[email protected] Running title: Recombination is related to chromatin structure Keywords: meiotic recombination, chromatin organization, 3D genome folding, PRDM9 binding, double strand breaks, crossovers 1 Downloaded from genome.cshlp.org on October 10, 2021 - Published by Cold Spring Harbor Laboratory Press 1 Abstract 2 Recombination enables reciprocal exchange of genomic information between parental chromo- 3 somes and successful segregation of homologous chromosomes during meiosis. Errors in this process 4 lead to negative health outcomes, while variability in recombination rate affects genome evolution. 5 In mammals, most crossovers occur in hotspots defined by PRDM9 motifs, though PRDM9 binding 6 peaks are not all equally hot. We hypothesize that dynamic patterns of meiotic genome folding are 7 linked to recombination activity. We apply an integrative bioinformatics approach to analyze how 8 three-dimensional (3D) chromosomal organization during meiosis relates to rates of double-strand- 9 break (DSB) and crossover (CO) formation at PRDM9 binding peaks. We show that active, spatially 10 accessible genomic regions during meiotic prophase are associated with DSB-favored loci, which fur- 11 ther adopt a transient locally active configuration in early prophase.