Histone methyltransferase that sequentially mono-, di-, and tri-methylates both 'Lys-4' (H3K4 and 'Lys-36' (H3K36 of histone H3 to produce respectively trimethylated 'Lys-4' (H3K4me3 and trimethylated 'Lys-36' (H3K36me3 histone H3 and plays a key role in meiotic prophase by determining hotspot localization thereby promoting meiotic recombination. Also can methylate all four core histones with H3 being the best substrate and the most highly modified. Is also able, on one hand, to mono and di-methylate H4K20 and on other hand to trimethylate H3K9 with the di-methylated H3K9 as the best substrate. During meiotic prophase, binds specific DNA sequences through its zinc finger domains thereby determining hotspot localization where it promotes local H3K4me3 and H3K36me3 enrichment on the same nucleosomes through its histone methyltransferase activity. Thereby promotes double-stranded breaks (DSB formation, at this subset of PRDM9-binding sites, that initiates meiotic recombination for the proper meiotic progression.