Molecular basis for methylation-sensitive editing by Cas9

• 成果类型: Article
• 署名作者: Roth, Mitchell O.; Shu, Yuerong; Zhao, Yu; Trasanidou, Despoina; Hoffman, Renee D.; Sudfeld, Christian; Bouzetos, Eugenios; Trasanidis, Nikolaos; Zawrotny, Michael; Gelasco, Mary K.; Medina, Megan L.; Das, Anuska; Rai, Jay; Goswami, Hemant N.; Wang, Bing; van der Oost, John; Li, Hong
• 署名单位: Van Andel Institute; Wageningen University & Research; Van Andel Institute; Imperial College London; State University System of Florida; Florida State University; State University System of Florida; Florida State University; St Jude Children's Research Hospital; Thermo Fisher Scientific
• 刊物名称: NATURE
• ISSN/ISSBN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-026-10384-z
• 发表日期: 2026-05-28
• 关键词: NON-CPG METHYLATION; dna methylation; CANCER EPIGENOME; crispr-cas9; gata3; mechanism; patterns; Mutation; reveals

摘要

The bacterial CRISPR-Cas9 (Cas9) nuclease has become a powerful genome manipulation tool for a wide range of organisms1, 2-3. However, it has yet to fully leverage the pervasive presence of DNA methylation in genomes4, 5, 6, 7, 8, 9-10. Here, to fill this gap, we report biochemical, structural and human genome-editing characterizations of a methylation-sensitive Cas9 (ThermoCas9). ThermoCas9 efficiently binds to and cleaves DNA upstream of its protospacer adjacent motif (PAM) 5 '-NNNNCGA-3 ' or 5 '-NNNNCCA-3 ' in vitro. Methylation of the fifth cytosine in either PAM sequence (5mCpG or 5mCpC), however, significantly inhibits ThermoCas9 activity. Cryo-electron microscopy structures of ThermoCas9 in pre-cleavage and post-cleavage states at 2.8 & Aring; and 2.2 & Aring; resolution, respectively, reveal the molecular basis for the stringent requirement of the unmethylated cytosine in PAM binding and provide guidance for further enzyme engineering. We demonstrate methylation-sensitive editing by ThermoCas9 in human cell lines with distinct DNA methylation landscapes. Moreover, we demonstrate that a catalytically enhanced ThermoCas9 efficiently targets luminal expression signature genes that are consistently hypomethylated in patients with breast cancer. Owing to its sensitivity to DNA methylation, ThermoCas9 can specifically target cells with disease-related hypomethylation, which adds another layer of precision to genome-editing technologies.