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Nyberg KG, Navales FG, Keles E, Nguyen JQ, Hertz LM, Carthew RW. Robust and heritable knockdown of gene expression using a self-cleaving ribozyme in Drosophila. Genetics 2024; 227:iyae067. [PMID: 38701221 PMCID: PMC11304983 DOI: 10.1093/genetics/iyae067] [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: 01/19/2024] [Revised: 04/11/2024] [Accepted: 04/20/2024] [Indexed: 05/05/2024] Open
Abstract
The current toolkit for genetic manipulation in the model animal Drosophila melanogaster is extensive and versatile but not without its limitations. Here, we report a powerful and heritable method to knockdown gene expression in D. melanogaster using the self-cleaving N79 hammerhead ribozyme, a modification of a naturally occurring ribozyme found in the parasite Schistosoma mansoni. A 111-bp ribozyme cassette, consisting of the N79 ribozyme surrounded by insulating spacer sequences, was inserted into 4 independent long noncoding RNA genes as well as the male-specific splice variant of doublesex using scarless CRISPR/Cas9-mediated genome editing. Ribozyme-induced RNA cleavage resulted in robust destruction of 3' fragments typically exceeding 90%. Single molecule RNA fluorescence in situ hybridization results suggest that cleavage and destruction can even occur for nascent transcribing RNAs. Knockdown was highly specific to the targeted RNA, with no adverse effects observed in neighboring genes or the other splice variants. To control for potential effects produced by the simple insertion of 111 nucleotides into genes, we tested multiple catalytically inactive ribozyme variants and found that a variant with scrambled N79 sequence best recapitulated natural RNA levels. Thus, self-cleaving ribozymes offer a novel approach for powerful gene knockdown in Drosophila, with potential applications for the study of noncoding RNAs, nuclear-localized RNAs, and specific splice variants of protein-coding genes.
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Affiliation(s)
- Kevin G Nyberg
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Fritz Gerald Navales
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Eren Keles
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Joseph Q Nguyen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Laura M Hertz
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Richard W Carthew
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons National Institute for Theory and Mathematics in Biology, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Evanston, IL 60208, USA
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2
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Quantitative neurogenetics: applications in understanding disease. Biochem Soc Trans 2021; 49:1621-1631. [PMID: 34282824 DOI: 10.1042/bst20200732] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/11/2021] [Accepted: 06/21/2021] [Indexed: 12/31/2022]
Abstract
Neurodevelopmental and neurodegenerative disorders (NNDs) are a group of conditions with a broad range of core and co-morbidities, associated with dysfunction of the central nervous system. Improvements in high throughput sequencing have led to the detection of putative risk genetic loci for NNDs, however, quantitative neurogenetic approaches need to be further developed in order to establish causality and underlying molecular genetic mechanisms of pathogenesis. Here, we discuss an approach for prioritizing the contribution of genetic risk loci to complex-NND pathogenesis by estimating the possible impacts of these loci on gene regulation. Furthermore, we highlight the use of a tissue-specificity gene expression index and the application of artificial intelligence (AI) to improve the interpretation of the role of genetic risk elements in NND pathogenesis. Given that NND symptoms are associated with brain dysfunction, risk loci with direct, causative actions would comprise genes with essential functions in neural cells that are highly expressed in the brain. Indeed, NND risk genes implicated in brain dysfunction are disproportionately enriched in the brain compared with other tissues, which we refer to as brain-specific expressed genes. In addition, the tissue-specificity gene expression index can be used as a handle to identify non-brain contexts that are involved in NND pathogenesis. Lastly, we discuss how using an AI approach provides the opportunity to integrate the biological impacts of risk loci to identify those putative combinations of causative relationships through which genetic factors contribute to NND pathogenesis.
