1
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Xing W, Li D, Wang W, Liu JJG, Chen C. Conformational dynamics of CasX (Cas12e) in mediating DNA cleavage revealed by single-molecule FRET. Nucleic Acids Res 2024:gkae604. [PMID: 38994558 DOI: 10.1093/nar/gkae604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/13/2024] Open
Abstract
CasX (also known as Cas12e), a Class 2 CRISPR-Cas system, shows promise in genome editing due to its smaller size compared to the widely used Cas9 and Cas12a. Although the structures of CasX-sgRNA-DNA ternary complexes have been resolved and uncover a distinctive NTSB domain, the dynamic behaviors of CasX are not well characterized. In this study, we employed single-molecule and biochemical assays to investigate the conformational dynamics of two CasX homologs, DpbCasX and PlmCasX, from DNA binding to target cleavage and fragment release. Our results indicate that CasX cleaves the non-target strand and the target strand sequentially with relative irreversible dynamics. The two CasX homologs exhibited different cleavage patterns and specificities. The dynamic characterization of CasX also reveals a PAM-proximal seed region, providing guidance for CasX-based effector design. Further studies elucidate the mechanistic basis for why modification of sgRNA and the NTSB domain can affect its activity. Interestingly, CasX has less effective target search efficiency than Cas9 and Cas12a, potentially accounting for its lower genome editing efficiency. This observation opens a new avenue for future protein engineering.
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Affiliation(s)
- Wenjing Xing
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Danyuan Li
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wenjuan Wang
- Technology Center for Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jun-Jie Gogo Liu
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chunlai Chen
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
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2
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Lim JJY, Murata Y, Yuri S, Kitamuro K, Kawai T, Isotani A. Generating an organ-deficient animal model using a multi-targeted CRISPR-Cas9 system. Sci Rep 2024; 14:10636. [PMID: 38724644 PMCID: PMC11082136 DOI: 10.1038/s41598-024-61167-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 05/02/2024] [Indexed: 05/12/2024] Open
Abstract
Gene-knockout animal models with organ-deficient phenotypes used for blastocyst complementation are generally not viable. Animals need to be maintained as heterozygous mutants, and homozygous mutant embryos yield only one-fourth of all embryos. In this study, we generated organ-deficient embryos using the CRISPR-Cas9-sgRNAms system that induces cell death with a single-guide RNA (sgRNAms) targeting multiple sites in the genome. The Cas9-sgRNAms system interrupted cell proliferation and induced cell ablation in vitro. The mouse model had Cas9 driven by the Foxn1 promoter with a ubiquitous expression cassette of sgRNAms at the Rosa26 locus (Foxn1Cas9; Rosa26_ms). It showed an athymic phenotype similar to that of nude mice but was not hairless. Eventually, a rat cell-derived thymus in an interspecies chimera was generated by blastocyst complementation of Foxn1Cas9; Rosa26_ms mouse embryos with rat embryonic stem cells. Theoretically, a half of the total embryos has the Cas9-sgRNAms system because Rosa26_ms could be maintained as homozygous.
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Affiliation(s)
- Jonathan Jun-Yong Lim
- Laboratory of Organ Developmental Engineering, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0912, Japan
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
| | - Yamato Murata
- Laboratory of Organ Developmental Engineering, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0912, Japan
| | - Shunsuke Yuri
- Laboratory of Organ Developmental Engineering, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0912, Japan
| | - Kohei Kitamuro
- Laboratory of Organ Developmental Engineering, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0912, Japan
| | - Taro Kawai
- Laboratory of Molecular Immunobiology, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0912, Japan
- Life Science Collaboration Center (LiSCo), Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192, Japan
| | - Ayako Isotani
- Laboratory of Organ Developmental Engineering, Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0912, Japan.
- Life Science Collaboration Center (LiSCo), Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192, Japan.
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3
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Mollashahi B, Latifi-Navid H, Owliaee I, Shamdani S, Uzan G, Jamehdor S, Naserian S. Research and Therapeutic Approaches in Stem Cell Genome Editing by CRISPR Toolkit. Molecules 2023; 28:molecules28041982. [PMID: 36838970 PMCID: PMC9961668 DOI: 10.3390/molecules28041982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
The most widely used genome editing toolkit is CRISPR (clustered regularly interspaced short palindromic repeats). It provides the possibility of replacing and modifying DNA and RNA nucleotides. Furthermore, with advancements in biological technology, inhibition and activation of the transcription of specific gene(s) has become possible. Bioinformatics tools that target the evolution of CRISPR-associated protein 9 (Cas9) turn this protein into a vehicle that is specific for a DNA or RNA region with single guide RNA (sgRNA). This toolkit could be used by researchers to investigate the function of stem cell gene(s). Here, in this review article, we cover recent developments and applications of this technique in stem cells for research and clinical purposes and discuss different CRISPR/Cas technologies for knock-out, knock-in, activation, or inhibition of gene expression. Additionally, a comparison of several deliveries and off-target detecting strategies is discussed.
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Affiliation(s)
- Behrouz Mollashahi
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy
| | - Hamid Latifi-Navid
- Department of Molecular Medicine, National Institute of Genetic Engineering and Biotechnology, Tehran 14965/161, Iran
| | - Iman Owliaee
- Department of Virology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamedan 6517838636, Iran
| | - Sara Shamdani
- INSERM UMR-S-MD 1197, Hôpital Paul Brousse, Paris-Saclay University, 94807 Villejuif, France
- CellMedEx, 94100 Saint Maur Des Fossés, France
| | - Georges Uzan
- INSERM UMR-S-MD 1197, Hôpital Paul Brousse, Paris-Saclay University, 94807 Villejuif, France
| | - Saleh Jamehdor
- Department of Virology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamedan 6517838636, Iran
- Correspondence: (S.J.); (S.N.)
| | - Sina Naserian
- INSERM UMR-S-MD 1197, Hôpital Paul Brousse, Paris-Saclay University, 94807 Villejuif, France
- CellMedEx, 94100 Saint Maur Des Fossés, France
- Correspondence: (S.J.); (S.N.)
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4
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Marino ND, Pinilla-Redondo R, Bondy-Denomy J. CRISPR-Cas12a targeting of ssDNA plays no detectable role in immunity. Nucleic Acids Res 2022; 50:6414-6422. [PMID: 35670674 PMCID: PMC9226536 DOI: 10.1093/nar/gkac462] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 05/12/2022] [Accepted: 05/23/2022] [Indexed: 12/17/2022] Open
Abstract
CRISPR-Cas12a (Cpf1) is a bacterial RNA-guided nuclease that cuts double-stranded DNA (dsDNA) at sites specified by a CRISPR RNA (crRNA) guide. Additional activities have been ascribed to this enzyme in vitro: site-specific (cis) single-stranded DNA (ssDNA) cleavage and indiscriminate (trans) degradation of ssDNA, RNA, and dsDNA after activation by a complementary target. The ability of Cas12a to cleave nucleic acids indiscriminately has been harnessed for many applications, including diagnostics, but it remains unknown if it contributes to bacterial immunity. Here, we provide evidence that cleavage of ssDNA in cis or in trans by Cas12a is insufficient to impact immunity. Using LbCas12a expressed in either Pseudomonas aeruginosa or Escherichia coli, we observed that cleavage of dsDNA targets did not elicit cell death or dormancy, suggesting insignificant levels of collateral damage against host RNA or DNA. Canonical immunity against invasive dsDNA also had no impact on the replicative fitness of co-infecting dsDNA phage, ssDNA phage or plasmid in trans. Lastly, crRNAs complementary to invasive ssDNA did not provide protection, suggesting that ssDNA cleavage does not occur in vivo or is insignificant. Overall, these results suggest that CRISPR-Cas12a immunity predominantly occurs via canonical targeting of dsDNA, and that the other activities do not significantly impact infection outcomes.
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Affiliation(s)
- Nicole D Marino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Rafael Pinilla-Redondo
- Section of Microbiology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
- Innovative Genomics Institute, Berkeley, CA 94720, USA
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5
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Smirnova VV, Shestakova ED, Nogina DS, Mishchenko PA, Prikazchikova TA, Zatsepin TS, Kulakovskiy IV, Shatsky IN, Terenin IM. Ribosomal leaky scanning through a translated uORF requires eIF4G2. Nucleic Acids Res 2022; 50:1111-1127. [PMID: 35018467 PMCID: PMC8789081 DOI: 10.1093/nar/gkab1286] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 12/07/2021] [Accepted: 12/18/2021] [Indexed: 11/21/2022] Open
Abstract
eIF4G2 (DAP5 or Nat1) is a homologue of the canonical translation initiation factor eIF4G1 in higher eukaryotes but its function remains poorly understood. Unlike eIF4G1, eIF4G2 does not interact with the cap-binding protein eIF4E and is believed to drive translation under stress when eIF4E activity is impaired. Here, we show that eIF4G2 operates under normal conditions as well and promotes scanning downstream of the eIF4G1-mediated 40S recruitment and cap-proximal scanning. Specifically, eIF4G2 facilitates leaky scanning for a subset of mRNAs. Apparently, eIF4G2 replaces eIF4G1 during scanning of 5′ UTR and the necessity for eIF4G2 only arises when eIF4G1 dissociates from the scanning complex. In particular, this event can occur when the leaky scanning complexes interfere with initiating or elongating 80S ribosomes within a translated uORF. This mechanism is therefore crucial for higher eukaryotes which are known to have long 5′ UTRs with highly frequent uORFs. We suggest that uORFs are not the only obstacle on the way of scanning complexes towards the main start codon, because certain eIF4G2 mRNA targets lack uORF(s). Thus, higher eukaryotes possess two distinct scanning complexes: the principal one that binds mRNA and initiates scanning, and the accessory one that rescues scanning when the former fails.
