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Sakono M, Oya T, Aoki M. Development of a Transcriptional Activator-Like Effector Protein to Accurately Discriminate Single Nucleotide Difference. Chembiochem 2023; 24:e202200486. [PMID: 36409599 DOI: 10.1002/cbic.202200486] [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: 08/19/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/22/2022]
Abstract
Transcriptional activator-like effector (TALE), a DNA-binding protein, is widely used in genome editing. However, the recognition of the target sequence by the TALE is adversely affected by the number of mismatches. Therefore, the association constant of DNA-TALE complex formation can be controlled by appropriately introducing a mismatch into the TALE recognition sequence. This study aimed to construct a TALE that can distinguish a single nucleotide difference. Our results show that a single mismatch present in repeats 2 or 3 of TALE did not interfere with the complex formation with DNA, whereas continuous mismatches present in repeats 2 and 3 significantly reduced association with the target DNA. Based on these findings, we constructed a detection system of the one nucleotide difference in gene with high accuracy and constructed a TALE-nuclease (TALEN) that selectively cleaves DNA with a single mismatch.
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Affiliation(s)
- Masafumi Sakono
- Department of Applied Chemistry, Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama, Toyama, 930-855, Japan
| | - Takuma Oya
- Department of Applied Chemistry, Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama, Toyama, 930-855, Japan
| | - Mio Aoki
- Department of Applied Chemistry, Faculty of Engineering, University of Toyama, 3190 Gofuku, Toyama, Toyama, 930-855, Japan
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2
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Boti MA, Athanasopoulou K, Adamopoulos PG, Sideris DC, Scorilas A. Recent Advances in Genome-Engineering Strategies. Genes (Basel) 2023; 14:129. [PMID: 36672870 PMCID: PMC9859587 DOI: 10.3390/genes14010129] [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: 12/10/2022] [Revised: 12/25/2022] [Accepted: 12/29/2022] [Indexed: 01/05/2023] Open
Abstract
In October 2020, the chemistry Nobel Prize was awarded to Emmanuelle Charpentier and Jennifer A. Doudna for the discovery of a new promising genome-editing tool: the genetic scissors of CRISPR-Cas9. The identification of CRISPR arrays and the subsequent identification of cas genes, which together represent an adaptive immunological system that exists not only in bacteria but also in archaea, led to the development of diverse strategies used for precise DNA editing, providing new insights in basic research and in clinical practice. Due to their advantageous features, the CRISPR-Cas systems are already employed in several biological and medical research fields as the most suitable technique for genome engineering. In this review, we aim to describe the CRISPR-Cas systems that have been identified among prokaryotic organisms and engineered for genome manipulation studies. Furthermore, a comprehensive comparison between the innovative CRISPR-Cas methodology and the previously utilized ZFN and TALEN editing nucleases is also discussed. Ultimately, we highlight the contribution of CRISPR-Cas methodology in modern biomedicine and the current plethora of available applications for gene KO, repression and/or overexpression, as well as their potential implementation in therapeutical strategies that aim to improve patients' quality of life.
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Affiliation(s)
| | | | - Panagiotis G. Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
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3
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Niklander SE, Hunter KD. A Protocol to Produce Genetically Edited Primary Oral Keratinocytes Using the CRISPR-Cas9 System. Methods Mol Biol 2023; 2588:217-229. [PMID: 36418691 DOI: 10.1007/978-1-0716-2780-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Nobel Prize awarded gene editing system, CRISPR-Cas9, is probably one of the greatest achievements of the last decades. CRISPR-Cas9 can introduce irreversible genomic changes in its target DNA by simple specifying a 20-nucleotide sequence within its RNA guide. Due to its simplicity, efficacy, and relative low cost in comparison with other genome editing systems, it has become the most common gene editing system used in research laboratories. Here we describe a step-by-step protocol to produce genetically edited primary oral keratinocytes using the CRISPR-Cas9 system.
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Affiliation(s)
- Sven E Niklander
- Unidad de Patología y Medicina Oral, Facultad de Odontologia, Universidad Andres Bello, Viña del Mar, Chile
| | - Keith D Hunter
- Unit of Oral and Maxillofacial Medicine and Pathology, School of Clinical Dentistry, University of Sheffield, Sheffield, UK. .,Oral Biology and Pathology, University of Pretoria, Pretoria, South Africa. .,Liverpool Head and Neck Centre, University of Liverpool, Liverpool, United Kingdom.