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3
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Değirmenci L, Geiger D, Rogé Ferreira FL, Keller A, Krischke B, Beye M, Steffan-Dewenter I, Scheiner R. CRISPR/Cas 9-Mediated Mutations as a New Tool for Studying Taste in Honeybees. Chem Senses 2021; 45:655-666. [PMID: 32968780 DOI: 10.1093/chemse/bjaa063] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Honeybees rely on nectar as their main source of carbohydrates. Sucrose, glucose, and fructose are the main components of plant nectars. Intriguingly, honeybees express only 3 putative sugar receptors (AmGr1, AmGr2, and AmGr3), which is in stark contrast to many other insects and vertebrates. The sugar receptors are only partially characterized. AmGr1 detects different sugars including sucrose and glucose. AmGr2 is assumed to act as a co-receptor only, while AmGr3 is assumedly a fructose receptor. We show that honeybee gustatory receptor AmGr3 is highly specialized for fructose perception when expressed in Xenopus oocytes. When we introduced nonsense mutations to the respective AmGr3 gene using CRISPR/Cas9 in eggs of female workers, the resulting mutants displayed almost a complete loss of responsiveness to fructose. In contrast, responses to sucrose were normal. Nonsense mutations introduced by CRISPR/Cas9 in honeybees can thus induce a measurable behavioral change and serve to characterize the function of taste receptors in vivo. CRISPR/Cas9 is an excellent novel tool for characterizing honeybee taste receptors in vivo. Biophysical receptor characterization in Xenopus oocytes and nonsense mutation of AmGr3 in honeybees unequivocally demonstrate that this receptor is highly specific for fructose.
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Affiliation(s)
- Laura Değirmenci
- Behavioral Physiology and Sociobiology, University of Würzburg, Biocenter, Am Hubland, Würzburg, Germany
| | - Dietmar Geiger
- Julius-von-Sachs-Institute, Molecular Plant Physiology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany
| | - Fábio Luiz Rogé Ferreira
- Julius-von-Sachs-Institute, Molecular Plant Physiology and Biophysics, University of Würzburg, Biocenter, Würzburg, Germany
| | - Alexander Keller
- Department of Bioinformatics, Biocenter, Am Hubland, Würzburg, Germany
| | - Beate Krischke
- Animal Ecology and Tropical Biology, University of Würzburg, Biocenter, Am Hubland, Würzburg, Germany
| | - Martin Beye
- Evolutionary Genetics, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Ingolf Steffan-Dewenter
- Animal Ecology and Tropical Biology, University of Würzburg, Biocenter, Am Hubland, Würzburg, Germany
| | - Ricarda Scheiner
- Behavioral Physiology and Sociobiology, University of Würzburg, Biocenter, Am Hubland, Würzburg, Germany
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4
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Rautela I, Uniyal P, Thapliyal P, Chauhan N, Bhushan Sinha V, Dev Sharma M. An extensive review to facilitate understanding of CRISPR technology as a gene editing possibility for enhanced therapeutic applications. Gene 2021; 785:145615. [PMID: 33775851 DOI: 10.1016/j.gene.2021.145615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 03/20/2021] [Accepted: 03/23/2021] [Indexed: 02/06/2023]
Abstract
CRISPR are the sequences in bacterial and archaeal genome which provide resistance against viral infections. They might be the natural part of bacterial genomes for providing protection against viruses like bacteriophages but science has successfully achieved their use in the benefit of man-kind by using them for the treatment of deadly diseases like cancer, AIDS or genetic disorders like sickle cell disease and Leber congenital amaurosis. CRISPR system is majorly divided into two classes i.e class I and class II, of which the class II CRISPR/Cas9 system performs site specific cleavage of DNA with a guide RNA Cas12 (Cpf1). With the new emerging discoveries it is being found that CRISPR not only works on double stranded DNA but can also be useful to induce any sort of site specific cleavage in RNA too by Cas13 earlier known as C2c2, which is a protein found in CRISPR system and has ability to cure viral infections in plants. CRISPR is being used in the field of gene manipulation and various animals models are available to serve this purpose with short lifespan, rapid reproducibility and lower maintenance cost. Many successful studies and experiments performed using CRISPR, reveals their potency and utility to bring revolution in the areas which were previously believed to be out of scope of science and medicine.
