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 (PubMed:16292313, PubMed:24095733, PubMed:27362481, PubMed:24785241, PubMed:29478809). Can also methylate all four core histones with H3 being the best substrate and the most highly modified (PubMed:24785241, PubMed:27362481). 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 (PubMed:24785241, PubMed:27362481). 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 (PubMed:22028627, PubMed:27362481, PubMed:29478809). Thereby promotes double-stranded breaks (DSB) formation, at this subset of PRDM9-binding sites, that initiates meiotic recombination for the proper meiotic progression (PubMed:16292313, PubMed:29478809). During meiotic progression hotspot-bound PRDM9 interacts with several complexes; in early leptonema binds CDYL and EHMT2 followed by EWSR1 and CXXC1 by the end of leptonema (PubMed:27932493). EWSR1 joins PRDM9 with the chromosomal axis through REC8 (PubMed:27932493). In this way, controls the DSB repair pathway, pairing of homologous chromosomes and sex body formation (PubMed:25894966, PubMed:16292313). Moreover plays a central role in the transcriptional activation of genes during early meiotic prophase thanks to H3K4me3 and H3K36me3 enrichment that represents a specific tag for epigenetic transcriptional activation (PubMed:16292313). In addition performs automethylation (PubMed:28126738). Acetylation and phosphorylation of histone H3 attenuate or prevent histone H3 methylation (PubMed:27362481). L-lysyl-[protein] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl-[protein] + S-adenosyl-L-homocysteine N(6),N(6)-dimethyl-L-lysyl-[protein] + S-adenosyl-L-methionine = H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl-[protein] + S-adenosyl-L-homocysteine L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-homocysteine L-lysyl(36)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(36)-[histone H3] + 3 S-adenosyl-L-homocysteine L-lysyl(9)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + 3 S-adenosyl-L-homocysteine L-lysyl(20)-[histone H4] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-homocysteine N(6)-methyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-methionine = H(+) + N(6),N(6)-dimethyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-homocysteine Homodimer (PubMed:24095733). Interacts with EHMT2 and CDYL; interaction only takes place when PRDM9 is bound to hotspot DNA (PubMed:27932493). Interacts with CXXC1; this interaction does not link PRDM9-activated recombination hotspot sites with DSB machinery and is not required for the hotspot recognition pathway (PubMed:27932493, PubMed:30365547). Forms a complex with EWSR1, REC8, SYCP3 and SYCP1; complex formation is dependent of phosphorylated form of REC8 and requires PRDM9 bound to hotspot DNA; EWSR1 joins PRDM9 with the chromosomal axis through REC8 (PubMed:27932493). Localizes in nuclei of pre-leptotene, leptotene, and early to mid-zygotene spermatocytes. Specifically expressed in germ cells entering meiotic prophase in female fetal gonads and in postnatal testis (PubMed:16292313). Expressed in early meiotic prophase (PubMed:27932493). Specifically expressed during meiotic prophase. Transiently increases in female gonads from 13.5 dpc to 16.5 dpc, the time during which meiosis proceeds from pre-meiotic replication to pachytene stages. Its expression is barely detectable in fetal male gonads. In adults, it is expressed in testis, but not in any other tissue tested. Abundance increases from 10 d post partum (dpp) to 18 dpp, during which time the first wave of spermatogenesis proceeds synchronously from pre-leptotene to pachytene stages. The C2H2-type zinc fingers determine the hotspot localization through its binding to specific DNA sequences (PubMed:22028627, PubMed:29478809). Variations in their sequence affect affinity towards DNA-binding motif (PubMed:22028627, PubMed:29478809). Mono-methylated; automethylated (PubMed:28126738). Tri-methylated; automethylated (PubMed:28126738). Mono-methylation is predominant; automethylation is lower and slower than H3 peptide methylation and is in a highest S-adenosyl-L-methionine concentration-dependent (PubMed:28126738). There are two major sites for automethylation at Lys-368 and Lys-374 (PubMed:28126738). Lysines can be simultaneously methylated, such as Lys-368(me3)/Lys-372(me1), Lys-368(me1)/Lys-374(me1) and Lys-368(me1)/Lys-372(me1)/Lys-374(me1) (PubMed:28126738). Automethylation is an intramolecular (cis) process (PubMed:28126738). Several alleles exist depending on both the number of zinc finger C2H2 type domains and their identity (PubMed:22028627). Each allele binds to a specific hotspot set (PubMed:29478809). Both polymorphisms in the zinc finger C2H2 type domains and in DNA target sequence control recombination at hotspot (PubMed:22028627). The affinity of each allele for its DNA-binding site can vary histone methyltransferase activity (PubMed:29478809). Knockout homozygous mice are sterile in both sexes. Represents a speciation gene in mus genus. Prdm9 is one of several genes responsible for hybrid sterility between M.musculus and house mouse (PubMed:19074312). Hybrid sterility is defined as a situation where parental forms, each fertile inter se, produce infertile offspring (PubMed:19074312). Intersubspecific hybrids of house mouse display spermatogenic failures that are due to variations in the Prdm9 gene (PubMed:19074312). Belongs to the class V-like SAM-binding methyltransferase superfamily. Firstly described as not catalyzing the monomethylation of unmethylated H3 peptide (PubMed:16292313). However other in vitro experiments described that can also methylate unmodified 'Lys-4' of histone H3 (PubMed:24095733, PubMed:24785241, PubMed:27362481).