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Satterlee JW, Alonso D, Gramazio P, Jenike KM, He J, Arrones A, Villanueva G, Plazas M, Ramakrishnan S, Benoit M, Gentile I, Hendelman A, Shohat H, Fitzgerald B, Robitaille GM, Green Y, Swartwood K, Passalacqua MJ, Gagnon E, Hilgenhof R, Huggins TD, Eizenga GC, Gur A, Rutten T, Stein N, Yao S, Poncet A, Bellot C, Frary A, Knapp S, Bendahmane M, Särkinen T, Gillis J, Van Eck J, Schatz MC, Eshed Y, Prohens J, Vilanova S, Lippman ZB. Convergent evolution of plant prickles by repeated gene co-option over deep time. Science 2024; 385:eado1663. [PMID: 39088611 DOI: 10.1126/science.ado1663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/06/2024] [Indexed: 08/03/2024]
Abstract
An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on the same genetic programs, particularly over long timescales. In this work, we genetically dissected repeated origins and losses of prickles-sharp epidermal projections-that convergently evolved in numerous plant lineages. Mutations in a cytokinin hormone biosynthetic gene caused at least 16 independent losses of prickles in eggplants and wild relatives in the genus Solanum. Homologs underlie prickle formation across angiosperms that collectively diverged more than 150 million years ago, including rice and roses. By developing new Solanum genetic systems, we leveraged this discovery to eliminate prickles in a wild species and an indigenously foraged berry. Our findings implicate a shared hormone activation genetic program underlying evolutionarily widespread and recurrent instances of plant morphological innovation.
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Affiliation(s)
- James W Satterlee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - David Alonso
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Katharine M Jenike
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jia He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Andrea Arrones
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Gloria Villanueva
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Srividya Ramakrishnan
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Matthias Benoit
- French National Institute for Agriculture, Food, and Environment, Laboratory of Plant-Microbe Interactions, Toulouse, France
| | - Iacopo Gentile
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Anat Hendelman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Hagai Shohat
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Blaine Fitzgerald
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Gina M Robitaille
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yumi Green
- Boyce Thompson Institute, Ithaca, NY, USA
| | | | - Michael J Passalacqua
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Edeline Gagnon
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | | | - Trevis D Huggins
- USDA-ARS, Dale Bumpers National Rice Research Center, Stuttgart, AR, USA
| | - Georgia C Eizenga
- USDA-ARS, Dale Bumpers National Rice Research Center, Stuttgart, AR, USA
| | - Amit Gur
- Cucurbits Section, Department of Vegetable Sciences, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishay, Israel
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- Crop Plant Genetics, Martin Luther University of Halle-Wittenberg, Halle (Saale), Germany
| | - Shengrui Yao
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, USA
- Sustainable Agriculture Sciences Center, New Mexico State University, Alcalde, NM, USA
| | - Adrien Poncet
- Laboratoire Reproduction et Developpement des Plantes, INRAE, CNRS, Universite Lyon, Ecole Normale Superieure de Lyon, Lyon, France
| | - Clement Bellot
- Laboratoire Reproduction et Developpement des Plantes, INRAE, CNRS, Universite Lyon, Ecole Normale Superieure de Lyon, Lyon, France
| | - Amy Frary
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | | | - Mohammed Bendahmane
- Laboratoire Reproduction et Developpement des Plantes, INRAE, CNRS, Universite Lyon, Ecole Normale Superieure de Lyon, Lyon, France
| | | | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Yuval Eshed
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Zachary B Lippman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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Mikami N, Nguyen CLK, Osawa Y, Kato K, Ishida M, Tanimoto Y, Morimoto K, Murata K, Kang W, Sugiyama F, Ema M, Takahashi S, Mizuno S. Deletion of Exoc7, but not Exoc3, in male germ cells causes severe spermatogenesis failure with spermatocyte aggregation in mice. Exp Anim 2024; 73:286-292. [PMID: 38325858 PMCID: PMC11254494 DOI: 10.1538/expanim.23-0171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/31/2024] [Indexed: 02/09/2024] Open
Abstract