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Affiliation(s)
- Victoria V Smirnova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Ekaterina D Shestakova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Daria S Nogina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Polina A Mishchenko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | | | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow 121205, Russia.,Chemistry Department, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Ivan V Kulakovskiy
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia.,Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Ilya M Terenin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia.,Sirius University of Science and Technology, Sochi, Olimpiyskiy ave. b.1, 354349, Russia
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6
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Zhou J, Chen P, Wang H, Liu H, Li Y, Zhang Y, Wu Y, Paek C, Sun Z, Lei J, Yin L. Cas12a variants designed for lower genome-wide off-target effect through stringent PAM recognition. Mol Ther 2022; 30:244-255. [PMID: 34687846 PMCID: PMC8753454 DOI: 10.1016/j.ymthe.2021.10.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/08/2021] [Accepted: 10/10/2021] [Indexed: 01/07/2023] Open
Abstract
Cas12a is an RNA-guided endonuclease that has been widely used for convenient multiplex gene editing with low off-target effects. To minimize off-targeting in gene editing, we engineered a variant of LbCas12a (termed Lb-K538R) with more stringent PAM recognition, lower off-targeting capability, and similar editing efficiency in vivo compared with LbCas12a. We also demonstrated that Lb2Cas12a from Lachnospiraceae bacterium MA2020 has extensive gene-editing activities in mammalian cells. Similar to Lb-K538R, the designed Lb2Cas12a variant (termed Lb2-K518R) not only had a more stringent PAM sequence change from YYN to TYN (Y is T or C, N is A, T, C, or G), but also displayed lower off-target effects, thereby enabling more potential target site selections with low off-targeting than the common TTTV (V is A, G, or C) PAM. To determine whether this type of mutation at the homologous position had similar effects in other Cas12a, As-K548R was evaluated. Based on the results of the genome-wide off-target test, As-K548R displayed lower off-target effects. Collectively, our findings indicate that the Cas proteins could be designed to be stringent in PAM recognition to reduce their off-target effects, which suggests a promising and practical approach for minimizing off-targets effects in genome editing.
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Affiliation(s)
- Jin Zhou
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Peng Chen
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hongjian Wang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Huan Liu
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yongzheng Li
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Youpeng Zhang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yankang Wu
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chonil Paek
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zaiqiao Sun
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jun Lei
- Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Lei Yin
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China,Corresponding author: Lei Yin, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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7
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Duan N, Tang S, Zeng B, Hu Z, Hu Q, Wu L, Zhou M, Liang D. An Episomal CRISPR/Cas12a System for Mediating Efficient Gene Editing. Life (Basel) 2021; 11:life11111262. [PMID: 34833137 PMCID: PMC8620414 DOI: 10.3390/life11111262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 12/16/2022] Open
Abstract
(1) Background: Gene editing technology, as represented by CRISPR is a powerful tool used in biomedical science. However, the editing efficiency of such technologies, especially in induced pluripotent stem cells (iPSCs) and other types of stem cells, is low which hinders its application in regenerative medicine; (2) Methods: A gene-editing system, COE, was designed and constructed based on CRISPR/Cas12a and Orip/EBNA1, and its editing efficiency was evaluated in human embryonic kidney 293T (HEK-293T) cells with flow cytometry and restriction fragment length polymorphism (RFLP) analysis. The COE was nucleofected into iPSCs, then, the editing efficiency was verified by a polymerase chain reaction and Sanger sequencing; (3) Results: With the extension of time, COE enables the generation of up to 90% insertion or deletion rates in HEK-293T cells. Furthermore, the deletion of a 2.5 kb fragment containing Exon 51 of the dystrophin gene (DMD) in iPSCs was achieved with high efficiency; out of 14 clones analyzed, 3 were positive. Additionally, the Exon 51-deleted iPSCs derived from cardiomyocytes had similar expression profiles to those of Duchenne muscular dystrophy (DMD) patient-specific iPSCs. Moreover, there was no residue of each component of the plasmid in the editing cells; (4) Conclusions: In this study, a novel, efficient, and safe gene-editing system, COE, was developed, providing a powerful tool for gene editing.
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8
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Janowski M, Milewska M, Zare P, Pękowska A. Chromatin Alterations in Neurological Disorders and Strategies of (Epi)Genome Rescue. Pharmaceuticals (Basel) 2021; 14:765. [PMID: 34451862 PMCID: PMC8399958 DOI: 10.3390/ph14080765] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/26/2022] Open
Abstract
Neurological disorders (NDs) comprise a heterogeneous group of conditions that affect the function of the nervous system. Often incurable, NDs have profound and detrimental consequences on the affected individuals' lives. NDs have complex etiologies but commonly feature altered gene expression and dysfunctions of the essential chromatin-modifying factors. Hence, compounds that target DNA and histone modification pathways, the so-called epidrugs, constitute promising tools to treat NDs. Yet, targeting the entire epigenome might reveal insufficient to modify a chosen gene expression or even unnecessary and detrimental to the patients' health. New technologies hold a promise to expand the clinical toolkit in the fight against NDs. (Epi)genome engineering using designer nucleases, including CRISPR-Cas9 and TALENs, can potentially help restore the correct gene expression patterns by targeting a defined gene or pathway, both genetically and epigenetically, with minimal off-target activity. Here, we review the implication of epigenetic machinery in NDs. We outline syndromes caused by mutations in chromatin-modifying enzymes and discuss the functional consequences of mutations in regulatory DNA in NDs. We review the approaches that allow modifying the (epi)genome, including tools based on TALENs and CRISPR-Cas9 technologies, and we highlight how these new strategies could potentially change clinical practices in the treatment of NDs.
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Affiliation(s)
| | | | | | - Aleksandra Pękowska
- Dioscuri Centre for Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteur Street, 02-093 Warsaw, Poland; (M.J.); (M.M.); (P.Z.)
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9
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Schonfeld E, Schonfeld E, Schonfeld D. Autocatalytic-protection for an unknown locus CRISPR-Cas countermeasure for undesired mutagenic chain reactions. J Theor Biol 2021; 528:110831. [PMID: 34274311 DOI: 10.1016/j.jtbi.2021.110831] [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: 09/08/2020] [Revised: 04/27/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022]
Abstract
The mutagenic chain reaction (MCR) is a genetic tool to use a CRISPR-Cas construct to introduce a homing endonuclease, allowing gene drive to influence whole populations in a minimal number of generations (Esvelt et al., 2014; Gantz and Bier, 2015; Gantz and Bier, 2016). The question arises: if an active genetic terror event is released into a population, could we prevent the total spread of the undesired allele (Gantz, et al., 2015; Webber et al., 2015)? Thus far, effective protection methods require knowledge of the terror locus (Grunwald et al., 2019). Here we introduce a novel approach, an autocatalytic-Protection for an Unknown Locus (a-PUL), whose aim is to spread through a population and arrest and decrease an active terror event's spread without any prior knowledge of the terror-modified locus, thus allowing later natural selection and ERACR drives to restore the normal locus (Hammond et al., 2017). a-PUL, using a mutagenic chain reaction, includes (i) a segment encoding a non-Cas9 endonuclease capable of homology-directed repair suggested as Type II endonuclease Cpf1 (Cas12a), (ii) a ubiquitously-expressed gene encoding a gRNA (gRNA1) with a U4AU4 3'-overhang specific to Cpf1 and with crRNA specific to some desired genomic sequence of non-coding DNA, (iii) a ubiquitously-expressed gene encoding two gRNAs (gRNA2/gRNA3) both with tracrRNA specific to Cas9 and crRNA specific to two distinct sites of the Cas9 locus, and (iv) homology arms flanking the Cpf1/gRNA1/gRNA2/gRNA3 cassette that are identical to the region surrounding the target cut directed by gRNA1 (Khan, 2016; Zetsche et al., 2015). We demonstrate the proof-of-concept and efficacy of our protection construct through a Graphical Markov model and computer simulation.
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Affiliation(s)
| | - Elan Schonfeld
- Multimedia Communications Laboratory, University of Illinois, Chicago, IL, United States
| | - Dan Schonfeld
- Multimedia Communications Laboratory, University of Illinois, Chicago, IL, United States
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10
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Abak A, Shoorei H, Taheri M, Ghafouri-Fard S. In vivo Engineering of Chromosome 19 q-arm by Employing the CRISPR/AsCpf1 and ddAsCpf1 Systems in Human Malignant Gliomas (Hypothesis). J Mol Neurosci 2021; 71:1648-1663. [PMID: 33990905 DOI: 10.1007/s12031-021-01855-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 04/23/2021] [Accepted: 05/03/2021] [Indexed: 11/29/2022]
Abstract
Deletions of the q13.3 region of chromosome 19 have been found commonly in all three main kinds of diffuse human malignant gliomas, powerfully demonstrating the existence of tumor suppressor genes in this region. Consistent with the previous studies, the most common deletion interval has been mapped to a roughly 4 Mb region of 19q13.3 between the APOC2 and HRC genes, between genetic markers D19S219 and D19S246. EML2 is a tumor suppressor gene that is located on 19q13.32 and is considerably methylated in high-grade gliomas. Notably, MIR330 gene that is situated within the non-coding intronic region of EML2 is also detected as an oncosuppressor-miR in a variety of cancers including gliomas. Additionally, glioma oncoprotein Bcl2L12 which is located on 19q13.33 is significantly overexpressed in glioblastoma multiform and has a pivotal role in cancer evolution and resistance to apoptosis. Other genes such as MIR519D and NOP53 are also discovered as tumor suppressor genes in gliomas which are located on 19q13.3 and 19q13.4, respectively. Therefore, we hypothesize that a CRISPR/AsCpf1-based genome engineering strategy might be utilized to attach these deleted sizeable chromosomal portions of genes coding tumor suppressors as vital parts of the chromosome 19 q-arm with the purpose of treatment of this chromosomal abnormality in gliomas. Also, we can concurrently employ the CRISPR-ddAsCpf1 strategy for the precise suppression of Bcl2L12 oncogene in glioma.
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Affiliation(s)
- Atefe Abak
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Shoorei
- Department of Anatomical Sciences, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics. Shahid, Beheshti University of Medical Sciences, Tehran, Iran.
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11
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Tálas A, Huszár K, Kulcsár PI, Varga JK, Varga É, Tóth E, Welker Z, Erdős G, Pach PF, Welker Á, Györgypál Z, Tusnády GE, Welker E. A method for characterizing Cas9 variants via a one-million target sequence library of self-targeting sgRNAs. Nucleic Acids Res 2021; 49:e31. [PMID: 33450024 PMCID: PMC8034649 DOI: 10.1093/nar/gkaa1220] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 11/16/2020] [Accepted: 01/06/2021] [Indexed: 12/26/2022] Open
Abstract
Detailed target-selectivity information and experiment-based efficacy prediction tools are primarily available for Streptococcus pyogenes Cas9 (SpCas9). One obstacle to develop such tools is the rarity of accurate data. Here, we report a method termed ‘Self-targeting sgRNA Library Screen’ (SLS) for assaying the activity of Cas9 nucleases in bacteria using random target/sgRNA libraries of self-targeting sgRNAs. Exploiting more than a million different sequences, we demonstrate the use of the method with the SpCas9-HF1 variant to analyse its activity and reveal motifs that influence its target-selectivity. We have also developed an algorithm for predicting the activity of SpCas9-HF1 with an accuracy matching those of existing tools. SLS is a facile alternative to the much more expensive and laborious approaches used currently and has the capability of delivering sufficient amount of data for most of the orthologs and variants of SpCas9.
