Zea mays Epigenomics

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. Overall design: 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.