Article
Cell Biology
Shuwen Zheng, Haiwen Zhong, Xiaoqing Zhou, Min Chen, Wansheng Li, Yin Zi, Yue Chi, Jinling Wang, Wei Zheng, Qingjian Zou, Liangxue Lai, Chengcheng Tang
Summary: This study used cytosine base editor (CBE) to edit the porcine endogenous retrovirus (PERV) genome in pigs, reducing cytotoxic effects. The results showed that using CBE can significantly improve the efficiency of PERV knockout and avoid severe DNA damage in pig cells.
Article
Plant Sciences
Zhen Liang, Yuqing Wu, Lingling Ma, Yingjie Guo, Yidong Ran
Summary: The study successfully targeted multiple genes in foxtail millet using the CRISPR/Cas9 single- and multi-gene editing systems, and generated mutant plants through genetic transformation. Base editing was achieved using two base editors, resulting in the creation of herbicide-tolerant mutant plants in foxtail millet. This system has the potential to enhance functional genomics analysis and genetic improvement in foxtail millet.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Kairen Tian, Xia Hong, Manman Guo, Yanni Li, Hao Wu, Qinggele Caiyin, Jianjun Qiao
Summary: This study reports the development of a CRISPR-based multi-loci editing system that can efficiently edit multiple loci in L. lactis, providing a powerful tool for industrial applications.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Plant Sciences
Kutubuddin A. Molla, Simon Sretenovic, Kailash C. Bansal, Yiping Qi
Summary: The development of CRISPR-Cas systems has revolutionized genome editing in plant genetics and breeding. The inefficiency of HDR in many plant species has led to the development of base editing and prime editing technologies, which allow for precise changes at a single-base resolution in the target genome. This Review provides an overview of the current status of base editors and prime editors in plants, covering both technological developments and biological applications.
Article
Medicine, Research & Experimental
Lurong Jiang, Jie Long, Yang Yang, Lifang Zhou, Jing Su, Fengming Qin, Wenling Tang, Rui Tao, Qiang Chen, Shaohua Yao
Summary: In this study, a subset of base editors derived from SaCas9 was designed, which increased the editing efficiency and expanded the editing window by changing the insertion position of the deaminase. These base editors also showed reduced non-specific editing.
Article
Biotechnology & Applied Microbiology
Qiurong Ren, Simon Sretenovic, Guanqing Liu, Zhaohui Zhong, Jiaheng Wang, Lan Huang, Xu Tang, Yachong Guo, Li Liu, Yuechao Wu, Jie Zhou, Yuxin Zhao, Han Yang, Yao He, Shishi Liu, Desuo Yin, Rocio Mayorga, Xuelian Zheng, Tao Zhang, Yiping Qi, Yong Zhang
Summary: In this study, the A3A/Y130F-CBE_V01 was identified as the most efficient C-to-T base editor in plants, showing applications in generating microRNA-resistant mRNA transcripts and herbicide-resistant allele evolution in rice. Additionally, the development and testing of multiple CBE_V02, CBE_V03, and CBE_V04 systems in rice protoplasts demonstrated improved editing activity and purity, with the CBE_V04 systems showing enhanced editing efficiency through focal recruitment of uracil DNA glycosylase inhibitors by engineered sgRNA scaffolds. Whole-genome sequencing revealed varying levels of off-target effects among different CBE systems, with PmCDA1-CBE_V04 and A3A/Y130F-CBE_V04 identified as high-efficiency, high-purity, and highly specific next-generation plant CBEs.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Plant Sciences
Juan Luo, Muhammad Abid, Jing Tu, Xinxia Cai, Yi Zhang, Puxin Gao, Hongwen Huang
Summary: In this study, three tRNA-gRNA expression cassettes were constructed and compared for their base editing efficiency in polyploid plant N. benthamiana. A3A-CBE was found to be the most efficient base editor, allowing comprehensive editing from C-1 to C-17 and higher editing efficiency under the TC base background. Analysis of target sites in transformed N. benthamiana showed that only A3A-CBE could perform C-to-T editing, with higher efficiency at T2 compared to T6. No off-target events were found in transformed N. benthamiana. Overall, A3A-CBE is confirmed as the most suitable vector for specific C to T conversion in N. benthamiana, providing valuable insights for breeding polyploid plants.
