ChIP was performed using antibody against H3K4me3 (Millipore, #07-473) as previously described (Billings et al. 2013 (link)). To obtain sufficient material for high-throughput sequencing, four ChIP reactions from a single preparation of spermatocyte chromatin were pooled after final DNA elution. ChIP DNA was concentrated using Agencourt AMPure XP beads (Beckman Coulter) following the manufacturer’s protocol. Quantitation of ChIP and input DNA was measured using the Qubit dsDNA HS assay (Life Technologies). Typically, 7–10 ng of ChIP DNA was obtained after concentration and used for the sequencing library preparation. For all samples, an equal amount of MNase-treated input DNA was sequenced as a control. Biological replicates for each genotype were prepared independently from different litters of mice. Libraries were prepared for sequencing using Bioo Scientific’s NEXTflex ChIP-Seq Kit (protocol version V11.11) without size selection. Amplification of the libraries was done with 20 µL ligation product, 16 µL water, 12 µL NEXTflex ChIP PCR master mix, 2 µL NEXTflex ChIP primer mix, and 14–18 cycles of PCR.