151
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Blitz IL, Fish MB, Cho KWY. Leapfrogging: primordial germ cell transplantation permits recovery of CRISPR/Cas9-induced mutations in essential genes. Development 2016; 143:2868-75. [PMID: 27385011 PMCID: PMC5004912 DOI: 10.1242/dev.138057] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 06/15/2016] [Indexed: 01/07/2023]
Abstract
CRISPR/Cas9 genome editing is revolutionizing genetic loss-of-function analysis but technical limitations remain that slow progress when creating mutant lines. First, in conventional genetic breeding schemes, mosaic founder animals carrying mutant alleles are outcrossed to produce F1 heterozygotes. Phenotypic analysis occurs in the F2 generation following F1 intercrosses. Thus, mutant analyses will require multi-generational studies. Second, when targeting essential genes, efficient mutagenesis of founders is often lethal, preventing the acquisition of mature animals. Reducing mutagenesis levels may improve founder survival, but results in lower, more variable rates of germline transmission. Therefore, an efficient approach to study lethal mutations would be useful. To overcome these shortfalls, we introduce 'leapfrogging', a method combining efficient CRISPR mutagenesis with transplantation of mutated primordial germ cells into a wild-type host. Tested using Xenopus tropicalis, we show that founders containing transplants transmit mutant alleles with high efficiency. F1 offspring from intercrosses between F0 animals that carry embryonic lethal alleles recapitulate loss-of-function phenotypes, circumventing an entire generation of breeding. We anticipate that leapfrogging will be transferable to other species.
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Affiliation(s)
- Ira L Blitz
- 4410 Natural Sciences Building 2, Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Margaret B Fish
- 4410 Natural Sciences Building 2, Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
| | - Ken W Y Cho
- 4410 Natural Sciences Building 2, Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
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152
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Guan L, Han Y, Zhu S, Lin J. Application of CRISPR-Cas system in gene therapy: Pre-clinical progress in animal model. DNA Repair (Amst) 2016; 46:1-8. [PMID: 27519625 DOI: 10.1016/j.dnarep.2016.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 07/29/2016] [Accepted: 07/29/2016] [Indexed: 12/26/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated proteins (Cas) belong to the crucial adaptive immune system, which exist in archaea and bacteria. Currently, CRISPR-Cas9 system has been modified and widely used to edit genome. In this review, we summarized the discovery, classification and mechanism of CRISPR-Cas system and further discussed the application of CRISPR-Cas9 in gene therapy, mainly in disease models.
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Affiliation(s)
- Lihong Guan
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China; Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, Henan, 453003, China
| | - Yawei Han
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan, 450002, China
| | - Shaoyi Zhu
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
| | - Juntang Lin
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China; Henan Key Laboratory of Medical Tissue Regeneration, Xinxiang, Henan, 453003, China; College of Biomedical Engineering, Xinxiang Medical University, Xinxiang, Henan, 453003, China.
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153
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Chugunova AA, Dontsova OA, Sergiev PV. Methods of genome engineering: a new era of molecular biology. BIOCHEMISTRY (MOSCOW) 2016; 81:662-77. [DOI: 10.1134/s0006297916070038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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154
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Young JJ, Kjolby RAS, Wu G, Wong D, Hsu SW, Harland RM. Noggin is required for first pharyngeal arch differentiation in the frog Xenopus tropicalis. Dev Biol 2016; 426:245-254. [PMID: 27364468 DOI: 10.1016/j.ydbio.2016.06.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 06/18/2016] [Accepted: 06/24/2016] [Indexed: 02/02/2023]
Abstract
The dorsal ventral axis of vertebrates requires high BMP activity for ventral development and inhibition of BMP activity for dorsal development. Presumptive dorsal regions of the embryo are protected from the ventralizing activity of BMPs by the secretion of BMP antagonists from the mesoderm. Noggin, one such antagonist, binds BMP ligands and prevents them from binding their receptors, however, a unique role for Noggin in amphibian development has remained unclear. Previously, we used zinc-finger nucleases to mutagenize the noggin locus in Xenopus tropicalis. Here, we report on the phenotype of noggin mutant frogs as a result of breeding null mutations to homozygosity. Early homozygous noggin mutant embryos are indistinguishable from wildtype siblings, with normal neural induction and neural tube closure. However, in late tadpole stages mutants present severe ventral craniofacial defects, notably a fusion of Meckel's cartilage to the palatoquadrate cartilage. Consistent with a noggin loss-of-function, mutants show expansions of BMP target gene expression and the mutant phenotype can be rescued with transient BMP inhibition. These results demonstrate that in amphibians, Noggin is dispensable for early embryonic patterning but is critical for cranial skeletogenesis.
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Affiliation(s)
- John J Young
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Rachel A S Kjolby
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Gloria Wu
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Daniel Wong
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Shu-Wei Hsu
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Richard M Harland
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
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155
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Shigeta M, Sakane Y, Iida M, Suzuki M, Kashiwagi K, Kashiwagi A, Fujii S, Yamamoto T, Suzuki KIT. Rapid and efficient analysis of gene function using CRISPR-Cas9 inXenopus tropicalisfounders. Genes Cells 2016; 21:755-71. [DOI: 10.1111/gtc.12379] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 04/22/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Mitsuki Shigeta
- Department of Mathematical and Life Sciences; Hiroshima University; 1-3-1 Kagamiyama Higashi-Hiroshima Hiroshima 739-8526 Japan
| | - Yuto Sakane
- Department of Mathematical and Life Sciences; Hiroshima University; 1-3-1 Kagamiyama Higashi-Hiroshima Hiroshima 739-8526 Japan
| | - Midori Iida
- Department of Bioscience and Bioinformatics; Kyushu Institute of Technology; 680-4 Kawazu Iizuka Fukuoka 820-8502 Japan
| | - Miyuki Suzuki
- Department of Mathematical and Life Sciences; Hiroshima University; 1-3-1 Kagamiyama Higashi-Hiroshima Hiroshima 739-8526 Japan
| | - Keiko Kashiwagi
- Institute for Amphibian Biology; Graduate School of Science; Hiroshima University; 1-3-1 Kagamiyama Higashi-Hiroshima Hiroshima 739-8526 Japan
| | - Akihiko Kashiwagi
- Institute for Amphibian Biology; Graduate School of Science; Hiroshima University; 1-3-1 Kagamiyama Higashi-Hiroshima Hiroshima 739-8526 Japan
| | - Satoshi Fujii
- Department of Bioscience and Bioinformatics; Kyushu Institute of Technology; 680-4 Kawazu Iizuka Fukuoka 820-8502 Japan
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences; Hiroshima University; 1-3-1 Kagamiyama Higashi-Hiroshima Hiroshima 739-8526 Japan
| | - Ken-ichi T. Suzuki
- Department of Mathematical and Life Sciences; Hiroshima University; 1-3-1 Kagamiyama Higashi-Hiroshima Hiroshima 739-8526 Japan
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156
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Nelles DA, Fang MY, O'Connell MR, Xu JL, Markmiller SJ, Doudna JA, Yeo GW. Programmable RNA Tracking in Live Cells with CRISPR/Cas9. Cell 2016; 165:488-96. [PMID: 26997482 PMCID: PMC4826288 DOI: 10.1016/j.cell.2016.02.054] [Citation(s) in RCA: 392] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 02/05/2016] [Accepted: 02/24/2016] [Indexed: 11/23/2022]
Abstract
RNA-programmed genome editing using CRISPR/Cas9 from Streptococcus pyogenes has enabled rapid and accessible alteration of specific genomic loci in many organisms. A flexible means to target RNA would allow alteration and imaging of endogenous RNA transcripts analogous to CRISPR/Cas-based genomic tools, but most RNA targeting methods rely on incorporation of exogenous tags. Here, we demonstrate that nuclease-inactive S. pyogenes CRISPR/Cas9 can bind RNA in a nucleic-acid-programmed manner and allow endogenous RNA tracking in living cells. We show that nuclear-localized RNA-targeting Cas9 (RCas9) is exported to the cytoplasm only in the presence of sgRNAs targeting mRNA and observe accumulation of ACTB, CCNA2, and TFRC mRNAs in RNA granules that correlate with fluorescence in situ hybridization. We also demonstrate time-resolved measurements of ACTB mRNA trafficking to stress granules. Our results establish RCas9 as a means to track RNA in living cells in a programmable manner without genetically encoded tags.
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Affiliation(s)
- David A Nelles
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Materials Science and Engineering Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark Y Fang
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Mitchell R O'Connell
- Department of Molecular and Cell Biology and Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jia L Xu
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Sebastian J Markmiller
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology and Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, Innovative Genomics Initiative and Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, Berkeley, CA 94720, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Materials Science and Engineering Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 1190777, Singapore.
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157
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Saito S, Ohkita M, Saito CT, Takahashi K, Tominaga M, Ohta T. Evolution of Heat Sensors Drove Shifts in Thermosensation between Xenopus Species Adapted to Different Thermal Niches. J Biol Chem 2016; 291:11446-59. [PMID: 27022021 DOI: 10.1074/jbc.m115.702498] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Indexed: 11/06/2022] Open
Abstract
Temperature is one of the most critical environmental factors affecting survival, and thus species that inhabit different thermal niches have evolved thermal sensitivities suitable for their respective habitats. During the process of shifting thermal niches, various types of genes expressed in diverse tissues, including those of the peripheral to central nervous systems, are potentially involved in the evolutionary changes in thermosensation. To elucidate the molecular mechanisms behind the evolution of thermosensation, thermal responses were compared between two species of clawed frogs (Xenopus laevis and Xenopus tropicalis) adapted to different thermal environments. X. laevis was much more sensitive to heat stimulation than X. tropicalis at the behavioral and neural levels. The activity and sensitivity of the heat-sensing TRPA1 channel were higher in X. laevis compared with those of X. tropicalis The thermal responses of another heat-sensing channel, TRPV1, also differed between the two Xenopus species. The species differences in Xenopus TRPV1 heat responses were largely determined by three amino acid substitutions located in the first three ankyrin repeat domains, known to be involved in the regulation of rat TRPV1 activity. In addition, Xenopus TRPV1 exhibited drastic species differences in sensitivity to capsaicin, contained in chili peppers, between the two Xenopus species. Another single amino acid substitution within Xenopus TRPV1 is responsible for this species difference, which likely alters the neural and behavioral responses to capsaicin. These combined subtle amino acid substitutions in peripheral thermal sensors potentially serve as a driving force for the evolution of thermal and chemical sensation.