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4
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Stepanichev MY. Using Genome Editing for Alzheimer’s Disease Therapy: from Experiment to Clinic. NEUROCHEM J+ 2021. [DOI: 10.1134/s1819712421040139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Wu Y, Tian T, Wu Y, Yang Y, Zhang Y, Qin X. Systematic Studies of the Circadian Clock Genes Impact on Temperature Compensation and Cell Proliferation Using CRISPR Tools. BIOLOGY 2021; 10:biology10111204. [PMID: 34827197 PMCID: PMC8614980 DOI: 10.3390/biology10111204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 12/24/2022]
Abstract
Simple Summary One of the major characteristics of the circadian clock is temperature compensation, and previous studies suggested a single clock gene may determine the temperature compensation. In this study, we report the first full collection of clock gene knockout cell lines using CRISPR/Cas9 tools. Our full collections indicate that the temperature compensation is a complex gene regulation system instead of being regulated by any single gene. Besides, we systematically compared the proliferation rates and circadian periods using our full collections, and we found that the cell growth rate is not dependent on the circadian period. Therefore, complex interaction between clock genes and their protein products may underlie the mechanism of temperature compensation, which needs further investigations. Abstract Mammalian circadian genes are capable of producing a self-sustained, autonomous oscillation whose period is around 24 h. One of the major characteristics of the circadian clock is temperature compensation. However, the mechanism underlying temperature compensation remains elusive. Previous studies indicate that a single clock gene may determine the temperature compensation in several model organisms. In order to understand the influence of each individual clock gene on the temperature compensation, twenty-three well-known mammalian clock genes plus Timeless and Myc genes were knocked out individually, using a powerful gene-editing tool, CRISPR/Cas9. First, Bmal1, Cry1, and Cry2 were knocked out as examples to verify that deleting genes by CRISPR is effective and precise. Cell lines targeting twenty-two genes were successfully edited in mouse fibroblast NIH3T3 cells, and off-target analysis indicated these genes were correctly knocked out. Through measuring the luciferase reporters, the circadian periods of each cell line were recorded under two different temperatures, 32.5 °C and 37 °C. The temperature compensation coefficient Q10 was subsequently calculated for each cell line. Estimations of the Q10 of these cell lines showed that none of the individual cell lines can adversely affect the temperature compensation. Cells with a longer period at lower temperature tend to have a shorter period at higher temperature, while cells with a shorter period at lower temperature tend to be longer at higher temperature. Thus, the temperature compensation is a fundamental property to keep cellular homeostasis. We further conclude that the temperature compensation is a complex gene regulation system instead of being regulated by any single gene. We also estimated the proliferation rates of these cell lines. After systematically comparing the proliferation rates and circadian periods, we found that the cell growth rate is not dependent on the circadian period.
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Affiliation(s)
- Yue Wu
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China; (Y.W.); (T.T.); (Y.W.); (Y.Y.)
| | - Tian Tian
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China; (Y.W.); (T.T.); (Y.W.); (Y.Y.)
| | - Yin Wu
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China; (Y.W.); (T.T.); (Y.W.); (Y.Y.)
| | - Yu Yang
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China; (Y.W.); (T.T.); (Y.W.); (Y.Y.)
| | - Yunfei Zhang
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China; (Y.W.); (T.T.); (Y.W.); (Y.Y.)
- Moeden Experiment Technology Center, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China
- Correspondence: (Y.Z.); (X.Q.)
| | - Ximing Qin
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China; (Y.W.); (T.T.); (Y.W.); (Y.Y.)
- Correspondence: (Y.Z.); (X.Q.)
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6
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CRISPR-Cas systems for genome editing of mammalian cells. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 181:15-30. [PMID: 34127192 DOI: 10.1016/bs.pmbts.2021.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In the past decade, ZFNs and TALENs have been used for targeted genome engineering and have gained scientific attention. It has demonstrated huge potential for gene knockout, knock-in, and indels in desired locations of genomes to understand molecular mechanism of diseases and also discover therapy. However, both the genome engineering techniques are still suffering from design, screening and validation in cell and higher organisms. CRISPR-Cas9 is a rapid, simple, specific, and versatile technology and it has been applied in many organisms including mammalian cells. CRISPR-Cas9 has been used for animal models to modify animal cells for understanding human disease for novel drug discovery and therapy. Additionally, base editing has also been discussed herewith for conversion of C/G-to-T/A or A/T-to-G/C without DNA cleavage or donor DNA templates for correcting mutations or altering gene functions. In this chapter, we highlight CRISPR-Cas9 and base editing for desired genome editing in mammalian cells for a better understanding of molecular mechanisms, and biotechnological and therapeutic applications.
