1
|
Mathuria A, Vora C, Ali N, Mani I. Advances in CRISPR-Cas systems for human bacterial disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 208:19-41. [PMID: 39266183 DOI: 10.1016/bs.pmbts.2024.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2024]
Abstract
Prokaryotic adaptive immune systems called CRISPR-Cas systems have transformed genome editing by allowing for precise genetic alterations through targeted DNA cleavage. This system comprises CRISPR-associated genes and repeat-spacer arrays, which generate RNA molecules that guide the cleavage of invading genetic material. CRISPR-Cas is classified into Class 1 (multi-subunit effectors) and Class 2 (single multi-domain effectors). Its applications span combating antimicrobial resistance (AMR), targeting antibiotic resistance genes (ARGs), resensitizing bacteria to antibiotics, and preventing horizontal gene transfer (HGT). CRISPR-Cas3, for example, effectively degrades plasmids carrying resistance genes, providing a precise method to disarm bacteria. In the context of ESKAPE pathogens, CRISPR technology can resensitize bacteria to antibiotics by targeting specific resistance genes. Furthermore, in tuberculosis (TB) research, CRISPR-based tools enhance diagnostic accuracy and facilitate precise genetic modifications for studying Mycobacterium tuberculosis. CRISPR-based diagnostics, leveraging Cas endonucleases' collateral cleavage activity, offer highly sensitive pathogen detection. These advancements underscore CRISPR's transformative potential in addressing AMR and enhancing infectious disease management.
Collapse
Affiliation(s)
- Anshu Mathuria
- Department of Biochemistry, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Chaitali Vora
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
| | - Namra Ali
- Department of Microbiology, Gargi College, University of Delhi, New Delhi, India
| | - Indra Mani
- Department of Microbiology, Gargi College, University of Delhi, New Delhi, India.
| |
Collapse
|
2
|
Allemailem KS, Almatroudi A, Rahmani AH, Alrumaihi F, Alradhi AE, Alsubaiyel AM, Algahtani M, Almousa RM, Mahzari A, Sindi AAA, Dobie G, Khan AA. Recent Updates of the CRISPR/Cas9 Genome Editing System: Novel Approaches to Regulate Its Spatiotemporal Control by Genetic and Physicochemical Strategies. Int J Nanomedicine 2024; 19:5335-5363. [PMID: 38859956 PMCID: PMC11164216 DOI: 10.2147/ijn.s455574] [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: 12/29/2023] [Accepted: 05/30/2024] [Indexed: 06/12/2024] Open
Abstract
The genome editing approach by clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (CRISPR/Cas9) is a revolutionary advancement in genetic engineering. Owing to its simple design and powerful genome-editing capability, it offers a promising strategy for the treatment of different infectious, metabolic, and genetic diseases. The crystal structure of Streptococcus pyogenes Cas9 (SpCas9) in complex with sgRNA and its target DNA at 2.5 Å resolution reveals a groove accommodating sgRNA:DNA heteroduplex within a bilobate architecture with target recognition (REC) and nuclease (NUC) domains. The presence of a PAM is significantly required for target recognition, R-loop formation, and strand scission. Recently, the spatiotemporal control of CRISPR/Cas9 genome editing has been considerably improved by genetic, chemical, and physical regulatory strategies. The use of genetic modifiers anti-CRISPR proteins, cell-specific promoters, and histone acetyl transferases has uplifted the application of CRISPR/Cas9 as a future-generation genome editing tool. In addition, interventions by chemical control, small-molecule activators, oligonucleotide conjugates and bioresponsive delivery carriers have improved its application in other areas of biological fields. Furthermore, the intermediation of physical control by using heat-, light-, magnetism-, and ultrasound-responsive elements attached to this molecular tool has revolutionized genome editing further. These strategies significantly reduce CRISPR/Cas9's undesirable off-target effects. However, other undesirable effects still offer some challenges for comprehensive clinical translation using this genome-editing approach. In this review, we summarize recent advances in CRISPR/Cas9 structure, mechanistic action, and the role of small-molecule activators, inhibitors, promoters, and physical approaches. Finally, off-target measurement approaches, challenges, future prospects, and clinical applications are discussed.
Collapse
Affiliation(s)
- Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Arwa Essa Alradhi
- General Administration for Infectious Disease Control, Ministry of Health, Riyadh 12382, Saudi Arabia
| | - Amal M Alsubaiyel
- Department of Pharmaceutics, College of Pharmacy, Qassim University, Buraydah 51452, Saudi Arabia
| | - Mohammad Algahtani
- Department of Laboratory & Blood Bank, Security Forces Hospital, Mecca 21955, Saudi Arabia
| | - Rand Mohammad Almousa
- Department of Education, General Directorate of Education, Qassim 52361, Saudi Arabia
| | - Ali Mahzari
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha 65527, Saudi Arabia
| | - Abdulmajeed A A Sindi
- Department of Basic Medical Sciences, Faculty of Applied Medical Sciences, Al-Baha University, Al-Baha 65527, Saudi Arabia
| | - Gasim Dobie
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Jazan University, Gizan 82911, Saudi Arabia
| | - Amjad Ali Khan
- Department of Basic Health Sciences, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| |
Collapse
|
3
|
Vora DS, Bhandari SM, Sundar D. DNA shape features improve prediction of CRISPR/Cas9 activity. Methods 2024; 226:120-126. [PMID: 38641083 DOI: 10.1016/j.ymeth.2024.04.012] [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: 11/02/2023] [Revised: 03/27/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024] Open
Abstract
The CRISPR/Cas9 genome editing technology has transformed basic and translational research in biology and medicine. However, the advances are hindered by off-target effects and a paucity in the knowledge of the mechanism of the Cas9 protein. Machine learning models have been proposed for the prediction of Cas9 activity at unintended sites, yet feature engineering plays a major role in the outcome of the predictors. This study evaluates the improvement in the performance of similar predictors upon inclusion of epigenetic and DNA shape feature groups in the conventionally used sequence-based Cas9 target and off-target datasets. The approach involved the utilization of neural networks trained on a diverse range of parameters, allowing us to systematically assess the performance increase for the meticulously designed datasets- (i) sequence only, (ii) sequence and epigenetic features, and (iii) sequence, epigenetic and DNA shape feature datasets. The addition of DNA shape information significantly improved predictive performance, evaluated by Akaike and Bayesian information criteria. The evaluation of individual feature importance by permutation and LIME-based methods also indicates that not only sequence features like mismatches and nucleotide composition, but also base pairing parameters like opening and stretch, that are indicative of distortion in the DNA-RNA hybrid in the presence of mismatches, influence model outcomes.
Collapse
Affiliation(s)
- Dhvani Sandip Vora
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India.
| | - Sakshi Manoj Bhandari
- Department of Mathematics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi 110016, India; School of Artificial Intelligence, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
| |
Collapse
|
4
|
Li M, Chen F, Yang Q, Tang Q, Xiao Z, Tong X, Zhang Y, Lei L, Li S. Biomaterial-Based CRISPR/Cas9 Delivery Systems for Tumor Treatment. Biomater Res 2024; 28:0023. [PMID: 38694229 PMCID: PMC11062511 DOI: 10.34133/bmr.0023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 03/25/2024] [Indexed: 05/04/2024] Open
Abstract
CRISPR/Cas9 gene editing technology is characterized by high specificity and efficiency, and has been applied to the treatment of human diseases, especially tumors involving multiple genetic modifications. However, the clinical application of CRISPR/Cas9 still faces some major challenges, the most urgent of which is the development of optimized delivery vectors. Biomaterials are currently the best choice for use in CRISPR/Cas9 delivery vectors owing to their tunability, biocompatibility, and efficiency. As research on biomaterial vectors continues to progress, hope for the application of the CRISPR/Cas9 system for clinical oncology therapy builds. In this review, we first detail the CRISPR/Cas9 system and its potential applications in tumor therapy. Then, we introduce the different delivery forms and compare the physical, viral, and non-viral vectors. In addition, we analyze the characteristics of different types of biomaterial vectors. We further review recent research progress in the use of biomaterials as vectors for CRISPR/Cas9 delivery to treat specific tumors. Finally, we summarize the shortcomings and prospects of biomaterial-based CRISPR/Cas9 delivery systems.
Collapse
Affiliation(s)
- Mengmeng Li
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya Hospital,
Central South University, Changsha 410011, Hunan, China
| | - Fenglei Chen
- College of Veterinary Medicine, Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses,
Yangzhou University, Yangzhou 225009, China
| | - Qian Yang
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya Hospital,
Central South University, Changsha 410011, Hunan, China
| | - Qinglai Tang
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya Hospital,
Central South University, Changsha 410011, Hunan, China
| | - Zian Xiao
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya Hospital,
Central South University, Changsha 410011, Hunan, China
| | - Xinying Tong
- Department of Hemodialysis, the Second Xiangya Hospital,
Central South University, Changsha 410011, Hunan, China
| | - Ying Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya Hospital,
Central South University, Changsha 410011, Hunan, China
| | - Lanjie Lei
- Institute of Translational Medicine,
Zhejiang Shuren University, Hangzhou 310015, Zhejiang, China
| | - Shisheng Li
- Department of Otorhinolaryngology Head and Neck Surgery, the Second Xiangya Hospital,
Central South University, Changsha 410011, Hunan, China
| |
Collapse
|
5
|
Saad FA, Saad JF, Siciliano G, Merlini L, Angelini C. Duchenne Muscular Dystrophy Gene Therapy. Curr Gene Ther 2024; 24:17-28. [PMID: 36411557 DOI: 10.2174/1566523223666221118160932] [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: 05/05/2022] [Revised: 09/27/2022] [Accepted: 10/11/2022] [Indexed: 11/23/2022]
Abstract
Duchenne and Becker muscular dystrophies are allelic X-linked recessive neuromuscular diseases affecting both skeletal and cardiac muscles. Therefore, owing to their single X chromosome, the affected boys receive pathogenic gene mutations from their unknowing carrier mothers. Current pharmacological drugs are palliative that address the symptoms of the disease rather than the genetic cause imbedded in the Dystrophin gene DNA sequence. Therefore, alternative therapies like gene drugs that could address the genetic cause of the disease at its root are crucial, which include gene transfer/implantation, exon skipping, and gene editing. Presently, it is possible through genetic reprogramming to engineer AAV vectors to deliver certain therapeutic cargos specifically to muscle or other organs regardless of their serotype. Similarly, it is possible to direct the biogenesis of exosomes to carry gene editing constituents or certain therapeutic cargos to specific tissue or cell type like brain and muscle. While autologous exosomes are immunologically inert, it is possible to camouflage AAV capsids, and lipid nanoparticles to evade the immune system recognition. In this review, we highlight current opportunities for Duchenne muscular dystrophy gene therapy, which has been known thus far as an incurable genetic disease. This article is a part of Gene Therapy of Rare Genetic Diseases thematic issue.