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Affiliation(s)
- Indra Rautela
- Department of Biotechnology, School of Applied and Life Sciences (SALS), Uttaranchal University, Dehradun 248001, Uttarakhand, India
| | - Pooja Uniyal
- Department of Biotechnology, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun 248001, Uttarakhand, India
| | - Priya Thapliyal
- Department of Biochemistry, H.N.B. Garhwal (A Central) University, Srinagar 246174, Uttarakhand, India
| | - Neha Chauhan
- Department of Medical Microbiology, College of Paramedical Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun 248001, Uttarakhand, India
| | | | - Manish Dev Sharma
- Department of Biotechnology, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun 248001, Uttarakhand, India.
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5
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Jain RG, Robinson KE, Fletcher SJ, Mitter N. RNAi-Based Functional Genomics in Hemiptera. INSECTS 2020; 11:E557. [PMID: 32825516 PMCID: PMC7564473 DOI: 10.3390/insects11090557] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 01/05/2023]
Abstract
RNA interference (RNAi) is a powerful approach for sequence-specific gene silencing, displaying tremendous potential for functional genomics studies in hemipteran insects. Exploiting RNAi allows the biological roles of critical genes to be defined and aids the development of RNAi-based biopesticides. In this review, we provide context to the rapidly expanding field of RNAi-based functional genomics studies in hemipteran insects. We highlight the most widely used RNAi delivery strategies, including microinjection, oral ingestion and topical application. Additionally, we discuss the key variables affecting RNAi efficacy in hemipteran insects, including insect life-stage, gene selection, the presence of nucleases, and the role of core RNAi machinery. In conclusion, we summarise the application of RNAi in functional genomics studies in Hemiptera, focusing on genes involved in reproduction, behaviour, metabolism, immunity and chemical resistance across 33 species belonging to 14 families.
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Affiliation(s)
| | - Karl E. Robinson
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Sciences, The University of Queensland, Brisbane 4072, Queensland, Australia; (R.G.J.); (S.J.F.); (N.M.)
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6
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Sonnen KF, Merten CA. Microfluidics as an Emerging Precision Tool in Developmental Biology. Dev Cell 2019; 48:293-311. [PMID: 30753835 DOI: 10.1016/j.devcel.2019.01.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/13/2018] [Accepted: 01/10/2019] [Indexed: 12/18/2022]
Abstract
Microfluidics has become a precision tool in modern biology. It enables omics data to be obtained from individual cells, as compared to averaged signals from cell populations, and it allows manipulation of biological specimens in entirely new ways. Cells and organisms can be perturbed at extraordinary spatiotemporal resolution, revealing mechanistic insights that would otherwise remain hidden. In this perspective article, we discuss the current and future impact of microfluidic technology in the field of developmental biology. In addition, we provide detailed information on how to start using this technology even without prior experience.
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Affiliation(s)
| | - Christoph A Merten
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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7
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Aquilina B, Cauchi RJ. Modelling motor neuron disease in fruit flies: Lessons from spinal muscular atrophy. J Neurosci Methods 2018; 310:3-11. [DOI: 10.1016/j.jneumeth.2018.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 04/06/2018] [Accepted: 04/07/2018] [Indexed: 12/25/2022]
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8
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Borman AM. Of mice and men and larvae: Galleria mellonella to model the early host-pathogen interactions after fungal infection. Virulence 2017; 9:9-12. [PMID: 28933671 PMCID: PMC5955190 DOI: 10.1080/21505594.2017.1382799] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Andrew M Borman
- a UK National Mycology Reference Laboratory (MRL) , Public Health England South-West , Bristol , UK
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9
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Knowlton MN, Smith CL. Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species. Mamm Genome 2017; 28:367-376. [PMID: 28589392 PMCID: PMC5569137 DOI: 10.1007/s00335-017-9698-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/27/2017] [Indexed: 12/29/2022]
Abstract
The widespread use of CRISPR/Cas and other targeted endonuclease technologies in many species has led to an explosion in the generation of new mutations and alleles. The ability to generate many different mutations from the same target sequence either by homology-directed repair with a donor sequence or non-homologous end joining-induced insertions and deletions necessitates a means for representing these mutations in literature and databases. Standardized nomenclature can be used to generate unambiguous, concise, and specific symbols to represent mutations and alleles. The research communities of a variety of species using CRISPR/Cas and other endonuclease-mediated mutation technologies have developed different approaches to naming and identifying such alleles and mutations. While some organism-specific research communities have developed allele nomenclature that incorporates the method of generation within the official allele or mutant symbol, others use metadata tags that include method of generation or mutagen. Organism-specific research community databases together with organism-specific nomenclature committees are leading the way in providing standardized nomenclature and metadata to facilitate the integration of data from alleles and mutations generated using CRISPR/Cas and other targeted endonucleases.