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Affiliation(s)
- Shigeru Saito
- From the Division of Cell Signaling, Okazaki Institute for Integrative Bioscience, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan, the Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan, and
| | - Masashi Ohkita
- the Department of Veterinary Pharmacology, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
| | - Claire T Saito
- From the Division of Cell Signaling, Okazaki Institute for Integrative Bioscience, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Kenji Takahashi
- the Department of Veterinary Pharmacology, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
| | - Makoto Tominaga
- From the Division of Cell Signaling, Okazaki Institute for Integrative Bioscience, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan, the Department of Physiological Sciences, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan, and
| | - Toshio Ohta
- the Department of Veterinary Pharmacology, Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
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158
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Watanabe Y, Grommen SVH, De Groef B. Corticotropin-releasing hormone: Mediator of vertebrate life stage transitions? Gen Comp Endocrinol 2016; 228:60-68. [PMID: 26874222 DOI: 10.1016/j.ygcen.2016.02.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 02/07/2016] [Accepted: 02/09/2016] [Indexed: 01/10/2023]
Abstract
Hormones, particularly thyroid hormones and corticosteroids, play critical roles in vertebrate life stage transitions such as amphibian metamorphosis, hatching in precocial birds, and smoltification in salmonids. Since they synergistically regulate several metabolic and developmental processes that accompany vertebrate life stage transitions, the existence of extensive cross-communication between the adrenal/interrenal and thyroidal axes is not surprising. Synergies of corticosteroids and thyroid hormones are based on effects at the level of tissue hormone sensitivity and gene regulation. In addition, in representative nonmammalian vertebrates, corticotropin-releasing hormone (CRH) stimulates hypophyseal thyrotropin secretion, and thus functions as a common regulator of both the adrenal/interrenal and thyroidal axes to release corticosteroids and thyroid hormones. The dual function of CRH has been speculated to control or affect the timing of vertebrate life history transitions across taxa. After a brief overview of recent insights in the molecular mechanisms behind the synergic actions of thyroid hormones and corticosteroids during life stage transitions, this review examines the evidence for a possible role of CRH in controlling vertebrate life stage transitions.
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Affiliation(s)
- Yugo Watanabe
- Department of Anatomy, Physiology and Microbiology, La Trobe University, Bundoora, Victoria 3086, Australia.
| | - Sylvia V H Grommen
- Department of Anatomy, Physiology and Microbiology, La Trobe University, Bundoora, Victoria 3086, Australia.
| | - Bert De Groef
- Department of Anatomy, Physiology and Microbiology, La Trobe University, Bundoora, Victoria 3086, Australia.
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159
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Plautz CZ, Williams HC, Grainger RM. Functional Cloning Using a Xenopus Oocyte Expression System. J Vis Exp 2016:e53518. [PMID: 26862700 DOI: 10.3791/53518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Identification of genes responsible for embryonic induction poses a number of challenges; to name a few, secreted molecules of interest may be low in abundance, may not be secreted but tethered to the signaling cell(s), or may require the presence of binding partners or upstream regulatory molecules. Thus in a search for gene products capable of eliciting an early lens-inductive response in competent ectoderm, we utilized an expression cloning system that would allow identification of paracrine or juxtacrine factors as well as transcriptional or other regulatory proteins. Pools of mRNA were injected into Xenopus oocytes, and responding tissue placed directly on the oocytes and co-cultured. Following functional cloning of ldb1 from a neural plate stage cDNA library based on its ability to elicit the expression of the early lens placode marker foxe3 in lens-competent animal cap ectoderm, we characterized the mRNA expression pattern, and assayed developmental progression following overexpression or knockdown of ldb1. This system is suitable in a very wide variety of contexts where identification of an inducer or its upstream regulatory molecules is sought using a functional response in competent tissue.
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160
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Ma D, Liu F. Genome Editing and Its Applications in Model Organisms. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 13:336-44. [PMID: 26762955 PMCID: PMC4747648 DOI: 10.1016/j.gpb.2015.12.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/03/2015] [Accepted: 12/16/2015] [Indexed: 12/22/2022]
Abstract
Technological advances are important for innovative biological research. Development of molecular tools for DNA manipulation, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly-interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas), has revolutionized genome editing. These approaches can be used to develop potential therapeutic strategies to effectively treat heritable diseases. In the last few years, substantial progress has been made in CRISPR/Cas technology, including technical improvements and wide application in many model systems. This review describes recent advancements in genome editing with a particular focus on CRISPR/Cas, covering the underlying principles, technological optimization, and its application in zebrafish and other model organisms, disease modeling, and gene therapy used for personalized medicine.
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Affiliation(s)
- Dongyuan Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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161
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Wen L, Shi YB. Regulation of growth rate and developmental timing by Xenopus thyroid hormone receptor α. Dev Growth Differ 2016; 58:106-15. [PMID: 26219216 PMCID: PMC6296368 DOI: 10.1111/dgd.12231] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 05/22/2015] [Accepted: 05/25/2015] [Indexed: 01/31/2023]
Abstract
Thyroid hormone (TH) is critical for vertebrate postembryonic development, a period around birth in mammals when plasma TH levels are high. Interestingly, TH receptors (TRs), especially TRα, are expressed prior to the synthesis and secretion of zygotic TH, suggesting the existence of unliganded TR during development. However, the role of unliganded TR during mammalian development has been difficult to study, in part due to the relatively weak phenotype of TR knockout mice. Amphibian metamorphosis resembles postembryonic development in mammals and is controlled by TH via TRs. Like in mammals, TRα gene is highly activated and is the major TR expressed prior to the synthesis of endogenous TH. By using TALEN (transcriptional activator like effector nucleases)-mediated gene editing approach, we and others have now shown that unliganded TRα has two independent functions during Xenopus premetamorphosis, i.e. inhibiting growth rate and slowing development. Furthermore, molecular and transgenic studies have shown that unliganded TRα accomplishes these via the recruitment of histone deacetylase (HDAC)-containing corepressor complexes to repress the expression of TH-inducible genes.
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Affiliation(s)
- Luan Wen
- Section on Molecular Morphogenesis, Program on Cell Regulation and Metabolism, National Institute of Child Health and Human Development, National Institutes of Health, Bldg. 18T, Rm. 106, Bethesda, Maryland 20892, USA
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Program on Cell Regulation and Metabolism, National Institute of Child Health and Human Development, National Institutes of Health, Bldg. 18T, Rm. 106, Bethesda, Maryland 20892, USA
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162
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Parant JM, Yeh JRJ. Approaches to Inactivate Genes in Zebrafish. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:61-86. [PMID: 27165349 DOI: 10.1007/978-3-319-30654-4_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Animal models of tumor initiation and tumor progression are essential components toward understanding cancer and designing/validating future therapies. Zebrafish is a powerful model for studying tumorigenesis and has been successfully exploited in drug discovery. According to the zebrafish reference genome, 82 % of disease-associated genes in the Online Mendelian Inheritance in Man (OMIM) database have clear zebrafish orthologues. Using a variety of large-scale random mutagenesis methods developed to date, zebrafish can provide a unique opportunity to identify gene mutations that may be associated with cancer predisposition. On the other hand, newer technologies enabling targeted mutagenesis can facilitate reverse cancer genetic studies and open the door for complex genetic analysis of tumorigenesis. In this chapter, we will describe the various technologies for conducting genome editing in zebrafish with special emphasis on the approaches to inactivate genes.
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Affiliation(s)
- John M Parant
- Department of Pharmacology and Toxicology, UAB Comprehensive Cancer Center, University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35294, USA.
| | - Jing-Ruey Joanna Yeh
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, 02129, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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163
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Farasat I, Salis HM. A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation. PLoS Comput Biol 2016; 12:e1004724. [PMID: 26824432 PMCID: PMC4732943 DOI: 10.1371/journal.pcbi.1004724] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 12/23/2015] [Indexed: 12/26/2022] Open
Abstract
The ability to precisely modify genomes and regulate specific genes will greatly accelerate several medical and engineering applications. The CRISPR/Cas9 (Type II) system binds and cuts DNA using guide RNAs, though the variables that control its on-target and off-target activity remain poorly characterized. Here, we develop and parameterize a system-wide biophysical model of Cas9-based genome editing and gene regulation to predict how changing guide RNA sequences, DNA superhelical densities, Cas9 and crRNA expression levels, organisms and growth conditions, and experimental conditions collectively control the dynamics of dCas9-based binding and Cas9-based cleavage at all DNA sites with both canonical and non-canonical PAMs. We combine statistical thermodynamics and kinetics to model Cas9:crRNA complex formation, diffusion, site selection, reversible R-loop formation, and cleavage, using large amounts of structural, biochemical, expression, and next-generation sequencing data to determine kinetic parameters and develop free energy models. Our results identify DNA supercoiling as a novel mechanism controlling Cas9 binding. Using the model, we predict Cas9 off-target binding frequencies across the lambdaphage and human genomes, and explain why Cas9's off-target activity can be so high. With this improved understanding, we propose several rules for designing experiments for minimizing off-target activity. We also discuss the implications for engineering dCas9-based genetic circuits.
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Affiliation(s)
- Iman Farasat
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Howard M. Salis
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Biological Engineering, Pennsylvania State University, University Park, Pennsylvania, United States of America
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164
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Roland AB, O’Connell LA. Poison frogs as a model system for studying the neurobiology of parental care. Curr Opin Behav Sci 2015. [DOI: 10.1016/j.cobeha.2015.10.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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165
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Square T, Romášek M, Jandzik D, Cattell MV, Klymkowsky M, Medeiros DM. CRISPR/Cas9-mediated mutagenesis in the sea lamprey Petromyzon marinus: a powerful tool for understanding ancestral gene functions in vertebrates. DEVELOPMENT (CAMBRIDGE, ENGLAND) 2015. [PMID: 26511928 DOI: 10.1242/dev.125609.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Lamprey is one of only two living jawless vertebrates, a group that includes the first vertebrates. Comparisons between lamprey and jawed vertebrates have yielded important insights into the origin and evolution of vertebrate physiology, morphology and development. Despite its key phylogenetic position, studies of lamprey have been limited by their complex life history, which makes traditional genetic approaches impossible. The CRISPR/Cas9 system is a bacterial defense mechanism that was recently adapted to achieve high-efficiency targeted mutagenesis in eukaryotes. Here we report CRISPR/Cas9-mediated disruption of the genes Tyrosinase and FGF8/17/18 in the sea lamprey Petromyzon marinus, and detail optimized parameters for producing mutant F0 embryos. Using phenotype and genotype analyses, we show that CRISPR/Cas9 is highly effective in the sea lamprey, with a majority of injected embryos developing into complete or partial mutants. The ability to create large numbers of mutant embryos without inbred lines opens exciting new possibilities for studying development in lamprey and other non-traditional model organisms with life histories that prohibit the generation of mutant lines.