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7
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Kondrateva E, Demchenko A, Lavrov A, Smirnikhina S. An overview of currently available molecular Cas-tools for precise genome modification. Gene 2020; 769:145225. [PMID: 33059029 DOI: 10.1016/j.gene.2020.145225] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/17/2022]
Abstract
CRISPR-Cas system was first mentioned in 1987, and over the years have been studied so active that now it becomes the state-of-the-art tool for genome editing. Its working principle is based on Cas nuclease ability to bind short RNA, which targets it to complementary DNA or RNA sequence for highly precise cleavage. This alone or together with donor DNA allows to modify targeted sequence in different ways. Considering the many limitations of using native CRISPR-Cas systems, scientists around the world are working on creating modified variants to improve their specificity and efficiency in different objects. In addition, the use of the Cas effectors' targeting function in complex systems with other proteins is a promising work direction, as a result of which new tools are created with features such as single base editing, editing DNA without break and donor DNA, activation and repression of transcription, epigenetic regulation, modifying of different repair pathways involvement etc. In this review, we decided to consider in detail exactly this issue of variants of Cas effectors, their modifications and fusion molecules, which improve DNA-targeting and expand the scope of Cas effectors.
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Affiliation(s)
- Ekaterina Kondrateva
- Research Centre for Medical Genetics, Laboratory of Genome Editing, Moscow 115522, Russia.
| | - Anna Demchenko
- Research Centre for Medical Genetics, Laboratory of Genome Editing, Moscow 115522, Russia
| | - Alexander Lavrov
- Research Centre for Medical Genetics, Laboratory of Genome Editing, Moscow 115522, Russia
| | - Svetlana Smirnikhina
- Research Centre for Medical Genetics, Laboratory of Genome Editing, Moscow 115522, Russia
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8
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Ahn CH, Ramya M, An HR, Park PM, Kim YJ, Lee SY, Jang S. Progress and Challenges in the Improvement of Ornamental Plants by Genome Editing. PLANTS 2020; 9:plants9060687. [PMID: 32481726 PMCID: PMC7356337 DOI: 10.3390/plants9060687] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/18/2020] [Accepted: 05/27/2020] [Indexed: 01/08/2023]
Abstract
Biotechnological approaches have been used to modify the floral color, size, and fragrance of ornamental plants, as well as to increase disease resistance and vase life. Together with the advancement of whole genome sequencing technologies, new plant breeding techniques have rapidly emerged in recent years. Compared to the early versions of gene editing tools, such as meganucleases (MNs), zinc fingers (ZFNs), and transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeat (CRISPR) is capable of altering a genome more efficiently and with higher accuracy. Most recently, new CRISPR systems, including base editors and prime editors, confer reduced off-target activity with improved DNA specificity and an expanded targeting scope. However, there are still controversial issues worldwide for the recognition of genome-edited plants, including whether genome-edited plants are genetically modified organisms and require a safety evaluation process. In the current review, we briefly summarize the current progress in gene editing systems and also introduce successful/representative cases of the CRISPR system application for the improvement of ornamental plants with desirable traits. Furthermore, potential challenges and future prospects in the use of genome-editing tools for ornamental plants are also discussed.
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Affiliation(s)
- Chang Ho Ahn
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
| | - Mummadireddy Ramya
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
| | - Hye Ryun An
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
| | - Pil Man Park
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
| | - Yae-Jin Kim
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
| | - Su Young Lee
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Wanju-gun, Jellabuk-do 55365, Korea; (C.H.A.); (M.R.); (H.R.A.); (P.M.P.); (Y.-J.K.)
- Correspondence: (S.Y.L.); (S.J.); Tel.: +82-238-6840 (S.Y.L.); +82-63-238-6677 (S.J.)
| | - Seonghoe Jang
- World Vegetable Center Korea Office (WKO), Wanju-gun, Jellabuk-do 55365, Korea
- Correspondence: (S.Y.L.); (S.J.); Tel.: +82-238-6840 (S.Y.L.); +82-63-238-6677 (S.J.)
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9
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Genome Editing of the SNAI1 Gene in Rhabdomyosarcoma: A Novel Model for Studies of Its Role. Cells 2020; 9:cells9051095. [PMID: 32354171 PMCID: PMC7290443 DOI: 10.3390/cells9051095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 12/16/2022] Open
Abstract
Genome editing (GE) tools and RNA interference technology enable the modulation of gene expression in cancer research. While GE mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 or transcription activator-like effector nucleases (TALEN) activity can be used to induce gene knockouts, shRNA interacts with the targeted transcript, resulting in gene knockdown. Here, we compare three different methods for SNAI1 knockout or knockdown in rhabdomyosarcoma (RMS) cells. RMS is the most common sarcoma in children and its development has been previously associated with SNAI1 transcription factor activity. To investigate the role of SNAI1 in RMS development, we compared CRISPR/Cas9, TALEN, and shRNA tools to identify the most efficient tool for the modulation of SNAI1 expression with biological effects. Subsequently, the genome sequence, transcript levels, and protein expression of SNAI1 were evaluated. The modulation of SNAI1 using three different approaches affected the morphology of the cells and modulated the expression of myogenic factors and HDAC1. Our study revealed a similar effectiveness of the tested methods. Nevertheless, the low efficiency of the GE tools was a limiting factor in obtaining biallelic gene knockouts. To conclude, we established and characterized three different models of SNAI1 knockout and knockdown that might be used in further studies investigating the role of SNAI1 in RMS.