Vesicular trafficking is essential for the transport of intracellularly produced functional molecules to the plasma membrane and extracellular space. The exocyst complex, composed of eight different proteins, is an important functional machinery for "tethering" in vesicular trafficking. Functional studies have been conducted in laboratory mice to identify the mechanisms by which the deletion of each exocyst factor affect various biological phenomena. Interestingly, each exocyst factor-deficient mutant exhibits a different phenotype. This discrepancy may be due to the function of the exocyst factor beyond its role as a component of the exocyst complex. Male germline-specific conditional knockout (cKO) mice of the Exoc1 gene, which encodes one of the exocyst factors EXOC1 (SEC3), exhibit severe spermatogenesis defects; however, whether this abnormality also occurs in mutants lacking other exocyst factors remains unknown. In this study, we found that exocyst factor EXOC3 (SEC6) was not required for spermatogenesis, but depletion of EXOC7 (EXO70) led to severe spermatogenesis defects. In addition to being a component of the exocyst complex, EXOC1 has other functions. Notably, male germ cell-specific Exoc7 cKO and Exoc1 cKO mice exhibited phenotypic similarities, suggesting the importance of the exocyst complex for spermatogenesis. The results of this study will contribute to further understanding of spermatogenesis from the aspect of vesicular trafficking.
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Affiliation(s)
- Natsuki Mikami
- Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Chi Lieu Kim Nguyen
- Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yuki Osawa
- Master's Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kanako Kato
- Laboratory Animal Resource Center and Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Miyuki Ishida
- Laboratory Animal Resource Center and Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoko Tanimoto
- Laboratory Animal Resource Center and Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kento Morimoto
- Doctoral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
- Research Fellow of the Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Kazuya Murata
- Laboratory Animal Resource Center and Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Woojin Kang
- Laboratory Animal Resource Center and Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center and Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Masatsugu Ema
- Department of Stem Cells and Human Disease Models, Research Center for Animal Life Science, Shiga University of Medical Science, Seta, Tsukinowa-cho, Otsu, Shiga 520-2192, Japan
| | - Satoru Takahashi
- Laboratory Animal Resource Center and Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center and Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
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McCabe CV, Price PD, Codner GF, Allan AJ, Caulder A, Christou S, Loeffler J, Mackenzie M, Malzer E, Mianné J, Nowicki KJ, O’Neill EJ, Pike FJ, Hutchison M, Petit-Demoulière B, Stewart ME, Gates H, Wells S, Sanderson ND, Teboul L. Long-read sequencing for fast and robust identification of correct genome-edited alleles: PCR-based and Cas9 capture methods. PLoS Genet 2024; 20:e1011187. [PMID: 38457464 PMCID: PMC10954187 DOI: 10.1371/journal.pgen.1011187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 03/20/2024] [Accepted: 02/20/2024] [Indexed: 03/10/2024] Open
Abstract
BACKGROUND Recent developments in CRISPR/Cas9 genome-editing tools have facilitated the introduction of precise alleles, including genetic intervals spanning several kilobases, directly into the embryo. However, the introduction of donor templates, via homology directed repair, can be erroneous or incomplete and these techniques often produce mosaic founder animals. Thus, newly generated alleles must be verified at the sequence level across the targeted locus. Screening for the presence of the desired mutant allele using traditional sequencing methods can be challenging due to the size of the interval to be sequenced, together with the mosaic nature of founders. METHODOLOGY/PRINCIPAL FINDINGS In order to help disentangle the genetic complexity of these animals, we tested the application of Oxford Nanopore Technologies long-read sequencing at the targeted locus and found that the achievable depth of sequencing is sufficient to offset the sequencing error rate associated with the technology used to validate targeted regions of interest. We have assembled an analysis workflow that facilitates interrogating the entire length of a targeted segment in a single read, to confirm that the intended mutant sequence is present in both heterozygous animals and mosaic founders. We used this workflow to compare the output of PCR-based and Cas9 capture-based targeted sequencing for validation of edited alleles. CONCLUSION Targeted long-read sequencing supports in-depth characterisation of all experimental models that aim to produce knock-in or conditional alleles, including those that contain a mix of genome-edited alleles. PCR- or Cas9 capture-based modalities bring different advantages to the analysis.
