1
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Qi T, Wang Y, Yang Y, Gao S, Liu J, Huang Q, Tian Y, Tang J, Zheng WV, Wang Y. Phage-assisted evolution of compact Cas9 variants targeting a simple NNG PAM. Nat Chem Biol 2024; 20:344-352. [PMID: 38052959 DOI: 10.1038/s41589-023-01481-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 10/12/2023] [Indexed: 12/07/2023]
Abstract
Compact Cas9 nucleases hold great promise for therapeutic applications. Although several compact Cas9 nucleases have been developed, many genomic loci still could not be edited due to a lack of protospacer adjacent motifs (PAMs). We previously developed a compact SlugCas9 recognizing an NNGG PAM. Here we demonstrate that SlugCas9 displays comparable activity to SpCas9. We developed a simple phage-assisted evolution to engineer SlugCas9 for unique PAM requirements. Interestingly, we generated a SlugCas9 variant (SlugCas9-NNG) that could recognize an NNG PAM, expanding the targeting scope. We further developed a SlugCas9-NNG-based adenine base editor and demonstrated that it could be delivered by a single adeno-associated virus to disrupt PCSK9 splice donor and splice acceptor. These genome editors greatly enhance our ability for in vivo genome editing.
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Affiliation(s)
- Tao Qi
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China
| | - Yao Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China
| | - Yuan Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China
| | - Siqi Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China
| | - Jingtong Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Yuwen Tian
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China
| | - Junnan Tang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Wei V Zheng
- Intervention and Cell Therapy Center, Peking University Shenzhen Hospital, Shenzhen, China.
| | - Yongming Wang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China.
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Fudan University, Shanghai, China.
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China.
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2
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Zhang C, Yang Y, Qi T, Zhang Y, Hou L, Wei J, Yang J, Shi L, Ong SG, Wang H, Wang H, Yu B, Wang Y. Prediction of base editor off-targets by deep learning. Nat Commun 2023; 14:5358. [PMID: 37660097 PMCID: PMC10475126 DOI: 10.1038/s41467-023-41004-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 08/21/2023] [Indexed: 09/04/2023] Open
Abstract
Due to the tolerance of mismatches between gRNA and targeting sequence, base editors frequently induce unwanted Cas9-dependent off-target mutations. Here, to develop models to predict such off-targets, we design gRNA-off- target pairs for adenine base editors (ABEs) and cytosine base editors (CBEs) and stably integrate them into the human cells. After five days of editing, we obtain valid efficiency datasets of 54,663 and 55,727 off-targets for ABEs and CBEs, respectively. We use the datasets to train deep learning models, resulting in ABEdeepoff and CBEdeepoff, which can predict off-target sites. We use these tools to predict off-targets for a panel of endogenous loci and achieve Spearman correlation values varying from 0.710 to 0.859. Finally, we develop an integrated tool that is freely accessible via an online web server http://www.deephf.com/#/bedeep/bedeepoff . These tools could facilitate minimizing the off-target effects of base editing.
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Affiliation(s)
- Chengdong Zhang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Yuan Yang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Tao Qi
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Yuening Zhang
- SJTU-Yale Joint Center for Biostatistics and Data Science, (Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology) Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Linghui Hou
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Jingjing Wei
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Jingcheng Yang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Leming Shi
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Sang-Ging Ong
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Illinois, USA
- Division of Cardiology, Department of Medicine, University of Illinois College of Medicine, Illinois, USA
| | - Hongyan Wang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
| | - Bo Yu
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China.
| | - Yongming Wang
- Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center; State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, 200438, China.
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China.