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Affiliation(s)
- Tyler Square
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Marek Romášek
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA Department of Zoology, Comenius University in Bratislava, Bratislava 84215, Slovakia
| | - Maria V Cattell
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA Department of Pediatrics, University of Colorado, Denver, Aurora, CO 80045, USA
| | - Michael Klymkowsky
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Daniel M Medeiros
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
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166
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Moody SA, Neilson KM, Kenyon KL, Alfandari D, Pignoni F. Using Xenopus to discover new genes involved in branchiootorenal spectrum disorders. Comp Biochem Physiol C Toxicol Pharmacol 2015; 178:16-24. [PMID: 26117063 PMCID: PMC4662879 DOI: 10.1016/j.cbpc.2015.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 12/14/2022]
Abstract
Congenital hearing loss is an important clinical problem because, without early intervention, affected children do not properly acquire language and consequently have difficulties developing social skills. Although most newborns in the US are screened for hearing deficits, even earlier diagnosis can be made with prenatal genetic screening. Genetic screening that identifies the relevant mutated gene can also warn about potential congenital defects in organs not related to hearing. We will discuss efforts to identify new candidate genes that underlie the Branchiootorenal spectrum disorders in which affected children have hearing deficits and are also at risk for kidney defects. Mutations in two genes, SIX1 and EYA1, have been identified in about half of the patients tested. To uncover new candidate genes, we have used the aquatic animal model, Xenopus laevis, to identify genes that are part of the developmental genetic pathway of Six1 during otic and kidney development. We have already identified a large number of potential Six1 transcriptional targets and candidate co-factor proteins that are expressed at the right time and in the correct tissues to interact with Six1 during development. We discuss the advantages of using this system for gene discovery in a human congenital hearing loss syndrome.
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Affiliation(s)
- Sally A Moody
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, Washington, DC, USA.
| | - Karen M Neilson
- Department of Anatomy and Regenerative Biology, George Washington University, School of Medicine and Health Sciences, Washington, DC, USA
| | - Kristy L Kenyon
- Department of Biology, Hobart and William Smith Colleges, Geneva, NY, USA
| | - Dominique Alfandari
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Francesca Pignoni
- Department of Ophthalmology, Upstate Medical University, Syracuse, NY, USA
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167
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Miyamoto K, Suzuki KIT, Suzuki M, Sakane Y, Sakuma T, Herberg S, Simeone A, Simpson D, Jullien J, Yamamoto T, Gurdon JB. The Expression of TALEN before Fertilization Provides a Rapid Knock-Out Phenotype in Xenopus laevis Founder Embryos. PLoS One 2015; 10:e0142946. [PMID: 26580070 PMCID: PMC4651567 DOI: 10.1371/journal.pone.0142946] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/28/2015] [Indexed: 01/08/2023] Open
Abstract
Recent advances in genome editing using programmable nucleases have revolutionized gene targeting in various organisms. Successful gene knock-out has been shown in Xenopus, a widely used model organism, although a system enabling less mosaic knock-out in founder embryos (F0) needs to be explored in order to judge phenotypes in the F0 generation. Here, we injected modified highly active transcription activator-like effector nuclease (TALEN) mRNA to oocytes at the germinal vesicle (GV) stage, followed by in vitro maturation and intracytoplasmic sperm injection, to achieve a full knock-out in F0 embryos. Unlike conventional injection methods to fertilized embryos, the injection of TALEN mRNA into GV oocytes allows expression of nucleases before fertilization, enabling them to work from an earlier stage. Using this procedure, most of developed embryos showed full knock-out phenotypes of the pigmentation gene tyrosinase and/or embryonic lethal gene pax6 in the founder generation. In addition, our method permitted a large 1 kb deletion. Thus, we describe nearly complete gene knock-out phenotypes in Xenopus laevis F0 embryos. The presented method will help to accelerate the production of knock-out frogs since we can bypass an extra generation of about 1 year in Xenopus laevis. Meantime, our method provides a unique opportunity to rapidly test the developmental effects of disrupting those genes that do not permit growth to an adult able to reproduce. In addition, the protocol shown here is considerably less invasive than the previously used host transfer since our protocol does not require surgery. The experimental scheme presented is potentially applicable to other organisms such as mammals and fish to resolve common issues of mosaicism in founders.
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Affiliation(s)
- Kei Miyamoto
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (KM); (KTS)
| | - Ken-ichi T. Suzuki
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
- * E-mail: (KM); (KTS)
| | - Miyuki Suzuki
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Yuto Sakane
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Tetsushi Sakuma
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - Sarah Herberg
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Angela Simeone
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - David Simpson
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Jerome Jullien
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
| | - Takashi Yamamoto
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Japan
| | - J. B. Gurdon
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
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168
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Bhattacharya D, Marfo CA, Li D, Lane M, Khokha MK. CRISPR/Cas9: An inexpensive, efficient loss of function tool to screen human disease genes in Xenopus. Dev Biol 2015; 408:196-204. [PMID: 26546975 DOI: 10.1016/j.ydbio.2015.11.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 10/21/2015] [Accepted: 11/02/2015] [Indexed: 01/01/2023]
Abstract
Congenital malformations are the major cause of infant mortality in the US and Europe. Due to rapid advances in human genomics, we can now efficiently identify sequence variants that may cause disease in these patients. However, establishing disease causality remains a challenge. Additionally, in the case of congenital heart disease, many of the identified candidate genes are either novel to embryonic development or have no known function. Therefore, there is a pressing need to develop inexpensive and efficient technologies to screen these candidate genes for disease phenocopy in model systems and to perform functional studies to uncover their role in development. For this purpose, we sought to test F0 CRISPR based gene editing as a loss of function strategy for disease phenocopy in the frog model organism, Xenopus tropicalis. We demonstrate that the CRISPR/Cas9 system can efficiently modify both alleles in the F0 generation within a few hours post fertilization, recapitulating even early disease phenotypes that are highly similar to knockdowns from morpholino oligos (MOs) in nearly all cases tested. We find that injecting Cas9 protein is dramatically more efficacious and less toxic than cas9 mRNA. We conclude that CRISPR based F0 gene modification in X. tropicalis is efficient and cost effective and readily recapitulates disease and MO phenotypes.
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Affiliation(s)
- Dipankan Bhattacharya
- Departments of Genetics and Pediatrics, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Chris A Marfo
- Departments of Genetics and Pediatrics, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Davis Li
- Departments of Genetics and Pediatrics, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Maura Lane
- Departments of Genetics and Pediatrics, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Mustafa K Khokha
- Departments of Genetics and Pediatrics, Yale University School of Medicine, New Haven, CT 06520, United States.
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169
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Square T, Romášek M, Jandzik D, Cattell MV, Klymkowsky M, Medeiros DM. CRISPR/Cas9-mediated mutagenesis in the sea lamprey Petromyzon marinus: a powerful tool for understanding ancestral gene functions in vertebrates. Development 2015; 142:4180-7. [PMID: 26511928 DOI: 10.1242/dev.125609] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 10/19/2015] [Indexed: 12/24/2022]
Abstract
Lamprey is one of only two living jawless vertebrates, a group that includes the first vertebrates. Comparisons between lamprey and jawed vertebrates have yielded important insights into the origin and evolution of vertebrate physiology, morphology and development. Despite its key phylogenetic position, studies of lamprey have been limited by their complex life history, which makes traditional genetic approaches impossible. The CRISPR/Cas9 system is a bacterial defense mechanism that was recently adapted to achieve high-efficiency targeted mutagenesis in eukaryotes. Here we report CRISPR/Cas9-mediated disruption of the genes Tyrosinase and FGF8/17/18 in the sea lamprey Petromyzon marinus, and detail optimized parameters for producing mutant F0 embryos. Using phenotype and genotype analyses, we show that CRISPR/Cas9 is highly effective in the sea lamprey, with a majority of injected embryos developing into complete or partial mutants. The ability to create large numbers of mutant embryos without inbred lines opens exciting new possibilities for studying development in lamprey and other non-traditional model organisms with life histories that prohibit the generation of mutant lines.
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Affiliation(s)
- Tyler Square
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Marek Romášek
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA Department of Zoology, Comenius University in Bratislava, Bratislava 84215, Slovakia
| | - Maria V Cattell
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA Department of Pediatrics, University of Colorado, Denver, Aurora, CO 80045, USA
| | - Michael Klymkowsky
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
| | - Daniel M Medeiros
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO 80309, USA
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170
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Amin NM, Womble M, Ledon-Rettig C, Hull M, Dickinson A, Nascone-Yoder N. Budgett's frog (Lepidobatrachus laevis): A new amphibian embryo for developmental biology. Dev Biol 2015; 405:291-303. [PMID: 26169245 PMCID: PMC4670266 DOI: 10.1016/j.ydbio.2015.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The large size and rapid development of amphibian embryos has facilitated ground-breaking discoveries in developmental biology. Here, we describe the embryogenesis of the Budgett's frog (Lepidobatrachus laevis), an unusual species with eggs that are over twice the diameter of laboratory Xenopus, and embryos that can tolerate higher temperatures to develop into a tadpole four times more rapidly. In addition to detailing their early development, we demonstrate that, like Xenopus, these embryos are amenable to explant culture assays and can express exogenous transcripts in a tissue-specific manner. Moreover, the steep developmental trajectory and large scale of Lepidobatrachus make it exceptionally well-suited for morphogenesis research. For example, the developing organs of the Budgett's frog are massive compared to those of most model species, and are composed of larger individual cells, thereby affording increased subcellular resolution of early vertebrate organogenesis. Furthermore, we found that complete limb regeneration, which typically requires months to achieve in most vertebrate models, occurs in a matter of days in the Budgett's tadpole, which substantially accelerates the pace of experimentation. Thus, the unusual combination of the greater size and speed of the Budgett's frog model provides inimitable advantages for developmental studies-and a novel inroad to address the mechanisms of spatiotemporal scaling during evolution.
