Homologous recombination is required for proper segregation of homologous 
chromosomes during meiosis. It occurs predominantly at recombination hotspots 
that are defined by the DNA binding specificity of the PRDM9 protein. PRDM9 
contains three conserved domains typically involved in regulation of 
transcription; yet, the role of PRDM9 in gene expression control is not clear. 
Here, we analyze the germline transcriptome of Prdm9-/- male mice in comparison 
to Prdm9+/+ males and find no apparent differences in the mRNA and miRNA 
profiles. We further explore the role of PRDM9 in meiosis by analyzing the 
effect of the KRAB, SSXRD, and post-SET zinc finger deletions in a cell culture 
expression system and the KRAB domain deletion in mice. We found that although 
the post-SET zinc finger and the KRAB domains are not essential for the 
methyltransferase activity of PRDM9 in cell culture, the KRAB domain mutant mice 
show only residual PRDM9 methyltransferase activity and undergo meiotic arrest. 
In aggregate, our data indicate that domains typically involved in regulation of 
gene expression do not serve that role in PRDM9, but are likely involved in 
setting the proper chromatin environment for initiation and completion of 
homologous recombination.