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Affiliation(s)
- András Tálas
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, Hungary
| | - Krisztina Huszár
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.,Gene Design Ltd, Szeged, Hungary
| | - Péter István Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.,Biospiral-2006 Ltd, Szeged, Hungary.,School of Ph.D. Studies, University of Szeged, Hungary
| | - Julia K Varga
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Éva Varga
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.,School of Ph.D. Studies, University of Szeged, Hungary.,Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Eszter Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | | | | | | | - Ágnes Welker
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Zoltán Györgypál
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Gábor E Tusnády
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Ervin Welker
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.,Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
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12
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Choi E, Koo T. CRISPR technologies for the treatment of Duchenne muscular dystrophy. Mol Ther 2021; 29:3179-3191. [PMID: 33823301 DOI: 10.1016/j.ymthe.2021.04.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/18/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023] Open
Abstract
The emerging clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing technologies have progressed remarkably in recent years, opening up the potential of precise genome editing as a therapeutic approach to treat various diseases. The CRISPR-CRISPR-associated (Cas) system is an attractive platform for the treatment of Duchenne muscular dystrophy (DMD), which is a neuromuscular disease caused by mutations in the DMD gene. CRISPR-Cas can be used to permanently repair the mutated DMD gene, leading to the expression of the encoded protein, dystrophin, in systems ranging from cells derived from DMD patients to animal models of DMD. However, the development of more efficient therapeutic approaches and delivery methods remains a great challenge for DMD. Here, we review various therapeutic strategies that use CRISPR-Cas to correct or bypass DMD mutations and discuss their therapeutic potential, as well as obstacles that lie ahead.
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Affiliation(s)
- Eunyoung Choi
- Department of Life and Nanopharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Taeyoung Koo
- Department of Life and Nanopharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul, Republic of Korea; Department of Biomedical and Pharmaceutical Sciences, Graduate School, Kyung Hee University, Seoul, Republic of Korea; Department of Pharmaceutical Science, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea.
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13
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Tran MH, Park H, Nobles CL, Karunadharma P, Pan L, Zhong G, Wang H, He W, Ou T, Crynen G, Sheptack K, Stiskin I, Mou H, Farzan M. A more efficient CRISPR-Cas12a variant derived from Lachnospiraceae bacterium MA2020. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:40-53. [PMID: 33738137 PMCID: PMC7940699 DOI: 10.1016/j.omtn.2021.02.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/14/2021] [Indexed: 12/26/2022]
Abstract
CRISPR effector proteins introduce double-stranded breaks into the mammalian genome, facilitating gene editing by non-homologous end-joining or homology-directed repair. Unlike the more commonly studied Cas9, the CRISPR effector protein Cas12a/Cpf1 recognizes a T-rich protospacer adjacent motif (PAM) and can process its own CRISPR RNA (crRNA) array, simplifying the use of multiple guide RNAs. We observed that the Cas12a ortholog of Lachnospiraceae bacterium MA2020 (Lb2Cas12a) edited mammalian genes with efficiencies comparable to those of AsCas12a and LbCas12a. Compared to these well-characterized Cas12a orthologs, Lb2Cas12a is smaller and recognizes a narrow set of PAM TTTV. We introduced two mutations into Lb2Cas12a, Q571K and C1003Y, that increased its cleavage efficiency for a range of target sequences beyond those of the commonly used Cas12a orthologs AsCas12a and LbCas12a. In addition to the canonical TTTV PAM, this variant, Lb2-KY, also efficiently cleaved target regions with CTTN PAMs. Finally, we demonstrated that Lb2-KY ribonucleoprotein (RNP) complexes edited two hemoglobin target regions useful for correcting common forms of sickle-cell anemia more efficiently than commercial AsCas12a RNP complexes. Thus, Lb2-KY has distinctive properties useful for modifying a range of clinically relevant targets in the human genome.
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Affiliation(s)
- Mai H Tran
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Hajeung Park
- X-ray Crystallography Core, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Christopher L Nobles
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Li Pan
- Genomics Core, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Guocai Zhong
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Haimin Wang
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Wenhui He
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Tianling Ou
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Gogce Crynen
- Bioinformatics and Statistics Core, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Kelly Sheptack
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Ian Stiskin
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Huihui Mou
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
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14
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Bloh K, Kanchana R, Bialk P, Banas K, Zhang Z, Yoo BC, Kmiec EB. Deconvolution of Complex DNA Repair (DECODR): Establishing a Novel Deconvolution Algorithm for Comprehensive Analysis of CRISPR-Edited Sanger Sequencing Data. CRISPR J 2021; 4:120-131. [PMID: 33571043 PMCID: PMC7898406 DOI: 10.1089/crispr.2020.0022] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
During CRISPR-directed gene editing, multiple gene repair mechanisms interact to produce a wide and largely unpredictable variety of sequence changes across an edited population of cells. Shortcomings inherent to previously available proposal-based insertion and deletion (indel) analysis software necessitated the development of a more comprehensive tool that could detect a larger range and variety of indels while maintaining the ease of use of tools currently available. To that end, we developed Deconvolution of Complex DNA Repair (DECODR). DECODR can detect indels formed from single or multi-guide CRISPR experiments without a limit on indel size. The software is accurate in determining the identities and positions of inserted and deleted bases in DNA extracts from both clonally expanded and bulk cell populations. The accurate identification and output of any potential indel allows for DECODR analysis to be executed in experiments utilizing potentially any configuration of donor DNA sequences, CRISPR-Cas, and endogenous DNA repair pathways.
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Affiliation(s)
- Kevin Bloh
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
- Department of Medical and Molecular Sciences, College of Health Sciences University of Delaware, Newark, Delaware, USA
| | - Rohan Kanchana
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
| | - Pawel Bialk
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
| | - Kelly Banas
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
- Department of Medical and Molecular Sciences, College of Health Sciences University of Delaware, Newark, Delaware, USA
| | - Zugui Zhang
- Value Institute, ChristianaCare, Newark, Delaware, USA
| | - Byung-Chun Yoo
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
| | - Eric B. Kmiec
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, ChristianaCare, Newark, Delaware, USA
- Department of Medical and Molecular Sciences, College of Health Sciences University of Delaware, Newark, Delaware, USA
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15
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Hanson B, Wood MJA, Roberts TC. Molecular correction of Duchenne muscular dystrophy by splice modulation and gene editing. RNA Biol 2021; 18:1048-1062. [PMID: 33472516 DOI: 10.1080/15476286.2021.1874161] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a currently incurable X-linked neuromuscular disorder, characterized by progressive muscle wasting and premature death, typically as a consequence of cardiac failure. DMD-causing mutations in the dystrophin gene are highly diverse, meaning that the development of a universally-applicable therapy to treat all patients is very challenging. The leading therapeutic strategy for DMD is antisense oligonucleotide-mediated splice modulation, whereby one or more specific exons are excluded from the mature dystrophin mRNA in order to correct the translation reading frame. Indeed, three exon skipping oligonucleotides have received FDA approval for use in DMD patients. Second-generation exon skipping drugs (i.e. peptide-antisense oligonucleotide conjugates) exhibit enhanced potency, and also induce dystrophin restoration in the heart. Similarly, multiple additional antisense oligonucleotide drugs targeting various exons are in clinical development in order to treat a greater proportion of DMD patient mutations. Relatively recent advances in the field of genome engineering (specifically, the development of the CRISPR/Cas system) have provided multiple promising therapeutic approaches for the RNA-directed genetic correction of DMD, including exon excision, exon reframing via the introduction of insertion/deletion mutations, disruption of splice signals to promote exon skipping, and the templated correction of point mutations by seamless homology directed repair or base editing technology. Potential limitations to the clinical translation of the splice modulation and gene editing approaches are discussed, including drug delivery, the importance of uniform dystrophin expression in corrected myofibres, safety issues (e.g. renal toxicity, viral vector immunogenicity, and off-target gene editing), and the high cost of therapy.
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Affiliation(s)
- Britt Hanson
- Department of Paediatrics, University of Oxford, Oxford, UK.,Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Matthew J A Wood
- Department of Paediatrics, University of Oxford, Oxford, UK.,MDUK Oxford Neuromuscular Centre, Oxford, UK
| | - Thomas C Roberts
- Department of Paediatrics, University of Oxford, Oxford, UK.,MDUK Oxford Neuromuscular Centre, Oxford, UK
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16
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Shin U, Brondani V. Analysis of Wild Type LbCpf1 Protein, and PAM Recognition Variants, in a Cellular Context. Front Genet 2021; 11:571591. [PMID: 33488667 PMCID: PMC7817983 DOI: 10.3389/fgene.2020.571591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022] Open
Abstract
Nucleases used in genome engineering induce hydrolysis of DNA phosphate backbone in a sequence-specific manner. So far CRISPR-Cas, the RNA-guided nucleases, is the most advanced genome engineering system. The CRISPR nucleases allows recognition of a particular genomic sequence with two distinct molecular interactions: first, by direct interaction between the nuclease and the protospacer-adjacent motif, wherein discrete amino acids interact with DNA base pairs; and second, by hybridization of the guide RNA with the target DNA sequence. Here we report the application of the single strand annealing cellular assay to analyze and quantify nuclease activity of wild type and mutant CRISPR-Cpf1. Using this heterologous marker system based on GFP activity, we observed a comparable PAM recognition selectivity with the NGS analysis. The heterologous marker system has revealed that LbCpf1 is a more specific nuclease than AsCpf1 in a cellular context. We controlled the in vitro activity of the Cpf1 nuclease complexes expressed in mammalian cells and demonstrated that they are responsible of the DNA cleavage at the target site. In addition, we generated and tested LbCpf1 variants with several combinations of mutations at the PAM-recognition positions G532, K538 and Y542. Finally, we showed that the results of the in vitro DNA cleavage assay with the wild type and mutants LbCpf1 corroborate with the selection of 6TG resistant cells associated to the genomic disruption of hprt gene.