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Affiliation(s)
- Nirav M Amin
- Department of Molecular Biomedical Sciences, 1060 William Moore Drive, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Mandy Womble
- Department of Molecular Biomedical Sciences, 1060 William Moore Drive, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Cristina Ledon-Rettig
- Department of Biology, Indiana University, 915 E, Third St., Bloomington, IN 47405, USA
| | - Margaret Hull
- Department of Molecular Biomedical Sciences, 1060 William Moore Drive, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA
| | - Amanda Dickinson
- Biology Department, Virginia Commonwealth University, 1000W, Cary St. Richmond, VA 23284, USA
| | - Nanette Nascone-Yoder
- Department of Molecular Biomedical Sciences, 1060 William Moore Drive, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607, USA.
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171
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Wang X, Zhou J, Cao C, Huang J, Hai T, Wang Y, Zheng Q, Zhang H, Qin G, Miao X, Wang H, Cao S, Zhou Q, Zhao J. Efficient CRISPR/Cas9-mediated biallelic gene disruption and site-specific knockin after rapid selection of highly active sgRNAs in pigs. Sci Rep 2015; 5:13348. [PMID: 26293209 PMCID: PMC4543986 DOI: 10.1038/srep13348] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 07/22/2015] [Indexed: 12/26/2022] Open
Abstract
Genetic engineering in livestock was greatly enhanced by the emergence of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9), which can be programmed with a single-guide RNA (sgRNA) to generate site-specific DNA breaks. However, the uncertainties caused by wide variations in sgRNA activity impede the utility of this system in generating genetically modified pigs. Here, we described a single blastocyst genotyping system to provide a simple and rapid solution to evaluate and compare the sgRNA efficiency at inducing indel mutations for a given gene locus. Assessment of sgRNA mutagenesis efficiencies can be achieved within 10 days from the design of the sgRNA. The most effective sgRNA selected by this system was successfully used to induce site-specific insertion through homology-directed repair at a frequency exceeding 13%. Additionally, the highly efficient gene deletion via the selected sgRNA was confirmed in pig fibroblast cells, which could serve as donor cells for somatic cell nuclear transfer. We further showed that direct cytoplasmic injection of Cas9 mRNA and the favorable sgRNA into zygotes could generate biallelic knockout piglets with an efficiency of up to 100%. Thus, our method considerably reduces the uncertainties and expands the practical possibilities of CRISPR/Cas9-mediated genome engineering in pigs.
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Affiliation(s)
- Xianlong Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinwei Zhou
- College of Veterinary Medicine, Sichuan Agriculture University, Ya’an, Sichuan 625014, China
| | - Chunwei Cao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiaojiao Huang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tang Hai
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanfang Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qiantao Zheng
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyong Zhang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guosong Qin
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangnan Miao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongmei Wang
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Suizhong Cao
- College of Veterinary Medicine, Sichuan Agriculture University, Ya’an, Sichuan 625014, China
| | - Qi Zhou
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianguo Zhao
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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172
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Firth AL, Menon T, Parker GS, Qualls SJ, Lewis BM, Ke E, Dargitz CT, Wright R, Khanna A, Gage FH, Verma IM. Functional Gene Correction for Cystic Fibrosis in Lung Epithelial Cells Generated from Patient iPSCs. Cell Rep 2015; 12:1385-90. [PMID: 26299960 DOI: 10.1016/j.celrep.2015.07.062] [Citation(s) in RCA: 224] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/06/2015] [Accepted: 07/29/2015] [Indexed: 12/21/2022] Open
Abstract
Lung disease is a major cause of death in the United States, with current therapeutic approaches serving only to manage symptoms. The most common chronic and life-threatening genetic disease of the lung is cystic fibrosis (CF) caused by mutations in the cystic fibrosis transmembrane regulator (CFTR). We have generated induced pluripotent stem cells (iPSCs) from CF patients carrying a homozygous deletion of F508 in the CFTR gene, which results in defective processing of CFTR to the cell membrane. This mutation was precisely corrected using CRISPR to target corrective sequences to the endogenous CFTR genomic locus, in combination with a completely excisable selection system, which significantly improved the efficiency of this correction. The corrected iPSCs were subsequently differentiated to mature airway epithelial cells where recovery of normal CFTR expression and function was demonstrated. This isogenic iPSC-based model system for CF could be adapted for the development of new therapeutic approaches.
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Affiliation(s)
- Amy L Firth
- The Salk Institute of Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Tushar Menon
- The Salk Institute of Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Gregory S Parker
- The Salk Institute of Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Susan J Qualls
- The Salk Institute of Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Benjamin M Lewis
- The Salk Institute of Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Eugene Ke
- The Salk Institute of Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Carl T Dargitz
- The Salk Institute of Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Rebecca Wright
- The Salk Institute of Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ajai Khanna
- Center for Gut Rehabilitation and Transplantation, Digestive Disease Institute and Lerner College of Medicine, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
| | - Fred H Gage
- The Salk Institute of Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Inder M Verma
- The Salk Institute of Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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173
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Shi Z, Wang F, Cui Y, Liu Z, Guo X, Zhang Y, Deng Y, Zhao H, Chen Y. Heritable CRISPR/Cas9‐mediated targeted integration in
Xenopus tropicalis. FASEB J 2015; 29:4914-23. [DOI: 10.1096/fj.15-273425] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/03/2015] [Indexed: 01/03/2023]
Affiliation(s)
- Zhaoying Shi
- Chinese Academy of Sciences Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouGuangdongChina
- Shenzhen Key Laboratory of Cell MicroenvironmentDepartment of BiologySouth University of Science and Technology of ChinaShenzhenGuangdongChina
| | - Fengqin Wang
- Chinese Academy of Sciences Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouGuangdongChina
- School of Life SciencesAnhui UniversityHefeiAnhuiChina
| | - Yan Cui
- Chinese Academy of Sciences Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouGuangdongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhongzhen Liu
- School of Biomedical Sciences, Faculty of MedicineThe Chinese University of Hong Kong, ShatinNew TerritoriesHong KongChina
| | - Xiaogang Guo
- Chinese Academy of Sciences Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouGuangdongChina
| | - Yanqi Zhang
- Chinese Academy of Sciences Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouGuangdongChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yi Deng
- Shenzhen Key Laboratory of Cell MicroenvironmentDepartment of BiologySouth University of Science and Technology of ChinaShenzhenGuangdongChina
| | - Hui Zhao
- School of Biomedical Sciences, Faculty of MedicineThe Chinese University of Hong Kong, ShatinNew TerritoriesHong KongChina
- Shenzhen Research InstituteThe Chinese University of Hong KongShenzhenGuangdongChina
| | - Yonglong Chen
- Chinese Academy of Sciences Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineSouth China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of SciencesGuangzhouGuangdongChina
- Shenzhen Key Laboratory of Cell MicroenvironmentDepartment of BiologySouth University of Science and Technology of ChinaShenzhenGuangdongChina
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174
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Igawa T, Watanabe A, Suzuki A, Kashiwagi A, Kashiwagi K, Noble A, Guille M, Simpson DE, Horb ME, Fujii T, Sumida M. Inbreeding Ratio and Genetic Relationships among Strains of the Western Clawed Frog, Xenopus tropicalis. PLoS One 2015. [PMID: 26222540 PMCID: PMC4519292 DOI: 10.1371/journal.pone.0133963] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains has not yet been clarified, and establishment of inbred strains has not yet been achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima University has maintained stocks of multiple X. tropicalis strains and conducted consecutive breeding as part of the National BioResource Project. In the present study we investigated the inbreeding ratio and genetic relationship of four inbred strains at IAB, as well as stocks from other institutions, using highly polymorphic microsatellite markers and mitochondrial haplotypes. Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains. The Ivory Coast strains clearly differed from the Nigerian strains genetically, and three subgroups were identified within both the Nigerian and Ivory Coast strains. It is noteworthy that the Ivory Coast strains have an evolutionary divergent genetic background. Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts.
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Affiliation(s)
- Takeshi Igawa
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- * E-mail:
| | - Ai Watanabe
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Atsushi Suzuki
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Akihiko Kashiwagi
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Keiko Kashiwagi
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Anna Noble
- School of Biological Sciences, Institute of Biomedical and Biomolecular Science, University of Portsmouth, Portsmouth, United Kingdom
| | - Matt Guille
- School of Biological Sciences, Institute of Biomedical and Biomolecular Science, University of Portsmouth, Portsmouth, United Kingdom
| | - David E. Simpson
- The Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Cambridge, United Kingdom
| | - Marko E. Horb
- Bell Center for Regenerative Biology and Tissue Engineering and National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA, United States of America
| | - Tamotsu Fujii
- Department of Health Sciences, Faculty of Human Culture & Science, Prefectural University of Hiroshima, Hiroshima, Japan
| | - Masayuki Sumida
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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175
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Yao S, He Z, Chen C. CRISPR/Cas9-Mediated Genome Editing of Epigenetic Factors for Cancer Therapy. Hum Gene Ther 2015; 26:463-71. [PMID: 26075804 DOI: 10.1089/hum.2015.067] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Shaohua Yao
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University , Chengdu, China
| | - Zhiyao He
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University , Chengdu, China
| | - Chong Chen
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University , Chengdu, China
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176
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Oliver D, Yuan S, McSwiggin H, Yan W. Pervasive Genotypic Mosaicism in Founder Mice Derived from Genome Editing through Pronuclear Injection. PLoS One 2015; 10:e0129457. [PMID: 26053263 PMCID: PMC4459985 DOI: 10.1371/journal.pone.0129457] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 05/09/2015] [Indexed: 01/12/2023] Open
Abstract
Genome editing technologies, especially the Cas9/CRISPR system, have revolutionized biomedical research over the past several years. Generation of novel alleles has been simplified to unprecedented levels, allowing for rapid expansion of available genetic tool kits for researchers. However, the issue of genotypic mosaicism has become evident, making stringent analyses of the penetrance of genome-edited alleles essential. Here, we report that founder mice, derived from pronuclear injection of ZFNs or a mix of guidance RNAs and Cas9 mRNAs, display consistent genotypic mosaicism for both deletion and insertion alleles. To identify founders with greater possibility of transmitting the mutant allele through the germline, we developed an effective germline genotyping method. The awareness of the inherent genotypic mosaicism issue with genome editing will allow for a more efficient implementation of the technologies, and the germline genotyping method will save valuable time and resources.