Collapse
Affiliation(s)
- Fawzy A Saad
- Department of Biology, Padua University School of Medicine, Via Trieste 75, Padova 35121, Italy
- Department of Gene Therapy, Saad Pharmaceuticals, Tornimäe 7-26, Tallinn, 10145, Estonia
| | - Jasen F Saad
- Department of Gene Therapy, Saad Pharmaceuticals, Tornimäe 7-26, Tallinn, 10145, Estonia
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, Pisa University School of Medicine, Pisa, Italy
| | - Luciano Merlini
- Department of Biomedical and Neuromotor Sciences, Bologna University School of Medicine, 40126 Bologna, Italy
| | - Corrado Angelini
- Department Neurosciences, Padova University School of Medicine, Padova, Italy
| |
Collapse
|
6
|
Yagci ZB, Kelkar GR, Johnson TJ, Sen D, Keung AJ. Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities. Methods Mol Biol 2024; 2842:23-55. [PMID: 39012589 DOI: 10.1007/978-1-0716-4051-7_2] [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] [Indexed: 07/17/2024]
Abstract
The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors (EEs) enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus-specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here, we present and discuss important design considerations and challenges regarding the biochemical and locus specificities of epigenome editors. These include how to: account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus-specificity by considering concentration, affinity, avidity, and sequestration effects.
Collapse
Affiliation(s)
- Z Begum Yagci
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Gautami R Kelkar
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Tyler J Johnson
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Dilara Sen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
| |
Collapse
|
7
|
Nayak V, Patra S, Singh KR, Ganguly B, Kumar DN, Panda D, Maurya GK, Singh J, Majhi S, Sharma R, Pandey SS, Singh RP, Kerry RG. Advancement in precision diagnosis and therapeutic for triple-negative breast cancer: Harnessing diagnostic potential of CRISPR-cas & engineered CAR T-cells mediated therapeutics. ENVIRONMENTAL RESEARCH 2023; 235:116573. [PMID: 37437865 DOI: 10.1016/j.envres.2023.116573] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/14/2023]
Abstract
Cancer is characterized by uncontrolled cell growth, disrupted regulatory pathways, and the accumulation of genetic mutations. These mutations across different types of cancer lead to disruptions in signaling pathways and alterations in protein expression related to cellular growth and proliferation. This review highlights the AKT signaling cascade and the retinoblastoma protein (pRb) regulating cascade as promising for novel nanotheranostic interventions. Through synergizing state-of-the-art gene editing tools like the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas system with nanomaterials and targeting AKT, there is potential to enhance cancer diagnostics significantly. Furthermore, the integration of modified CAR-T cells into multifunctional nanodelivery systems offers a promising approach for targeted cancer inhibition, including the eradication of cancer stem cells (CSCs). Within the context of highly aggressive and metastatic Triple-negative Breast Cancer (TNBC), this review specifically focuses on devising innovative nanotheranostics. For both pre-clinical and post-clinical TNBC detection, the utilization of the CRISPR-Cas system, guided by RNA (gRNA) and coupled with a fluorescent reporter specifically designed to detect TNBC's mutated sequence, could be promising. Additionally, a cutting-edge approach involving the engineering of TNBC-specific iCAR and syn-Notch CAR T-cells, combined with the co-delivery of a hybrid polymeric nano-liposome encapsulating a conditionally replicative adenoviral vector (CRAdV) against CSCs, could present an intriguing intervention strategy. This review thus paves the way for exciting advancements in the field of nanotheranostics for the treatment of TNBC and beyond.
Collapse
Affiliation(s)
- Vinayak Nayak
- Indian Council of Agricultural Research- National Institute on Foot and Mouth Disease- International Center for Foot and Mouth Disease, Bhubaneswar, Odisha, India
| | - Sushmita Patra
- Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Navi-Mumbai 410210, India
| | - Kshitij Rb Singh
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu, Kitakyushu, Japan.
| | - Bristy Ganguly
- Fish Health Management Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha, India
| | - Das Nishant Kumar
- PG Department of Biotechnology, Utkal University, Bhubaneswar, Odisha, India
| | - Deepak Panda
- PG Department of Biotechnology, Utkal University, Bhubaneswar, Odisha, India
| | - Ganesh Kumar Maurya
- Zoology Section, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Jay Singh
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Sanatan Majhi
- PG Department of Biotechnology, Utkal University, Bhubaneswar, Odisha, India
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Shyam S Pandey
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu, Kitakyushu, Japan.
| | - Ravindra Pratap Singh
- Department of Biotechnology, Indira Gandhi National Tribal University, Amarkantak, Madhya Pradesh, India.
| | - Rout George Kerry
- PG Department of Biotechnology, Utkal University, Bhubaneswar, Odisha, India.
| |
Collapse
|
8
|
Ludwik KA, Telugu N, Schommer S, Stachelscheid H, Diecke S. ASSURED-optimized CRISPR protocol for knockout/SNP knockin in hiPSCs. STAR Protoc 2023; 4:102406. [PMID: 37481731 PMCID: PMC10382939 DOI: 10.1016/j.xpro.2023.102406] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/21/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
CRISPR-Cas9 technology coupled with human induced pluripotent stem cells allows precise disease modeling in pluripotent cells and subsequently derived specialized cell types. Here, we present an optimized CRISPR-Cas9 pipeline, ASSURED (affordable, successful, specific, user-friendly, rapid, efficient, and deliverable), to produce gene-modified single-cell-derived knockout or single-nucleotide-polymorphism-modified knockin hiPSCs clones. We describe steps for analyzing targeted genomic sequence and designing guide RNAs and homology repair template. We then detail the CRISPR-Cas9 delivery workflow, evaluation of editing efficiency, and automated cell isolation followed by clone screening.
Collapse
Affiliation(s)
- Katarzyna A Ludwik
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Unit Pluripotent Stem Cells & Organoids, 13353 Berlin, Germany
| | - Narasimha Telugu
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Sandra Schommer
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Harald Stachelscheid
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Unit Pluripotent Stem Cells & Organoids, 13353 Berlin, Germany.
| | - Sebastian Diecke
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research) (partner site), Berlin, Germany.
| |
Collapse
|
9
|
Guo C, Ma X, Gao F, Guo Y. Off-target effects in CRISPR/Cas9 gene editing. Front Bioeng Biotechnol 2023; 11:1143157. [PMID: 36970624 PMCID: PMC10034092 DOI: 10.3389/fbioe.2023.1143157] [Citation(s) in RCA: 76] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
Gene editing stands for the methods to precisely make changes to a specific nucleic acid sequence. With the recent development of the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, gene editing has become efficient, convenient and programmable, leading to promising translational studies and clinical trials for both genetic and non-genetic diseases. A major concern in the applications of the CRISPR/Cas9 system is about its off-target effects, namely the deposition of unexpected, unwanted, or even adverse alterations to the genome. To date, many methods have been developed to nominate or detect the off-target sites of CRISPR/Cas9, which laid the basis for the successful upgrades of CRISPR/Cas9 derivatives with enhanced precision. In this review, we summarize these technological advancements and discuss about the current challenges in the management of off-target effects for future gene therapy.
Collapse
Affiliation(s)
- Congting Guo
- School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Peking University Institute of Cardiovascular Sciences, Beijing, China
| | - Xiaoteng Ma
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Fei Gao
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
- *Correspondence: Fei Gao, ; Yuxuan Guo,
| | - Yuxuan Guo
- School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- Peking University Institute of Cardiovascular Sciences, Beijing, China
- Ministry of Education Key Laboratory of Molecular Cardiovascular Science, Beijing, China
- Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
- *Correspondence: Fei Gao, ; Yuxuan Guo,
| |
Collapse
|
10
|
Hwang S, Maxwell KL. Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type II Anti-CRISPR Proteins. J Mol Biol 2023; 435:168041. [PMID: 36893938 DOI: 10.1016/j.jmb.2023.168041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 03/09/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated proteins) systems provide bacteria and archaea with an adaptive immune response against invasion by mobile genetic elements like phages, plasmids, and transposons. These systems have been repurposed as very powerful biotechnological tools for gene editing applications in both bacterial and eukaryotic systems. The discovery of natural off-switches for CRISPR-Cas systems, known as anti-CRISPR proteins, provided a mechanism for controlling CRISPR-Cas activity and opened avenues for the development of more precise editing tools. In this review, we focus on the inhibitory mechanisms of anti-CRISPRs that are active against type II CRISPR-Cas systems and briefly discuss their biotechnological applications.
