Highly parallel profiling of the activities and specificities of Cas12a variants in human cells
Abstract Several Cas12a variants have been developed to broaden its targeting range, improve the gene editing specificity or the efficiency. However, selecting the appropriate Cas12a among the many orthologs for a given target sequence remains difficult. Here, we perform high-throughput analyses to...
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Nature Portfolio
2025-03-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-57150-9 |
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| author | Peng Chen Yankang Wu Hongjian Wang Huan Liu Jin Zhou Jingli Chen Jun Lei Zaiqiao Sun Chonil Paek Lei Yin |
| author_facet | Peng Chen Yankang Wu Hongjian Wang Huan Liu Jin Zhou Jingli Chen Jun Lei Zaiqiao Sun Chonil Paek Lei Yin |
| author_sort | Peng Chen |
| collection | DOAJ |
| description | Abstract Several Cas12a variants have been developed to broaden its targeting range, improve the gene editing specificity or the efficiency. However, selecting the appropriate Cas12a among the many orthologs for a given target sequence remains difficult. Here, we perform high-throughput analyses to evaluate the activity and compatibility with specific PAMs of 24 Cas12a variants and develop deep learning models for these Cas12a variants to predict gene editing activities at target sequences of interest. Furthermore, we reveal and enhance the truncation in the integrated tag sequence that may hinder off-targeting detection for Cas12a by GUIDE-seq. This enhanced system, which we term enGUIDE-seq, is used to evaluate and compare the off-targeting and translocations of these Cas12a variants. |
| format | Article |
| id | doaj-art-de1fcf27aac84a67b0606cce6e7ceae8 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-de1fcf27aac84a67b0606cce6e7ceae82025-08-20T03:40:50ZengNature PortfolioNature Communications2041-17232025-03-0116111310.1038/s41467-025-57150-9Highly parallel profiling of the activities and specificities of Cas12a variants in human cellsPeng Chen0Yankang Wu1Hongjian Wang2Huan Liu3Jin Zhou4Jingli Chen5Jun Lei6Zaiqiao Sun7Chonil Paek8Lei Yin9Department of Pediatric Research Institute; Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children’s Hospital of Chongqing Medical University, School of Basic Medical Sciences, Chongqing Medical UniversityState Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan UniversityState Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan UniversityState Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan UniversityDepartment of Pediatric Research Institute; Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children’s Hospital of Chongqing Medical University, School of Basic Medical Sciences, Chongqing Medical UniversitySchool of Medicine, Wuhan University of Science and TechnologyDepartment of Pediatric Research Institute; Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children’s Hospital of Chongqing Medical University, School of Basic Medical Sciences, Chongqing Medical UniversityState Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan UniversityState Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan UniversityDepartment of Pediatric Research Institute; Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children’s Hospital of Chongqing Medical University, School of Basic Medical Sciences, Chongqing Medical UniversityAbstract Several Cas12a variants have been developed to broaden its targeting range, improve the gene editing specificity or the efficiency. However, selecting the appropriate Cas12a among the many orthologs for a given target sequence remains difficult. Here, we perform high-throughput analyses to evaluate the activity and compatibility with specific PAMs of 24 Cas12a variants and develop deep learning models for these Cas12a variants to predict gene editing activities at target sequences of interest. Furthermore, we reveal and enhance the truncation in the integrated tag sequence that may hinder off-targeting detection for Cas12a by GUIDE-seq. This enhanced system, which we term enGUIDE-seq, is used to evaluate and compare the off-targeting and translocations of these Cas12a variants.https://doi.org/10.1038/s41467-025-57150-9 |
| spellingShingle | Peng Chen Yankang Wu Hongjian Wang Huan Liu Jin Zhou Jingli Chen Jun Lei Zaiqiao Sun Chonil Paek Lei Yin Highly parallel profiling of the activities and specificities of Cas12a variants in human cells Nature Communications |
| title | Highly parallel profiling of the activities and specificities of Cas12a variants in human cells |
| title_full | Highly parallel profiling of the activities and specificities of Cas12a variants in human cells |
| title_fullStr | Highly parallel profiling of the activities and specificities of Cas12a variants in human cells |
| title_full_unstemmed | Highly parallel profiling of the activities and specificities of Cas12a variants in human cells |
| title_short | Highly parallel profiling of the activities and specificities of Cas12a variants in human cells |
| title_sort | highly parallel profiling of the activities and specificities of cas12a variants in human cells |
| url | https://doi.org/10.1038/s41467-025-57150-9 |
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