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3
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Gao S, Wang Y, Qi T, Wei J, Hu Z, Liu J, Sun S, Liu H, Wang Y. Genome editing with natural and engineered CjCas9 orthologs. Mol Ther 2023; 31:1177-1187. [PMID: 36733251 PMCID: PMC10124074 DOI: 10.1016/j.ymthe.2023.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 01/01/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
CjCas9 is one of the smallest CRISPR-associated (Cas9) nucleases for mammalian genome editing. However, it requires a long N4RYAC (R = A or G; Y = C or T) protospacer-adjacent motif (PAM), limiting its DNA targeting scope. In this study, we investigated the PAMs of three CjCas9 orthologs, including Hsp1Cas9, Hsp2Cas9, and CcuCas9, by performing a GFP-activation assay. Interestingly, Hsp1Cas9 and CcuCas9 recognized unique N4RAA and N4CNA PAMs, respectively. We further generated an Hsp1Cas9-Hsp2Cas9 chimeric Cas9 (Hsp1-Hsp2Cas9), which recognized a simple N4CY PAM. Genome-wide off-target analysis revealed that Hsp1-Hsp2Cas9 has very few off-targets compared to SpCas9. By analyzing the crystal structure of CjCas9, we identified eight mutations that can improve the specificity and generate a high-fidelity Hsp1-Hsp2Cas9-Y. Hsp1-Hsp2Cas9-Y enables the knockout of B4GALNT2 and CMAH in porcine fetal fibroblasts (PFFs). Moreover, we developed a high-fidelity Hsp1-Hsp2Cas9-KY which displayed undetectable off-targets revealed by GUIDE-seq at four tested loci. These natural and engineered Cas9 nucleases enabled efficient genome editing in multiple mammalian cells, expanding the DNA targeting scope.
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Affiliation(s)
- Siqi Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Yao Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Tao Qi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Jingjing Wei
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Ziying Hu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Jingtong Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Shuna Sun
- Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China.
| | - Huihui Liu
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing 102300, China.
| | - Yongming Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China.
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4
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Osadchiy IS, Kamalyan SO, Tumashova KY, Georgiev PG, Maksimenko OG. CRISPR/Cas9 Essential Gene Editing in Drosophila. Acta Naturae 2023; 15:70-74. [PMID: 37538801 PMCID: PMC10395781 DOI: 10.32607/actanaturae.11874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/04/2023] [Indexed: 08/05/2023] Open
Abstract
Since the addition of the CRISPR/Cas9 technology to the genetic engineering toolbox, the problems of low efficiency and off-target effects hamper its widespread use in all fields of life sciences. Furthermore, essential gene knockout usually results in failure and it is often not obvious whether the gene of interest is an essential one. Here, we report on a new strategy to improve the CRISPR/Cas9 genome editing, which is based on the idea that editing efficiency is tightly linked to how essential the gene to be modified is. The more essential the gene, the less the efficiency of the editing and the larger the number of off-targets, due to the survivorship bias. Considering this, we generated deletions of three essential genes in Drosophila: trf2, top2, and mep-1, using fly strains with previous target gene overexpression ("pre-rescued" genetic background).
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Affiliation(s)
- I. S. Osadchiy
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russian Federation
| | - S. O. Kamalyan
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russian Federation
| | - K. Y. Tumashova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russian Federation
| | - P. G. Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russian Federation
| | - O. G. Maksimenko
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russian Federation
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5
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Huber A, Dijkstra C, Ernst M, Eissmann MF. Generation of gene-of-interest knockouts in murine organoids using CRISPR-Cas9. STAR Protoc 2023; 4:102076. [PMID: 36853714 PMCID: PMC9918790 DOI: 10.1016/j.xpro.2023.102076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/11/2022] [Accepted: 01/09/2023] [Indexed: 02/03/2023] Open
Abstract
Gene-of-interest knockout organoids present a powerful and versatile research tool to study a gene's effects on many biological and pathological processes. Here, we present a straightforward and broadly applicable protocol to generate gene knockouts in mouse organoids using CRISPR-Cas9 technology. We describe the processes of transient transfecting organoids with pre-assembled CRISPR-Cas9 ribonucleoprotein complexes, organoid cell sorting, and establishing clonal organoid culture pairs. We then detail how to confirm the knockout via Western blot analysis.
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Affiliation(s)
- Anne Huber
- Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia.
| | - Christine Dijkstra
- Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia
| | - Matthias Ernst
- Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia
| | - Moritz F Eissmann
- Olivia Newton-John Cancer Research Institute and La Trobe School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia.