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10
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Generation of IL17RB Knockout Cell Lines Using CRISPR/Cas9-Based Genome Editing. Methods Mol Biol 2020. [PMID: 31939193 DOI: 10.1007/978-1-0716-0247-8_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
CRISPR/Cas9-based genome editing is an inexpensive and efficient tool for genetic modification. Here we present a methodological approach of establishing interleukin-17 receptor B (IL17RB) knockout cell lines using CRISPR/Cas9-mediated genomic deletion. IL17RB gene encodes for a cytokine receptor that specifically binds to IL17B and IL17E and overexpressed in various cancers. The method involves CRISPR design, CRISPR cloning, delivery of CRISPR clone into cells, and verification of IL17RB gene deletion by deletion screening primer design, genomic DNA extraction, and polymerase chain reaction (PCR). Similar approaches can be used for generating mammalian cell lines with gene knockout for other genes of interest.
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11
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Barrass SV, Butcher SJ. Advances in high-throughput methods for the identification of virus receptors. Med Microbiol Immunol 2019; 209:309-323. [PMID: 31865406 PMCID: PMC7248041 DOI: 10.1007/s00430-019-00653-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/02/2019] [Indexed: 12/26/2022]
Abstract
Viruses have evolved many mechanisms to invade host cells and establish successful infections. The interaction between viral attachment proteins and host cell receptors is the first and decisive step in establishing such infections, initiating virus entry into the host cells. Therefore, the identification of host receptors is fundamental in understanding pathogenesis and tissue tropism. Furthermore, receptor identification can inform the development of antivirals, vaccines, and diagnostic technologies, which have a substantial impact on human health. Nevertheless, due to the complex nature of virus entry, the redundancy in receptor usage, and the limitations in current identification methods, many host receptors remain elusive. Recent advances in targeted gene perturbation, high-throughput screening, and mass spectrometry have facilitated the discovery of virus receptors in recent years. In this review, we compare the current methods used within the field to identify virus receptors, focussing on genomic- and interactome-based approaches.
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Affiliation(s)
- Sarah V Barrass
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme and Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
| | - Sarah J Butcher
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme and Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
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12
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Ryu N, Kim MA, Choi DG, Kim YR, Sonn JK, Lee KY, Kim UK. CRISPR/Cas9-mediated genome editing of splicing mutation causing congenital hearing loss. Gene 2019; 703:83-90. [PMID: 30898719 DOI: 10.1016/j.gene.2019.03.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 03/10/2019] [Accepted: 03/12/2019] [Indexed: 01/04/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has ushered in a new era of gene therapy. In this study, we aimed to demonstrate precise CRISPR/Cas9-mediated genome editing of the splicing mutation c.919-2A > G in intron 7 of the SLC26A4 gene, which is the second most common causative gene of congenital hearing loss. We designed candidate single-guide RNAs (sgRNAs) aimed to direct the targeting of Staphylococcus aureus Cas9 to either exon 7 or exon 8 of SLC26A4. Several of the designed sgRNAs showed targeting activity, with average indel efficiencies ranging from approximately 14% to 25%. The usage of dual sgRNAs delivered both into Neuro2a cells and primary mouse embryonic fibroblasts resulted in the successful removal of large genomic fragments within the target locus. We subsequently evaluated genome editing in the presence of artificial donor templates to induce precise target modification via homology-directed repair. Using this approach, two different donor plasmids successfully introduced silent mutations within the c.919-2A region of Slc26a4 without evident off-target activities. Overall, these results indicate that CRISPR/Cas9-mediated correction of mutations in the Slc26a4 gene is a feasible therapeutic option for restoration of hearing loss.
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Affiliation(s)
- Nari Ryu
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Min-A Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Deok-Gyun Choi
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Ye-Ri Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jong Kyung Sonn
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyu-Yup Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea.
| | - Un-Kyung Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea.