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Affiliation(s)
| | - Peter D. Price
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Gemma F. Codner
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | | | - Adam Caulder
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | | | - Jorik Loeffler
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | | | - Elke Malzer
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Joffrey Mianné
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | | | | | - Fran J. Pike
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Marie Hutchison
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Benoit Petit-Demoulière
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, Illkirch, France
| | | | - Hilary Gates
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
- Mammalian Genetics Unit, MRC Harwell, Oxfordshire, United Kingdom
| | - Sara Wells
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
| | - Nicholas D. Sanderson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell, Oxfordshire, United Kingdom
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Sato R, Nanasato Y, Takata N, Nagano S, Fukatsu E, Fujino T, Yamaguchi K, Moriguchi Y, Shigenobu S, Suzuki Y, Kasahara M, Ueno S. Efficient selection of a biallelic and nonchimeric gene-edited tree using Oxford Nanopore Technologies sequencing. TREE PHYSIOLOGY 2024; 44:tpad158. [PMID: 38145493 DOI: 10.1093/treephys/tpad158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/12/2023] [Indexed: 12/27/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 nuclease system is a versatile and essential biotechnological tool in the life sciences that allows efficient genome editing. When generating gene-edited trees, T0-generation plants are often used for subsequent analysis because of the time that is required to obtain the desired mutants via crossing. However, T0-generation plants exhibit various unexpected mutations, which emphasizes the need to identify mutants with expected mutation patterns. The two critical checkpoints in this process are to confirm the expected mutation patterns in both alleles and to exclude somatic chimeric plants. In this study, we generated gene-edited Cryptomeria japonica plants and established a method to determine chimerism and mutation patterns using fragment analysis and Oxford Nanopore Technologies (ONT)-based amplicon sequencing. In the first screening, fragment analysis, i.e., indel detection via amplicon analysis, was used to predict indel mutation patterns in both alleles and to discriminate somatic chimeric plants in 188 candidate mutants. In the second screening, we precisely determined the mutation patterns and chimerism in the mutants using ONT-based amplicon sequencing, where confirmation of both alleles can be achieved using allele-specific markers flanking the single guide RNA target site. In the present study, a bioinformatic analysis procedure was developed and provided for the rapid and accurate determination of DNA mutation patterns using ONT-based amplicon sequencing. As ONT amplicon sequencing has a low running cost compared with other long-read analysis methods, such as PacBio, it is a powerful tool in plant genetics and biotechnology to select gene-edited plants with expected indel patterns in the T0-generation.
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Affiliation(s)
- Ryosuke Sato
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki 319-1301, Japan
| | - Yoshihiko Nanasato
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki 319-1301, Japan
| | - Naoki Takata
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki 319-1301, Japan
| | - Soichiro Nagano
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki 319-1301, Japan
| | - Eitaro Fukatsu
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 3809-1 Ishi, Juo, Hitachi, Ibaraki 319-1301, Japan
| | - Takeshi Fujino
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Katushi Yamaguchi
- Trans-Scale Biology Center, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Yoshinari Moriguchi
- Faculty of Agriculture, Niigata University, 8050 Ikarashi 2-Nocho, Nishi-ku, Niigata 950-2181, Japan
| | - Shuji Shigenobu
- Trans-Scale Biology Center, National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Masahiro Kasahara
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
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Tamari T, Ikeda Y, Morimoto K, Kobayashi K, Mizuno-Iijima S, Ayabe S, Kuno A, Mizuno S, Yoshiki A. A universal method for generating knockout mice in multiple genetic backgrounds using zygote electroporation. Biol Open 2023; 12:bio059970. [PMID: 37623822 PMCID: PMC10497038 DOI: 10.1242/bio.059970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023] Open
Abstract
Genetically engineered mouse models are essential tools for understanding mammalian gene functions and disease pathogenesis. Genome editing allows the generation of these models in multiple inbred strains of mice without backcrossing. Zygote electroporation dramatically removed the barrier for introducing the CRISPR-Cas9 complex in terms of cost and labour. Here, we demonstrate that the generalised zygote electroporation method is also effective for generating knockout mice in multiple inbred strains. By combining in vitro fertilisation and electroporation, we obtained founders for knockout alleles in eight common inbred strains. Long-read sequencing analysis detected not only intended mutant alleles but also differences in read frequency of intended and unintended alleles among strains. Successful germline transmission of knockout alleles demonstrated that our approach can establish mutant mice targeting the same locus in multiple inbred strains for phenotyping analysis, contributing to reverse genetics and human disease research.