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6
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Wang S, Tao C, Mao H, Hou L, Wang Y, Qi T, Yang Y, Ong SG, Hu S, Chai R, Wang Y. Identification of SaCas9 orthologs containing a conserved serine residue that determines simple NNGG PAM recognition. PLoS Biol 2022; 20:e3001897. [PMID: 36449487 PMCID: PMC9710800 DOI: 10.1371/journal.pbio.3001897] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 10/31/2022] [Indexed: 12/04/2022] Open
Abstract
Due to different nucleotide preferences at target sites, no single Cas9 is capable of editing all sequences. Thus, this highlights the need to establish a Cas9 repertoire covering all sequences for efficient genome editing. Cas9s with simple protospacer adjacent motif (PAM) requirements are particularly attractive to allow for a wide range of genome editing, but identification of such Cas9s from thousands of Cas9s in the public database is a challenge. We previously identified PAMs for 16 SaCas9 orthologs. Here, we compared the PAM-interacting (PI) domains in these orthologs and found that the serine residue corresponding to SaCas9 N986 was associated with the simple NNGG PAM requirement. Based on this discovery, we identified five additional SaCas9 orthologs that recognize the NNGG PAM. We further identified three amino acids that determined the NNGG PAM requirement of SaCas9. Finally, we engineered Sha2Cas9 and SpeCas9 to generate high-fidelity versions of Cas9s. Importantly, these natural and engineered Cas9s displayed high activities and distinct nucleotide preferences. Our study offers a new perspective to identify SaCas9 orthologs with NNGG PAM requirements, expanding the Cas9 repertoire.
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Affiliation(s)
- Shuai Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chen Tao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Huilin Mao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Linghui Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yao Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tao Qi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuan Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sang-Ging Ong
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, Illinois, United States of America
- Division of Cardiology, Department of Medicine, University of Illinois College of Medicine, Chicago, Illinois, United States of America
| | - Shijun Hu
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, China
- * E-mail: (SH); (RC); (YW)
| | - Renjie Chai
- State Key Laboratory of Bioelectronics, Department of Otolaryngology Head and Neck Surgery, Zhongda Hospital, School of Life Sciences and Technology, Advanced Institute for Life and Health, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, China
- Co-Innovation Center of Neuroregeneration, Nantong University, Nantong, China
- Department of Otolaryngology Head and Neck Surgery, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- * E-mail: (SH); (RC); (YW)
| | - Yongming Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
- * E-mail: (SH); (RC); (YW)
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7
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Wei J, Hou L, Liu J, Wang Z, Gao S, Qi T, Gao S, Sun S, Wang Y. Closely related type II-C Cas9 orthologs recognize diverse PAMs. eLife 2022; 11:77825. [PMID: 35959889 PMCID: PMC9433092 DOI: 10.7554/elife.77825] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
The RNA-guided CRISPR/Cas9 system is a powerful tool for genome editing, but its targeting scope is limited by the protospacer-adjacent motif (PAM). To expand the target scope, it is crucial to develop a CRISPR toolbox capable of recognizing multiple PAMs. Here, using a GFP-activation assay, we tested the activities of 29 type II-C orthologs closely related to Nme1Cas9, 25 of which are active in human cells. These orthologs recognize diverse PAMs with variable length and nucleotide preference, including purine-rich, pyrimidine-rich, and mixed purine and pyrimidine PAMs. We characterized in depth the activity and specificity of Nsp2Cas9. We also generated a chimeric Cas9 nuclease that recognizes a simple N4C PAM, representing the most relaxed PAM preference for compact Cas9s to date. These Cas9 nucleases significantly enhance our ability to perform allele-specific genome editing.
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Affiliation(s)
- Jingjing Wei
- State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Linghui Hou
- State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Jingtong Liu
- State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Ziwen Wang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Siqi Gao
- State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Tao Qi
- State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Song Gao
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shuna Sun
- National Children's Medical Center, Children's Hospital of Fudan University, Shanghai, China
| | - Yongming Wang
- State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
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8
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Wang S, Mao H, Hou L, Hu Z, Wang Y, Qi T, Tao C, Yang Y, Zhang C, Li M, Liu H, Hu S, Chai R, Wang Y. Compact SchCas9 Recognizes the Simple NNGR PAM. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104789. [PMID: 34874112 PMCID: PMC8811835 DOI: 10.1002/advs.202104789] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/11/2021] [Indexed: 05/20/2023]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)/SaCas9 is the most popular tool for in vivo genome editing due to its high efficiency and small genome. The authors previously developed four SaCas9 orthologs as genome-editing tools. Here, to expand the targeting scope, they investigate the diversity of protospacer adjacent motifs (PAMs) by screening a list of 16 SaCas9 orthologs, twelve of which display editing activity in mammalian cells. They recognize five types of PAMs: NNGRRT, NNGRRR, NNGRC, NNGA, and NNGR. Importantly, SchCas9 recognizes the simple NNGR PAM, representing the most relaxed PAM preference of compact Cas9s to date. It is further demonstrated that SchCas9 enables efficient genome editing in multiple human cell lines. Altogether, these compact Cas9 tools offer a new option for both basic research and clinical applications.