Article
Biochemistry & Molecular Biology
Jibiao Fan, Leisheng Shi, Qi Liu, Zhipeng Zhu, Fan Wang, Runxian Song, Jimeng Su, Degui Zhou, Xiao Chen, Kailong Li, Lixiang Xue, Lichao Sun, Fengbiao Mao
Summary: CRISPRbase is a powerful tool that integrates over 1,252,935 records of base editing outcomes from more than 50 cell types and 17 species. It helps evaluate the editing precision of different base editing systems and assesses the editing window, efficiency, and product purity. The study found that most cancer-related off-target mutations were damaging to protein functions but had a weak effect on carcinogenesis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Qiqi Jing, Weiwei Liu, Haoyun Jiang, Yaya Liao, Qiang Yang, Yuyun Xing
Summary: In this study, five ABEs were used to generate A-to-G (T-to-C) conversions in five genome loci in porcine fetal fibroblasts. Different editing efficiencies and activity windows were observed in these targeting regions using different editors. The strategy of two sgRNAs in one vector showed superior editing efficiency. ABE-mediated start-codon mutation in APOE resulted in the silencing of its protein expression and elimination of the majority of its mRNA. No off-target DNA site was detected, but substantial off-target RNA events were present in the ABE-edited cells.
Article
Biology
Zhiquan Liu, Siyu Chen, Wanhua Xie, Hao Yu, Liangxue Lai, Zhanjun Li
Summary: Researchers have revisited and engineered a compact Cas9 orthologue derived from Neisseria cinerea (NcCas9) for efficient genome editing in mammal cells. NcCas9 can recognize a PAM sequence (N4GYAT) that existing Cas9s cannot, and by optimizing its architecture and spacer length, editing efficacy is improved. NcCas9-derived Base editors can efficiently generate base conversions, and six anti-CRISPR proteins were identified as off-switches for NcCas9. NcCas9 successfully generated efficient editing of mouse embryos by microinjection of NcCas9 mRNA and the corresponding sgRNA.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Savio D. Rodrigues, Mansour Karimi, Lennert Impens, Els Van Lerberge, Griet Coussens, Stijn Aesaert, Debbie Rombaut, Dominique Holtappels, Heba M. M. Ibrahim, Marc Van Montagu, Jeroen Wagemans, Thomas B. Jacobs, Barbara De Coninck, Laurens Pauwels
Summary: Agrobacterium spp. are important plant pathogens that can be genetically modified using CRISPR-mediated base editing to introduce targeted point mutations, improving the efficiency and functionality of the strains for plant transformation and gene editing. The method developed in this study has shown high efficiency and potential for future advancements in engineering Agrobacterium strains.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Yangning Sun, Qi Chen, Yanbing Cheng, Xi Wang, Zixin Deng, Fuling Zhou, Yuhui Sun
Summary: This study engineered blue-light-activated base editors (BLBEs) by combining photoswitches magnets with DNA deaminases. The BLBEs system showed efficient base editing with low off-target effects. This study is of great significance for promoting the development of optogenetic genome engineering.
Review
Biochemistry & Molecular Biology
Kartik L. Rallapalli, Alexis C. Komor
Summary: DNA-editing enzymes can change the genetic identity of modified base or regulate gene expression. With the development of CRISPR-Cas systems, interest in DNA-editing enzymes has grown due to their ability to target specific genomic loci. In this review, we highlight the repurposing and redesigning of DNA-editing enzymes into programmable base editors, including deaminases, glycosylases, methyltransferases, and demethylases. The remarkable engineering efforts showcased in this review serve as a model for repurposing and engineering other enzyme families. Collectively, these base editors enable programmable point mutation introduction and gene expression modulation through targeted chemical modifications of nucleobases.
ANNUAL REVIEW OF BIOCHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Zhiquan Liu, Siyu Chen, Wanhua Xie, Yuning Song, Jinze Li, Liangxue Lai, Zhanjun Li
Summary: This study demonstrates the potential of compact CRISPR-Cas9 systems for gene therapy. The researchers optimized and expanded the targeting scope of a small Cas9 ortholog called SpaCas9, which showed efficient genome editing in vivo. They also engineered SpaCas9 variants to further expand the capabilities of compact Cas9 systems. The results showed that SpaCas9 has distinct protospacer adjacent motifs (PAMs) and a small size, making it a valuable tool for gene modifications and therapeutic applications.