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Affiliation(s)
- Ujin Shin
- Center for Genome Engineering, Institute for Basic Science, Daejeon, South Korea
| | - Vincent Brondani
- Center for Genome Engineering, Institute for Basic Science, Daejeon, South Korea
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17
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Tóth E, Varga É, Kulcsár PI, Kocsis-Jutka V, Krausz SL, Nyeste A, Welker Z, Huszár K, Ligeti Z, Tálas A, Welker E. Improved LbCas12a variants with altered PAM specificities further broaden the genome targeting range of Cas12a nucleases. Nucleic Acids Res 2020; 48:3722-3733. [PMID: 32107556 PMCID: PMC7144938 DOI: 10.1093/nar/gkaa110] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 02/07/2020] [Accepted: 02/24/2020] [Indexed: 12/26/2022] Open
Abstract
The widespread use of Cas12a (formerly Cpf1) nucleases for genome engineering is limited by their requirement for a rather long TTTV protospacer adjacent motif (PAM) sequence. Here we have aimed to loosen these PAM constraints and have generated new PAM mutant variants of the four Cas12a orthologs that are active in mammalian and plant cells, by combining the mutations of their corresponding RR and RVR variants with altered PAM specificities. LbCas12a-RVRR showing the highest activity was selected for an in-depth characterization of its PAM preferences in mammalian cells, using a plasmid-based assay. The consensus PAM sequence of LbCas12a-RVRR resembles a TNTN motif, but also includes TACV, TTCV CTCV and CCCV. The D156R mutation in improved LbCas12a (impLbCas12a) was found to further increase the activity of that variant in a PAM-dependent manner. Due to the overlapping but still different PAM preferences of impLbCas12a and the recently reported enAsCas12a variant, they complement each other to provide increased efficiency for genome editing and transcriptome modulating applications.
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Affiliation(s)
- Eszter Tóth
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary
| | - Éva Varga
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged H-6726, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary
| | - Péter István Kulcsár
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged H-6726, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary
| | - Virág Kocsis-Jutka
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,ProteoScientia Kft, Cserhátszentiván, H-3066, Hungary
| | - Sarah Laura Krausz
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, H-1085, Hungary
| | - Antal Nyeste
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary.,ProteoScientia Kft, Cserhátszentiván, H-3066, Hungary
| | | | - Krisztina Huszár
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Biospirál-2006 Kft., Szeged, H-6726, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged H-6726, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary
| | - András Tálas
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, H-1085, Hungary
| | - Ervin Welker
- Institute of Enzymology, Research Centre of Natural Sciences of the Hungarian Academy of Sciences, Budapest H-1117, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary
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18
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Zhang J, Zhang D, Zhu J, Liu H, Liang S, Luo Y. Efficient Multiplex Genome Editing in Streptomyces via Engineered CRISPR-Cas12a Systems. Front Bioeng Biotechnol 2020; 8:726. [PMID: 32695773 PMCID: PMC7338789 DOI: 10.3389/fbioe.2020.00726] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 06/09/2020] [Indexed: 02/05/2023] Open
Abstract
Streptomyces strains produce a great number of valuable natural products. With the development of genome sequencing, a vast number of biosynthetic gene clusters with high potential for use in the discovery of valuable clinical drugs have been revealed. Therefore, emerging needs for tools to manipulate these biosynthetic pathways are presented. Although the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas 9) system has exhibited great capabilities for gene editing in multiple Streptomyces strains, it has failed to work in some newly discovered strains and some important industrial strains. Additionally, the protospacer adjacent motif (PAM) recognition scope of this system sometimes limits its applications for generating precise site mutations and insertions. Here, we developed three efficient CRISPR-FnCas12a systems for multiplex genome editing in several Streptomyces strains. Each system exhibited advantages for different applications. The CRISPR-FnCas12a1 system was efficiently applied in the industrial strain Streptomyces hygroscopicus, in which SpCas9 does not work well. The CRISPR-FnCas12a2 system was used to delete large fragments ranging from 21.4 to 128 kb. Additionally, the CRISPR-FnCas12a3 system employing the engineered FnCas12a mutant EP16, which recognizes a broad spectrum of PAM sequences, was used to precisely perform site mutations and insertions. The CRISPR-FnCas12a3 system addressed the limitation of TTN PAM recognition in Streptomyces strains with high GC contents. In summary, all the CRISPR-FnCas12a systems developed in this study are powerful tools for precise and multiplex genome editing in Streptomyces strains.
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Affiliation(s)
- Jun Zhang
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Dan Zhang
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Jie Zhu
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Huayi Liu
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Shufang Liang
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
| | - Yunzi Luo
- Department of Gastroenterology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Frontiers Science Center of Synthetic Biology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
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19
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Alok A, Sandhya D, Jogam P, Rodrigues V, Bhati KK, Sharma H, Kumar J. The Rise of the CRISPR/Cpf1 System for Efficient Genome Editing in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:264. [PMID: 32296449 PMCID: PMC7136500 DOI: 10.3389/fpls.2020.00264] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/19/2020] [Indexed: 05/20/2023]
Abstract
Cpf1, an endonuclease of the class 2 CRISPR family, fills the gaps that were previously faced in the world of genome engineering tools, which include the TALEN, ZFN, and CRISPR/Cas9. Other simultaneously discovered nucleases were not able to carry out re-engineering at the same region due to the loss of a target site after first-time engineering. Cpf1 acts as a dual nuclease, functioning as an endoribonuclease to process crRNA and endodeoxyribonuclease to cleave target sequences and generate double-stranded breaks. Additionally, Cpf1 allows for multiplexed genome editing, as a single crRNA array transcript can target multiple loci in the genome. The CRISPR/Cpf1 system enables gene deletion, insertion, base editing, and locus tagging in monocot as well as in dicot plants with fewer off-target effects. This tool has been efficiently demonstrated into tobacco, rice, soybean, wheat, etc. This review covers the development and applications of Cpf1 mediated genome editing technology in plants.
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Affiliation(s)
- Anshu Alok
- University Institute of Engineering and Technology, Panjab University, Chandigarh, India
- *Correspondence: Anshu Alok,
| | - Dulam Sandhya
- Department of Biotechnology, Kakatiya University, Warangal, India
| | - Phanikanth Jogam
- Department of Biotechnology, Kakatiya University, Warangal, India
| | - Vandasue Rodrigues
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kaushal K. Bhati
- Louvain Institute of Biomolecular Science, UCLouvain, Louvain-la-Neuve, Belgium
| | - Himanshu Sharma
- CSK Himachal Pradesh Agricultural University, Palampur, India
| | - Jitendra Kumar
- Department of Plant Pathology, University of Minnesota, Minneapolis, MN, United States
- Jitendra Kumar,
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20
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Bernabé‐Orts JM, Casas‐Rodrigo I, Minguet EG, Landolfi V, Garcia‐Carpintero V, Gianoglio S, Vázquez‐Vilar M, Granell A, Orzaez D. Assessment of Cas12a-mediated gene editing efficiency in plants. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1971-1984. [PMID: 30950179 PMCID: PMC6737022 DOI: 10.1111/pbi.13113] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 02/19/2019] [Accepted: 03/20/2019] [Indexed: 05/17/2023]
Abstract
The CRISPR/Cas12a editing system opens new possibilities for plant genome engineering. To obtain a comparative assessment of RNA-guided endonuclease (RGEN) types in plants, we adapted the CRISPR/Cas12a system to the GoldenBraid (GB) modular cloning platform and compared the efficiency of Acidaminococcus (As) and Lachnospiraceae (Lb) Cas12a variants with the previously described GB-assembled Streptococcus pyogenes Cas9 (SpCas9) constructs in eight Nicotiana benthamiana loci using transient expression. All three nucleases showed drastic target-dependent differences in efficiency, with LbCas12 producing higher mutagenesis rates in five of the eight loci assayed, as estimated with the T7E1 endonuclease assay. Attempts to engineer crRNA direct repeat (DR) had little effect improving on-target efficiency for AsCas12a and resulted deleterious in the case of LbCas12a. To complete the assessment of Cas12a activity, we carried out genome editing experiments in three different model plants, namely N. benthamiana, Solanum lycopersicum and Arabidopsis thaliana. For the latter, we also resequenced Cas12a-free segregating T2 lines to assess possible off-target effects. Our results showed that the mutagenesis footprint of Cas12a is enriched in deletions of -10 to -2 nucleotides and included in some instances complex rearrangements in the surroundings of the target sites. We found no evidence of off-target mutations neither in related sequences nor somewhere else in the genome. Collectively, this study shows that LbCas12a is a viable alternative to SpCas9 for plant genome engineering.
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Affiliation(s)
- Joan Miquel Bernabé‐Orts
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Iván Casas‐Rodrigo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
- Present address:
Department of Biosystems Science and EngineeringEidgenössische Technische Hochschule (ETH) ZurichBaselSwitzerland
| | - Eugenio G. Minguet
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Viola Landolfi
- Department of Agricultural, Forest and Food SciencesUniversity of TorinoGrugliascoItaly
| | - Victor Garcia‐Carpintero
- Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV‐UPV)Universitat Politècnica de ValènciaValenciaSpain
| | - Silvia Gianoglio
- Department of Agricultural, Forest and Food SciencesUniversity of TorinoGrugliascoItaly
| | - Marta Vázquez‐Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP)Consejo Superior de Investigaciones CientíficasUniversidad Politécnica de ValenciaValenciaSpain
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21
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Zhang L, Sun R, Yang M, Peng S, Cheng Y, Chen C. Conformational Dynamics and Cleavage Sites of Cas12a Are Modulated by Complementarity between crRNA and DNA. iScience 2019; 19:492-503. [PMID: 31437752 PMCID: PMC6710298 DOI: 10.1016/j.isci.2019.08.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/15/2019] [Accepted: 08/02/2019] [Indexed: 12/26/2022] Open
Abstract
Cas12a is an RNA-guided endonuclease, which displays great potentials and several advantages over the well-known Cas9 in genome editing and engineering. Here, we established a quantitative kinetic scheme to describe the conformational dynamics of Cas12a/crRNA/dsDNA ternary complexes. The highly dynamic nature of Cas12a complexes, including their reversible formation, disassembly, and transition between different conformational states, is likely to be one of the key aspects contributing to their high specificity. The non-target strand is cleaved when its cleavage sites are released from DNA duplex after DNase activation of Cas12a. Cleaved non-target strand stabilizes target strand pre-cleavage states to permit subsequent cleavage and to ensure two DNA strands cleaved in a well-defined order. The extent of complementarity between crRNA and DNA modulates the relative stabilities of target strand pre-cleavage states targeting different cleavage sites. Our discoveries provide insights to fully elucidate the working mechanisms of Cas12a and to optimize it for genome engineering. Dynamic processes of Cas12a contribute to its high specificity Cleavage sites of non-target strand are released from duplex after DNase activation Cleaved non-target strand stabilizes target strand pre-cleavage states Multiple target strand pre-cleavage states target different cleavage sites
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Affiliation(s)
- Lujia Zhang
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Ruirui Sun
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Mengyi Yang
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Sijia Peng
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Yongxin Cheng
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Chunlai Chen
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.