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Affiliation(s)
- Shuai Wang
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesZhongshan HospitalFudan UniversityShanghai200438China
| | - Huilin Mao
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesZhongshan HospitalFudan UniversityShanghai200438China
| | - Linghui Hou
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesZhongshan HospitalFudan UniversityShanghai200438China
| | - Ziying Hu
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesZhongshan HospitalFudan UniversityShanghai200438China
| | - Yao Wang
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesZhongshan HospitalFudan UniversityShanghai200438China
| | - Tao Qi
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesZhongshan HospitalFudan UniversityShanghai200438China
| | - Chen Tao
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesZhongshan HospitalFudan UniversityShanghai200438China
| | - Yuan Yang
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesZhongshan HospitalFudan UniversityShanghai200438China
| | - Chengdong Zhang
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesZhongshan HospitalFudan UniversityShanghai200438China
| | - Miaomiao Li
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesZhongshan HospitalFudan UniversityShanghai200438China
| | - Huihui Liu
- Experimental Center of Forestry in North ChinaChinese Academy of ForestryBeijing102300China
| | - Shijun Hu
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular ScienceCollaborative Innovation Center of HematologyState Key Laboratory of Radiation Medicine and ProtectionMedical CollegeSoochow UniversitySuzhou215000China
| | - Renjie Chai
- State Key Laboratory of BioelectronicsSchool of Life Sciences and TechnologyJiangsu Province High‐Tech Key Laboratory for Bio‐Medical ResearchSoutheast UniversityNanjing210096China
- Co‐Innovation Center of NeuroregenerationNantong UniversityNantong226001China
| | - Yongming Wang
- State Key Laboratory of Genetic EngineeringSchool of Life SciencesZhongshan HospitalFudan UniversityShanghai200438China
- Shanghai Engineering Research Center of Industrial MicroorganismsShanghai200438China
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9
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Hu Z, Zhang C, Wang D, Gao S, Ong SG, Wang Y, Zheng WV. A Highly Sensitive GFP Activation Assay for Detection of DNA Cleavage in Cells. Front Cell Dev Biol 2021; 9:771248. [PMID: 34869366 PMCID: PMC8636026 DOI: 10.3389/fcell.2021.771248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/21/2021] [Indexed: 12/02/2022] Open
Abstract
CRISPR/Cas9 nucleases hold great potential for gene therapy, but they frequently induce unwanted off-target cleavage. We previously developed a GFP activation assay for detection of DNA cleavage in cells. Here, we demonstrate two novel applications of this assay. First, we use this assay to confirm off-target cleavage that cannot be detected by targeted deep sequencing in cells before. Second, we use this approach to detect multiple alternative PAMs recognized by SpCas9. These noncanonical PAMs are associated with low cleavage activity, but targets associated with these PAMs must be considered as potential off-target sites. Taken together, the GFP activation assay is a powerful platform for DNA cleavage detection in cells.
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Affiliation(s)
- Ziying Hu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China.,Centre for Assisted Reproduction, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chengdong Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Daqi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Siqi Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Sang-Ging Ong
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL, United States.,Division of Cardiology, Department of Medicine, University of Illinois College of Medicine, Chicago, IL, United States
| | - Yongming Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Wei V Zheng
- Intervention and Cell Therapy Center, Peking University Shenzhen Hospital, Shenzhen, China
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10
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Gao N, Zhang C, Hu Z, Li M, Wei J, Wang Y, Liu H. Characterization of Brevibacillus laterosporus Cas9 (BlatCas9) for Mammalian Genome Editing. Front Cell Dev Biol 2020; 8:583164. [PMID: 33195228 PMCID: PMC7604293 DOI: 10.3389/fcell.2020.583164] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/24/2020] [Indexed: 11/30/2022] Open
Abstract
Compact CRISPR/Cas9 systems that can be delivered by AAV for in vivo genome editing hold great promise for clinical applications. Brevibacillus laterosporus Cas9 (BlatCas9) is a compact Cas9 nuclease that has been identified for plant genome editing. Here, we characterize BlatCas9 as an alternative tool for mammalian genome editing. We demonstrate that BlatCas9 prefers a N4CNAA protospacer adjacent motif (PAM), but N4C PAM is also editable in mammalian cells. We next demonstrate that BlatCas9 enables genome editing in a variety of cell types. Furthermore, BlatCas9 can be packaged into AAV for genome editing. Finally, we characterize the specificity of BlatCas9. In summary, BlatCas9 offers an alternative tool for both basic research and clinical applications.