Collapse
Affiliation(s)
- Sungwon Hwang
- Department of Biochemistry. University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON M5G 1M1, Canada. https://twitter.com/s1hwang_21
| | - Karen L Maxwell
- Department of Biochemistry. University of Toronto, 661 University Avenue, Suite 1600, Toronto, ON M5G 1M1, Canada.
| |
Collapse
|
11
|
Hu LF, Li YX, Wang JZ, Zhao YT, Wang Y. Controlling CRISPR-Cas9 by guide RNA engineering. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1731. [PMID: 35393779 DOI: 10.1002/wrna.1731] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/15/2022] [Indexed: 01/31/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system is a product of million years of evolution by microbes to fight against invading genetic materials. Around 10 years ago, scientists started to repurpose the CRISPR as genetic tools by molecular engineering approaches. The guide RNA provides a versatile and unique platform for the innovation to improve and expand the application of CRISPR-Cas9 system. In this review, we will first introduce the basic sequence and structure of guide RNA and its role during the function of CRISPR-Cas9. We will then summarize recent progress on the development of various guide RNA engineering strategies. These strategies have been dedicated to improve the performance of CRISPR-Cas9, to achieve precise spatiotemporal control of CRISPR-Cas9, and to broaden the application of CRISPR-Cas9. Finally, we will briefly discuss the uniqueness and advantage of guide RNA-engineering based systems versus those with engineered Cas9 proteins and speculate potential future directions in guide RNA engineering. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Methods > RNA Nanotechnology Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
Collapse
Affiliation(s)
- Lu-Feng Hu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Yu-Xuan Li
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jia-Zhen Wang
- College of Life Sciences, Peking University, Beijing, China
| | - Yu-Ting Zhao
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yangming Wang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| |
Collapse
|
12
|
Reid W, Williams AE, Sanchez-Vargas I, Lin J, Juncu R, Olson KE, Franz AWE. Assessing single-locus CRISPR/Cas9-based gene drive variants in the mosquito Aedes aegypti via single-generation crosses and modeling. G3 (BETHESDA, MD.) 2022; 12:jkac280. [PMID: 36250791 PMCID: PMC9713460 DOI: 10.1093/g3journal/jkac280] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/09/2022] [Indexed: 07/29/2023]
Abstract
The yellow fever mosquito Aedes aegypti is a major vector of arthropod-borne viruses, including dengue, chikungunya, and Zika viruses. A novel approach to mitigate arboviral infections is to generate mosquitoes refractory to infection by overexpressing antiviral effector molecules. Such an approach requires a mechanism to spread these antiviral effectors through a population, for example, by using CRISPR/Cas9-based gene drive systems. Critical to the design of a single-locus autonomous gene drive is that the selected genomic locus is amenable to both gene drive and appropriate expression of the antiviral effector. In our study, we used reverse engineering to target 2 intergenic genomic loci, which had previously shown to be highly permissive for antiviral effector gene expression, and we further investigated the use of 3 promoters (nanos, β2-tubulin, or zpg) for Cas9 expression. We then quantified the accrual of insertions or deletions (indels) after single-generation crossings, measured maternal effects, and assessed fitness costs associated with various transgenic lines to model the rate of gene drive fixation. Overall, MGDrivE modeling suggested that when an autonomous gene drive is placed into an intergenic locus, the gene drive system will eventually be blocked by the accrual of gene drive blocking resistance alleles and ultimately be lost in the population. Moreover, while genomic locus and promoter selection were critically important for the initial establishment of the autonomous gene drive, it was the fitness of the gene drive line that most strongly influenced the persistence of the gene drive in the simulated population. As such, we propose that when autonomous CRISPR/Cas9-based gene drive systems are anchored in an intergenic locus, they temporarily result in a strong population replacement effect, but as gene drive-blocking indels accrue, the gene drive becomes exhausted due to the fixation of CRISPR resistance alleles.
Collapse
Affiliation(s)
- William Reid
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Adeline E Williams
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Irma Sanchez-Vargas
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Jingyi Lin
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Rucsanda Juncu
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Ken E Olson
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Alexander W E Franz
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| |
Collapse
|
13
|
Tao S, Chen H, Li N, Liang W. The Application of the CRISPR-Cas System in Antibiotic Resistance. Infect Drug Resist 2022; 15:4155-4168. [PMID: 35942309 PMCID: PMC9356603 DOI: 10.2147/idr.s370869] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/17/2022] [Indexed: 11/28/2022] Open
Abstract
The emergence and global epidemic of antimicrobial resistance (AMR) poses a serious threat to global public health in recent years. AMR genes are shared between bacterial pathogens mainly via horizontal gene transfer (HGT) on mobile genetic elements (MGEs), thereby accelerating the spread of antimicrobial resistance (AMR) and increasing the burden of drug resistance. There is an urgent need to develop new strategies to control bacterial infections and the spread of antimicrobial resistance. The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) are an RNA-guided adaptive immune system in prokaryotes that recognizes and defends against invasive genetic elements such as phages and plasmids. Because of its specifically target and cleave DNA sequences encoding antibiotic resistance genes, CRISPR/Cas system has been developed into a new gene-editing tool for the prevention and control of bacterial drug resistance. CRISPR-Cas plays a potentially important role in controlling horizontal gene transfer and limiting the spread of antibiotic resistance. In this review, we will introduce the structure and working mechanism of CRISPR-Cas systems, followed by delivery strategies, and then focus on the relationship between antimicrobial resistance and CRISPR-Cas. Moreover, the challenges and prospects of this research field are discussed, thereby providing a reference for the prevention and control of the spread of antibiotic resistance.
Collapse
Affiliation(s)
- Shuan Tao
- School of Medical, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, People’s Republic of China
- Lianyungang Clinical College of Jiangsu University, Lianyungang, Jiangsu Province, 222023, People’s Republic of China
| | - Huimin Chen
- School of Medical, Jiangsu University, Zhenjiang, Jiangsu Province, 212013, People’s Republic of China
| | - Na Li
- Bengbu Medical College, Bengbu, Anhui Province, 233030, People’s Republic of China
| | - Wei Liang
- Lianyungang Clinical College of Jiangsu University, Lianyungang, Jiangsu Province, 222023, People’s Republic of China
| |
Collapse
|
14
|
Harmsen TJW, Pritchard CEJ, Riepsaame J, van de Vrugt HJ, Huijbers IJ, Te Riele H. HideRNAs protect against CRISPR-Cas9 re-cutting after successful single base-pair gene editing. Sci Rep 2022; 12:9606. [PMID: 35688932 PMCID: PMC9187658 DOI: 10.1038/s41598-022-13688-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/26/2022] [Indexed: 12/05/2022] Open
Abstract
Promiscuous activity of the Streptococcus pyogenes DNA nuclease CRISPR-Cas9 can result in destruction of a successfully modified sequence obtained by templated repair of a Cas9-induced DNA double-strand break. To avoid re-cutting, additional target-site-disruptions (TSDs) are often introduced on top of the desired base-pair alteration in order to suppress target recognition. These TSDs may lower the efficiency of introducing the intended mutation and can cause unexpected phenotypes. Alternatively, successfully edited sites can be protected against Cas9 re-cutting activity. This method exploits the finding that Cas9 complexed to trimmed guideRNAs can still tightly bind specific genomic sequences but lacks nuclease activity. We show here that the presence of a guideRNA plus a trimmed guideRNA that matches the successfully mutated sequence, which we call hideRNA, can enhance the recovery of precise single base-pair substitution events tenfold. The benefit of hideRNAs in generating a single point mutation was demonstrated in cell lines using plasmid-based delivery of CRISPR-Cas9 components and in mouse zygotes injected with Cas9/guideRNA plus Cas9/hideRNA ribonucleoprotein complexes. However, hRNA protection sometimes failed, which likely reflects an unfavorable affinity of hRNA/Cas9 versus gRNA/Cas9 for the DNA target site. HideRNAs can easily be implemented into current gene editing protocols and facilitate the recovery of single base-pair substitution. As such, hideRNAs are of great value in gene editing experiments demanding high accuracy.
Collapse
Affiliation(s)
- Tim J W Harmsen
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Plant Sciences and Natural Products, Institute of Biology Leiden (IBL), Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Colin E J Pritchard
- Mouse Clinic for Cancer and Aging Research, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Joey Riepsaame
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, Oxford, UK
| | - Henri J van de Vrugt
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Department of Clinical Genetics, Section Oncogenetics, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands
| | - Ivo J Huijbers
- Mouse Clinic for Cancer and Aging Research, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Hein Te Riele
- Division of Tumor Biology and Immunology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
| |
Collapse
|
15
|
Antony JS, Hinz JM, Wyrick JJ. Tips, Tricks, and Potential Pitfalls of CRISPR Genome Editing in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2022; 10:924914. [PMID: 35706506 PMCID: PMC9190257 DOI: 10.3389/fbioe.2022.924914] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/16/2022] [Indexed: 12/26/2022] Open
Abstract
The versatility of clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) genome editing makes it a popular tool for many research and biotechnology applications. Recent advancements in genome editing in eukaryotic organisms, like fungi, allow for precise manipulation of genetic information and fine-tuned control of gene expression. Here, we provide an overview of CRISPR genome editing technologies in yeast, with a particular focus on Saccharomyces cerevisiae. We describe the tools and methods that have been previously developed for genome editing in Saccharomyces cerevisiae and discuss tips and experimental tricks for promoting efficient, marker-free genome editing in this model organism. These include sgRNA design and expression, multiplexing genome editing, optimizing Cas9 expression, allele-specific editing in diploid cells, and understanding the impact of chromatin on genome editing. Finally, we summarize recent studies describing the potential pitfalls of using CRISPR genome targeting in yeast, including the induction of background mutations.
