本文采用的英格恩产品: CCAA细胞凋亡检测试剂盒(PI)
Molecular basis for methylation-sensitive editing by Cas9
Affiliations
- 1 Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
- 2 Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, Netherlands.
- 3 Stichting Sanquin Bloedvoorziening, Amsterdam, Netherlands.
- 4 Graduate School, Van Andel Institute, Grand Rapids, MI, USA.
- 5 Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Hematology, Department of Immunology and Inflammation, Imperial College London, London, UK.
- 6 Institute of Molecular Biophysics, Tallahassee, FL, USA.
- 7 Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA.
- 8 Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA.
- 9 Materials and Structural Analysis Division, Thermo Fisher Scientific, Hillsboro, OR, USA.
- 10 Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, Netherlands. john.vanderoost@wur.nl.
- 11 Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA. hong.li@vai.org.
- 12 Graduate School, Van Andel Institute, Grand Rapids, MI, USA. hong.li@vai.org.
- PMID: 41986708
- PMCID: PMC13216068
- DOI: 10.1038/s41586-026-10384-z
Abstract
The bacterial CRISPR-Cas9 (Cas9) nuclease has become a powerful genome manipulation tool for a wide range of organisms1-3. However, it has yet to fully leverage the pervasive presence of DNA methylation in genomes4-10. 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 Å and 2.2 Å 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.