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Affiliation(s)
- Ning Gao
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, China.,State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Chengdong Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Ziying Hu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Miaomiao Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Jingjing Wei
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Yongming Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
| | - Huihui Liu
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, China
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11
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Qi T, Wu F, Xie Y, Gao S, Li M, Pu J, Li D, Lan F, Wang Y. Base Editing Mediated Generation of Point Mutations Into Human Pluripotent Stem Cells for Modeling Disease. Front Cell Dev Biol 2020. [PMID: 33102492 DOI: 10.3389/fcell.2020.590581.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are a powerful platform for disease modeling and drug discovery. However, the introduction of known pathogenic mutations into hPSCs is a time-consuming and labor-intensive process. Base editing is a newly developed technology that enables facile introduction of point mutations into specific loci within the genome of living cells. Here, we design an all-in-one episomal vector that expresses a single guide RNA (sgRNA) with an adenine base editor (ABE) or a cytosine base editor (CBE). Both ABE and CBE can efficiently introduce mutations into cells, A-to-G and C-to-T, respectively. We introduce disease-specific mutations of long QT syndrome into hPSCs to model LQT1, LQT2, and LQT3. Electrophysiological analysis of hPSC-derived cardiomyocytes (hPSC-CMs) using multi-electrode arrays (MEAs) reveals that edited hPSC-CMs display significant increases in duration of the action potential. Finally, we introduce the novel Brugada syndrome-associated mutation into hPSCs, demonstrating that this mutation can cause abnormal electrophysiology. Our study demonstrates that episomal encoded base editors (epi-BEs) can efficiently generate mutation-specific disease hPSC models.
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Affiliation(s)
- Tao Qi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fujian Wu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuquan Xie
- Department of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Siqi Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Miaomiao Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jun Pu
- Department of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Feng Lan
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongming Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
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12
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Qi T, Wu F, Xie Y, Gao S, Li M, Pu J, Li D, Lan F, Wang Y. Base Editing Mediated Generation of Point Mutations Into Human Pluripotent Stem Cells for Modeling Disease. Front Cell Dev Biol 2020; 8:590581. [PMID: 33102492 PMCID: PMC7546412 DOI: 10.3389/fcell.2020.590581] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) are a powerful platform for disease modeling and drug discovery. However, the introduction of known pathogenic mutations into hPSCs is a time-consuming and labor-intensive process. Base editing is a newly developed technology that enables facile introduction of point mutations into specific loci within the genome of living cells. Here, we design an all-in-one episomal vector that expresses a single guide RNA (sgRNA) with an adenine base editor (ABE) or a cytosine base editor (CBE). Both ABE and CBE can efficiently introduce mutations into cells, A-to-G and C-to-T, respectively. We introduce disease-specific mutations of long QT syndrome into hPSCs to model LQT1, LQT2, and LQT3. Electrophysiological analysis of hPSC-derived cardiomyocytes (hPSC-CMs) using multi-electrode arrays (MEAs) reveals that edited hPSC-CMs display significant increases in duration of the action potential. Finally, we introduce the novel Brugada syndrome-associated mutation into hPSCs, demonstrating that this mutation can cause abnormal electrophysiology. Our study demonstrates that episomal encoded base editors (epi-BEs) can efficiently generate mutation-specific disease hPSC models.
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Affiliation(s)
- Tao Qi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fujian Wu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuquan Xie
- Department of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Siqi Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Miaomiao Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jun Pu
- Department of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Feng Lan
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongming Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China.,Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
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13
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Hu Z, Wang S, Zhang C, Gao N, Li M, Wang D, Wang D, Liu D, Liu H, Ong SG, Wang H, Wang Y. A compact Cas9 ortholog from Staphylococcus Auricularis (SauriCas9) expands the DNA targeting scope. PLoS Biol 2020; 18:e3000686. [PMID: 32226015 PMCID: PMC7145270 DOI: 10.1371/journal.pbio.3000686] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 04/09/2020] [Accepted: 03/12/2020] [Indexed: 11/19/2022] Open
Abstract
Compact CRISPR/Cas9 systems that can be packaged into an adeno-associated virus (AAV) hold great promise for gene therapy. Unfortunately, currently available small Cas9 nucleases either display low activity or require a long protospacer adjacent motif (PAM) sequence, limiting their extensive applications. Here, we screened a panel of Cas9 nucleases and identified a small Cas9 ortholog from Staphylococcus auricularis (SauriCas9), which recognizes a simple NNGG PAM, displays high activity for genome editing, and is compact enough to be packaged into an AAV for genome editing. Moreover, the conversion of adenine and cytosine bases can be achieved by fusing SauriCas9 to the cytidine and adenine deaminase. Therefore, SauriCas9 holds great potential for both basic research and clinical applications.