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22
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Tóth E, Czene BC, Kulcsár PI, Krausz SL, Tálas A, Nyeste A, Varga É, Huszár K, Weinhardt N, Ligeti Z, Borsy AÉ, Fodor E, Welker E. Mb- and FnCpf1 nucleases are active in mammalian cells: activities and PAM preferences of four wild-type Cpf1 nucleases and of their altered PAM specificity variants. Nucleic Acids Res 2019; 46:10272-10285. [PMID: 30239882 PMCID: PMC6212782 DOI: 10.1093/nar/gky815] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 09/11/2018] [Indexed: 01/02/2023] Open
Abstract
Cpf1s, the RNA-guided nucleases of the class II clustered regularly interspaced short palindromic repeats system require a short motive called protospacer adjacent motif (PAM) to be present next to the targeted sequence for their activity. The TTTV PAM sequence of As- and LbCpf1 nucleases is relatively rare in the genome of higher eukaryotic organisms. Here, we show that two other Cpf1 nucleases, Fn- and MbCpf1, which have been reported to utilize a shorter, more frequently occurring PAM sequence (TTN) when tested in vitro, carry out efficient genome modification in mammalian cells. We found that all four Cpf1 nucleases showed similar activities and TTTV PAM preferences. Our approach also revealed that besides their activities their PAM preferences are also target dependent. To increase the number of the available targets for Fn- and MbCpf1 we generated their RVR and RR mutants with altered PAM specificity and compared them to the wild-type and analogous As- and LbCpf1 variants. The mutants gained new PAM specificities but retained their activity on targets with TTTV PAMs, redefining RR-Cpf1's PAM-specificities as TTYV/TCCV, respectively. These variants may become versatile substitutes for wild-type Cpf1s by providing an expanded range of targets for genome engineering applications.
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Affiliation(s)
- Eszter Tóth
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Bernadett C Czene
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.,Gene Design Kft., Szeged, H-6726, Hungary
| | - Péter I Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.,Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, H-6726, Hungary
| | - Sarah L Krausz
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, H-1085, Hungary
| | - András Tálas
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, H-1085, Hungary
| | - Antal Nyeste
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Éva Varga
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Krisztina Huszár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary
| | - Nóra Weinhardt
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.,Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, H-6726, Hungary.,Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.,Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, H-6726, Hungary
| | - Adrienn É Borsy
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.,Biospirál-2006 Kft., Szeged, H-6726, Hungary
| | - Elfrieda Fodor
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6726, Hungary.,Biospirál-2006 Kft., Szeged, H-6726, Hungary
| | - Ervin Welker
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, H-1117, Hungary.,Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6726, Hungary
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23
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Zhang J, Yang F, Yang Y, Jiang Y, Huo YX. Optimizing a CRISPR-Cpf1-based genome engineering system for Corynebacterium glutamicum. Microb Cell Fact 2019; 18:60. [PMID: 30909908 PMCID: PMC6432761 DOI: 10.1186/s12934-019-1109-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/19/2019] [Indexed: 11/10/2022] Open
Abstract
Background Corynebacterium glutamicum is an important industrial strain for the production of a diverse range of chemicals. Cpf1 nucleases are highly specific and programmable, with efficiencies comparable to those of Cas9. Although the Francisella novicida (Fn) CRISPR-Cpf1 system has been adapted for genome editing in C. glutamicum, the editing efficiency is currently less than 15%, due to false positives caused by the poor targeting efficiency of the crRNA. Results To address this limitation, a screening strategy was developed in this study to systematically evaluate crRNA targeting efficiency in C. glutamicum. We quantitatively examined various parameters of the C. glutamicum CRISPR-Cpf1 system, including the protospacer adjacent motif (PAM) sequence, the length of the spacer sequence, and the type of repair template. We found that the most efficient C. glutamicum crRNA contained a 5′-NYTV-3′ PAM and a 21 bp spacer sequence. Moreover, we observed that linear DNA could be used to repair double strand breaks. Conclusions Here, we identified optimized PAM-related parameters for the CRISPR-Cpf1 system in C. glutamicum. Our study sheds light on the function of the FnCpf1 endonuclease and Cpf1-based genome editing. This optimized system, with higher editing efficiency, could be used to increase the production of bulk chemicals, such as isobutyrate, in C. glutamicum. Electronic supplementary material The online version of this article (10.1186/s12934-019-1109-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiao Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Fayu Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China
| | - Yunpeng Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China.,UCLA Institute of Advancement (Suzhou), 10 Yueliangwan Road, Suzhou Industrial Park, Suzhou, 215123, China
| | - Yu Jiang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Sciences, Beijing Institute of Technology, No. 5 South Zhongguancun Street, Beijing, 100081, China. .,UCLA Institute of Advancement (Suzhou), 10 Yueliangwan Road, Suzhou Industrial Park, Suzhou, 215123, China.
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24
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Prowse TA, Adikusuma F, Cassey P, Thomas P, Ross JV. A Y-chromosome shredding gene drive for controlling pest vertebrate populations. eLife 2019; 8:41873. [PMID: 30767891 PMCID: PMC6398975 DOI: 10.7554/elife.41873] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 02/13/2019] [Indexed: 11/16/2022] Open
Abstract
Self-replicating gene drives that modify sex ratios or infer a fitness cost could be used to control populations of invasive alien species. The targeted deletion of Y sex chromosomes using CRISPR technology offers a new approach for sex bias that could be incorporated within gene-drive designs. We introduce a novel gene-drive strategy termed Y-CHromosome deletion using Orthogonal Programmable Endonucleases (Y-CHOPE), incorporating a programmable endonuclease that ‘shreds’ the Y chromosome, thereby converting XY males into fertile XO females. Firstly, we demonstrate that the CRISPR/Cas12a system can eliminate the Y chromosome in embryonic stem cells with high efficiency (c. 90%). Next, using stochastic, individual-based models of a pest mouse population, we show that a Y-shredding drive that progressively depletes the pool of XY males could effect population eradication through mate limitation. Our molecular and modeling data suggest that a Y-CHOPE gene drive could be a viable tool for vertebrate pest control.
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Affiliation(s)
- Thomas Aa Prowse
- School of Mathematical Sciences, The University of Adelaide, Adelaide, Australia
| | - Fatwa Adikusuma
- School of Medicine, The University of Adelaide, Adelaide, Australia.,South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Phillip Cassey
- The Centre for Applied Conservation Science, The University of Adelaide, Adelaide, Australia.,School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Paul Thomas
- School of Medicine, The University of Adelaide, Adelaide, Australia.,South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Joshua V Ross
- School of Mathematical Sciences, The University of Adelaide, Adelaide, Australia
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25
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Zhang Y, Long C, Bassel-Duby R, Olson EN. Myoediting: Toward Prevention of Muscular Dystrophy by Therapeutic Genome Editing. Physiol Rev 2018; 98:1205-1240. [PMID: 29717930 DOI: 10.1152/physrev.00046.2017] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Muscular dystrophies represent a large group of genetic disorders that significantly impair quality of life and often progress to premature death. There is no effective treatment for these debilitating diseases. Most therapies, developed to date, focus on alleviating the symptoms or targeting the secondary effects, while the underlying gene mutation is still present in the human genome. The discovery and application of programmable nucleases for site-specific DNA double-stranded breaks provides a powerful tool for precise genome engineering. In particular, the CRISPR/Cas system has revolutionized the genome editing field and is providing a new path for disease treatment by targeting the disease-causing genetic mutations. In this review, we provide a historical overview of genome-editing technologies, summarize the most recent advances, and discuss potential strategies and challenges for permanently correcting genetic mutations that cause muscular dystrophies.
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Affiliation(s)
- Yu Zhang
- Department of Molecular Biology, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center , Dallas, Texas
| | - Chengzu Long
- Department of Molecular Biology, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center , Dallas, Texas
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center , Dallas, Texas
| | - Eric N Olson
- Department of Molecular Biology, Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center , Dallas, Texas
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26
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Lee SH, Kim S, Hur JK. CRISPR and Target-Specific DNA Endonucleases for Efficient DNA Knock-in in Eukaryotic Genomes. Mol Cells 2018; 41:943-952. [PMID: 30486613 PMCID: PMC6277560 DOI: 10.14348/molcells.2018.0408] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/08/2018] [Accepted: 11/08/2018] [Indexed: 01/23/2023] Open
Abstract
The discovery and mechanistic understanding of target-specific genome engineering technologies has led to extremely effective and specific genome editing in higher organisms. Target-specific genetic modification technology is expected to have a leading position in future gene therapy development, and has a ripple effect on various basic and applied studies. However, several problems remain and hinder efficient and specific editing of target genomic loci. The issues are particularly critical in precise targeted insertion of external DNA sequences into genomes. Here, we discuss some recent efforts to overcome such problems and present a perspective of future genome editing technologies.