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Affiliation(s)
| | - Cynthia L Smith
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, 04609, USA
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10
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Huang Q, Cao Y, Liu Z, Tan Y, Liu Y. Efficient gene replacements in ku70 disruption strain of Aspergillus chevalieri var. intermedius. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1251828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Qingqing Huang
- Department of Life Science, Guizhou Normal University, Guiyang, China
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yang Cao
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Zuoyi Liu
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yumei Tan
- Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yongxiang Liu
- Guizhou Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, China
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11
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Mino RE, Rogers SL, Risinger AL, Rohena C, Banerjee S, Bhat MA. Drosophila Ringmaker regulates microtubule stabilization and axonal extension during embryonic development. J Cell Sci 2016; 129:3282-94. [PMID: 27422099 DOI: 10.1242/jcs.187294] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 07/13/2016] [Indexed: 11/20/2022] Open
Abstract
Axonal growth and targeting are fundamental to the organization of the nervous system, and require active engagement of the cytoskeleton. Polymerization and stabilization of axonal microtubules is central to axonal growth and maturation of neuronal connectivity. Studies have suggested that members of the tubulin polymerization promoting protein (TPPP, also known as P25α) family are involved in cellular process extension. However, no in vivo knockout data exists regarding its role in axonal growth during development. Here, we report the characterization of Ringmaker (Ringer; CG45057), the only Drosophila homolog of long p25α proteins. Immunohistochemical analyses indicate that Ringer expression is dynamically regulated in the embryonic central nervous system (CNS). ringer-null mutants show cell misplacement, and errors in axonal extension and targeting. Ultrastructural examination of ringer mutants revealed defective microtubule morphology and organization. Primary neuronal cultures of ringer mutants exhibit defective axonal extension, and Ringer expression in cells induced microtubule stabilization and bundling into rings. In vitro assays showed that Ringer directly affects tubulin, and promotes microtubule bundling and polymerization. Together, our studies uncover an essential function of Ringer in axonal extension and targeting through proper microtubule organization.
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Affiliation(s)
- Rosa E Mino
- Department of Physiology, University of Texas School of Medicine, Health Science Center, San Antonio, TX 78229, USA
| | - Stephen L Rogers
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - April L Risinger
- Department of Pharmacology, University of Texas School of Medicine, Health Science Center, San Antonio, TX 78229, USA
| | - Cristina Rohena
- Department of Pharmacology, University of Texas School of Medicine, Health Science Center, San Antonio, TX 78229, USA Department of Medicine, University of California, San Diego, CA 92093, USA
| | - Swati Banerjee
- Department of Physiology, University of Texas School of Medicine, Health Science Center, San Antonio, TX 78229, USA
| | - Manzoor A Bhat
- Department of Physiology, University of Texas School of Medicine, Health Science Center, San Antonio, TX 78229, USA
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12
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Koutroumpa FA, Monsempes C, François MC, de Cian A, Royer C, Concordet JP, Jacquin-Joly E. Heritable genome editing with CRISPR/Cas9 induces anosmia in a crop pest moth. Sci Rep 2016; 6:29620. [PMID: 27403935 PMCID: PMC4940732 DOI: 10.1038/srep29620] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/17/2016] [Indexed: 12/20/2022] Open
Abstract
Lepidoptera suffer critical lack of genetic tools and heritable genome edition has been achieved only in a few model species. Here we demonstrate that the CRISPR/Cas9 system is highly efficient for genome editing in a non-model crop pest Lepidoptera, the noctuid moth Spodoptera littoralis. We knocked-out the olfactory receptor co-receptor Orco gene to investigate its function in Lepidoptera olfaction. We find that 89.6% of the injected individuals carried Orco mutations, 70% of which transmitted them to the next generation. CRISPR/Cas9-mediated Orco knockout caused defects in plant odor and sex pheromone olfactory detection in homozygous individuals. Our work genetically defines Orco as an essential OR partner for both host and mate detection in Lepidoptera, and demonstrates that CRISPR/Cas9 is a simple and highly efficient genome editing technique in noctuid pests opening new routes for gene function analysis and the development of novel pest control strategies.