Collapse
Affiliation(s)
- Jacob S. Antony
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
| | - John M. Hinz
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
- *Correspondence: John J. Wyrick,
| |
Collapse
|
16
|
enChIP-Seq Analyzer: A Software Program to Analyze and Interpret enChIP-Seq Data for the Detection of Physical Interactions between Genomic Regions. Genes (Basel) 2022; 13:genes13030472. [PMID: 35328026 PMCID: PMC8949577 DOI: 10.3390/genes13030472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 02/05/2023] Open
Abstract
Accumulating evidence suggests that the physical interactions between genomic regions play critical roles in the regulation of genome functions, such as transcription and epigenetic regulation. Various methods to detect the physical interactions between genomic regions have been developed. We recently developed a method to search for genomic regions interacting with a locus of interest in a non-biased manner that combines pull-down of the locus using engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) and next-generation sequencing (NGS) analysis (enChIP-Seq). The clustered regularly interspaced short palindromic repeats (CRISPR) system, consisting of a nuclease-dead form of Cas9 (dCas9) and a guide RNA (gRNA), or transcription activator-like (TAL) proteins, can be used for enChIP. In enChIP-Seq, it is necessary to compare multiple datasets of enChIP-Seq data to unambiguously detect specific interactions. However, it is not always easy to analyze enChIP-Seq datasets to subtract non-specific interactions or identify common interactions. To facilitate such analysis, we developed the enChIP-Seq analyzer software. It enables easy extraction of common signals as well as subtraction of non-specific signals observed in negative control samples, thereby streamlining extraction of specific enChIP-Seq signals. enChIP-Seq analyzer will help users analyze enChIP-Seq data and identify physical interactions between genomic regions.
Collapse
|
17
|
Wang X, Li X, Ma Y, He J, Liu X, Yu G, Yin H, Zhang H. Inhibition mechanisms of CRISPR-Cas9 by AcrIIA17 and AcrIIA18. Nucleic Acids Res 2022; 50:512-521. [PMID: 34893860 PMCID: PMC8754659 DOI: 10.1093/nar/gkab1197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/16/2021] [Accepted: 11/23/2021] [Indexed: 12/27/2022] Open
Abstract
Mobile genetic elements such as phages and plasmids have evolved anti-CRISPR proteins (Acrs) to suppress CRISPR-Cas adaptive immune systems. Recently, several phage and non-phage derived Acrs including AcrIIA17 and AcrIIA18 have been reported to inhibit Cas9 through modulation of sgRNA. Here, we show that AcrIIA17 and AcrIIA18 inactivate Cas9 through distinct mechanisms. AcrIIA17 inhibits Cas9 activity through interference with Cas9-sgRNA binary complex formation. In contrast, AcrIIA18 induces the truncation of sgRNA in a Cas9-dependent manner, generating a shortened sgRNA incapable of triggering Cas9 activity. The crystal structure of AcrIIA18, combined with mutagenesis studies, reveals a crucial role of the N-terminal β-hairpin in AcrIIA18 for sgRNA cleavage. The enzymatic inhibition mechanism of AcrIIA18 is different from those of the other reported type II Acrs. Our results add new insights into the mechanistic understanding of CRISPR-Cas9 inhibition by Acrs, and also provide valuable information in the designs of tools for conditional manipulation of CRISPR-Cas9.
Collapse
Affiliation(s)
- Xiaoshen Wang
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xuzichao Li
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yongjian Ma
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jiaqi He
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xiang Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Guimei Yu
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hang Yin
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Heng Zhang
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| |
Collapse
|
18
|
Pan S, Zhang H. Discovery in CRISPR-Cas9 system. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2021; 46:1392-1402. [PMID: 35232910 PMCID: PMC10930580 DOI: 10.11817/j.issn.1672-7347.2021.210169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Indexed: 06/14/2023]
Abstract
The 2020 Nobel Prize in Chemistry was awarded to the American scientist Jennifer A. Doudna and the French scientist Emmanuelle Charpentier, in recognition of their discovery in one of the greatest weapons in genetic technology: CRISPR-Cas9 gene scissors. The CRISPR-Cas system is a bacterial defense immune system against exogenous genetic material. Because the system can specifically recognize and cut DNA, this technology is widely used for precise editing of animal, plant, and microbial DNA. The discovery of CRISPR-Cas9 gene scissors enables the tedious and complicated cell gene editing work to be completed in a few weeks or even less, which has promoted the development of gene editing technology in various fields and brought revolutionary influence to the field of life sciences. At the same time, CRISPR gene editing technology has become one of the new therapies for tumors because of its large number of targets and relatively simple operation, and it also makes gene therapy possible. Although the technology still needs to solve technical problems such as off-target and promoter inefficiency, the CRISPR-Cas system will show its unique advantages in more fields with the continuous development of life science and basic medicine.
Collapse
Affiliation(s)
- Shaowei Pan
- Department of Pathophysiology, School of Basic Medical Science, Central South University, Changsha 410013, China.
| | - Huali Zhang
- Department of Pathophysiology, School of Basic Medical Science, Central South University, Changsha 410013, China.
| |
Collapse
|
19
|
Liu Y, Zhao N, Kanemaki MT, Yamamoto Y, Sadamura Y, Ito Y, Tokunaga M, Stasevich TJ, Kimura H. Visualizing looping of two endogenous genomic loci using synthetic zinc-finger proteins with anti-FLAG and anti-HA frankenbodies in living cells. Genes Cells 2021; 26:905-926. [PMID: 34465007 PMCID: PMC8893316 DOI: 10.1111/gtc.12893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 12/17/2022]
Abstract
In eukaryotic nuclei, chromatin loops mediated through cohesin are critical structures that regulate gene expression and DNA replication. Here, we demonstrate a new method to see endogenous genomic loci using synthetic zinc-finger proteins harboring repeat epitope tags (ZF probes) for signal amplification via binding of tag-specific intracellular antibodies, or frankenbodies, fused with fluorescent proteins. We achieve this in two steps: First, we develop an anti-FLAG frankenbody that can bind FLAG-tagged proteins in diverse live-cell environments. The anti-FLAG frankenbody complements the anti-HA frankenbody, enabling two-color signal amplification from FLAG- and HA-tagged proteins. Second, we develop a pair of cell-permeable ZF probes that specifically bind two endogenous chromatin loci predicted to be involved in chromatin looping. By coupling our anti-FLAG and anti-HA frankenbodies with FLAG- and HA-tagged ZF probes, we simultaneously see the dynamics of the two loci in single living cells. This shows a close association between the two loci in the majority of cells, but the loci markedly separate from the triggered degradation of the cohesin subunit RAD21. Our ability to image two endogenous genomic loci simultaneously in single living cells provides a proof of principle that ZF probes coupled with frankenbodies are useful new tools for exploring genome dynamics in multiple colors.
Collapse
Affiliation(s)
- Yang Liu
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ning Zhao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems, Mishima, Japan.,Department of Genetics, SOKENDAI, Mishima, Japan
| | - Yotaro Yamamoto
- Life Science Research Laboratories, Fujifilm Wako Pure Chemical, Amagasaki, Japan
| | - Yoshifusa Sadamura
- Life Science Research Laboratories, Fujifilm Wako Pure Chemical, Amagasaki, Japan
| | - Yuma Ito
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Makio Tokunaga
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.,Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan
| | - Hiroshi Kimura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.,Cell Biology Center and World Research Hub Initiative, Tokyo Institute of Technology, Yokohama, Japan
| |
Collapse
|
20
|
Sledzinski P, Dabrowska M, Nowaczyk M, Olejniczak M. Paving the way towards precise and safe CRISPR genome editing. Biotechnol Adv 2021; 49:107737. [PMID: 33785374 DOI: 10.1016/j.biotechadv.2021.107737] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 03/11/2021] [Accepted: 03/19/2021] [Indexed: 12/13/2022]
Abstract
As the possibilities of CRISPR-Cas9 technology have been revealed, we have entered a new era of research aimed at increasing its specificity and safety. This stage of technology development is necessary not only for its wider application in the clinic but also in basic research to better control the process of genome editing. Research during the past eight years has identified some factors influencing editing outcomes and led to the development of highly specific endonucleases, modified guide RNAs and computational tools supporting experiments. More recently, large-scale experiments revealed a previously overlooked feature: Cas9 can generate reproducible mutation patterns. As a result, it has become apparent that Cas9-induced double-strand break (DSB) repair is nonrandom and can be predicted to some extent. Here, we review the present state of knowledge regarding the specificity and safety of CRISPR-Cas9 technology to define gRNA, protein and target-related problems and solutions. These issues include sequence-specific off-target effects, immune responses, genetic variation and chromatin accessibility. We present new insights into the role of DNA repair in genome editing and define factors influencing editing outcomes. In addition, we propose practical guidelines for increasing the specificity of editing and discuss novel perspectives in improvement of this technology.
Collapse
Affiliation(s)
- Pawel Sledzinski
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland
| | - Magdalena Dabrowska
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland
| | - Mateusz Nowaczyk
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland
| | - Marta Olejniczak
- Department of Genome Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego 12/14, 61-704, Poland.
| |
Collapse
|
21
|
CRISPR/Cas Technology in Pig-to-Human Xenotransplantation Research. Int J Mol Sci 2021; 22:ijms22063196. [PMID: 33801123 PMCID: PMC8004187 DOI: 10.3390/ijms22063196] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023] Open
Abstract
CRISPR/Cas (clustered regularly interspaced short palindromic repeats linked to Cas nuclease) technology has revolutionized many aspects of genetic engineering research. Thanks to it, it became possible to study the functions and mechanisms of biology with greater precision, as well as to obtain genetically modified organisms, both prokaryotic and eukaryotic. The changes introduced by the CRISPR/Cas system are based on the repair paths of the single or double strand DNA breaks that cause insertions, deletions, or precise integrations of donor DNA. These changes are crucial for many fields of science, one of which is the use of animals (pigs) as a reservoir of tissues and organs for xenotransplantation into humans. Non-genetically modified animals cannot be used to save human life and health due to acute immunological reactions resulting from the phylogenetic distance of these two species. This review is intended to collect and summarize the advantages as well as achievements of the CRISPR/Cas system in pig-to-human xenotransplantation research. In addition, it demonstrates barriers and limitations that require careful evaluation before attempting to experiment with this technology.