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Affiliation(s)
- Daniel Oliver
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Shuiqiao Yuan
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Hayden McSwiggin
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America
- * E-mail:
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177
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Webber DM, MacLeod SL, Bamshad MJ, Shaw GM, Finnell RH, Shete SS, Witte JS, Erickson SW, Murphy LD, Hobbs C. Developments in our understanding of the genetic basis of birth defects. ACTA ACUST UNITED AC 2015; 103:680-91. [PMID: 26033863 DOI: 10.1002/bdra.23385] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Birth defects are a major cause of morbidity and mortality worldwide. There has been much progress in understanding the genetic basis of familial and syndromic forms of birth defects. However, the etiology of nonsydromic birth defects is not well-understood. Although there is still much work to be done, we have many of the tools needed to accomplish the task. Advances in next-generation sequencing have introduced a sea of possibilities, from disease-gene discovery to clinical screening and diagnosis. These advances have been fruitful in identifying a host of candidate disease genes, spanning the spectrum of birth defects. With the advent of CRISPR-Cas9 gene editing, researchers now have a precise tool for characterizing this genetic variation in model systems. Work in model organisms has also illustrated the importance of epigenetics in human development and birth defects etiology. Here we review past and current knowledge in birth defects genetics. We describe genotyping and sequencing methods for the detection and analysis of rare and common variants. We remark on the utility of model organisms and explore epigenetics in the context of structural malformation. We conclude by highlighting approaches that may provide insight into the complex genetics of birth defects.
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Affiliation(s)
- Daniel M Webber
- Division of Birth Defects Research, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Stewart L MacLeod
- Division of Birth Defects Research, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Michael J Bamshad
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington
| | - Gary M Shaw
- Stanford University School of Medicine, Stanford, California
| | - Richard H Finnell
- Dell Pediatric Research Institute, Department of Nutritional Sciences, The University of Texas at Austin, Austin, Texas
| | - Sanjay S Shete
- Department of Epidemiology, MD Anderson Cancer Center, Houston, Texas
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Stephen W Erickson
- Department of Biostatistics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Linda D Murphy
- Division of Birth Defects Research, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Charlotte Hobbs
- Division of Birth Defects Research, Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
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178
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Schweickert A, Feistel K. The Xenopus Embryo: An Ideal Model System to Study Human Ciliopathies. CURRENT PATHOBIOLOGY REPORTS 2015. [DOI: 10.1007/s40139-015-0074-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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179
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Abstract
Diseases affecting endodermal organs like the pancreas, lung and gastrointestinal (GI) tract have a substantial impact on human welfare. Since many of these are congenital defects that arise as a result of defects during development broad efforts are focused on understanding the development of these organs so as to better identify risk factors, disease mechanisms and therapeutic targets. Studies implementing model systems, like the amphibian Xenopus, have contributed immensely to our understanding of signaling (e.g. Wnt, FGF, BMP, RA) pathways and gene regulation (e.g. hhex, ptf1a, ngn3) that underlie normal development as well as disease progression. Recent advances in genome engineering further enhance the capabilities of the Xenopus model system for pursuing biomedical research, and will undoubtedly result in a boom of new information underlying disease mechanisms ultimately leading to advancements in diagnosis and therapy.
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180
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Wen L, Hasebe T, Miller TC, Ishizuya-Oka A, Shi YB. A requirement for hedgehog signaling in thyroid hormone-induced postembryonic intestinal remodeling. Cell Biosci 2015; 5:13. [PMID: 25859319 PMCID: PMC4391142 DOI: 10.1186/s13578-015-0004-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 03/13/2015] [Indexed: 12/25/2022] Open
Abstract
Background Intestinal remodeling during amphibian metamorphosis has long been studied as a model for the formation of the adult organs in vertebrates, especially the formation of adult organ-specific stem cells. Like all other processes during metamorphosis, this process is controlled by thyroid hormone (T3), which affects cell fate and behavior through transcriptional regulation of target genes by binding to T3 receptors (TRs). Earlier studies have shown that Sonic hedgehog (Shh) is induced by T3 in the developing adult stem cells and that the Shh receptor and other downstream components are present in the connective tissue and at lower levels in the muscles at the climax of intestinal remodeling. However, no in vivo studies have carried out to investigate whether Shh produced in the adult cells can regulate the connective tissue to promote intestinal maturation. Results We have addressed this issue by treating tadpoles with Shh inhibitor cyclopamine. We showed that cyclopamine but not the structurally related chemical tomatidine inhibited the expression of Shh response genes BMP4, Snai2, and Twist1. More importantly, we showed that cyclopamine reduced the cell proliferation of both the developing adult stem cells as well as cells in the other intestinal tissues at the climax of metamorphosis, leading to delayed/incomplete remodeling of the intestine at the end of metamorphosis. We further revealed that both Snai2 and Twist1 were strongly upregulated during metamorphosis in the intestine and their expression was restricted to the connective tissue. Conclusions Our results suggest that Shh indeed signals the connective tissue whereby it can increase adult stem cell proliferation and promote formation of the adult intestine.
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Affiliation(s)
- Luan Wen
- Section on Molecular Morphogenesis, Program on Cell Regulation and Metabolism, National Institute of Child Health and Human Development, National Institutes of Health, Bldg. 18 T, Rm. 106, Bethesda, MD 20892 USA
| | - Takashi Hasebe
- Department of Biology, Nippon Medical School, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-0023 Japan
| | - Thomas C Miller
- Section on Molecular Morphogenesis, Program on Cell Regulation and Metabolism, National Institute of Child Health and Human Development, National Institutes of Health, Bldg. 18 T, Rm. 106, Bethesda, MD 20892 USA
| | - Atsuko Ishizuya-Oka
- Department of Biology, Nippon Medical School, 1-7-1 Kyonan-cho, Musashino, Tokyo 180-0023 Japan
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Program on Cell Regulation and Metabolism, National Institute of Child Health and Human Development, National Institutes of Health, Bldg. 18 T, Rm. 106, Bethesda, MD 20892 USA
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181
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Nakayama T, Fisher M, Nakajima K, Odeleye AO, Zimmerman KB, Fish MB, Yaoita Y, Chojnowski JL, Lauderdale JD, Netland PA, Grainger RM. Xenopus pax6 mutants affect eye development and other organ systems, and have phenotypic similarities to human aniridia patients. Dev Biol 2015; 408:328-44. [PMID: 25724657 DOI: 10.1016/j.ydbio.2015.02.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/13/2015] [Accepted: 02/16/2015] [Indexed: 02/06/2023]
Abstract
Mutations in the Pax6 gene cause ocular defects in both vertebrate and invertebrate animal species, and the disease aniridia in humans. Despite extensive experimentation on this gene in multiple species, including humans, we still do not understand the earliest effects on development mediated by this gene. This prompted us to develop pax6 mutant lines in Xenopus tropicalis taking advantage of the utility of the Xenopus system for examining early development and in addition to establish a model for studying the human disease aniridia in an accessible lower vertebrate. We have generated mutants in pax6 by using Transcription Activator-Like Effector Nuclease (TALEN) constructs for gene editing in X. tropicalis. Embryos with putative null mutations show severe eye abnormalities and changes in brain development, as assessed by changes in morphology and gene expression. One gene that we found is downregulated very early in development in these pax6 mutants is myc, a gene involved in pluripotency and progenitor cell maintenance and likely a mediator of some key pax6 functions in the embryo. Changes in gene expression in the developing brain and pancreas reflect other important functions of pax6 during development. In mutations with partial loss of pax6 function eye development is initially relatively normal but froglets show an underdeveloped iris, similar to the classic phenotype (aniridia) seen in human patients with PAX6 mutations. Other eye abnormalities observed in these froglets, including cataracts and corneal defects, are also common in human aniridia. The frog model thus allows us to examine the earliest deficits in eye formation as a result of pax6 lesions, and provides a useful model for understanding the developmental basis for the aniridia phenotype seen in humans.
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Affiliation(s)
- Takuya Nakayama
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Marilyn Fisher
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Keisuke Nakajima
- Division of Embryology and Genetics, Institute for Amphibian Biology, Hiroshima University, Higashihiroshima 739-8526, Japan
| | - Akinleye O Odeleye
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Keith B Zimmerman
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Margaret B Fish
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Yoshio Yaoita
- Division of Embryology and Genetics, Institute for Amphibian Biology, Hiroshima University, Higashihiroshima 739-8526, Japan
| | - Jena L Chojnowski
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - James D Lauderdale
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Peter A Netland
- Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Robert M Grainger
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA; Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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182
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Miyamoto K, Simpson D, Gurdon JB. Manipulation and in vitro maturation of Xenopus laevis oocytes, followed by intracytoplasmic sperm injection, to study embryonic development. J Vis Exp 2015:e52496. [PMID: 25742326 PMCID: PMC4354630 DOI: 10.3791/52496] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Amphibian eggs have been widely used to study embryonic development. Early embryonic development is driven by maternally stored factors accumulated during oogenesis. In order to study roles of such maternal factors in early embryonic development, it is desirable to manipulate their functions from the very beginning of embryonic development. Conventional ways of gene interference are achieved by injection of antisense oligonucleotides (oligos) or mRNA into fertilized eggs, enabling under- or over-expression of specific proteins, respectively. However, these methods normally require more than several hours until protein expression is affected, and, hence, the interference of gene functions is not effective during early embryonic stages. Here, we introduce an experimental system in which expression levels of maternal proteins can be altered before fertilization. Xenopus laevis oocytes obtained from ovaries are defolliculated by incubating with enzymes. Antisense oligos or mRNAs are injected into defolliculated oocytes at the germinal vesicle (GV) stage. These oocytes are in vitro matured to eggs at the metaphase II (MII) stage, followed by intracytoplasmic sperm injection (ICSI). By this way, up to 10% of ICSI embryos can reach the swimming tadpole stage, thus allowing functional tests of specific gene knockdown or overexpression. This approach can be a useful way to study roles of maternally stored factors in early embryonic development.