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13
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Sibbritt T, Osteil P, Fan X, Sun J, Salehin N, Knowles H, Shen J, Tam PPL. Gene Editing of Mouse Embryonic and Epiblast Stem Cells. Methods Mol Biol 2019; 1940:77-95. [PMID: 30788819 DOI: 10.1007/978-1-4939-9086-3_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Efficient and reliable methods for gene editing are critical for the generation of loss-of-gene function stem cells and genetically modified mice. Here, we outline the application of CRISPR-Cas9 technology for gene editing in mouse embryonic stem cells (mESCs) to generate knockout ESC chimeras for the fast-tracked analysis of gene function. Furthermore, we describe the application of gene editing directly to mouse epiblast stem cells (mEpiSCs) for modelling germ layer differentiation in vitro.
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Affiliation(s)
- Tennille Sibbritt
- The University of Sydney, Children's Medical Research Institute, Westmead, NSW, Australia
- The University of Sydney, School of Medical Sciences, Camperdown, NSW, Australia
| | - Pierre Osteil
- The University of Sydney, Children's Medical Research Institute, Westmead, NSW, Australia
- The University of Sydney, School of Medical Sciences, Camperdown, NSW, Australia
| | - Xiaochen Fan
- The University of Sydney, Children's Medical Research Institute, Westmead, NSW, Australia
| | - Jane Sun
- The University of Sydney, Children's Medical Research Institute, Westmead, NSW, Australia
| | - Nazmus Salehin
- The University of Sydney, Children's Medical Research Institute, Westmead, NSW, Australia
| | - Hilary Knowles
- The University of Sydney, Children's Medical Research Institute, Westmead, NSW, Australia
| | - Joanne Shen
- The University of Sydney, Children's Medical Research Institute, Westmead, NSW, Australia
| | - Patrick P L Tam
- The University of Sydney, Children's Medical Research Institute, Westmead, NSW, Australia.
- The University of Sydney, School of Medical Sciences, Camperdown, NSW, Australia.
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14
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Simón JE, Rodríguez ÁS, Santiago Vispo N. CRISPR-Cas9: A Precise Approach to Genome Engineering. Ther Innov Regul Sci 2018; 52:701-707. [DOI: 10.1177/2168479018762798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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15
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Sorlien EL, Witucki MA, Ogas J. Efficient Production and Identification of CRISPR/Cas9-generated Gene Knockouts in the Model System Danio rerio. J Vis Exp 2018. [PMID: 30222157 PMCID: PMC6231919 DOI: 10.3791/56969] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Characterization of the clustered, regularly interspaced, short, palindromic repeat (CRISPR) system of Streptococcus pyogenes has enabled the development of a customizable platform to rapidly generate gene modifications in a wide variety of organisms, including zebrafish. CRISPR-based genome editing uses a single guide RNA (sgRNA) to target a CRISPR-associated (Cas) endonuclease to a genomic DNA (gDNA) target of interest, where the Cas endonuclease generates a double-strand break (DSB). Repair of DSBs by error-prone mechanisms lead to insertions and/or deletions (indels). This can cause frameshift mutations that often introduce a premature stop codon within the coding sequence, thus creating a protein-null allele. CRISPR-based genome engineering requires only a few molecular components and is easily introduced into zebrafish embryos by microinjection. This protocol describes the methods used to generate CRISPR reagents for zebrafish microinjection and to identify fish exhibiting germline transmission of CRISPR-modified genes. These methods include in vitro transcription of sgRNAs, microinjection of CRISPR reagents, identification of indels induced at the target site using a PCR-based method called a heteroduplex mobility assay (HMA), and characterization of the indels using both a low throughput and a powerful next-generation sequencing (NGS)-based approach that can analyze multiple PCR products collected from heterozygous fish. This protocol is streamlined to minimize both the number of fish required and the types of equipment needed to perform the analyses. Furthermore, this protocol is designed to be amenable for use by laboratory personal of all levels of experience including undergraduates, enabling this powerful tool to be economically employed by any research group interested in performing CRISPR-based genomic modification in zebrafish.
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Affiliation(s)
| | | | - Joseph Ogas
- Department of Biochemistry, Purdue University;
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Chaterji S, Ahn EH, Kim DH. CRISPR Genome Engineering for Human Pluripotent Stem Cell Research. Theranostics 2017; 7:4445-4469. [PMID: 29158838 PMCID: PMC5695142 DOI: 10.7150/thno.18456] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 08/24/2017] [Indexed: 12/13/2022] Open
Abstract
The emergence of targeted and efficient genome editing technologies, such as repurposed bacterial programmable nucleases (e.g., CRISPR-Cas systems), has abetted the development of cell engineering approaches. Lessons learned from the development of RNA-interference (RNA-i) therapies can spur the translation of genome editing, such as those enabling the translation of human pluripotent stem cell engineering. In this review, we discuss the opportunities and the challenges of repurposing bacterial nucleases for genome editing, while appreciating their roles, primarily at the epigenomic granularity. First, we discuss the evolution of high-precision, genome editing technologies, highlighting CRISPR-Cas9. They exist in the form of programmable nucleases, engineered with sequence-specific localizing domains, and with the ability to revolutionize human stem cell technologies through precision targeting with greater on-target activities. Next, we highlight the major challenges that need to be met prior to bench-to-bedside translation, often learning from the path-to-clinic of complementary technologies, such as RNA-i. Finally, we suggest potential bioinformatics developments and CRISPR delivery vehicles that can be deployed to circumvent some of the challenges confronting genome editing technologies en route to the clinic.