Collapse
|
22
|
Wang H, Lu H, Lei YS, Gong CY, Chen Z, Luan YQ, Li Q, Jian YZ, Wang HZ, Wu FL, Tao CL, Shen H, Bo HB, Shao HW, Zhang WF. Development of a Self-Restricting CRISPR-Cas9 System to Reduce Off-Target Effects. Mol Ther Methods Clin Dev 2020; 18:390-401. [PMID: 32695841 PMCID: PMC7358219 DOI: 10.1016/j.omtm.2020.06.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/05/2020] [Indexed: 12/26/2022]
Abstract
Development of the CRISPR-Cas9 gene-editing system has given rise to a new era of gene editing with wide applications in biology, medicine, agriculture, and other fields. However, the overexpression of Cas9 nuclease causes off-target effects and may trigger an immune response in vivo. Therefore, we constructed a self-restricting CRISPR-Cas9 system, where the target gene sequence corresponding to the guide RNA (gRNA) is inserted on either end of the Cas9 promoter. When double-strand breaks (DSBs) are induced in the target gene sequence, the Cas9 promoter is cut off and transcription ceases. With this system, expression of Cas9 protein at 60 h after transfection is only 10% that of the wild-type system, with about 70% promoter deletion efficiency. The target site editing efficiency and homologous recombination efficiency of the self-restricting system remain at about 50% and 30%, respectively, while the frequency of off-target indel formation decreased by 76.7%. Further, the number of indel types was also reduced from 13 to 2. Because this system does not include additional gRNA sequences, the possibility of introducing new off-target mutations is decreased. Importantly, this system is composed of a single plasmid, which could potentially be easily introduced in vivo using a viral vector or nanoparticles.
Collapse
Affiliation(s)
- Hui Wang
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Hua Lu
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Ying-Shou Lei
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Chen-Yu Gong
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Zhao Chen
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Ying-Qiao Luan
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Qiang Li
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Ying-Zhen Jian
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Hao-Zheng Wang
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Feng-Lin Wu
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Chang-Li Tao
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Han Shen
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Hua-Ben Bo
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Hong-Wei Shao
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Wen-Feng Zhang
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| |
Collapse
|
23
|
Shin J, Oh JW. Development of CRISPR/Cas9 system for targeted DNA modifications and recent improvements in modification efficiency and specificity. BMB Rep 2020. [PMID: 32580834 PMCID: PMC7396914 DOI: 10.5483/bmbrep.2020.53.7.070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The targeted nuclease clustered, regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR/Cas) system has recently emerged as a prominent gene manipulation method. Because of its ease in programming targeted DNA/protein binding through RNA in a vast range of organisms, this prokaryotic defense system is a versatile tool with many applications in the research field as well as high potential in agricultural and clinical improvements. This review will present a brief history that led to its discovery and adaptation. We also present some of its restrictions, and modifications that have been performed to overcome such restrictions, focusing specifically on the most common CRISPR/Cas9 mediated non-homologous end joint repair.
Collapse
Affiliation(s)
- Juhyun Shin
- Department of Surgery, Chungnam National University College of Medicine, Daejeon, Korea
| | - Jae-Wook Oh
- Department of Surgery, Chungnam National University College of Medicine, Daejeon, Korea
| |
Collapse
|
24
|
Lee HJ, Kim HJ, Lee SJ. CRISPR-Cas9-mediated pinpoint microbial genome editing aided by target-mismatched sgRNAs. Genome Res 2020; 30:768-775. [PMID: 32327447 PMCID: PMC7263196 DOI: 10.1101/gr.257493.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/21/2020] [Indexed: 01/24/2023]
Abstract
Genome editing has been revolutionized by the CRISPR-Cas9 system. CRISPR-Cas9 is composed of single-molecular guide RNA (sgRNA) and a proteinaceous Cas9 nuclease, which recognizes a specific target sequence and a protospacer adjacent motif (PAM) sequence and, subsequently, cleaves the targeted DNA sequence. This CRISPR-Cas9 system has been used as an efficient negative-selection tool to cleave unedited or unchanged target DNAs during site-specific mutagenesis and, consequently, obtain microbial cells with desired mutations. This study aimed to investigate the genome editing efficiency of the CRISPR-Cas9 system for in vivo oligonucleotide-directed mutagenesis in bacteria. This system successfully introduced two- to four-base mutations in galK in Escherichia coli with high editing efficiencies (81%−86%). However, single-point mutations (T504A or C578A) were rarely introduced with very low editing efficiencies (<3%), probably owing to mismatch tolerance. To resolve this issue, we designed one- or two-base mismatches in the sgRNA sequence to recognize target sequences in galK in E. coli. A single-point nucleotide mutation (T504A or C578A in the galK gene) was successfully introduced in 36%−95% of negatively selected E. coli cells using single-base mismatched sgRNAs. Sixteen targets were randomly selected through genome-wide single-base editing experiments using mismatched sgRNAs. Consequently, out of 48 desired single-base mutations, 25 single bases were successfully edited, using mismatched sgRNAs. Finally, applicable design rules for target-mismatched sgRNAs were provided for single-nucleotide editing in microbial genomes.
Collapse
Affiliation(s)
- Ho Joung Lee
- Department of Systems Biotechnology, and Institute of Microbiomics, Chung-Ang University, Anseong 17546, South Korea
| | - Hyun Ju Kim
- Department of Systems Biotechnology, and Institute of Microbiomics, Chung-Ang University, Anseong 17546, South Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, and Institute of Microbiomics, Chung-Ang University, Anseong 17546, South Korea
| |
Collapse
|
25
|
Bratovič M, Fonfara I, Chylinski K, Gálvez EJC, Sullivan TJ, Boerno S, Timmermann B, Boettcher M, Charpentier E. Bridge helix arginines play a critical role in Cas9 sensitivity to mismatches. Nat Chem Biol 2020; 16:587-595. [PMID: 32123387 DOI: 10.1038/s41589-020-0490-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/30/2020] [Indexed: 12/31/2022]
Abstract
The RNA-programmable DNA-endonuclease Cas9 is widely used for genome engineering, where a high degree of specificity is required. To investigate which features of Cas9 determine the sensitivity to mismatches along the target DNA, we performed in vitro biochemical assays and bacterial survival assays in Escherichia coli. We demonstrate that arginines in the Cas9 bridge helix influence guide RNA, and target DNA binding and cleavage. They cluster in two groups that either increase or decrease the Cas9 sensitivity to mismatches. We show that the bridge helix is essential for R-loop formation and that R63 and R66 reduce Cas9 specificity by stabilizing the R-loop in the presence of mismatches. Additionally, we identify Q768 that reduces sensitivity of Cas9 to protospacer adjacent motif-distal mismatches. The Cas9_R63A/Q768A variant showed increased specificity in human cells. Our results provide a firm basis for function- and structure-guided mutagenesis to increase Cas9 specificity for genome engineering.
Collapse
Affiliation(s)
- Majda Bratovič
- Max Planck Unit for the Science of Pathogens, Berlin, Germany.,Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, Berlin, Germany.,Institute for Biology, Humboldt University, Berlin, Germany.,Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ines Fonfara
- Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, Berlin, Germany.,Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,The Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Krzysztof Chylinski
- The Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, Umeå, Sweden.,Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.,Protein Technologies Facility, The Vienna Biocenter Core Facilities GmbH (VBCF), Vienna, Austria
| | - Eric J C Gálvez
- Max Planck Unit for the Science of Pathogens, Berlin, Germany.,Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Stefan Boerno
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michael Boettcher
- Max Planck Unit for the Science of Pathogens, Berlin, Germany.,Medical Faculty, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, Berlin, Germany. .,Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, Berlin, Germany. .,Institute for Biology, Humboldt University, Berlin, Germany. .,Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany. .,The Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, Umeå, Sweden.
| |
Collapse
|
26
|
Jacinto FV, Link W, Ferreira BI. CRISPR/Cas9-mediated genome editing: From basic research to translational medicine. J Cell Mol Med 2020; 24:3766-3778. [PMID: 32096600 PMCID: PMC7171402 DOI: 10.1111/jcmm.14916] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/23/2019] [Accepted: 11/13/2019] [Indexed: 12/26/2022] Open
Abstract
The recent development of the CRISPR/Cas9 system as an efficient and accessible programmable genome‐editing tool has revolutionized basic science research. CRISPR/Cas9 system‐based technologies have armed researchers with new powerful tools to unveil the impact of genetics on disease development by enabling the creation of precise cellular and animal models of human diseases. The therapeutic potential of these technologies is tremendous, particularly in gene therapy, in which a patient‐specific mutation is genetically corrected in order to treat human diseases that are untreatable with conventional therapies. However, the translation of CRISPR/Cas9 into the clinics will be challenging, since we still need to improve the efficiency, specificity and delivery of this technology. In this review, we focus on several in vitro, in vivo and ex vivo applications of the CRISPR/Cas9 system in human disease‐focused research, explore the potential of this technology in translational medicine and discuss some of the major challenges for its future use in patients.
