Nakamura Nao, Yoshimi Sae, Kikuchi Amika, Onoda Hiroki, Kori Satomi, Nakanishi Makoto, Nishiyama Atsuya, Arita Kyohei
Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Kanagawa, Japan.
Synchrotron Radiation Research Center, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya 464-8603, Aichi, Japan.
Structure. 2025 Sep 4;33(9):1510-1518.e5. doi: 10.1016/j.str.2025.06.005. Epub 2025 Jul 10.
The ubiquitin signal generated by UHRF1 is essential for DNA methylation maintenance by recruiting DNA methyltransferase 1 (DNMT1) to hemimethylated DNA through strong binding of its replication foci targeting sequence (RFTS) domain to ubiquitinated histone H3. The ubiquitin-specific protease 7 (USP7) forms a complex with DNMT1 and removes ubiquitin from H3. However, it remains unknown how USP7 deubiquitinates ubiquitinated H3 upon strong binding of the DNMT1 RFTS domain. Here, we show the activation mechanism of USP7 by combining biochemical and structural studies. USP7 is inactive toward ubiquitinated H3 in complex with the RFTS domain. However, when complexed with DNMT1, USP7 efficiently deubiquitinates ubiquitinated H3. Cryogenic electron microscopy (cryo-EM) single particle analysis revealed that USP7 bound to DNMT1 undergoes an open (inactive) and closed (active) conformational transition. Our findings provide mechanistic insights into the activation of USP7 upon binding to DNMT1 and contribute to a better understanding of the deubiquitination process in DNA methylation maintenance.
由UHRF1产生的泛素信号对于DNA甲基化维持至关重要，它通过其复制灶靶向序列（RFTS）结构域与泛素化组蛋白H3的强结合，将DNA甲基转移酶1（DNMT1）招募到半甲基化DNA上。泛素特异性蛋白酶7（USP7）与DNMT1形成复合物，并从H3上去除泛素。然而，在DNMT1的RFTS结构域强结合后，USP7如何去泛素化泛素化的H3仍不清楚。在这里，我们通过结合生化和结构研究展示了USP7的激活机制。USP7与RFTS结构域形成复合物时，对泛素化的H3无活性。然而，当与DNMT1复合时，USP7能有效地去泛素化泛素化的H3。低温电子显微镜（cryo-EM）单颗粒分析显示，与DNMT1结合的USP7会发生开放（无活性）和闭合（有活性）的构象转变。我们的研究结果为USP7与DNMT1结合后的激活机制提供了深入见解，并有助于更好地理解DNA甲基化维持中的去泛素化过程。