Article
Biotechnology & Applied Microbiology
Yaru Chen, Meijie Cheng, Yan Li, Lin Wang, Lixia Fang, Yingxiu Cao, Hao Song
Summary: This study developed a rapid and efficient multiplex base editing system that significantly improved extracellular electron transfer in microbes by deactivating multiple genes. The system was applied successfully in genome manipulation and combinatorial engineering in Shewanella, enhancing our ability to understand and apply extracellular electron transfer.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2023)
Article
Biology
Jingke Xie, Xingyun Huang, Xia Wang, Shixue Gou, Yanhui Liang, Fangbing Chen, Nan Li, Zhen Ouyang, Quanjun Zhang, Weikai Ge, Qin Jin, Hui Shi, Zhenpeng Zhuang, Xiaozhu Zhao, Meng Lian, Jiaowei Wang, Yinghua Ye, Longquan Quan, Han Wu, Kepin Wang, Liangxue Lai
Article
Biotechnology & Applied Microbiology
Nan Li, Shixue Gou, Jiaowei Wang, Quanjun Zhang, Xingyun Huang, Jingke Xie, Li Li, Qin Jin, Zhen Ouyang, Fangbing Chen, Weikai Ge, Hui Shi, Yanhui Liang, Zhenpeng Zhuang, Xiaozhu Zhao, Meng Lian, Yinghua Ye, Longquan Quan, Han Wu, Liangxue Lai, Kepin Wang
Summary: The study successfully rescued lethal phenotypes in newborn HT1 rabbits by delivering CRISPR-Cas9 and donor templates, allowing the rabbits to reach adulthood normally and give birth to offspring. The liver and kidney structures and functions were normal, with gene corrections efficient enough to recover liver function and reduce damage.
Article
Genetics & Heredity
Menglong Chen, Hui Shi, Shixue Gou, Xiaomin Wang, Lei Li, Qin Jin, Han Wu, Huili Zhang, Yaqin Li, Liang Wang, Huan Li, Jinfu Lin, Wenjing Guo, Zhiwu Jiang, Xiaoyu Yang, Anding Xu, Yuling Zhu, Cheng Zhang, Liangxue Lai, Xiaoping Li
Summary: This study demonstrated the high efficiency of large-scale excision of mutant DMD exons in restoring dystrophin protein expression in a patient-derived stem cell model. CRISPR-mediated genome editing with Cas12a showed similar efficacy to Cas9 in correcting DMD mutations. In a PDX DMD mouse model, over 10% of human DMD muscle fibers expressed dystrophin after treatment with large-scale excision strategies, indicating functional restoration of dystrophin in vivo.
Article
Medicine, Research & Experimental
Ding Zhao, Yuqiang Qian, Jinze Li, Zhanjun Li, Liangxue Lai
Summary: This study shows that ABE8.17 systems can efficiently induce base editing in mouse and rabbit embryos, as well as accurately mimic clinical point mutations in rabbits. ABE8.17-NL, created by eliminating the linker, achieved efficient base editing within a narrowed window in human cells.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2022)
Letter
Cell Biology
Yingqi Jia, Tian Wang, Ding Zhao, Zhiquan Liu, Tingting Sui, Siyu Chen, Jinze Li, Liangxue Lai, Zhanjun Li
JOURNAL OF MOLECULAR CELL BIOLOGY
(2023)
Article
Biology
Zhiquan Liu, Siyu Chen, Wanhua Xie, Hao Yu, Liangxue Lai, Zhanjun Li
Summary: Researchers have revisited and engineered a compact Cas9 orthologue derived from Neisseria cinerea (NcCas9) for efficient genome editing in mammal cells. NcCas9 can recognize a PAM sequence (N4GYAT) that existing Cas9s cannot, and by optimizing its architecture and spacer length, editing efficacy is improved. NcCas9-derived Base editors can efficiently generate base conversions, and six anti-CRISPR proteins were identified as off-switches for NcCas9. NcCas9 successfully generated efficient editing of mouse embryos by microinjection of NcCas9 mRNA and the corresponding sgRNA.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Feiyu Zhao, Tao Zhang, Xiaodi Sun, Xiyun Zhang, Letong Chen, Hejun Wang, Jinze Li, Peng Fan, Liangxue Lai, Tingting Sui, Zhanjun Li
Summary: The authors develop an Interaction, Dynamics and Conservation (IDC) strategy combined with AlphaFold2 to generate compact variants of Cas13 and construct an RNA base editor. This study provides a feasible strategy for downsizing CRISPR/Cas13 systems and enables targeted degradation of RNAs and RNA editing.
NATURE COMMUNICATIONS
(2023)