Collapse
Affiliation(s)
- Filipe V Jacinto
- Centre for Biomedical Research (CBMR), Faro, Portugal.,Departamento de Medicina e Ciências Biomedicas (DCBM), Universidade do Algarve, Faro, Portugal.,Algarve Biomedical Center (ABC), Faro, Portugal
| | - Wolfgang Link
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain
| | - Bibiana I Ferreira
- Centre for Biomedical Research (CBMR), Faro, Portugal.,Departamento de Medicina e Ciências Biomedicas (DCBM), Universidade do Algarve, Faro, Portugal.,Algarve Biomedical Center (ABC), Faro, Portugal
| |
Collapse
|
27
|
Li J, Hong S, Chen W, Zuo E, Yang H. Advances in detecting and reducing off-target effects generated by CRISPR-mediated genome editing. J Genet Genomics 2019; 46:513-521. [PMID: 31911131 DOI: 10.1016/j.jgg.2019.11.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/05/2019] [Accepted: 11/14/2019] [Indexed: 12/26/2022]
Abstract
CRISPR-mediated genome editing is a revolutionary technology for genome manipulation that uses the CRISPR-Cas systems and base editors. Currently, poor efficiency and off-target problems have impeded the application of CRISPR systems. The on-target efficiency has been improved in several advanced versions of CRISPR systems, whereas the off-target detection still remains a key challenge. Here, we outline the different versions of CRISPR systems and off-target detection strategies, discuss the merits and limitations of off-target detection methods, and provide potential implications for further gene editing research.
Collapse
Affiliation(s)
- Jinjing Li
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China; Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Shunyan Hong
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China; Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China
| | - Wanjin Chen
- Department of Neurology and Institute of Neurology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China; Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, 350005, China.
| | - Erwei Zuo
- Lingnan Guangdong Laboratory of Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| |
Collapse
|
28
|
Therapeutic application of the CRISPR system: current issues and new prospects. Hum Genet 2019; 138:563-590. [DOI: 10.1007/s00439-019-02028-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 05/13/2019] [Indexed: 12/23/2022]
|
29
|
Patsali P, Turchiano G, Papasavva P, Romito M, Loucari CC, Stephanou C, Christou S, Sitarou M, Mussolino C, Cornu TI, Antoniou MN, Lederer CW, Cathomen T, Kleanthous M. Correction of IVS I-110(G>A) β-thalassemia by CRISPR/Cas-and TALEN-mediated disruption of aberrant regulatory elements in human hematopoietic stem and progenitor cells. Haematologica 2019; 104:e497-e501. [PMID: 31004018 DOI: 10.3324/haematol.2018.215178] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Petros Patsali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Giandomenico Turchiano
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg, Germany
| | - Panayiota Papasavva
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Marianna Romito
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg, Germany
| | - Constantinos C Loucari
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Coralea Stephanou
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Department of Medical and Molecular Genetics, King's College London, London, UK
| | | | - Maria Sitarou
- Thalassemia Center, Cyprus Ministry of Health, Cyprus
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg, Germany
| | - Tatjana I Cornu
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg, Germany
| | - Michael N Antoniou
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Carsten W Lederer
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus .,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany .,Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus .,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| |
Collapse
|
30
|
Abstract
The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here we present and discuss important design considerations and challenges regarding the biochemical and locus specificities of epigenome editors. These include how to account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus specificity by considering concentration, affinity, avidity, and sequestration effects.
Collapse
|
31
|
WareJoncas Z, Campbell JM, Martínez-Gálvez G, Gendron WAC, Barry MA, Harris PC, Sussman CR, Ekker SC. Precision gene editing technology and applications in nephrology. Nat Rev Nephrol 2018; 14:663-677. [PMID: 30089813 PMCID: PMC6591726 DOI: 10.1038/s41581-018-0047-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The expanding field of precision gene editing is empowering researchers to directly modify DNA. Gene editing is made possible using synonymous technologies: a DNA-binding platform to molecularly locate user-selected genomic sequences and an associated biochemical activity that serves as a functional editor. The advent of accessible DNA-targeting molecular systems, such as zinc-finger nucleases, transcription activator-like effectors (TALEs) and CRISPR-Cas9 gene editing systems, has unlocked the ability to target nearly any DNA sequence with nucleotide-level precision. Progress has also been made in harnessing endogenous DNA repair machineries, such as non-homologous end joining, homology-directed repair and microhomology-mediated end joining, to functionally manipulate genetic sequences. As understanding of how DNA damage results in deletions, insertions and modifications increases, the genome becomes more predictably mutable. DNA-binding platforms such as TALEs and CRISPR can also be used to make locus-specific epigenetic changes and to transcriptionally enhance or suppress genes. Although many challenges remain, the application of precision gene editing technology in the field of nephrology has enabled the generation of new animal models of disease as well as advances in the development of novel therapeutic approaches such as gene therapy and xenotransplantation.
Collapse
Affiliation(s)
- Zachary WareJoncas
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Jarryd M Campbell
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | | | - William A C Gendron
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Michael A Barry
- Translational Polycystic Kidney Disease Center, Mayo Clinic, Rochester, MN, USA
| | - Peter C Harris
- Translational Polycystic Kidney Disease Center, Mayo Clinic, Rochester, MN, USA
| | - Caroline R Sussman
- Translational Polycystic Kidney Disease Center, Mayo Clinic, Rochester, MN, USA
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.
- Translational Polycystic Kidney Disease Center, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
32
|
Moore CT, Christie KA, Marshall J, Nesbit MA. Personalised genome editing – The future for corneal dystrophies. Prog Retin Eye Res 2018; 65:147-165. [DOI: 10.1016/j.preteyeres.2018.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/19/2018] [Accepted: 01/22/2018] [Indexed: 12/21/2022]
|
33
|
Katigbak A, Robert F, Paquet M, Pelletier J. Inducible Genome Editing with Conditional CRISPR/Cas9 Mice. G3 (BETHESDA, MD.) 2018; 8:1627-1635. [PMID: 29519936 PMCID: PMC5940154 DOI: 10.1534/g3.117.300327] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 03/06/2018] [Indexed: 01/07/2023]
Abstract
Genetically engineered mouse models (GEMMs) are powerful tools by which to probe gene function in vivo, obtain insight into disease etiology, and identify modifiers of drug response. Increased sophistication of GEMMs has led to the design of tissue-specific and inducible models in which genes of interest are expressed or ablated in defined tissues or cellular subtypes. Here we describe the generation of a transgenic mouse harboring a doxycycline-regulated Cas9 allele for inducible genome engineering. This model provides a flexible platform for genome engineering since editing is achieved by exogenous delivery of sgRNAs and should allow for the modeling of a range of biological and pathological processes.
Collapse
Affiliation(s)
- Alexandra Katigbak
- Department of Biochemistry, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec
| | - Francis Robert
- Department of Biochemistry, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec
| | - Marilène Paquet
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec
| | - Jerry Pelletier
- Department of Biochemistry, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec
- The Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Québec, Canada, H3G 1Y6
- Department of Oncology, McGill University, Montreal, Québec, Canada, H3G 1Y6
| |
Collapse
|
34
|
Gutierrez-Guerrero A, Sanchez-Hernandez S, Galvani G, Pinedo-Gomez J, Martin-Guerra R, Sanchez-Gilabert A, Aguilar-González A, Cobo M, Gregory P, Holmes M, Benabdellah K, Martin F. Comparison of Zinc Finger Nucleases Versus CRISPR-Specific Nucleases for Genome Editing of the Wiskott-Aldrich Syndrome Locus. Hum Gene Ther 2018; 29:366-380. [DOI: 10.1089/hum.2017.047] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Alejandra Gutierrez-Guerrero
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Sabina Sanchez-Hernandez
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Giuseppe Galvani
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Javier Pinedo-Gomez
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Rocio Martin-Guerra
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Almudena Sanchez-Gilabert
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Araceli Aguilar-González
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Marién Cobo
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
- LentiStem Biotech, Granada, Spain
| | - Philip Gregory
- Sangamo BioSciences, Point Richmond Tech Center, Richmond, California
| | - Michael Holmes
- Sangamo BioSciences, Point Richmond Tech Center, Richmond, California
| | - Karim Benabdellah
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
- LentiStem Biotech, Granada, Spain
| | - Francisco Martin
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
- LentiStem Biotech, Granada, Spain
| |
Collapse
|
35
|
Stephenson AA, Raper AT, Suo Z. Bidirectional Degradation of DNA Cleavage Products Catalyzed by CRISPR/Cas9. J Am Chem Soc 2018; 140:3743-3750. [PMID: 29461055 DOI: 10.1021/jacs.7b13050] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Since the initial characterization of Streptococcus pyogenes CRISPR/Cas9 as a powerful gene-editing tool, it has been widely accepted that Cas9 generates blunt-ended DNA products by concerted cleavage of the target (tDNA) and non-target (ntDNA) strands three nucleotides away from the protospacer adjacent motif (PAM) by HNH and RuvC nuclease active sites, respectively. Following initial DNA cleavage, RuvC catalyzes 3'→5' degradation of the ntDNA resulting in DNA products of various lengths. Here, we found that Cas9 selects multiple sites for initial ntDNA cleavage and preferentially generates staggered-ended DNA products containing single-nucleotide 5'-overhangs. We also quantitatively evaluated 3'→5' post-cleavage trimming (PCT) activity of RuvC to find that ntDNA degradation continues up to the -10 position on the PAM distal DNA product and is kinetically significant when compared to extremely slow DNA product release. We also discovered a previously unidentified 5'→3' PCT activity of RuvC which can shorten the PAM proximal ntDNA product by precisely one nucleotide with a comparable rate as the 3'→5' PCT activity. Taken together, our results demonstrate that RuvC-catalyzed PCT ultimately generates DNA fragments with heterogeneous ends following initial DNA cleavage including a PAM proximal fragment with a blunt end and a PAM distal fragment with a staggered-end, 3'-recessed on the ntDNA strand. These kinetic and biochemical findings underline the importance of temporal control of Cas9 during gene-editing experiments and help explain the patterns of nucleotide insertions at sites of Cas9-catalyzed gene modification in vivo.