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Affiliation(s)
- Seung Hwan Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Sunghyun Kim
- Department of Pathology, College of Medicine, Kyung Hee University, Seoul 02447,
Korea
| | - Junho K Hur
- Department of Pathology, College of Medicine, Kyung Hee University, Seoul 02447,
Korea
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27
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Smirnikhina SA, Anuchina AA, Lavrov AV. Ways of improving precise knock-in by genome-editing technologies. Hum Genet 2018; 138:1-19. [DOI: 10.1007/s00439-018-1953-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/29/2018] [Indexed: 02/07/2023]
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28
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Zhou M, Hu Z, Qiu L, Zhou T, Feng M, Hu Q, Zeng B, Li Z, Sun Q, Wu Y, Liu X, Wu L, Liang D. Seamless Genetic Conversion of SMN2 to SMN1 via CRISPR/Cpf1 and Single-Stranded Oligodeoxynucleotides in Spinal Muscular Atrophy Patient-Specific Induced Pluripotent Stem Cells. Hum Gene Ther 2018; 29:1252-1263. [PMID: 29598153 DOI: 10.1089/hum.2017.255] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a kind of neuromuscular disease characterized by progressive motor neuron loss in the spinal cord. It is caused by mutations in the survival motor neuron 1 (SMN1) gene. SMN1 has a paralogous gene, survival motor neuron 2 (SMN2), in humans that is present in almost all SMA patients. The generation and genetic correction of SMA patient-specific induced pluripotent stem cells (iPSCs) is a viable, autologous therapeutic strategy for the disease. Here, c-Myc-free and non-integrating iPSCs were generated from the urine cells of an SMA patient using an episomal iPSC reprogramming vector, and a unique crRNA was designed that does not have similar sequences (≤3 mismatches) anywhere in the human reference genome. In situ gene conversion of the SMN2 gene to an SMN1-like gene in SMA-iPSCs was achieved using CRISPR/Cpf1 and single-stranded oligodeoxynucleotide with a high efficiency of 4/36. Seamlessly gene-converted iPSC lines contained no exogenous sequences and retained a normal karyotype. Significantly, the SMN expression and gems localization were rescued in the gene-converted iPSCs and their derived motor neurons. This is the first report of an efficient gene conversion mediated by Cpf1 homology-directed repair in human cells and may provide a universal gene therapeutic approach for most SMA patients.
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Affiliation(s)
- Miaojin Zhou
- 1 Center for Medical Genetics, School of Life Sciences, Central South University , Hunan, China
| | - Zhiqing Hu
- 1 Center for Medical Genetics, School of Life Sciences, Central South University , Hunan, China
| | - Liyan Qiu
- 1 Center for Medical Genetics, School of Life Sciences, Central South University , Hunan, China
| | - Tao Zhou
- 1 Center for Medical Genetics, School of Life Sciences, Central South University , Hunan, China
| | - Mai Feng
- 1 Center for Medical Genetics, School of Life Sciences, Central South University , Hunan, China
| | - Qian Hu
- 1 Center for Medical Genetics, School of Life Sciences, Central South University , Hunan, China
| | - Baitao Zeng
- 1 Center for Medical Genetics, School of Life Sciences, Central South University , Hunan, China
| | - Zhuo Li
- 1 Center for Medical Genetics, School of Life Sciences, Central South University , Hunan, China
| | - Qianru Sun
- 1 Center for Medical Genetics, School of Life Sciences, Central South University , Hunan, China
| | - Yong Wu
- 1 Center for Medical Genetics, School of Life Sciences, Central South University , Hunan, China
| | - Xionghao Liu
- 1 Center for Medical Genetics, School of Life Sciences, Central South University , Hunan, China
| | - Lingqian Wu
- 1 Center for Medical Genetics, School of Life Sciences, Central South University , Hunan, China
- 2 Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Desheng Liang
- 1 Center for Medical Genetics, School of Life Sciences, Central South University , Hunan, China
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29
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Strohkendl I, Saifuddin FA, Rybarski JR, Finkelstein IJ, Russell R. Kinetic Basis for DNA Target Specificity of CRISPR-Cas12a. Mol Cell 2018; 71:816-824.e3. [PMID: 30078724 PMCID: PMC6679935 DOI: 10.1016/j.molcel.2018.06.043] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/13/2018] [Accepted: 06/26/2018] [Indexed: 12/26/2022]
Abstract
Class 2 CRISPR-Cas nucleases are programmable genome editing tools with promising applications in human health and disease. However, DNA cleavage at off-target sites that resemble the target sequence is a pervasive problem that remains poorly understood mechanistically. Here, we use quantitative kinetics to dissect the reaction steps of DNA targeting by Acidaminococcus sp Cas12a (also known as Cpf1). We show that Cas12a binds DNA tightly in two kinetically separable steps. Protospacer-adjacent motif (PAM) recognition is followed by rate-limiting R-loop propagation, leading to inevitable DNA cleavage of both strands. Despite functionally irreversible binding, Cas12a discriminates strongly against mismatches along most of the DNA target sequence. This result implies substantial reversibility during R-loop formation-a late transition state-and defies common descriptions of a "seed" region. Our results provide a quantitative basis for the DNA cleavage patterns measured in vivo and observations of greater reported target specificity for Cas12a than for the Cas9 nuclease.
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Affiliation(s)
- Isabel Strohkendl
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Fatema A Saifuddin
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - James R Rybarski
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Rick Russell
- Department of Molecular Biosciences and the Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
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30
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Swarts DC, Jinek M. Cas9 versus Cas12a/Cpf1: Structure-function comparisons and implications for genome editing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1481. [DOI: 10.1002/wrna.1481] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Daan C. Swarts
- Department of Biochemistry; University of Zurich; Zurich Switzerland
| | - Martin Jinek
- Department of Biochemistry; University of Zurich; Zurich Switzerland
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31
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Koo T, Park SW, Jo DH, Kim D, Kim JH, Cho HY, Kim J, Kim JH, Kim JS. CRISPR-LbCpf1 prevents choroidal neovascularization in a mouse model of age-related macular degeneration. Nat Commun 2018; 9:1855. [PMID: 29748595 PMCID: PMC5945874 DOI: 10.1038/s41467-018-04175-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 04/06/2018] [Indexed: 12/26/2022] Open
Abstract
LbCpf1, derived from Lachnospiraceae bacterium ND2006, is a CRISPR RNA-guided endonuclease and holds promise for therapeutic applications. Here we show that LbCpf1 can be used for therapeutic gene editing in a mouse model of age-related macular degeneration (AMD). The intravitreal delivery of LbCpf1, targeted to two angiogenesis-associated genes encoding vascular endothelial growth factor A (Vegfa) and hypoxia inducing factor 1a (Hif1a), using adeno-associated virus, led to efficient gene disruption with no apparent off-target effects in the retina and retinal pigment epithelium (RPE) cells. Importantly, LbCpf1 targeted to Vegfa or Hif1a in RPE cells reduced the area of laser-induced choroidal neovascularization as efficiently as aflibercept, an anti-VEGF drug currently used in the clinic, without inducing cone dysfunction. Unlike aflibercept, LbCpf1 targeted to Vegfa or Hif1a achieved a long-term therapeutic effect on CNV, potentially avoiding repetitive injections. Taken together, these results indicate that LbCpf1-mediated in vivo genome editing to ablate pathologic angiogenesis provides an effective strategy for the treatment of AMD and other neovascularization-associated diseases.
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Affiliation(s)
- Taeyoung Koo
- Center for Genome Engineering, Institute for Basic Science, Seoul, 151-747, Republic of Korea
- Department of Basic Science, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Sung Wook Park
- FARB Laboratory, Biomedical Research Institute, Seoul National University Hospital, Seoul, 03082, Republic of Korea
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Dong Hyun Jo
- FARB Laboratory, Biomedical Research Institute, Seoul National University Hospital, Seoul, 03082, Republic of Korea
| | - Daesik Kim
- Department of Chemistry, Seoul National University, Seoul, 151-747, South Korea
| | - Jin Hyoung Kim
- FARB Laboratory, Biomedical Research Institute, Seoul National University Hospital, Seoul, 03082, Republic of Korea
| | - Hee-Yeon Cho
- Center for Genome Engineering, Institute for Basic Science, Seoul, 151-747, Republic of Korea
| | - Jeungeun Kim
- Department of Chemistry, Seoul National University, Seoul, 151-747, South Korea
| | - Jeong Hun Kim
- FARB Laboratory, Biomedical Research Institute, Seoul National University Hospital, Seoul, 03082, Republic of Korea.
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Seoul, 151-747, Republic of Korea.
- Department of Basic Science, University of Science and Technology, Daejeon, 34113, Republic of Korea.
- Department of Chemistry, Seoul National University, Seoul, 151-747, South Korea.
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32
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Islam W. CRISPR-Cas9; an efficient tool for precise plant genome editing. Mol Cell Probes 2018; 39:47-52. [PMID: 29621557 DOI: 10.1016/j.mcp.2018.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 03/30/2018] [Accepted: 03/31/2018] [Indexed: 01/09/2023]
Abstract
Efficient plant genome editing is dependent upon induction of double stranded DNA breaks (DSBs) through site specified nucleases. These DSBs initiate the process of DNA repair which can either base upon homologous recombination (HR) or non-homologous end jointing (NHEJ). Recently, CRISPR-Cas9 mechanism got highlighted as revolutionizing genetic tool due to its simpler frame work along with the broad range of adaptability and applications. So, in this review, I have tried to sum up the application of this biotechnological tool in plant genome editing. Furthermore, I have tried to explain successful adaptation of CRISPR in various plant species where it is used for the successful generation of stable mutations in a steadily growing number of species through NHEJ. The review also sheds light upon other biotechnological approaches relying upon single DNA lesion induction such as genomic deletion or pair wise nickases for evasion of offsite effects.
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Affiliation(s)
- Waqar Islam
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fuzhou, 350002, China; Govt.of Punjab, Agriculture Department, Lahore, Pakistan.
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33
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Sansbury BM, Wagner AM, Nitzan E, Tarcic G, Kmiec EB. CRISPR-Directed In Vitro Gene Editing of Plasmid DNA Catalyzed by Cpf1 (Cas12a) Nuclease and a Mammalian Cell-Free Extract. CRISPR J 2018; 1:191-202. [PMID: 30687813 PMCID: PMC6345151 DOI: 10.1089/crispr.2018.0006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/27/2018] [Accepted: 04/06/2018] [Indexed: 12/20/2022] Open
Abstract
Extraordinary efforts are underway to offer greater versatility and broader applications for CRISPR-directed gene editing. Here, we report the establishment of a system for studying this process in a mammalian cell-free extract prepared from HEK-293 human embryonic kidney cells. A ribonucleoprotein (RNP) particle and a mammalian cell-free extract coupled with a genetic readout are used to generate and identify specific deletions or insertions within a plasmid target. A Cpf1 (Cas12a) RNP induces a double-stranded break, and the cell-free extract provides the appropriate enzymatic activities to direct specific deletion through resection and homology directed repair in the presence of single- and double-stranded donor DNA. This cell-free system establishes a foundation to study the heterogeneous products of gene editing, as well as the relationship between nonhomologous end joining and homology directed repair and related regulatory circuitries simultaneously in a controlled environment.