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Affiliation(s)
| | | | | | - Anne de Cian
- CNRS UMR 7196, INSERM U1154, Museum National d'Histoire Naturelle, Paris, France
| | - Corinne Royer
- INSA-Lyon, Villeurbanne F-69621, France.,INRA, UMR203 BF2I, Biologie Fonctionnelle Insecte et Interaction, F-69621, France
| | - Jean-Paul Concordet
- CNRS UMR 7196, INSERM U1154, Museum National d'Histoire Naturelle, Paris, France
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13
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Nishizawa-Yokoi A, Cermak T, Hoshino T, Sugimoto K, Saika H, Mori A, Osakabe K, Hamada M, Katayose Y, Starker C, Voytas DF, Toki S. A Defect in DNA Ligase4 Enhances the Frequency of TALEN-Mediated Targeted Mutagenesis in Rice. PLANT PHYSIOLOGY 2016; 170:653-66. [PMID: 26668331 PMCID: PMC4734567 DOI: 10.1104/pp.15.01542] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/10/2015] [Indexed: 05/02/2023]
Abstract
We have established methods for site-directed mutagenesis via transcription activator-like effector nucleases (TALENs) in the endogenous rice (Oryza sativa) waxy gene and demonstrated stable inheritance of TALEN-induced somatic mutations to the progeny. To analyze the role of classical nonhomologous end joining (cNHEJ) and alternative nonhomologous end joining (altNHEJ) pathways in TALEN-induced mutagenesis in plant cells, we investigated whether a lack of DNA Ligase4 (Lig4) affects the kinetics of TALEN-induced double-strand break repair in rice cells. Deep-sequencing analysis revealed that the frequency of all types of mutations, namely deletion, insertion, combination of insertion with deletion, and substitution, in lig4 null mutant calli was higher than that in a lig4 heterozygous mutant or the wild type. In addition, the ratio of large deletions (greater than 10 bp) and deletions repaired by microhomology-mediated end joining (MMEJ) to total deletion mutations in lig4 null mutant calli was higher than that in the lig4 heterozygous mutant or wild type. Furthermore, almost all insertions (2 bp or greater) were shown to be processed via copy and paste of one or more regions around the TALENs cleavage site and rejoined via MMEJ regardless of genetic background. Taken together, our findings indicate that the dysfunction of cNHEJ leads to a shift in the repair pathway from cNHEJ to altNHEJ or synthesis-dependent strand annealing.
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Affiliation(s)
- Ayako Nishizawa-Yokoi
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Tomas Cermak
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Tomoki Hoshino
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Kazuhiko Sugimoto
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Hiroaki Saika
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Akiko Mori
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Keishi Osakabe
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Masao Hamada
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Yuichi Katayose
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Colby Starker
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Daniel F Voytas
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
| | - Seiichi Toki
- Plant Genome Engineering Research Unit (A.N.-Y., H.S., A.M., S.T.), Rice Applied Genomics Research Unit (T.H., K.S.), and Advanced Genomics Laboratory (M.H., Y.K.), National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan;Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (T.C., C.S., D.F.V.);Center for Collaboration among Agriculture, Industry, and Commerce, University of Tokushima, Tokushima 770-8503, Japan (K.O.); andKihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan (S.T.)
