G-quadruplex structures act as a novel recognition motif for the meiosis-specific histone methyltransferase PRDM9

The protein PRDM9 plays a crucial role in human meiotic recombination by depositing activating histone marks, which recruit the meiotic recombination machinery. This protein identifies DNA through a specific zinc-finger array, binding to certain sequence motifs with G-rich strands that can form stable DNA structures, specifically G-quadruplexes (G4s). These G4s may serve as an additional binding site for PRDM9, influencing the chromatin environment to promote meiotic recombination.

Analyzing PRDM9 binding sites in combination with G4 motifs using computational techniques revealed that G4 structures are among the most common features at PRDM9 binding sites. The enrichment of G4 motifs was particularly strong for highly stable G4s, regardless of loop length. Further experiments using electrophoretic mobility shift assays demonstrated that PRDM9 can bind short, single-stranded G4-forming oligonucleotides, with binding strength correlated to G4 stability.

This binding phenomenon was observed across various G4 motifs and was enhanced by increasing the potassium concentration or introducing a G4-stabilizing ligand.

Moreover, PRDM9 was shown to bind an artificial G4-forming sequence not found in the human genome, which was rendered non-functional when the G4 motif was altered to prevent structure formation. These findings collectively suggest that stable G4 structures aid PRDM9 recruitment by creating discrete regions of increased local chromatin accessibility. This accessibility is believed to contribute to the initiation of meiotic recombination.