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Affiliation(s)
- Kei Miyamoto
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge; Department of Zoology, University of Cambridge;
| | - David Simpson
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge; Department of Zoology, University of Cambridge
| | - John B Gurdon
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge; Department of Zoology, University of Cambridge
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183
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Nakajima K, Yaoita Y. Development of a new approach for targeted gene editing in primordial germ cells using TALENs in Xenopus. Biol Open 2015; 4:259-66. [PMID: 25661867 PMCID: PMC4359732 DOI: 10.1242/bio.201410926] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 12/09/2014] [Indexed: 11/20/2022] Open
Abstract
A gene of interest can be efficiently modified using transcription activator-like effector nucleases (TALENs) (Christian et al., 2010;Li et al., 2011). However, if a target gene is essential for development, growth and fertility, use of TALENs with high mutagenic activity in F0 frogs could result in developmental disorders or sterility, which would reduce the number of F1 progeny and make F1 phenotypical analysis difficult. We used the 3' untranslated region of DEADSouth gene (DS-3') of Xenopus tropicalis to solve this problem, because the addition of the DS-3' to mRNA is known to induce primordial germ cell (PGC)-specific expression and reduce the stability in somatic cells of mRNA in Xenopus laevis. At first, we inserted the X. tropicalis DS-3' downstream of the EGFP termination codon and confirmed that the EGFP expression was specifically detected in PGCs for three weeks. Therefore, we inserted the DS-3' downstream of the termination codon of the TALEN coding sequence. The tyrosinase gene was selected as the target gene for TALEN because the bi-allelic mutation of this gene is easily discernible by the albino phenotype. When fertilized eggs were microinjected with TALEN mRNAs fused to the DS-3', their sperm and oocytes had a high rate (84-100%) of target-gene modification in contrast to the lower rate (0-45%) of nucleotide alteration observed in somatic cells.
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Affiliation(s)
- Keisuke Nakajima
- Division of Embryology and Genetics, Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashihiroshima 739-8526, Japan
| | - Yoshio Yaoita
- Division of Embryology and Genetics, Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashihiroshima 739-8526, Japan
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184
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Generation of BAC transgenic tadpoles enabling live imaging of motoneurons by using the urotensin II-related peptide (ust2b) gene as a driver. PLoS One 2015; 10:e0117370. [PMID: 25658845 PMCID: PMC4319907 DOI: 10.1371/journal.pone.0117370] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 12/22/2014] [Indexed: 12/13/2022] Open
Abstract
Xenopus is an excellent tetrapod model for studying normal and pathological motoneuron ontogeny due to its developmental morpho-physiological advantages. In mammals, the urotensin II-related peptide (UTS2B) gene is primarily expressed in motoneurons of the brainstem and the spinal cord. Here, we show that this expression pattern was conserved in Xenopus and established during the early embryonic development, starting at the early tailbud stage. In late tadpole stage, uts2b mRNA was detected both in the hindbrain and in the spinal cord. Spinal uts2b+ cells were identified as axial motoneurons. In adult, however, the uts2b expression was only detected in the hindbrain. We assessed the ability of the uts2b promoter to drive the expression of a fluorescent reporter in motoneurons by recombineering a green fluorescent protein (GFP) into a bacterial artificial chromosome (BAC) clone containing the entire X. tropicalis uts2b locus. After injection of this construction in one-cell stage embryos, a transient GFP expression was observed in the spinal cord of about a quarter of the resulting animals from the early tailbud stage and up to juveniles. The GFP expression pattern was globally consistent with that of the endogenous uts2b in the spinal cord but no fluorescence was observed in the brainstem. A combination of histological and electrophysiological approaches was employed to further characterize the GFP+ cells in the larvae. More than 98% of the GFP+ cells expressed choline acetyltransferase, while their projections were co-localized with α-bungarotoxin labeling. When tail myotomes were injected with rhodamine dextran amine crystals, numerous double-stained GFP+ cells were observed. In addition, intracellular electrophysiological recordings of GFP+ neurons revealed locomotion-related rhythmic discharge patterns during fictive swimming. Taken together our results provide evidence that uts2b is an appropriate driver to express reporter genes in larval motoneurons of the Xenopus spinal cord.
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185
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Perry KJ, Henry JQ. CRISPR/Cas9-mediated genome modification in the mollusc, Crepidula fornicata. Genesis 2015; 53:237-44. [PMID: 25529990 DOI: 10.1002/dvg.22843] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/12/2014] [Accepted: 12/17/2014] [Indexed: 12/20/2022]
Abstract
The discovery and application of the CRISPR/Cas9 genome editing method has greatly enhanced the ease with which transgenic manipulation can occur. We applied this technology to the mollusc, Crepidula fornicata, and have successfully created transgenic embryos expressing mCherry fused to endogenous β-catenin. Specific integration of the fluorescent reporter was achieved by homologous recombination with a β-catenin-specific donor DNA containing the mCherry coding sequence. This fluorescent gene knock-in strategy permits in vivo observations of β-catenin expression during embryonic development and represents the first demonstration of CRISPR/Cas9-mediated transgenesis in the Lophotrochozoa superphylum. The CRISPR/Cas9 method is a powerful and economical tool for genome modification and presents an option for analysis of gene expression in not only major model systems, but also in those more diverse species that may not have been amenable to the classic methods of transgenesis. This approach will allow one to generate transgenic lines of snails for future studies.
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Affiliation(s)
- Kimberly J Perry
- Department of Cell and Developmental Biology, University of Illinois, Urbana, Illinois, 61801
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186
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Abstract
Targeted mutagenesis based on homologous recombination has been a powerful tool for understanding the mechanisms underlying development, normal physiology, and disease. A recent breakthrough in genome engineering technology based on the class of RNA-guided endonucleases, such as clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas9, is further revolutionizing biology and medical studies. The simplicity of the CRISPR-Cas9 system has enabled its widespread applications in generating germline animal models, somatic genome engineering, and functional genomic screening and in treating genetic and infectious diseases. This technology will likely be used in all fields of biomedicine, ranging from basic research to human gene therapy.
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Affiliation(s)
- Xiao Yang
- State Key Laboratory of Proteomics, Collaborative Innovation Center for Cardiovascular Disorders, Genetic Laboratory of Development and Disease, Institute of Biotechnology, Beijing, 100071 China
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187
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Aluru N, Karchner SI, Franks DG, Nacci D, Champlin D, Hahn ME. Targeted mutagenesis of aryl hydrocarbon receptor 2a and 2b genes in Atlantic killifish (Fundulus heteroclitus). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 158:192-201. [PMID: 25481785 PMCID: PMC4272816 DOI: 10.1016/j.aquatox.2014.11.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/17/2014] [Accepted: 11/18/2014] [Indexed: 06/04/2023]
Abstract
Understanding molecular mechanisms of toxicity is facilitated by experimental manipulations, such as disruption of function by gene targeting, that are especially challenging in non-standard model species with limited genomic resources. While loss-of-function approaches have included gene knock-down using morpholino-modified oligonucleotides and random mutagenesis using mutagens or retroviruses, more recent approaches include targeted mutagenesis using zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology. These latter methods provide more accessible opportunities to explore gene function in non-traditional model species. To facilitate evaluation of toxic mechanisms for important categories of aryl hydrocarbon pollutants, whose actions are known to be receptor mediated, we used ZFN and CRISPR-Cas9 approaches to generate aryl hydrocarbon receptor 2a (AHR2a) and AHR2b gene mutations in Atlantic killifish (Fundulus heteroclitus) embryos. This killifish is a particularly valuable non-traditional model, with multiple paralogs of AHR whose functions are not well characterized. In addition, some populations of this species have evolved resistance to toxicants such as halogenated aromatic hydrocarbons. AHR-null killifish will be valuable for characterizing the role of the individual AHR paralogs in evolved resistance, as well as in normal development. We first used five-finger ZFNs targeting exons 1 and 3 of AHR2a. Subsequently, CRISPR-Cas9 guide RNAs were designed to target regions in exon 2 and 3 of AHR2a and AHR2b. We successfully induced frameshift mutations in AHR2a exon 3 with ZFN and CRISPR-Cas9 guide RNAs, with mutation frequencies of 10% and 16%, respectively. In AHR2b, mutations were induced using CRISPR-Cas9 guide RNAs targeting sites in both exon 2 (17%) and exon 3 (63%). We screened AHR2b exon 2 CRISPR-Cas9-injected embryos for off-target effects in AHR paralogs. No mutations were observed in closely related AHR genes (AHR1a, AHR1b, AHR2a, AHRR) in the CRISPR-Cas9-injected embryos. Overall, our results demonstrate that targeted genome-editing methods are efficient in inducing mutations at specific loci in embryos of a non-traditional model species, without detectable off-target effects in paralogous genes.
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Affiliation(s)
- Neelakanteswar Aluru
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; Superfund Research Program, Boston University School of Public Health, Boston, MA, USA.
| | - Sibel I Karchner
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; Superfund Research Program, Boston University School of Public Health, Boston, MA, USA
| | - Diana G Franks
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; Superfund Research Program, Boston University School of Public Health, Boston, MA, USA
| | - Diane Nacci
- Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, Environmental Protection Agency, Narragansett, RI 02882, USA
| | - Denise Champlin
- Office of Research and Development, National Health and Environmental Effects Research Laboratory, Atlantic Ecology Division, Environmental Protection Agency, Narragansett, RI 02882, USA
| | - Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA; Superfund Research Program, Boston University School of Public Health, Boston, MA, USA
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188
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Abstract
The advent of facile genome engineering using the bacterial RNA-guided CRISPR-Cas9 system in animals and plants is transforming biology. We review the history of CRISPR (clustered regularly interspaced palindromic repeat) biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism, which has set the stage for remarkable developments using this technology to modify, regulate, or mark genomic loci in a wide variety of cells and organisms from all three domains of life. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way toward fundamental discoveries in biology, with applications in all branches of biotechnology, as well as strategies for human therapeutics.
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Affiliation(s)
- Jennifer A Doudna
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA. Department of Chemistry, University of California, Berkeley, CA 94720, USA. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Emmanuelle Charpentier
- Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany. Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, S-90187 Umeå, Sweden. Hannover Medical School, D-30625 Hannover, Germany.