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14
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Tokunaga A, Anai H, Hanada K. Mechanisms of gene targeting in higher eukaryotes. Cell Mol Life Sci 2016; 73:523-33. [PMID: 26507245 PMCID: PMC11108335 DOI: 10.1007/s00018-015-2073-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/14/2015] [Accepted: 10/14/2015] [Indexed: 10/22/2022]
Abstract
Targeted genome modifications using techniques that alter the genomic information of interest have contributed to multiple studies in both basic and applied biology. Traditionally, in gene targeting, the target-site integration of a targeting vector by homologous recombination is used. However, this strategy has several technical problems. The first problem is the extremely low frequency of gene targeting, which makes obtaining recombinant clones an extremely labor intensive task. The second issue is the limited number of biomaterials to which gene targeting can be applied. Traditional gene targeting hardly occurs in most of the human adherent cell lines. However, a new approach using designer nucleases that can introduce site-specific double-strand breaks in genomic DNAs has increased the efficiency of gene targeting. This new method has also expanded the number of biomaterials to which gene targeting could be applied. Here, we summarize various strategies for target gene modification, including a comparison of traditional gene targeting with designer nucleases.
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Affiliation(s)
- Akinori Tokunaga
- The Tokunaga Laboratory, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan
- Section of Physiology, Department of Integrative Aging Neuroscience, National Center for Geriatrics and Gerontology (NCGG), 7-430, Morioka-cho, Obu, Aichi, 474-8511, Japan
| | - Hirofumi Anai
- Clinical Engineering Research Center, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan
| | - Katsuhiro Hanada
- Clinical Engineering Research Center, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita, 879-5593, Japan.
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15
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Riordan SM, Heruth DP, Zhang LQ, Ye SQ. Application of CRISPR/Cas9 for biomedical discoveries. Cell Biosci 2015; 5:33. [PMID: 26137216 PMCID: PMC4487574 DOI: 10.1186/s13578-015-0027-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/13/2015] [Indexed: 12/26/2022] Open
Abstract
The Clustered Regions of Interspersed Palindromic Repeats-Cas9 (CRISPR/Cas9), a viral defense system found in bacteria and archaea, has emerged as a tour de force genome editing tool. The CRISPR/Cas9 system is much easier to customize and optimize because the site selection for DNA cleavage is guided by a short sequence of RNA rather than an engineered protein as in the systems of zinc finger nucleases (ZFN), transcription activator–like effector nucleases (TALEN), and meganucleases. Although it still suffers from some off-target effects, the CRISPR/Cas9 system has been broadly and successfully applied for biomedical discoveries in a number of areas. In this review, we present a brief history and development of the CRISPR system and focus on the application of this genome editing technology for biomedical discoveries. We then present concise concluding remarks and future directions for this fast moving field.
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Affiliation(s)
- Sean M Riordan
- Department of Pediatrics, The Children's Mercy Hospital, Kansas City, MO USA
| | - Daniel P Heruth
- Department of Pediatrics, The Children's Mercy Hospital, Kansas City, MO USA
| | - Li Q Zhang
- Department of Pediatrics, The Children's Mercy Hospital, Kansas City, MO USA
| | - Shui Qing Ye
- Department of Pediatrics, The Children's Mercy Hospital, Kansas City, MO USA ; Department of Biomedical and Health Informatics, University of Missouri Kansas City School of Medicine, Kansas City, MO USA
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16
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Xu J, Ren X, Sun J, Wang X, Qiao HH, Xu BW, Liu LP, Ni JQ. A Toolkit of CRISPR-Based Genome Editing Systems in Drosophila. J Genet Genomics 2015; 42:141-9. [PMID: 25953352 DOI: 10.1016/j.jgg.2015.02.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 02/11/2015] [Accepted: 02/26/2015] [Indexed: 12/13/2022]
Abstract
The last couple of years have witnessed an explosion in development of CRISPR-based genome editing technologies in cell lines as well as in model organisms. In this review, we focus on the applications of this popular system in Drosophila. We discuss the effectiveness of the CRISPR/Cas9 systems in terms of delivery, mutagenesis detection, parameters affecting efficiency, and off-target issues, with an emphasis on how to apply this powerful tool to characterize gene functions.
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Affiliation(s)
- Jiang Xu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua Fly Center, Tsinghua University, Beijing 100084, China; School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China; College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | - Xingjie Ren
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jin Sun
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xia Wang
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Huan-Huan Qiao
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Bo-Wen Xu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lu-Ping Liu
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua Fly Center, Tsinghua University, Beijing 100084, China
| | - Jian-Quan Ni
- Gene Regulatory Lab, School of Medicine, Tsinghua University, Beijing 100084, China.
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