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17
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A novel magneto-DNA duplex probe for bacterial DNA detection based on exonuclease III-aided cycling amplification. Talanta 2015; 132:59-64. [DOI: 10.1016/j.talanta.2014.08.054] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/18/2014] [Accepted: 08/20/2014] [Indexed: 12/21/2022]
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18
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Xiong JS, Ding J, Li Y. Genome-editing technologies and their potential application in horticultural crop breeding. HORTICULTURE RESEARCH 2015; 2:15019. [PMID: 26504570 PMCID: PMC4595993 DOI: 10.1038/hortres.2015.19] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/09/2015] [Indexed: 05/19/2023]
Abstract
Plant breeding, one of the oldest agricultural activities, parallels human civilization. Many crops have been domesticated to satisfy human's food and aesthetical needs, including numerous specialty horticultural crops such as fruits, vegetables, ornamental flowers, shrubs, and trees. Crop varieties originated through selection during early human civilization. Other technologies, such as various forms of hybridization, mutation, and transgenics, have also been invented and applied to crop breeding over the past centuries. The progress made in these breeding technologies, especially the modern biotechnology-based breeding technologies, has had a great impact on crop breeding as well as on our lives. Here, we first review the developmental process and applications of these technologies in horticultural crop breeding. Then, we mainly describe the principles of the latest genome-editing technologies and discuss their potential applications in the genetic improvement of horticultural crops. The advantages and challenges of genome-editing technologies in horticultural crop breeding are also discussed.
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Affiliation(s)
- Jin-Song Xiong
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, The People's Republic of China
- ()
| | - Jing Ding
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, The People's Republic of China
| | - Yi Li
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095, The People's Republic of China
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269, USA
- ()
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19
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Affiliation(s)
- Katherine E. Tansey
- *To whom correspondence should be addressed; MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, CF24 4HQ, UK; tel: +44-029-20-688-457, fax: +44-029-20-687-068, e-mail:
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20
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Day JJ, Kennedy AJ, Sweatt JD. DNA methylation and its implications and accessibility for neuropsychiatric therapeutics. Annu Rev Pharmacol Toxicol 2014; 55:591-611. [PMID: 25340930 DOI: 10.1146/annurev-pharmtox-010814-124527] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this review, we discuss the potential pharmacological targeting of a set of powerful epigenetic mechanisms: DNA methylation control systems in the central nervous system (CNS). Specifically, we focus on the possible use of these targets for novel future treatments for learning and memory disorders. We first describe several unique pharmacological attributes of epigenetic mechanisms, especially DNA cytosine methylation, as potential drug targets. We then present an overview of the existing literature regarding DNA methylation control pathways and enzymes in the nervous system, particularly as related to synaptic function, plasticity, learning and memory. Lastly, we speculate upon potential categories of CNS cognitive disorders that might be amenable to methylomic targeting.
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Affiliation(s)
- Jeremy J Day
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama 35294; , ,
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21
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Kim DS, Ross PJ, Zaslavsky K, Ellis J. Optimizing neuronal differentiation from induced pluripotent stem cells to model ASD. Front Cell Neurosci 2014; 8:109. [PMID: 24782713 PMCID: PMC3990101 DOI: 10.3389/fncel.2014.00109] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 03/25/2014] [Indexed: 01/01/2023] Open
Abstract
Autism spectrum disorder (ASD) is an early-onset neurodevelopmental disorder characterized by deficits in social communication, and restricted and repetitive patterns of behavior. Despite its high prevalence, discovery of pathophysiological mechanisms underlying ASD has lagged due to a lack of appropriate model systems. Recent advances in induced pluripotent stem cell (iPSC) technology and neural differentiation techniques allow for detailed functional analyses of neurons generated from living individuals with ASD. Refinement of cortical neuron differentiation methods from iPSCs will enable mechanistic studies of specific neuronal subpopulations that may be preferentially impaired in ASD. In this review, we summarize recent accomplishments in differentiation of cortical neurons from human pluripotent stems cells and efforts to establish in vitro model systems to study ASD using personalized neurons.