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189
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Ma Y, Zhang L, Huang X. Genome modification by CRISPR/Cas9. FEBS J 2014; 281:5186-93. [PMID: 25315507 DOI: 10.1111/febs.13110] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/21/2014] [Accepted: 10/03/2014] [Indexed: 12/20/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas)9-mediated genome modification enables us to edit the genomes of a variety of organisms rapidly and efficiently. The advantages of the CRISPR-Cas9 system have made it an increasingly popular genetic engineering tool for biological and therapeutic applications. Moreover, CRISPR-Cas9 has been employed to recruit functional domains that repress/activate gene expression or label specific genomic loci in living cells or organisms, in order to explore developmental mechanisms, gene expression regulation, and animal behavior. One major concern about this system is its specificity; although CRISPR-Cas9-mediated off-target mutation has been broadly studied, more efforts are required to further improve the specificity of CRISPR-Cas9. We will also discuss the potential applications of CRISPR-Cas9.
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Affiliation(s)
- Yuanwu Ma
- Key Laboratory of Human Disease Comparative Medicine, Ministry of Health, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing, China
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190
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Karpinka JB, Fortriede JD, Burns KA, James-Zorn C, Ponferrada VG, Lee J, Karimi K, Zorn AM, Vize PD. Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes. Nucleic Acids Res 2014; 43:D756-63. [PMID: 25313157 PMCID: PMC4384024 DOI: 10.1093/nar/gku956] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Xenbase (http://www.xenbase.org), the Xenopus frog model organism database, integrates a wide variety of data from this biomedical model genus. Two closely related species are represented: the allotetraploid Xenopus laevis that is widely used for microinjection and tissue explant-based protocols, and the diploid Xenopus tropicalis which is used for genetics and gene targeting. The two species are extremely similar and protocols, reagents and results from each species are often interchangeable. Xenbase imports, indexes, curates and manages data from both species; all of which are mapped via unique IDs and can be queried in either a species-specific or species agnostic manner. All our services have now migrated to a private cloud to achieve better performance and reliability. We have added new content, including providing full support for morpholino reagents, used to inhibit mRNA translation or splicing and binding to regulatory microRNAs. New genomes assembled by the JGI for both species and are displayed in Gbrowse and are also available for searches using BLAST. Researchers can easily navigate from genome content to gene page reports, literature, experimental reagents and many other features using hyperlinks. Xenbase has also greatly expanded image content for figures published in papers describing Xenopus research via PubMedCentral.
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Affiliation(s)
- J Brad Karpinka
- University of Calgary-Computer Science, Calgary, Alberta, Canada
| | - Joshua D Fortriede
- Cincinnati Children's Research Foundation-Division of Developmental Biology, Cincinnati, OH, USA
| | - Kevin A Burns
- Cincinnati Children's Research Foundation-Division of Developmental Biology, Cincinnati, OH, USA
| | - Christina James-Zorn
- Cincinnati Children's Research Foundation-Division of Developmental Biology, Cincinnati, OH, USA
| | - Virgilio G Ponferrada
- Cincinnati Children's Research Foundation-Division of Developmental Biology, Cincinnati, OH, USA
| | - Jacqueline Lee
- University of Calgary-Computer Science, Calgary, Alberta, Canada
| | - Kamran Karimi
- University of Calgary-Computer Science, Calgary, Alberta, Canada
| | - Aaron M Zorn
- Cincinnati Children's Research Foundation-Division of Developmental Biology, Cincinnati, OH, USA
| | - Peter D Vize
- University of Calgary-Computer Science, Calgary, Alberta, Canada University of Calgary-Biological Sciences, Calgary, Alberta, Canada
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191
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Targeted mutagenesis in Atlantic salmon (Salmo salar L.) using the CRISPR/Cas9 system induces complete knockout individuals in the F0 generation. PLoS One 2014; 9:e108622. [PMID: 25254960 PMCID: PMC4177897 DOI: 10.1371/journal.pone.0108622] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/23/2014] [Indexed: 12/26/2022] Open
Abstract
Understanding the biological function behind key proteins is of great concern in Atlantic salmon, both due to a high commercial importance and an interesting life history. Until recently, functional studies in salmonids appeared to be difficult. However, the recent discovery of targeted mutagenesis using the CRISPR/Cas9 (clustered regularly interspaced palindromic repeats/CRISPR-associated) system enables performing functional studies in Atlantic salmon to a great extent. We used the CRISPR/Cas9 system to target two genes involved in pigmentation, tyrosinase (tyr) and solute carrier family 45, member 2 (slc45a2). Embryos were assayed for mutation rates at the 17 somite stage, where 40 and 22% of all injected embryos showed a high degree of mutation induction for slc45a2 and tyr, respectively. At hatching this mutation frequency was also visible for both targeted genes, displaying a graded phenotype ranging from complete lack of pigmentation to partial loss and normal pigmentation. CRISPRslc45a2/Cas9 injected embryos showing a complete lack of pigmentation or just a few spots of pigments also lacked wild type sequences when assaying more than 80 (slc45a2) sequence clones from whole embryos. This indicates that CRISPR/Cas9 can induce double-allelic knockout in the F0 generation. However, types and frequency of indels might affect the phenotype. Therefore, the variation of indels was assayed in the graded pigmentation phenotypes produced by CRISPR/Cas9-slc45a2. The results show a tendency for fewer types of indels formed in juveniles completely lacking pigmentation compared to juveniles displaying partial pigmentation. Another interesting observation was a high degree of the same indel type in different juveniles. This study shows for the first time successful use of the CRISPR/Cas9 technology in a marine cold water species. Targeted double-allelic mutations were obtained and, though the level of mosaicism has to be considered, we demonstrate that F0 fish can be used for functional studies in Atlantic salmon.
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192
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Xenopus mutant reveals necessity of rax for specifying the eye field which otherwise forms tissue with telencephalic and diencephalic character. Dev Biol 2014; 395:317-330. [PMID: 25224223 DOI: 10.1016/j.ydbio.2014.09.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 08/20/2014] [Accepted: 09/05/2014] [Indexed: 01/23/2023]
Abstract
The retinal anterior homeobox (rax) gene encodes a transcription factor necessary for vertebrate eye development. rax transcription is initiated at the end of gastrulation in Xenopus, and is a key part of the regulatory network specifying anterior neural plate and retina. We describe here a Xenopus tropicalis rax mutant, the first mutant analyzed in detail from a reverse genetic screen. As in other vertebrates, this nonsense mutation results in eyeless animals, and is lethal peri-metamorphosis. Tissue normally fated to form retina in these mutants instead forms tissue with characteristics of diencephalon and telencephalon. This implies that a key role of rax, in addition to defining the eye field, is in preventing alternative forebrain identities. Our data highlight that brain and retina regions are not determined by the mid-gastrula stage but are by the neural plate stage. An RNA-Seq analysis and in situ hybridization assays for early gene expression in the mutant revealed that several key eye field transcription factors (e.g. pax6, lhx2 and six6) are not dependent on rax activity through neurulation. However, these analyses identified other genes either up- or down-regulated in mutant presumptive retinal tissue. Two neural patterning genes of particular interest that appear up-regulated in the rax mutant RNA-seq analysis are hesx1 and fezf2. These genes were not previously known to be regulated by rax. The normal function of rax is to partially repress their expression by an indirect mechanism in the presumptive retina region in wildtype embryos, thus accounting for the apparent up-regulation in the rax mutant. Knock-down experiments using antisense morpholino oligonucleotides directed against hesx1 and fezf2 show that failure to repress these two genes contributes to transformation of presumptive retinal tissue into non-retinal forebrain identities in the rax mutant.
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193
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Abstract
The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system is poised to transform developmental biology by providing a simple, efficient method to precisely manipulate the genome of virtually any developing organism. This RNA-guided nuclease (RGN)-based approach already has been effectively used to induce targeted mutations in multiple genes simultaneously, create conditional alleles, and generate endogenously tagged proteins. Illustrating the adaptability of RGNs, the genomes of >20 different plant and animal species as well as multiple cell lines and primary cells have been successfully modified. Here we review the current and potential uses of RGNs to investigate genome function during development.
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Affiliation(s)
- Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | - Brian V Jenkins
- Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Kate M O'Connor-Giles
- Laboratory of Genetics, Laboratory of Cell and Molecular Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jill Wildonger
- Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
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194
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Yen ST, Zhang M, Deng JM, Usman SJ, Smith CN, Parker-Thornburg J, Swinton PG, Martin JF, Behringer RR. Somatic mosaicism and allele complexity induced by CRISPR/Cas9 RNA injections in mouse zygotes. Dev Biol 2014; 393:3-9. [PMID: 24984260 PMCID: PMC4166609 DOI: 10.1016/j.ydbio.2014.06.017] [Citation(s) in RCA: 226] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 12/20/2022]
Abstract
Tyrosinase is the rate-limiting enzyme for the production of melanin pigmentation. In the mouse and other animals, homozygous null mutations in the Tyrosinase gene (Tyr) result in the absence of pigmentation, i.e. albinism. Here we used the CRISPR/Cas9 system to generate mono- and bi-allelic null mutations in the Tyr locus by zygote injection of two single-guide and Cas9 RNAs. Injection into C57BL/6N wild-type embryos resulted in one completely albino founder carrying two different Tyr mutations. In addition, three pigmentation mosaics and fully pigmented littermates were obtained that transmitted new mutant Tyr alleles to progeny in test crosses with albinos. Injection into Tyr heterozygous (B6CBAF1/J×FVB/NJ) zygotes resulted in the generation of numerous albinos and also mice with a graded range of albino mosaicism. Deep sequencing revealed that the majority of the albinos and the mosaics had more than two new mutant alleles. These visual phenotypes and molecular genotypes highlight the somatic mosaicism and allele complexity in founders that occurs for targeted genes during CRISPR/Cas9-mediated mutagenesis by zygote injection in mice.
