Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1

The PHD finger protein 1 (PHF1) is essential in epigenetic regulation and genome maintenance. Here, we demonstrate that the Tudor domain of human PHF1 binds to histone H3 trimethylated at Lys36 (H3K36me3). We report a 1.9 Å resolution crystal structure of the Tudor domain in complex with H3K36me3 and describe the molecular mechanism of H3K36me3 recognition using NMR analysis. Binding of PHF1 to H3K36me3 inhibits the ability of the Polycomb PRC2 complex to methylate H3K27 in vitro and in vivo. Laser micro-irradiation data reveal that PHF1 is transiently recruited to DNA double-strand breaks (DSBs), and PHF1 mutants impaired in the H3K36me3 interaction exhibit reduced retention at DSB sites. Together, our findings suggest that PHF1 can mediate deposition of the repressive H3K27me3 mark and acts as an early DNA damage response cofactor. The human Polycomblike (PCL) protein PHF1 associates with pivotal nuclear complexes including PRC2 (Polycomb repressive complex 2) and Ku70-Ku80 and is involved in transcription regulatory and DNA damage repair pathways. The PRC2 complex possesses intrinsic histone lysine methyltransferase (HKMT) activity1–3. It methylates Lys27 of Correspondence should be addressed to: T.G.K