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Affiliation(s)
- Tomohiro Tamari
- Model Generation & Breeding Service, The Jackson Laboratory Japan, Inc., 955 Kamibayashi, Ishioka, Ibaraki 315-0138, Japan
- Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
- Doctoral Program in Biomedical Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoshihisa Ikeda
- Model Generation & Breeding Service, The Jackson Laboratory Japan, Inc., 955 Kamibayashi, Ishioka, Ibaraki 315-0138, Japan
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kento Morimoto
- Doctoral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
- Research Fellow of the Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Keiko Kobayashi
- Model Generation & Breeding Service, The Jackson Laboratory Japan, Inc., 955 Kamibayashi, Ishioka, Ibaraki 315-0138, Japan
| | - Saori Mizuno-Iijima
- Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shinya Ayabe
- Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Akihiro Kuno
- Department of Anatomy and Embryology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center in Trans-Border Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
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6
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Kobayashi R, Horii T, Hatada I. Efficient Detection of Flox Mice Using In Vitro Cre Recombination. Methods Mol Biol 2023; 2637:149-159. [PMID: 36773145 DOI: 10.1007/978-1-0716-3016-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Advances in CRISPR/Cas9 genome editing technologies have allowed for the rapid generation of Cre-loxP conditional knockout mice. However, current strategies for genotyping flox mice, typically based on Sanger sequencing following cloning of target sequences from dozens of pups, are time-consuming. Here, we describe a rapid screening method for flox mice, using in vitro Cre recombination that can be performed using simple enzymatic reactions and enables detection of functional flox mouse within 1 day. In addition, we introduce an efficient strategy for subsequent sequence analysis by cloning of floxed regions using the In-Fusion system. Our genotyping pipeline reduces laborious tasks and thus contributes to the rapid selection of accurately edited flox mice.
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Affiliation(s)
- Ryosuke Kobayashi
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Takuro Horii
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan.
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7
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Yoshiki A, Ballard G, Perez AV. Genetic quality: a complex issue for experimental study reproducibility. Transgenic Res 2022; 31:413-430. [PMID: 35751794 PMCID: PMC9489590 DOI: 10.1007/s11248-022-00314-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022]
Abstract
Laboratory animal research involving mice, requires consideration of many factors to be controlled. Genetic quality is one factor that is often overlooked but is essential for the generation of reproducible experimental results. Whether experimental research involves inbred mice, spontaneous mutant, or genetically modified strains, exercising genetic quality through careful breeding, good recordkeeping, and prudent quality control steps such as validation of the presence of mutations and verification of the genetic background, will help ensure that experimental results are accurate and that reference controls are representative for the particular experiment. In this review paper, we will discuss various techniques used for the generation of genetically altered mice, and the different aspects to be considered regarding genetic quality, including inbred strains and substrains used, quality check controls during and after genetic manipulation and breeding. We also provide examples for when to use the different techniques and considerations on genetic quality checks. Further, we emphasize on the importance of establishing an in-house genetic quality program.
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Affiliation(s)
- Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, Tsukuba, 3050074, Japan.
| | - Gregory Ballard
- Comparative Medicine and Quality, The Jackson Laboratory, Bar Harbor, ME 04609, USA
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