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Affiliation(s)
- Brett M Sansbury
- Department of Medical Laboratory Sciences, University of Delaware, Newark, Delaware.,Gene Editing Insitute, Helen F. Graham Cancer Center & Research Institute, Christiana Care Health System, Newark, Delaware
| | - Amanda M Wagner
- Gene Editing Insitute, Helen F. Graham Cancer Center & Research Institute, Christiana Care Health System, Newark, Delaware
| | - Erez Nitzan
- NovellusDx, Jerusalem Bio-Park, Hadassah Ein-Kerem Medical Center Campus, Jerusalem, Israel
| | - Gabi Tarcic
- NovellusDx, Jerusalem Bio-Park, Hadassah Ein-Kerem Medical Center Campus, Jerusalem, Israel
| | - Eric B Kmiec
- Department of Medical Laboratory Sciences, University of Delaware, Newark, Delaware.,Gene Editing Insitute, Helen F. Graham Cancer Center & Research Institute, Christiana Care Health System, Newark, Delaware
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Bewg WP, Ci D, Tsai CJ. Genome Editing in Trees: From Multiple Repair Pathways to Long-Term Stability. FRONTIERS IN PLANT SCIENCE 2018; 9:1732. [PMID: 30532764 PMCID: PMC6265510 DOI: 10.3389/fpls.2018.01732] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 11/07/2018] [Indexed: 05/19/2023]
Abstract
The CRISPR technology continues to diversify with a broadening array of applications that touch all kingdoms of life. The simplicity, versatility and species-independent nature of the CRISPR system offers researchers a previously unattainable level of precision and control over genomic modifications. Successful applications in forest, fruit and nut trees have demonstrated the efficacy of CRISPR technology at generating null mutations in the first generation. This eliminates the lengthy process of multigenerational crosses to obtain homozygous knockouts (KO). The high degree of genome heterozygosity in outcrossing trees is both a challenge and an opportunity for genome editing: a challenge because sequence polymorphisms at the target site can render CRISPR editing ineffective; yet an opportunity because the power and specificity of CRISPR can be harnessed for allele-specific editing. Examination of CRISPR/Cas9-induced mutational profiles from published tree studies reveals the potential involvement of multiple DNA repair pathways, suggesting that the influence of sequence context at or near the target sites can define mutagenesis outcomes. For commercial production of elite trees that rely on vegetative propagation, available data suggest an excellent outlook for stable CRISPR-induced mutations and associated phenotypes over multiple clonal generations.
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Affiliation(s)
- William Patrick Bewg
- Warnell School of Forestry and Natural Resources, Department of Genetics, and Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Dong Ci
- Warnell School of Forestry and Natural Resources, Department of Genetics, and Department of Plant Biology, University of Georgia, Athens, GA, United States
- Department of Bioscience and Biotechnology, Beijing Forestry University, Beijing, China
| | - Chung-Jui Tsai
- Warnell School of Forestry and Natural Resources, Department of Genetics, and Department of Plant Biology, University of Georgia, Athens, GA, United States
- *Correspondence: Chung-Jui Tsai,
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35
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The Conspicuity of CRISPR-Cpf1 System as a Significant Breakthrough in Genome Editing. Curr Microbiol 2017; 75:107-115. [DOI: 10.1007/s00284-017-1406-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/23/2017] [Indexed: 12/20/2022]
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36
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Kulcsár PI, Tálas A, Huszár K, Ligeti Z, Tóth E, Weinhardt N, Fodor E, Welker E. Crossing enhanced and high fidelity SpCas9 nucleases to optimize specificity and cleavage. Genome Biol 2017; 18:190. [PMID: 28985763 PMCID: PMC6389135 DOI: 10.1186/s13059-017-1318-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/11/2017] [Indexed: 12/19/2022] Open
Abstract
Background The propensity for off-target activity of Streptococcus pyogenes Cas9 (SpCas9) has been considerably decreased by rationally engineered variants with increased fidelity (eSpCas9; SpCas9-HF1). However, a subset of targets still generate considerable off-target effects. To deal specifically with these targets, we generated new “Highly enhanced Fidelity” nuclease variants (HeFSpCas9s) containing mutations from both eSpCas9 and SpCas9-HF1 and examined these improved nuclease variants side by side to decipher the factors that affect their specificities and to determine the optimal nuclease for applications sensitive to off-target effects. Results These three increased-fidelity nucleases can routinely be used only with perfectly matching 20-nucleotide-long spacers, a matching 5′ G extension being more detrimental to their activities than a mismatching one. HeFSpCas9 exhibit substantially improved specificity for those targets for which eSpCas9 and SpCas9-HF1 have higher off-target propensity. The targets can also be ranked by their cleavability and off-target effects manifested by the increased fidelity nucleases. Furthermore, we show that the mutations in these variants may diminish the cleavage, but not the DNA-binding, of SpCas9s. Conclusions No single nuclease variant shows generally superior fidelity; instead, for highest specificity cleavage, each target needs to be matched with an appropriate high-fidelity nuclease. We provide here a framework for generating new nuclease variants for targets that currently have no matching optimal nuclease, and offer a simple means for identifying the optimal nuclease for targets in the absence of accurate target-ranking prediction tools. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1318-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Péter István Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.,University of Szeged, Szeged, Hungary
| | - András Tálas
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,School of Ph.D. Studies, Semmelweis University, Budapest, Hungary
| | - Krisztina Huszár
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.,Gene Design Kft, Szeged, Hungary
| | - Zoltán Ligeti
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,Gene Design Kft, Szeged, Hungary
| | - Eszter Tóth
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Nóra Weinhardt
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.,University of Szeged, Szeged, Hungary
| | - Elfrieda Fodor
- Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Ervin Welker
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary. .,Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary.
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Pineda M, Moghadam F, Ebrahimkhani MR, Kiani S. Engineered CRISPR Systems for Next Generation Gene Therapies. ACS Synth Biol 2017; 6:1614-1626. [PMID: 28558198 DOI: 10.1021/acssynbio.7b00011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An ideal in vivo gene therapy platform provides safe, reprogrammable, and precise strategies which modulate cell and tissue gene regulatory networks with a high temporal and spatial resolution. Clustered regularly interspaced short palindromic repeats (CRISPR), a bacterial adoptive immune system, and its CRISPR-associated protein 9 (Cas9), have gained attention for the ability to target and modify DNA sequences on demand with unprecedented flexibility and precision. The precision and programmability of Cas9 is derived from its complexation with a guide-RNA (gRNA) that is complementary to a desired genomic sequence. CRISPR systems open-up widespread applications including genetic disease modeling, functional screens, and synthetic gene regulation. The plausibility of in vivo genetic engineering using CRISPR has garnered significant traction as a next generation in vivo therapeutic. However, there are hurdles that need to be addressed before CRISPR-based strategies are fully implemented. Some key issues center on the controllability of the CRISPR platform, including minimizing genomic-off target effects and maximizing in vivo gene editing efficiency, in vivo cellular delivery, and spatial-temporal regulation. The modifiable components of CRISPR systems: Cas9 protein, gRNA, delivery platform, and the form of CRISPR system delivered (DNA, RNA, or ribonucleoprotein) have recently been engineered independently to design a better genome engineering toolbox. This review focuses on evaluating CRISPR potential as a next generation in vivo gene therapy platform and discusses bioengineering advancements that can address challenges associated with clinical translation of this emerging technology.
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Affiliation(s)
- Michael Pineda
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
| | - Farzaneh Moghadam
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
| | - Mo R. Ebrahimkhani
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
- Center for Regenerative
Medicine, Mayo Clinic, Phoenix, Arizona 85054, United States
| | - Samira Kiani
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85281, United States
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Cebrian-Serrano A, Davies B. CRISPR-Cas orthologues and variants: optimizing the repertoire, specificity and delivery of genome engineering tools. Mamm Genome 2017; 28:247-261. [PMID: 28634692 PMCID: PMC5569134 DOI: 10.1007/s00335-017-9697-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/26/2017] [Indexed: 12/17/2022]
Abstract
Robust and cost-effective genome editing in a diverse array of cells and model organisms is now possible thanks to the discovery of the RNA-guided endonucleases of the CRISPR-Cas system. The commonly used Cas9 of Streptococcus pyogenes shows high levels of activity but, depending on the application, has been associated with some shortcomings. Firstly, the enzyme has been shown to cause mutagenesis at genomic sequences resembling the target sequence. Secondly, the stringent requirement for a specific motif adjacent to the selected target site can limit the target range of this enzyme. Lastly, the physical size of Cas9 challenges the efficient delivery of genomic engineering tools based on this enzyme as viral particles for potential therapeutic applications. Related and parallel strategies have been employed to address these issues. Taking advantage of the wealth of structural information that is becoming available for CRISPR-Cas effector proteins, Cas9 has been redesigned by mutagenizing key residues contributing to activity and target recognition. The protein has also been shortened and redesigned into component subunits in an attempt to facilitate its efficient delivery. Furthermore, the CRISPR-Cas toolbox has been expanded by exploring the properties of Cas9 orthologues and other related effector proteins from diverse bacterial species, some of which exhibit different target site specificities and reduced molecular size. It is hoped that the improvements in accuracy, target range and efficiency of delivery will facilitate the therapeutic application of these site-specific nucleases.
