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Bryant WB, Yang A, Griffin SH, Zhang W, Rafiq AM, Han W, Deak F, Mills MK, Long X, Miano JM. CRISPR-Cas9 Long-Read Sequencing for Mapping Transgenes in the Mouse Genome. CRISPR J 2023; 6:163-175. [PMID: 37071672 PMCID: PMC10123806 DOI: 10.1089/crispr.2022.0099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/12/2023] [Indexed: 04/19/2023] Open
Abstract
Microinjected transgenes, both large and small, are known to insert randomly into the mouse genome. Traditional methods of mapping a transgene are challenging, thus complicating breeding strategies and accurate interpretation of phenotypes, particularly when a transgene disrupts critical coding or noncoding sequences. As the vast majority of transgenic mouse lines remain unmapped, we developed CRISPR-Cas9 Long-Read Sequencing (CRISPR-LRS) to ascertain transgene integration loci. This novel approach mapped a wide size range of transgenes and uncovered more complex transgene-induced host genome re-arrangements than previously appreciated. CRISPR-LRS offers a facile, informative approach to establish robust breeding practices and will enable researchers to study a gene without confounding genetic issues. Finally, CRISPR-LRS will find utility in rapidly and accurately interrogating gene/genome editing fidelity in experimental and clinical settings.
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Affiliation(s)
- W. Bart Bryant
- Department of Medicine and Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Allison Yang
- Department of Medicine and Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Susan H. Griffin
- Department of Medicine and Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Wei Zhang
- Department of Medicine and Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Ashiq M. Rafiq
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Weiping Han
- Department of Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Ferenc Deak
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Mary Katherine Mills
- Department of Department of Biology and Geology, University of South Carolina Aiken, Aiken, South Carolina, USA
| | - Xiaochun Long
- Department of Medicine and Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
| | - Joseph M. Miano
- Department of Medicine and Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, Georgia, USA
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Kaneda R, Saeki Y, Getachew D, Matsumoto A, Furuya M, Ogawa N, Motoya T, Rafiq AM, Jahan E, Udagawa J, Hashimoto R, Otani H. Interkinetic nuclear migration in the tracheal and esophageal epithelia of the mouse embryo: Possible implications for tracheo-esophageal anomalies. Congenit Anom (Kyoto) 2018; 58:62-70. [PMID: 28782137 DOI: 10.1111/cga.12241] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/18/2017] [Accepted: 07/31/2017] [Indexed: 02/02/2023]
Abstract
Interkinetic nuclear migration (INM) is a cell polarity-based phenomenon in which progenitor cell nuclei migrate along the apico-basal axis of the pseudostratified epithelium in synchrony with the cell cycle. INM is suggested to be at least partially cytoskeleton-dependent and to regulate not only the proliferation/differentiation of stem/progenitor cells but also the localized/overall size and shape of organs/tissues. INM occurs in all three of the germ-layer derived epithelia, including the endoderm-derived gut. However, INM has not been documented in the esophagus and respiratory tube arising from the anterior foregut. Esophageal atresia with or without trachea-esophageal fistula (EA/TEF) is a relatively common developmental defect. Transcription factors and signaling molecules have been implicated in EA/TEF, but the etiology of EA/TEF-which has been suggested to involve cell polarity-related mechanisms-remains highly controversial. In the present study, we first examined whether INM exists in the trachea and esophagus of mouse embryos at embryonic day 11.5 (E11.5), just after separation of the two tubes from the anterior foregut. By labeling the DNA-synthesizing stem cell nuclei with 5-ethynyl-2'-deoxyuridine, a nucleotide analogue, and statistically analyzing chronological changes in the distribution pattern of the labeled nuclei by using multidimensional scaling, we showed the existence of INM in both the esophagus and trachea, with differences in the INM magnitude and cycle pattern. We further showed morphological changes from the INM-based pseudostratified single layer to the stratified multilayer in the esophageal epithelium in association with a temporal loss/perturbation of AB polarity, suggesting a possible relation with the pathogenesis of EA/TEF.
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Affiliation(s)
- Ryo Kaneda
- Department of Development Biology, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Yuko Saeki
- Department of Development Biology, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Dereje Getachew
- Department of Development Biology, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Akihiro Matsumoto
- Department of Development Biology, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Motohide Furuya
- Department of Development Biology, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Noriko Ogawa
- Department of Development Biology, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Tomoyuki Motoya
- Department of Development Biology, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Ashiq M Rafiq
- Center for the Promotion of Project Research, Organization for Research, Shimane University, Matsue, Japan
| | - Esrat Jahan
- Department of Development Biology, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Jun Udagawa
- Division of Anatomy and Cell Biology, Department of Anatomy, Shiga University of Medical Science, Otsu, Japan
| | - Ryuju Hashimoto
- Department of Clinical Nursing, Faculty of Medicine, Shimane University, Izumo, Japan
| | - Hiroki Otani
- Department of Development Biology, Faculty of Medicine, Shimane University, Izumo, Japan
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