In mouse and human meiosis, DNA double-strand breaks (DSBs) initiate homologous recombination and occur at specific sites called hotspots. The localization of these sites is determined by the sequence-specific DNA binding domain of the PRDM9 histone methyl transferase. Here, we performed an extensive analysis of PRDM9 binding in mouse spermatocytes. Unexpectedly, we identified a noncanonical recruitment of PRDM9 to sites that lack recombination activity and the PRDM9 binding consensus motif. These sites include gene promoters, where PRDM9 is recruited in a DSB-dependent manner. Another subset reveals DSB-independent interactions between PRDM9 and genomic sites, such as the binding sites for the insulator protein CTCF. We propose that these DSB-independent sites result from interactions between hotspot-bound PRDM9 and genomic sequences located on the chromosome axis.

The work leading to the H3K4me3 results received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 262055. This work was supported by the Agence Nationale de la Recherche (ANR-15-CE12-0010-01/DaSiRe). B.d.M. was funded by grants from the Centre National pour la Recherche Scientifique (CNRS) and the European Research Council Executive Agency under the European Community's Seventh Framework Programme (FP7/2007-2013 grant agreement no. [322788]).