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Affiliation(s)
- Dae-Sung Kim
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children Toronto, ON, Canada
| | - P Joel Ross
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children Toronto, ON, Canada
| | - Kirill Zaslavsky
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children Toronto, ON, Canada ; Department of Molecular Genetics, University of Toronto Toronto, ON, Canada
| | - James Ellis
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children Toronto, ON, Canada ; Department of Molecular Genetics, University of Toronto Toronto, ON, Canada
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22
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Zhang M, Wang F, Li S, Wang Y, Bai Y, Xu X. TALE: A tale of genome editing. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:25-32. [DOI: 10.1016/j.pbiomolbio.2013.11.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 10/10/2013] [Accepted: 11/17/2013] [Indexed: 11/16/2022]
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23
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Tang JCY, Szikra T, Kozorovitskiy Y, Teixiera M, Sabatini BL, Roska B, Cepko CL. A nanobody-based system using fluorescent proteins as scaffolds for cell-specific gene manipulation. Cell 2013; 154:928-39. [PMID: 23953120 PMCID: PMC4096992 DOI: 10.1016/j.cell.2013.07.021] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 05/31/2013] [Accepted: 07/15/2013] [Indexed: 01/22/2023]
Abstract
Fluorescent proteins are commonly used to label cells across organisms, but the unmodified forms cannot control biological activities. Using GFP-binding proteins derived from Camelid antibodies, we co-opted GFP as a scaffold for inducing formation of biologically active complexes, developing a library of hybrid transcription factors that control gene expression only in the presence of GFP or its derivatives. The modular design allows for variation in key properties such as DNA specificity, transcriptional potency, and drug dependency. Production of GFP controlled cell-specific gene expression and facilitated functional perturbations in the mouse retina and brain. Further, retrofitting existing transgenic GFP mouse and zebrafish lines for GFP-dependent transcription enabled applications such as optogenetic probing of neural circuits. This work establishes GFP as a multifunctional scaffold and opens the door to selective manipulation of diverse GFP-labeled cells across transgenic lines. This approach may also be extended to exploit other intracellular products as cell-specific scaffolds in multicellular organisms.
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Affiliation(s)
- Jonathan C Y Tang
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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24
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Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat Protoc 2013. [PMID: 24157548 DOI: 10.1038/nprot.2013.143.] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Targeted nucleases are powerful tools for mediating genome alteration with high precision. The RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system can be used to facilitate efficient genome engineering in eukaryotic cells by simply specifying a 20-nt targeting sequence within its guide RNA. Here we describe a set of tools for Cas9-mediated genome editing via nonhomologous end joining (NHEJ) or homology-directed repair (HDR) in mammalian cells, as well as generation of modified cell lines for downstream functional studies. To minimize off-target cleavage, we further describe a double-nicking strategy using the Cas9 nickase mutant with paired guide RNAs. This protocol provides experimentally derived guidelines for the selection of target sites, evaluation of cleavage efficiency and analysis of off-target activity. Beginning with target design, gene modifications can be achieved within as little as 1-2 weeks, and modified clonal cell lines can be derived within 2-3 weeks.
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Affiliation(s)
- F Ann Ran
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,McGovern Institute for Brain Research, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, USA.,Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Patrick D Hsu
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,McGovern Institute for Brain Research, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, USA.,Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jason Wright
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA
| | - Vineeta Agarwala
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,Program in Biophysics, Harvard University, MIT, Cambridge, Massachusetts, USA.,Harvard-MIT Division of Health Sciences and Technology, MIT, Cambridge, Massachusetts, USA
| | - David A Scott
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,McGovern Institute for Brain Research, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, USA.,Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA
| | - Feng Zhang
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, USA.,McGovern Institute for Brain Research, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, Massachusetts, USA.,Department of Biological Engineering, MIT, Cambridge, Massachusetts, USA
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25
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Abstract
Targeted nucleases are powerful tools for mediating genome alteration with high precision. The RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system can be used to facilitate efficient genome engineering in eukaryotic cells by simply specifying a 20-nt targeting sequence within its guide RNA. Here we describe a set of tools for Cas9-mediated genome editing via nonhomologous end joining (NHEJ) or homology-directed repair (HDR) in mammalian cells, as well as generation of modified cell lines for downstream functional studies. To minimize off-target cleavage, we further describe a double-nicking strategy using the Cas9 nickase mutant with paired guide RNAs. This protocol provides experimentally derived guidelines for the selection of target sites, evaluation of cleavage efficiency and analysis of off-target activity. Beginning with target design, gene modifications can be achieved within as little as 1-2 weeks, and modified clonal cell lines can be derived within 2-3 weeks.
