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Locating and Characterizing a Transgene Integration Site by Nanopore Sequencing

Author(s)
Nicholls, Peter K.; Bellott, Daniel W.; Cho, Ting-Jan; Pyntikova, Tatyana; Page, David C.
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Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/
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Abstract
The introduction of foreign DNA into cells and organisms has facilitated much of modern biological research, and it promises to become equally important in clinical practice. Locating sites of foreign DNA incorporation in mammalian genomes has proven burdensome, so the genomic location of most transgenes remains unknown. To address this challenge, we applied nanopore sequencing in search of the site of integration of Tg(Pou5f1-EGFP)2Mnn (also known as Oct4:EGFP), a widely used fluorescent reporter in mouse germ line research. Using this nanopore-based approach, we identified the site of Oct4: EGFP transgene integration near the telomere of Chromosome 9. This methodology simultaneously yielded an estimate of transgene copy number, provided direct evidence of transgene inversions, revealed contaminating E. coli genomic DNA within the transgene array, validated the integrity of neighboring genes, and enabled definitive genotyping. We suggest that such an approach provides a rapid, cost-effective method for identifying and analyzing transgene integration sites.
Date issued
2019-05
URI
https://hdl.handle.net/1721.1/125096
Department
Whitehead Institute for Biomedical Research; Massachusetts Institute of Technology. Department of Biology
Journal
G3
Publisher
Genetics Society of America
Citation
Nicholls, Peter K. et al. “Locating and Characterizing a Transgene Integration Site by Nanopore Sequencing.” G3 9 (2019): 1481-1486 © 2019 The Author(s)
Version: Final published version
ISSN
2160-1836

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