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Affiliation(s)
- Shuo-Ting Yen
- Program in Developmental Biology, Baylor College of Medicine, USA; Department of Genetics, University of Texas M.D. Anderson Cancer Center, USA
| | - Min Zhang
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, USA
| | - Jian Min Deng
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, USA
| | - Shireen J Usman
- Department of Genetics, University of Texas M.D. Anderson Cancer Center, USA
| | - Chad N Smith
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, USA
| | - Jan Parker-Thornburg
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, USA
| | | | - James F Martin
- Program in Developmental Biology, Baylor College of Medicine, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, USA; Texas Heart Institute, Houston, TX 77030, USA
| | - Richard R Behringer
- Program in Developmental Biology, Baylor College of Medicine, USA; Department of Genetics, University of Texas M.D. Anderson Cancer Center, USA.
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195
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Sasaki H, Yoshida K, Hozumi A, Sasakura Y. CRISPR/Cas9-mediated gene knockout in the ascidian Ciona intestinalis. Dev Growth Differ 2014; 56:499-510. [PMID: 25212715 PMCID: PMC4231237 DOI: 10.1111/dgd.12149] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 06/18/2014] [Accepted: 06/22/2014] [Indexed: 01/25/2023]
Abstract
Knockout of genes with CRISPR/Cas9 is a newly emerged approach to investigate functions of genes in various organisms. We demonstrate that CRISPR/Cas9 can mutate endogenous genes of the ascidian Ciona intestinalis, a splendid model for elucidating molecular mechanisms for constructing the chordate body plan. Short guide RNA (sgRNA) and Cas9 mRNA, when they are expressed in Ciona embryos by means of microinjection or electroporation of their expression vectors, introduced mutations in the target genes. The specificity of target choice by sgRNA is relatively high compared to the reports from some other organisms, and a single nucleotide mutation at the sgRNA dramatically reduced mutation efficiency at the on-target site. CRISPR/Cas9-mediated mutagenesis will be a powerful method to study gene functions in Ciona along with another genome editing approach using TALE nucleases.
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Affiliation(s)
- Haruka Sasaki
- Shimoda Marine Research Center, University of TsukubaShimoda, Shizuoka, 415-0025, Japan
| | - Keita Yoshida
- Shimoda Marine Research Center, University of TsukubaShimoda, Shizuoka, 415-0025, Japan
| | - Akiko Hozumi
- Shimoda Marine Research Center, University of TsukubaShimoda, Shizuoka, 415-0025, Japan
| | - Yasunori Sasakura
- Shimoda Marine Research Center, University of TsukubaShimoda, Shizuoka, 415-0025, Japan
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196
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Horii T, Hatada I. Genome engineering using the CRISPR/Cas system. World J Med Genet 2014; 4:69-76. [DOI: 10.5496/wjmg.v4.i3.69] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/12/2014] [Accepted: 05/19/2014] [Indexed: 02/06/2023] Open
Abstract
Recently, an epoch-making genome engineering technology using clustered regularly at interspaced short palindromic repeats (CRISPR) and CRISPR associated (Cas) nucleases, was developed. Previous technologies for genome manipulation require the time-consuming design and construction of genome-engineered nucleases for each target and have, therefore, not been widely used in mouse research where standard techniques based on homologous recombination are commonly used. The CRISPR/Cas system only requires the design of sequences complementary to a target locus, making this technology fast and straightforward. In addition, CRISPR/Cas can be used to generate mice carrying mutations in multiple genes in a single step, an achievement not possible using other methods. Here, we review the uses of this technology in genetic analysis and manipulation, including achievements made possible to date and the prospects for future therapeutic applications.
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197
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Porro F, Bockor L, De Caneva A, Bortolussi G, Muro AF. Generation of Ugt1-deficient murine liver cell lines using TALEN technology. PLoS One 2014; 9:e104816. [PMID: 25118822 PMCID: PMC4132024 DOI: 10.1371/journal.pone.0104816] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/17/2014] [Indexed: 12/22/2022] Open
Abstract
The Crigler-Najjar Syndrome Type I (CNSI) is a rare genetic disorder caused by mutations in the Ugt1a1 gene. It is characterized by unconjugated hyperbilirubinemia that may result in severe neurologic damage and death if untreated. To date, liver transplantation is the only curative treatment. With the aim of generating mutant cell lines of the Ugt1 gene, we utilized the TALEN technology to introduce site-specific mutations in Ugt1 exon 4. We report a fast and efficient method to perform gene knockout in tissue culture cells, based on the use of TALEN pairs targeting restriction enzyme (RE) sites in the region of interest. This strategy overcame the presence of allele-specific single nucleotide polymorphisms (SNPs) and pseudogenes, conditions that limit INDELs' detection by Surveyor. We obtained liver-derived murine N-Muli cell clones having INDELs with efficiency close to 40%, depending on the TALEN pair and RE target site. Sequencing of the target locus and WB analysis of the isolated cell clones showed a high proportion of biallelic mutations in cells treated with the most efficient TALEN pair. Ugt glucuronidation activity was reduced basal levels in the biallelic mutant clones. These mutant liver-derived cell lines could be a very useful tool to study biochemical aspects of Ugt1 enzyme activity in a more natural context, such as substrate specificity, requirement of specific co-factors, the study of inhibitors and other pharmacological aspects, and to correlate enzyme activity to the presence of specific mutations in the gene, by adding back to the mutant cell clones specific variants of the Ugt1 gene. In addition, since genome editing has recently emerged as a potential therapeutic approach to cure genetic diseases, the definition of the most efficient TALEN pair could be an important step towards setting up a platform to perform genome editing in CNSI.
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Affiliation(s)
- Fabiola Porro
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, TS, Italy
| | - Luka Bockor
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, TS, Italy
| | - Alessia De Caneva
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, TS, Italy
| | - Giulia Bortolussi
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, TS, Italy
| | - Andrés F. Muro
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, TS, Italy
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198
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CRISPR-mediated genomic deletion of Sox2 in the axolotl shows a requirement in spinal cord neural stem cell amplification during tail regeneration. Stem Cell Reports 2014; 3:444-59. [PMID: 25241743 PMCID: PMC4266004 DOI: 10.1016/j.stemcr.2014.06.018] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/28/2014] [Accepted: 06/30/2014] [Indexed: 12/26/2022] Open
Abstract
The salamander is the only tetrapod that functionally regenerates all cell types of the limb and spinal cord (SC) and thus represents an important regeneration model, but the lack of gene-knockout technology has limited molecular analysis. We compared transcriptional activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPRs) in the knockout of three loci in the axolotl and find that CRISPRs show highly penetrant knockout with less toxic effects compared to TALENs. Deletion of Sox2 in up to 100% of cells yielded viable F0 larvae with normal SC organization and ependymoglial cell marker expression such as GFAP and ZO-1. However, upon tail amputation, neural stem cell proliferation was inhibited, resulting in spinal-cord-specific regeneration failure. In contrast, the mesodermal blastema formed normally. Sox3 expression during development, but not regeneration, most likely allowed embryonic survival and the regeneration-specific phenotype. This analysis represents the first tissue-specific regeneration phenotype from the genomic deletion of a gene in the axolotl.
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199
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Martel B, Moineau S. CRISPR-Cas: an efficient tool for genome engineering of virulent bacteriophages. Nucleic Acids Res 2014; 42:9504-13. [PMID: 25063295 PMCID: PMC4132740 DOI: 10.1093/nar/gku628] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteriophages are now widely recognized as major players in a wide variety of ecosystems. Novel genes are often identified in newly isolated phages as well as in environmental metavirome studies. Most of these novel viral genes have unknown functions but appear to be coding for small, non-structural proteins. To understand their biological role, very efficient genetic tools are required to modify them, especially in the genome of virulent phages. We first show that specific point mutations and large deletions can be engineered in the genome of the virulent phage 2972 using the Streptococcus thermophilus CRISPR-Cas Type II-A system as a selective pressure to increase recombination efficiencies. Of significance, all the plaques tested contained recombinant phages with the desired mutation. Furthermore, we show that the CRISPR-Cas engineering system can be used to efficiently introduce a functional methyltransferase gene into a virulent phage genome. Finally, synthetic CRISPR bacteriophage insensitive mutants were constructed by cloning a spacer-repeat unit in a low-copy vector illustrating the possibility to target multiple regions of the phage genome. Taken together, this data shows that the CRISPR-Cas system is an efficient and adaptable tool for editing the otherwise intractable genomes of virulent phages and to better understand phage-host interactions.
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Affiliation(s)
- Bruno Martel
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec city, Quebec, G1V 0A6, Canada Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Quebec City, Quebec, G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec city, Quebec, G1V 0A6, Canada Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Quebec City, Quebec, G1V 0A6, Canada
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200
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Nemudryi AA, Valetdinova KR, Medvedev SP, Zakian SM. TALEN and CRISPR/Cas Genome Editing Systems: Tools of Discovery. Acta Naturae 2014; 6:19-40. [PMID: 25349712 PMCID: PMC4207558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Precise studies of plant, animal and human genomes enable remarkable opportunities of obtained data application in biotechnology and medicine. However, knowing nucleotide sequences isn't enough for understanding of particular genomic elements functional relationship and their role in phenotype formation and disease pathogenesis. In post-genomic era methods allowing genomic DNA sequences manipulation, visualization and regulation of gene expression are rapidly evolving. Though, there are few methods, that meet high standards of efficiency, safety and accessibility for a wide range of researchers. In 2011 and 2013 novel methods of genome editing appeared - this are TALEN (Transcription Activator-Like Effector Nucleases) and CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats)/Cas9 systems. Although TALEN and CRISPR/Cas9 appeared recently, these systems have proved to be effective and reliable tools for genome engineering. Here we generally review application of these systems for genome editing in conventional model objects of current biology, functional genome screening, cell-based human hereditary disease modeling, epigenome studies and visualization of cellular processes. Additionally, we review general strategies for designing TALEN and CRISPR/Cas9 and analyzing their activity. We also discuss some obstacles researcher can face using these genome editing tools.
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Affiliation(s)
- A. A. Nemudryi
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
| | - K. R. Valetdinova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
- Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
| | - S. P. Medvedev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
- Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
| | - S. M. Zakian
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 10, Novosibirsk, Russia, 630090
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Prosp., 8, Novosibirsk, Russia, 630090
- Meshalkin Novosibirsk State Research Institute of Circulation Pathology, Ministry of Health of the Russian Federation, Rechkunovskaya Str., 15, Novosibirsk, Russia, 630055
- Novosibirsk State University, Pirogova Str., 2, Novosibirsk, Russia, 630090
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