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26
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Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, Trevino A, Scott DA, Inoue A, Matoba S, Zhang Y, Zhang F. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 2013; 154:1380-9. [PMID: 23992846 PMCID: PMC3856256 DOI: 10.1016/j.cell.2013.08.021] [Citation(s) in RCA: 2402] [Impact Index Per Article: 218.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 08/13/2013] [Accepted: 08/14/2013] [Indexed: 12/12/2022]
Abstract
Targeted genome editing technologies have enabled a broad range of research and medical applications. The Cas9 nuclease from the microbial CRISPR-Cas system is targeted to specific genomic loci by a 20 nt guide sequence, which can tolerate certain mismatches to the DNA target and thereby promote undesired off-target mutagenesis. Here, we describe an approach that combines a Cas9 nickase mutant with paired guide RNAs to introduce targeted double-strand breaks. Because individual nicks in the genome are repaired with high fidelity, simultaneous nicking via appropriately offset guide RNAs is required for double-stranded breaks and extends the number of specifically recognized bases for target cleavage. We demonstrate that using paired nicking can reduce off-target activity by 50- to 1,500-fold in cell lines and to facilitate gene knockout in mouse zygotes without sacrificing on-target cleavage efficiency. This versatile strategy enables a wide variety of genome editing applications that require high specificity.
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Affiliation(s)
- F. Ann Ran
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Patrick D. Hsu
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chie-Yu Lin
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Silvana Konermann
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alexandro Trevino
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - David A. Scott
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Azusa Inoue
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Shogo Matoba
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yi Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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27
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Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 2013. [PMID: 23873081 DOI: 10.1038/npbt.2647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
The Streptococcus pyogenes Cas9 (SpCas9) nuclease can be efficiently targeted to genomic loci by means of single-guide RNAs (sgRNAs) to enable genome editing. Here, we characterize SpCas9 targeting specificity in human cells to inform the selection of target sites and avoid off-target effects. Our study evaluates >700 guide RNA variants and SpCas9-induced indel mutation levels at >100 predicted genomic off-target loci in 293T and 293FT cells. We find that SpCas9 tolerates mismatches between guide RNA and target DNA at different positions in a sequence-dependent manner, sensitive to the number, position and distribution of mismatches. We also show that SpCas9-mediated cleavage is unaffected by DNA methylation and that the dosage of SpCas9 and sgRNA can be titrated to minimize off-target modification. To facilitate mammalian genome engineering applications, we provide a web-based software tool to guide the selection and validation of target sequences as well as off-target analyses.
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Affiliation(s)
- Patrick D Hsu
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA. [4]
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28
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Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 2013; 31:827-32. [PMID: 23873081 PMCID: PMC3969858 DOI: 10.1038/nbt.2647] [Citation(s) in RCA: 3228] [Impact Index Per Article: 293.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 06/30/2013] [Indexed: 12/15/2022]
Abstract
The Streptococcus pyogenes Cas9 (SpCas9) nuclease can be efficiently targeted to genomic loci by means of single-guide RNAs (sgRNAs) to enable genome editing. Here, we characterize SpCas9 targeting specificity in human cells to inform the selection of target sites and avoid off-target effects. Our study evaluates >700 guide RNA variants and SpCas9-induced indel mutation levels at >100 predicted genomic off-target loci in 293T and 293FT cells. We find that SpCas9 tolerates mismatches between guide RNA and target DNA at different positions in a sequence-dependent manner, sensitive to the number, position and distribution of mismatches. We also show that SpCas9-mediated cleavage is unaffected by DNA methylation and that the dosage of SpCas9 and sgRNA can be titrated to minimize off-target modification. To facilitate mammalian genome engineering applications, we provide a web-based software tool to guide the selection and validation of target sequences as well as off-target analyses.
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Affiliation(s)
- Patrick D Hsu
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA. [4]
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29
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Abstract
The Streptococcus pyogenes Cas9 (SpCas9) nuclease can be efficiently targeted to genomic loci by means of single-guide RNAs (sgRNAs) to enable genome editing. Here, we characterize SpCas9 targeting specificity in human cells to inform the selection of target sites and avoid off-target effects. Our study evaluates >700 guide RNA variants and SpCas9-induced indel mutation levels at >100 predicted genomic off-target loci in 293T and 293FT cells. We find that SpCas9 tolerates mismatches between guide RNA and target DNA at different positions in a sequence-dependent manner, sensitive to the number, position and distribution of mismatches. We also show that SpCas9-mediated cleavage is unaffected by DNA methylation and that the dosage of SpCas9 and sgRNA can be titrated to minimize off-target modification. To facilitate mammalian genome engineering applications, we provide a web-based software tool to guide the selection and validation of target sequences as well as off-target analyses.
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