Collapse
|
36
|
CRISPR interference-based specific and efficient gene inactivation in the brain. Nat Neurosci 2018; 21:447-454. [PMID: 29403034 DOI: 10.1038/s41593-018-0077-5] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 12/28/2017] [Indexed: 12/21/2022]
Abstract
CRISPR-Cas9 has been demonstrated to delete genes in postmitotic neurons. Compared to the establishment of proliferative cell lines or animal strains, it is more challenging to acquire a highly homogeneous consequence of gene editing in a stable neural network. Here we show that dCas9-based CRISPR interference (CRISPRi) can efficiently silence genes in neurons. Using a pseudotarget fishing strategy, we demonstrate that CRISPRi shows superior targeting specificity without detectable off-target activity. Furthermore, CRISPRi can achieve multiplex inactivation of genes fundamental for neurotransmitter release with high efficiency. By developing conditional CRISPRi tools targeting synaptotagmin I (Syt1), we modified the excitatory to inhibitory balance in the dentate gyrus of the mouse hippocampus and found that the dentate gyrus has distinct regulatory roles in learning and affective processes in mice. We therefore recommend CRISPRi as a useful tool for more rapid investigation of gene function in the mammalian brain.
Collapse
|
37
|
Fujita T, Kitaura F, Yuno M, Suzuki Y, Sugano S, Fujii H. Locus-specific ChIP combined with NGS analysis reveals genomic regulatory regions that physically interact with the Pax5 promoter in a chicken B cell line. DNA Res 2017; 24:537-548. [PMID: 28586432 PMCID: PMC5737561 DOI: 10.1093/dnares/dsx023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/04/2017] [Indexed: 12/05/2022] Open
Abstract
Chromosomal interactions regulate genome functions, such as transcription, via dynamic chromosomal organization in the nucleus. In this study, we attempted to identify genomic regions that physically bind to the promoter region of the Pax5 gene, which encodes a master regulator for B cell lineage commitment, in a chicken B cell line, DT40, with the goal of obtaining mechanistic insight into transcriptional regulation through chromosomal interaction. We found that the Pax5 promoter bound to multiple genomic regions using locus-specific chromatin immunoprecipitation (locus-specific ChIP), a method for locus-specific isolation of target genomic regions, in combination with next-generation sequencing (NGS). Comparing chromosomal interactions in wild-type DT40 with those in a macrophage-like counterpart, we found that some of the identified chromosomal interactions were organized in a B cell-specific manner. In addition, deletion of a B cell-specific interacting genomic region in chromosome 11, which was marked by active enhancer histone modifications, resulted in moderate but significant down-regulation of Pax5 transcription. Together, these results suggested that Pax5 transcription in DT40 is regulated by B cell-specific inter-chromosomal interactions. Moreover, these analyses showed that locus-specific ChIP combined with NGS analysis is useful for non-biased identification of functional genomic regions that physically interact with a locus of interest.
Collapse
Affiliation(s)
- Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori 036-8562, Japan.,Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Fusako Kitaura
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Miyuki Yuno
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.,Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.,Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Minato-ku, Tokyo 108-8639, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori 036-8562, Japan.,Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| |
Collapse
|
38
|
Chen YC, Farzadfard F, Gharaei N, Chen WCW, Cao J, Lu TK. Randomized CRISPR-Cas Transcriptional Perturbation Screening Reveals Protective Genes against Alpha-Synuclein Toxicity. Mol Cell 2017; 68:247-257.e5. [PMID: 28985507 PMCID: PMC5702536 DOI: 10.1016/j.molcel.2017.09.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 06/05/2017] [Accepted: 09/12/2017] [Indexed: 01/09/2023]
Abstract
The genome-wide perturbation of transcriptional networks with CRISPR-Cas technology has primarily involved systematic and targeted gene modulation. Here, we developed PRISM (Perturbing Regulatory Interactions by Synthetic Modulators), a screening platform that uses randomized CRISPR-Cas transcription factors (crisprTFs) to globally perturb transcriptional networks. By applying PRISM to a yeast model of Parkinson's disease (PD), we identified guide RNAs (gRNAs) that modulate transcriptional networks and protect cells from alpha-synuclein (αSyn) toxicity. One gRNA identified in this screen outperformed the most protective suppressors of αSyn toxicity reported previously, highlighting PRISM's ability to identify modulators of important phenotypes. Gene expression profiling revealed genes differentially modulated by this strong protective gRNA that rescued yeast from αSyn toxicity when overexpressed. Human homologs of top-ranked hits protected against αSyn-induced cell death in a human neuronal PD model. Thus, high-throughput and unbiased perturbation of transcriptional networks via randomized crisprTFs can reveal complex biological phenotypes and effective disease modulators.
Collapse
Affiliation(s)
- Ying-Chou Chen
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Fahim Farzadfard
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; MIT Microbiology Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering and Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Nava Gharaei
- MCO Graduate Program, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - William C W Chen
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jicong Cao
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; MIT Microbiology Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering and Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
39
|
|
40
|
Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. Nature 2017; 550:407-410. [PMID: 28931002 PMCID: PMC5918688 DOI: 10.1038/nature24268] [Citation(s) in RCA: 769] [Impact Index Per Article: 109.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/12/2017] [Indexed: 12/12/2022]
Abstract
The RNA-guided CRISPR-Cas9 nuclease from Streptococcus pyogenes (SpCas9) has been widely repurposed for genome editing1–4. High-fidelity (SpCas9-HF1) and enhanced specificity (eSpCas9(1.1)) variants exhibit substantially reduced off-target cleavage in human cells, but the mechanism of target discrimination and the potential to further improve fidelity were unknown5–9. Using single-molecule Förster resonance energy transfer (smFRET) experiments, we show that both SpCas9-HF1 and eSpCas9(1.1) are trapped in an inactive state10 when bound to mismatched targets. We find that a non-catalytic domain within Cas9, REC3, recognizes target complementarity and governs the HNH nuclease to regulate overall catalytic competence. Exploiting this observation, we designed a new hyper-accurate Cas9 variant (HypaCas9) that demonstrates high genome-wide specificity without compromising on-target activity in human cells. These results offer a more comprehensive model to rationalize and modify the balance between target recognition and nuclease activation for precision genome editing.
Collapse
|
41
|
Yang YJ, Wang Y, Li ZF, Gong Y, Zhang P, Hu WC, Sheng DH, Li YZ. Increasing on-target cleavage efficiency for CRISPR/Cas9-induced large fragment deletion in Myxococcus xanthus. Microb Cell Fact 2017; 16:142. [PMID: 28814300 PMCID: PMC5559782 DOI: 10.1186/s12934-017-0758-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/09/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The CRISPR/Cas9 system is a powerful tool for genome editing, in which the sgRNA binds and guides the Cas9 protein for the sequence-specific cleavage. The protocol is employable in different organisms, but is often limited by cell damage due to the endonuclease activity of the introduced Cas9 and the potential off-target DNA cleavage from incorrect guide by the 20 nt spacer. RESULTS In this study, after resolving some critical limits, we have established an efficient CRISPR/Cas9 system for the deletion of large genome fragments related to the biosynthesis of secondary metabolites in Myxococcus xanthus cells. We revealed that the high expression of a codon-optimized cas9 gene in M. xanthus was cytotoxic, and developed a temporally high expression strategy to reduce the cell damage from high expressions of Cas9. We optimized the deletion protocol by using the tRNA-sgRNA-tRNA chimeric structure to ensure correct sgRNA sequence. We found that, in addition to the position-dependent nucleotide preference, the free energy of a 20 nt spacer was a key factor for the deletion efficiency. CONCLUSIONS By using the developed protocol, we achieved the CRISPR/Cas9-induced deletion of large biosynthetic gene clusters for secondary metabolites in M. xanthus DK1622 and its epothilone-producing mutant. The findings and the proposals described in this paper were suggested to be workable in other organisms, for example, other Gram negative bacteria with high GC content.
Collapse
Affiliation(s)
- Ying-jie Yang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Ye Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Zhi-feng Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Ya Gong
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Peng Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Wen-chao Hu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Duo-hong Sheng
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| | - Yue-zhong Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, 250100 People’s Republic of China
| |
Collapse
|
42
|
Farboud B. Targeted genome editing in Caenorhabditis elegans using CRISPR/Cas9. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [PMID: 28810059 DOI: 10.1002/wdev.287] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/04/2017] [Accepted: 07/05/2017] [Indexed: 12/26/2022]
Abstract
Utilization of programmable nucleases to generate DNA lesions at precise endogenous sequences has transformed the ability to edit genomes from microbes to plants and animals. This is especially true in organisms that previously lacked the means to engineer precise genomic changes, like Caenorhabditis elegans. C. elegans is a 1 mm long free-living, nonparasitic, nematode worm, which is easily cultivated in a laboratory. Its detailed genetic map and relatively compact genome (~100 megabases) helped make it the first metazoan to have its entire genome sequenced. With detailed sequence information came development of numerous molecular tools to dissect gene function. Initially absent from this toolbox, however, were methods to make precise edits at chosen endogenous loci. Adapting site-specific nucleases for use in C. elegans, revolutionized studies of C. elegans biology. Zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and then CRISPR-associated protein 9 (Cas9) were used to target specific endogenous DNA sequences to make double-strand DNA breaks (DSBs). Precise changes could be engineered by providing repair templates targeting the DSB in trans. The ease of programming Cas9 to bind and cleave DNA sequences with few limitations has led to its widespread use in C. elegans research and sped the development of strategies to facilitate mutant recovery. Numerous innovative CRISPR/Cas9 methodologies are now primed for use in C. elegans. WIREs Dev Biol 2017, 6:e287. doi: 10.1002/wdev.287 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Behnom Farboud
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| |
Collapse
|
43
|
Kim SK, Kim H, Ahn WC, Park KH, Woo EJ, Lee DH, Lee SG. Efficient Transcriptional Gene Repression by Type V-A CRISPR-Cpf1 from Eubacterium eligens. ACS Synth Biol 2017; 6:1273-1282. [PMID: 28375596 DOI: 10.1021/acssynbio.6b00368] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Clustered regularly interspaced short palindromic repeats interference (CRISPRi) is an emerging technology for artificial gene regulation. Type II CRISPR-Cas endonuclease Cas9 is the most widely used protein for gene regulation with CRISPRi. Here, we present type V-A CRISPR-Cas endonuclease Cpf1-based CRISPRi. We constructed an l-rhamnose-inducible CRISPRi system with DNase-deactivated Cpf1 from Eubacterium eligens (EedCpf1) and compared its performance with catalytically deactivated Cas9 from Streptococcus pyogenes (SpdCas9). In contrast to SpdCas9, EedCpf1 showed stronger gene repression when it was targeted to the template strand than when it was targeted to the nontemplate strand of the 5' untranslated region or coding DNA sequences. EedCpf1 exhibited no strand bias when targeted to the promoter, and preferentially used the 5'-TTTV-3' (V = A, G, or C) protospacer adjacent motif. Multiplex repression of the EedCpf1-based CRISPRi system was demonstrated using episomal and chromosomal gene targets. Our findings will guide an efficient EedCpf1-mediated CRISPRi genetic control.