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Affiliation(s)
| | - Benjamin Davies
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
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39
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Zhang X, Wang J, Cheng Q, Zheng X, Zhao G, Wang J. Multiplex gene regulation by CRISPR-ddCpf1. Cell Discov 2017; 3:17018. [PMID: 28607761 PMCID: PMC5460296 DOI: 10.1038/celldisc.2017.18] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 04/24/2017] [Indexed: 12/14/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/dCas9 system has been widely applied in both transcriptional regulation and epigenetic studies. However, for multiple targets, independent expression of multiple single guide RNAs (sgRNAs) is needed, which is less convenient. To address the problem, we employed a DNase-dead Cpf1 mutant (ddCpf1) for multiplex gene regulation. We demonstrated that ddCpf1 alone could be employed for gene repression in Escherichia coli, and the repression was more effective with CRISPR RNAs (crRNAs) specifically targeting to the template strand of its target genes, which was different from that of dCas9. When targeting the promoter region, both strands showed effective repression by the ddCpf1/crRNA complex. The whole-transcriptome RNA-seq technique was further employed to demonstrate the high specificity of ddCpf1-mediated repression. Besides, we proved that the remaining RNase activity in ddCpf1 was capable of processing a precursor CRISPR array to simply generate multiple mature crRNAs in vivo, facilitating multiplex gene regulation. With the employment of this multiplex gene regulation strategy, we also showed how to quickly screen a library of candidate targets, that is, the two-component systems in E. coli. Therefore, based on our findings here, the CRISPR-ddCpf1 system may be further developed and widely applied in both biological research and clinical studies.
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Affiliation(s)
- Xiaochun Zhang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingman Wang
- State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Shenzhen Second People’s Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
- Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qiuxiang Cheng
- Shanghai Tolo Biotechnology Company Limited, Shanghai, China
| | - Xuan Zheng
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guoping Zhao
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jin Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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40
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He ZY, Men K, Qin Z, Yang Y, Xu T, Wei YQ. Non-viral and viral delivery systems for CRISPR-Cas9 technology in the biomedical field. SCIENCE CHINA. LIFE SCIENCES 2017; 60:458-467. [PMID: 28527117 DOI: 10.1007/s11427-017-9033-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/16/2017] [Indexed: 02/08/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) system provides a novel genome editing technology that can precisely target a genomic site to disrupt or repair a specific gene. Some CRISPR-Cas9 systems from different bacteria or artificial variants have been discovered or constructed by biologists, and Cas9 nucleases and single guide RNAs (sgRNA) are the major components of the CRISPR-Cas9 system. These Cas9 systems have been extensively applied for identifying therapeutic targets, identifying gene functions, generating animal models, and developing gene therapies. Moreover, CRISPR-Cas9 systems have been used to partially or completely alleviate disease symptoms by mutating or correcting related genes. However, the efficient transfer of CRISPR-Cas9 system into cells and target organs remains a challenge that affects the robust and precise genome editing activity. The current review focuses on delivery systems for Cas9 mRNA, Cas9 protein, or vectors encoding the Cas9 gene and corresponding sgRNA. Non-viral delivery of Cas9 appears to help Cas9 maintain its on-target effect and reduce off-target effects, and viral vectors for sgRNA and donor template can improve the efficacy of genome editing and homology-directed repair. Safe, efficient, and producible delivery systems will promote the application of CRISPR-Cas9 technology in human gene therapy.
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Affiliation(s)
- Zhi-Yao He
- Department of Pharmacy, and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Ke Men
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Zhou Qin
- Department of Pharmacy, and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Yang Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
| | - Ting Xu
- Department of Pharmacy, and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China.
| | - Yu-Quan Wei
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China
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41
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Swarts DC, van der Oost J, Jinek M. Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a. Mol Cell 2017; 66:221-233.e4. [PMID: 28431230 PMCID: PMC6879319 DOI: 10.1016/j.molcel.2017.03.016] [Citation(s) in RCA: 337] [Impact Index Per Article: 48.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/06/2017] [Accepted: 03/23/2017] [Indexed: 12/26/2022]
Abstract
The CRISPR-associated protein Cas12a (Cpf1), which has been repurposed for genome editing, possesses two distinct nuclease activities: endoribonuclease activity for processing its own guide RNAs and RNA-guided DNase activity for target DNA cleavage. To elucidate the molecular basis of both activities, we determined crystal structures of Francisella novicida Cas12a bound to guide RNA and in complex with an R-loop formed by a non-cleavable guide RNA precursor and a full-length target DNA. Corroborated by biochemical experiments, these structures reveal the mechanisms of guide RNA processing and pre-ordering of the seed sequence in the guide RNA that primes Cas12a for target DNA binding. Furthermore, the R-loop complex structure reveals the strand displacement mechanism that facilitates guide-target hybridization and suggests a mechanism for double-stranded DNA cleavage involving a single active site. Together, these insights advance our mechanistic understanding of Cas12a enzymes and may contribute to further development of genome editing technologies.
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MESH Headings
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- CRISPR-Associated Proteins/chemistry
- CRISPR-Associated Proteins/genetics
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- Catalysis
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Endonucleases/chemistry
- Endonucleases/genetics
- Endonucleases/metabolism
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Francisella/enzymology
- Francisella/genetics
- Gene Editing/methods
- Models, Molecular
- Nucleic Acid Conformation
- Protein Conformation
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Guide, CRISPR-Cas Systems/chemistry
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Structure-Activity Relationship
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Affiliation(s)
- Daan C Swarts
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6708WE Wageningen, the Netherlands
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland.
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42
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Zhang Y, Long C, Li H, McAnally JR, Baskin KK, Shelton JM, Bassel-Duby R, Olson EN. CRISPR-Cpf1 correction of muscular dystrophy mutations in human cardiomyocytes and mice. SCIENCE ADVANCES 2017; 3:e1602814. [PMID: 28439558 PMCID: PMC5389745 DOI: 10.1126/sciadv.1602814] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 02/14/2017] [Indexed: 05/07/2023]
Abstract
Duchenne muscular dystrophy (DMD), caused by mutations in the X-linked dystrophin gene (DMD), is characterized by fatal degeneration of striated muscles. Dilated cardiomyopathy is one of the most common lethal features of the disease. We deployed Cpf1, a unique class 2 CRISPR (clustered regularly interspaced short palindromic repeats) effector, to correct DMD mutations in patient-derived induced pluripotent stem cells (iPSCs) and mdx mice, an animal model of DMD. Cpf1-mediated genomic editing of human iPSCs, either by skipping of an out-of-frame DMD exon or by correcting a nonsense mutation, restored dystrophin expression after differentiation to cardiomyocytes and enhanced contractile function. Similarly, pathophysiological hallmarks of muscular dystrophy were corrected in mdx mice following Cpf1-mediated germline editing. These findings are the first to show the efficiency of Cpf1-mediated correction of genetic mutations in human cells and an animal disease model and represent a significant step toward therapeutic translation of gene editing for correction of DMD.
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MESH Headings
- Animals
- CRISPR-Cas Systems
- Dystrophin/genetics
- Dystrophin/metabolism
- Humans
- Mice
- Mice, Inbred mdx
- Muscular Dystrophy, Animal/genetics
- Muscular Dystrophy, Animal/metabolism
- Muscular Dystrophy, Animal/pathology
- Muscular Dystrophy, Animal/therapy
- Muscular Dystrophy, Duchenne/genetics
- Muscular Dystrophy, Duchenne/metabolism
- Muscular Dystrophy, Duchenne/pathology
- Muscular Dystrophy, Duchenne/therapy
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
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Affiliation(s)
- Yu Zhang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chengzu Long
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hui Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John R. McAnally
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kedryn K. Baskin
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John M. Shelton
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eric N. Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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43
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Czapiński J, Kiełbus M, Kałafut J, Kos M, Stepulak A, Rivero-Müller A. How to Train a Cell-Cutting-Edge Molecular Tools. Front Chem 2017; 5:12. [PMID: 28344971 PMCID: PMC5344921 DOI: 10.3389/fchem.2017.00012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/20/2017] [Indexed: 12/28/2022] Open
Abstract
In biological systems, the formation of molecular complexes is the currency for all cellular processes. Traditionally, functional experimentation was targeted to single molecular players in order to understand its effects in a cell or animal phenotype. In the last few years, we have been experiencing rapid progress in the development of ground-breaking molecular biology tools that affect the metabolic, structural, morphological, and (epi)genetic instructions of cells by chemical, optical (optogenetic) and mechanical inputs. Such precise dissection of cellular processes is not only essential for a better understanding of biological systems, but will also allow us to better diagnose and fix common dysfunctions. Here, we present several of these emerging and innovative techniques by providing the reader with elegant examples on how these tools have been implemented in cells, and, in some cases, organisms, to unravel molecular processes in minute detail. We also discuss their advantages and disadvantages with particular focus on their translation to multicellular organisms for in vivo spatiotemporal regulation. We envision that further developments of these tools will not only help solve the processes of life, but will give rise to novel clinical and industrial applications.
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Affiliation(s)
- Jakub Czapiński
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
- Postgraduate School of Molecular Medicine, Medical University of WarsawWarsaw, Poland
| | - Michał Kiełbus
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Joanna Kałafut
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Michał Kos
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Andrzej Stepulak
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi UniversityTurku, Finland
- Department of Biosciences, Åbo Akademi UniversityTurku, Finland
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44
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Abstract
Since the rapid emergence of clustered regulatory interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system, developed as a genome engineering tool in 2012–2013, most researchers in the life science field have had a fixated interest in this fascinating technology. CRISPR-Cas9 is an RNA-guided DNA endonuclease system, which consists of Cas9 nuclease defining a few targeting base via protospacer adjacent motif complexed with easily customizable single guide RNA targeting around 20-bp genomic sequence. Although Streptococcus pyogenes Cas9 (SpCas9), one of the Cas9 proteins that applications in genome engineering were first demonstrated, still has wide usage because of its high nuclease activity and broad targeting range, there are several limitations such as large molecular weight and potential off-target effect. In this commentary, we describe various improvements and alternatives of CRISPR-Cas systems, including engineered Cas9 variants, Cas9 homologs, and novel Cas proteins other than Cas9. These variations enable flexible genome engineering with high efficiency and specificity, orthogonal genetic control at multiple gene loci, gene knockdown, or fluorescence imaging of transcripts mediated by RNA targeting, and beyond.
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Affiliation(s)
- Shota Nakade
- a Department of Mathematical and Life Sciences, Graduate School of Science , Hiroshima University , Hiroshima , Japan
| | - Takashi Yamamoto
- a Department of Mathematical and Life Sciences, Graduate School of Science , Hiroshima University , Hiroshima , Japan
| | - Tetsushi Sakuma
- a Department of Mathematical and Life Sciences, Graduate School of Science , Hiroshima University , Hiroshima , Japan
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45
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Guichard SM. CRISPR–Cas9 for Drug Discovery in Oncology. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1016/bs.armc.2017.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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