Genomic features shaping the landscape of meiotic double-strand break hotspots in maize [ChIP-Seq]

To generate the double-strand break (DSB) hotspot map in maize, we used a chromatin immunoprecipitation (ChIP) approach, in which chromatin from flowers containing zygotene meiocytes was enriched in fragments associated with RAD51. To identify sites occupied by RAD51, we compared the genomic distribution of RAD51 ChIP-seq reads to (i) Illumina-sequenced meiotic input chromatin that was not subjected to ChIP, (ii) ChIP products generated by using pre-immune IgG, instead of the anti-RAD51 antibody, on meiotic chromatin, and (iii) ChIP products generated using the anti-RAD51 antibody on leaf tissue chromatin. RAD51 ChIP-seq was also performed on the meiotic chromatin of a POOR HOMOLOGOUS SYNAPSIS1 (phs1) mutant.