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Significance Accessibility of antigen receptor gene segments to recombination-activating gene (RAG), the V(D)J recombinase, is correlated with marks of active chromatin. One mark, histone H3 at lysine 4 (H3K4me3), binds to a plant homeodomain (PHD) in the RAG-2 subunit; mutations that abolish binding of the PHD to H3K4me3 also impair V(D)J recombination. Engagement of H3K4me3 by RAG-2 enhances substrate binding and catalysis, which are functions of RAG-1. We show that H3K4me3 acts through the PHD to induce conformational changes in an autoinhibitory domain residing within RAG-2 as well as in substrate-binding and catalytic regions of RAG-1. Our data suggest that H3K4me3 promotes displacement of the autoinhibitory domain as well as concomitant conformational alterations in RAG-1 that favor increased substrate affinity and catalytic rate.

H3K4me3 induces allosteric conformational changes in the DNA-binding and catalytic regions of the V(D)J recombinase