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Affiliation(s)
- Ziying Hu
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shuai Wang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chengdong Zhang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ning Gao
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Miaomiao Li
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Deqian Wang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Daqi Wang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dong Liu
- School of Life Sciences, Co-innovation Center of Neuroregeneration, Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, China
| | - Huihui Liu
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, China
| | - Sang-Ging Ong
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, Illinois, United States of America
- Division of Cardiology, Department of Medicine, University of Illinois College of Medicine, Chicago, Illinois, United States of America
| | - Hongyan Wang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yongming Wang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- School of Life Sciences, Co-innovation Center of Neuroregeneration, Jiangsu Key Laboratory of Neuroregeneration, Nantong University, Nantong, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, China
- * E-mail:
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14
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Sarsaiya S, Shi J, Chen J. Bioengineering tools for the production of pharmaceuticals: current perspective and future outlook. Bioengineered 2019; 10:469-492. [PMID: 31656120 PMCID: PMC6844412 DOI: 10.1080/21655979.2019.1682108] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/08/2019] [Accepted: 10/11/2019] [Indexed: 01/18/2023] Open
Abstract
The bioengineering tools have significant advantages through less time-consuming and utilized as a promising stage for the production of pharmaceutical bioproducts under the single platform. This review highlighted the advantages and current improvement in the plant, animal and microbial bioengineering tools and outlines feasible approaches by biological and process's bioengineering levels for advancing the economic feasibility of pharmaceutical's production. The critical analysis results revealed that system biology and synthetic biology along with advanced bioengineering tools like transcriptome, proteome, metabolome and nano bioengineering tools have shown a promising impact on the development of pharmaceutical's bioproducts. Tools to overcome and resolve the accompanying encounters of pharmaceutical's production that include nano bioengineering tools are also discussed. As a summary and prospect, it also gives new insight into the challenges and possible breakthrough of the development of pharmaceutical's bioproducts through bioengineering tools.
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Affiliation(s)
- Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, China
| | - Jingshan Shi
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Jishuang Chen
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
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15
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Rakow S, Pullamsetti SS, Bauer UM, Bouchard C. Assaying epigenome functions of PRMTs and their substrates. Methods 2019; 175:53-65. [PMID: 31542509 DOI: 10.1016/j.ymeth.2019.09.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/09/2019] [Accepted: 09/16/2019] [Indexed: 12/20/2022] Open
Abstract
Among the widespread and increasing number of identified post-translational modifications (PTMs), arginine methylation is catalyzed by the protein arginine methyltransferases (PRMTs) and regulates fundamental processes in cells, such as gene regulation, RNA processing, translation, and signal transduction. As epigenetic regulators, PRMTs play key roles in pluripotency, differentiation, proliferation, survival, and apoptosis, which are essential biological programs leading to development, adult homeostasis but also pathological conditions including cancer. A full understanding of the molecular mechanisms that underlie PRMT-mediated gene regulation requires the genome wide mapping of each player, i.e., PRMTs, their substrates and epigenetic marks, methyl-marks readers as well as interaction partners, in a thorough and unambiguous manner. However, despite the tremendous advances in high throughput sequencing technologies and the numerous efforts from the scientific community, the epigenomic profiling of PRMTs as well as their histone and non-histone substrates still remains a big challenge owing to obvious limitations in tools and methodologies. This review will summarize the present knowledge about the genome wide mapping of PRMTs and their substrates as well as the technical approaches currently in use. The limitations and pitfalls of the technical tools along with conventional approaches will be then discussed in detail. Finally, potential new strategies for chromatin profiling of PRMTs and histone substrates will be proposed and described.
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Affiliation(s)
- Sinja Rakow
- Institute for Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Hans-Meerwein-Str. 2, BMFZ, 35043 Marburg, Germany
| | - Soni Savai Pullamsetti
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Uta-Maria Bauer
- Institute for Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Hans-Meerwein-Str. 2, BMFZ, 35043 Marburg, Germany
| | - Caroline Bouchard
- Institute for Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Hans-Meerwein-Str. 2, BMFZ, 35043 Marburg, Germany.
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