Collapse
Affiliation(s)
- Seong Keun Kim
- Synthetic
Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Biosystems
and Bioengineering Program, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Haseong Kim
- Synthetic
Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Biosystems
and Bioengineering Program, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Woo-Chan Ahn
- Disease
Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Kwang-Hyun Park
- Disease
Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Eui-Jeon Woo
- Disease
Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Bio-Analytical
Science Program, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Dae-Hee Lee
- Synthetic
Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Biosystems
and Bioengineering Program, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Seung-Goo Lee
- Synthetic
Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Biosystems
and Bioengineering Program, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| |
Collapse
|
44
|
Lin J, Zhou Y, Liu J, Chen J, Chen W, Zhao S, Wu Z, Wu N. Progress and Application of CRISPR/Cas Technology in Biological and Biomedical Investigation. J Cell Biochem 2017; 118:3061-3071. [DOI: 10.1002/jcb.26198] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 06/06/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Jiachen Lin
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
| | - Yangzhong Zhou
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
- Department of Internal Medicine, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
| | - Jiaqi Liu
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Department of Breast Surgical Oncology, National Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Jia Chen
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
| | - Weisheng Chen
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
| | - Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
- Department of Central Laboratory, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| |
Collapse
|
45
|
Abstract
Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) systems employ the dual RNA-guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific double-stranded breaks in target DNA. Target recognition strictly requires the presence of a short protospacer adjacent motif (PAM) flanking the target site, and subsequent R-loop formation and strand scission are driven by complementary base pairing between the guide RNA and target DNA, Cas9-DNA interactions, and associated conformational changes. The use of CRISPR-Cas9 as an RNA-programmable DNA targeting and editing platform is simplified by a synthetic single-guide RNA (sgRNA) mimicking the natural dual trans-activating CRISPR RNA (tracrRNA)-CRISPR RNA (crRNA) structure. This review aims to provide an in-depth mechanistic and structural understanding of Cas9-mediated RNA-guided DNA targeting and cleavage. Molecular insights from biochemical and structural studies provide a framework for rational engineering aimed at altering catalytic function, guide RNA specificity, and PAM requirements and reducing off-target activity for the development of Cas9-based therapies against genetic diseases.
Collapse
Affiliation(s)
- Fuguo Jiang
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720; ,
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720; ,
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
- Department of Chemistry, University of California, Berkeley, California 94720
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720
| |
Collapse
|
46
|
Fujita T, Yuno M, Suzuki Y, Sugano S, Fujii H. Identification of physical interactions between genomic regions by enChIP-Seq. Genes Cells 2017; 22:506-520. [PMID: 28474362 DOI: 10.1111/gtc.12492] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 03/22/2017] [Indexed: 01/23/2023]
Abstract
Physical interactions between genomic regions play critical roles in the regulation of genome functions, including gene expression. Here, we show the feasibility of using engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) in combination with next-generation sequencing (NGS) (enChIP-Seq) to detect such interactions. In enChIP-Seq, the target genomic region is captured by an engineered DNA-binding complex, such as a clustered regularly interspaced short palindromic repeats (CRISPR) system consisting of a catalytically inactive form of Cas9 and a single guide RNA. Subsequently, the genomic regions that physically interact with the target genomic region in the captured complex are sequenced by NGS. Using enChIP-Seq, we found that the 5'HS5 locus, which is involved in the regulation of globin genes expression at the β-globin locus, interacts with multiple genomic regions upon erythroid differentiation in the human erythroleukemia cell line K562. Genes near the genomic regions inducibly associated with the 5'HS5 locus were transcriptionally up-regulated in the differentiated state, suggesting the existence of a coordinated transcription mechanism mediated by physical interactions between these loci. Thus, enChIP-Seq might be a potentially useful tool for detecting physical interactions between genomic regions in a nonbiased manner, which would facilitate elucidation of the molecular mechanisms underlying regulation of genome functions.
Collapse
Affiliation(s)
- Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Miyuki Yuno
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.,Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.,Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| |
Collapse
|
47
|
Komor AC, Badran AH, Liu DR. CRISPR-Based Technologies for the Manipulation of Eukaryotic Genomes. Cell 2017; 168:20-36. [PMID: 27866654 PMCID: PMC5235943 DOI: 10.1016/j.cell.2016.10.044] [Citation(s) in RCA: 602] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 10/20/2016] [Accepted: 10/22/2016] [Indexed: 12/18/2022]
Abstract
The CRISPR-Cas9 RNA-guided DNA endonuclease has contributed to an explosion of advances in the life sciences that have grown from the ability to edit genomes within living cells. In this Review, we summarize CRISPR-based technologies that enable mammalian genome editing and their various applications. We describe recent developments that extend the generality, DNA specificity, product selectivity, and fundamental capabilities of natural CRISPR systems, and we highlight some of the remarkable advancements in basic research, biotechnology, and therapeutics science that these developments have facilitated.
Collapse
Affiliation(s)
- Alexis C Komor
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - Ahmed H Badran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
| | - David R Liu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.
| |
Collapse
|
48
|
Zhang K, Raboanatahiry N, Zhu B, Li M. Progress in Genome Editing Technology and Its Application in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:177. [PMID: 28261237 PMCID: PMC5306361 DOI: 10.3389/fpls.2017.00177] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/27/2017] [Indexed: 05/19/2023]
Abstract
Genome editing technology (GET) is a versatile approach that has progressed rapidly as a mechanism to alter the genotype and phenotype of organisms. However, conventional genome modification using GET cannot satisfy current demand for high-efficiency and site-directed mutagenesis, retrofitting of artificial nucleases has developed into a new avenue within this field. Based on mechanisms to recognize target genes, newly-developed GETs can generally be subdivided into three cleavage systems, protein-dependent DNA cleavage systems (i.e., zinc-finger nucleases, ZFN, and transcription activator-like effector nucleases, TALEN), RNA-dependent DNA cleavage systems (i.e., clustered regularly interspaced short palindromic repeats-CRISPR associated proteins, CRISPR-Cas9, CRISPR-Cpf1, and CRISPR-C2c1), and RNA-dependent RNA cleavage systems (i.e., RNA interference, RNAi, and CRISPR-C2c2). All these techniques can lead to double-stranded (DSB) or single-stranded breaks (SSB), and result in either random mutations via non-homologous end-joining (NHEJ) or targeted mutation via homologous recombination (HR). Thus, site-directed mutagenesis can be induced via targeted gene knock-out, knock-in, or replacement to modify specific characteristics including morphology-modification, resistance-enhancement, and physiological mechanism-improvement along with plant growth and development. In this paper, an non-comprehensive review on the development of different GETs as applied to plants is presented.
Collapse
Affiliation(s)
- Kai Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
| | - Nadia Raboanatahiry
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Bin Zhu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and TechnologyWuhan, China
- Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang Normal UniversityHuanggang, China
- *Correspondence: Maoteng Li
| |
Collapse
|
49
|
Shen S, Loh TJ, Shen H, Zheng X, Shen H. CRISPR as a strong gene editing tool. BMB Rep 2017; 50:20-24. [PMID: 27616359 PMCID: PMC5319660 DOI: 10.5483/bmbrep.2017.50.1.128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/16/2016] [Accepted: 09/07/2016] [Indexed: 11/20/2022] Open
Abstract
Clustered regularly-interspaced short palindromic repeats (CRISPR) is a new and effective genetic editing tool. CRISPR was initially found in bacteria to protect it from virus invasions. In the first step, specific DNA strands of virus are identified by guide RNA that is composed of crRNA and tracrRNA. Then RNAse III is required for producing crRNA from pre-crRNA. In The second step, a crRNA:tracrRNA:Cas9 complex guides RNase III to cleave target DNA. After cleavage of DNA by CRISPR-Cas9, DNA can be fixed by Non- Homologous End Joining (NHEJ) and Homology Directed Repair (HDR). Whereas NHEJ is simple and random, HDR is much more complex and accurate. Gene editing by CRISPR is able to be applied to various biological field such as agriculture and treating genetic diseases in human. [BMB Reports 2017; 50(1): 20-24].
Collapse
Affiliation(s)
- Shengfu Shen
- Willston Northampton School, Easthampton, MA 01027,
USA
| | - Tiing Jen Loh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
| | - Hongling Shen
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
| | - Xuexiu Zheng
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
| | - Haihong Shen
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
| |
Collapse
|
50
|
RNA-guided Genome Editing Tool CRISPR-Cas9: Its Applications and Achievements in Model and Crop Plants. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2016. [DOI: 10.22207/jpam.10.4.75] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|