PRDM9-directed recombination hotspots depleted near meiotically transcribed genes

•We used existing data to computationally test hypotheses about the interaction of different genomic processes.•We find that PRDM9-associated hotspots are decoupled from pachytene transcription but not leptotene/zygotene transcription.•We were able to model recombination hotspot location as a function of PRDM9 affinity sites and pachytene transcription using zero-inflated Poisson models.•We found an enrichment of retrotransposons in genomic windows that are rich in recombination hotspots but poor in PRDM9 affinity sites and pachytene transcription.