Whole-genome sequencing identifies I-SceI-mediated transgene integration sites in Xenopus tropicalis snai2: eGFP line

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Author(s)Wang, Jian
Author(s)Lu, Congyu
Author(s)Wei, Shuo
Date Accessioned2022-03-30T17:32:00Z
Date Available2022-03-30T17:32:00Z
Publication Date2022-02-16
DescriptionThis article has been accepted for publication in G3: Genes | Genomes | Genetics Published by Oxford University Press. The version of record is available at: https://doi.org/10.1093/g3journal/jkac037en_US
AbstractTransgenesis with the meganuclease I-SceI is a safe and efficient method, but the underlying mechanisms remain unclear due to the lack of information on transgene localization. Using I-SceI, we previously developed a transgenic Xenopus tropicalis line expressing enhanced green fluorescent protein driven by the neural crest-specific snai2 promoter/enhancer, which is a powerful tool for studying neural crest development and craniofacial morphogenesis. Here we carried out whole-genome shotgun sequencing for the snai2: eGFP embryos to identify the transgene integration sites. With a 19x sequencing coverage, we estimated that 6 copies of the transgene were inserted into the X. tropicalis genome in the hemizygous transgenic embryos. Two transgene integration loci adjacent to each other were identified in a non-coding region on Chromosome 1, possibly as a result of duplication after a single transgene insertion. Interestingly, genomic DNA at the boundaries of the transgene integration loci contains short sequences homologous to the I-SceI recognition site, suggesting that the integration was not random but probably mediated by sequence homology. To our knowledge, our work represents the first genome-wide sequencing study on a transgenic organism generated with I-SceI, which is useful for evaluating the potential genetic effects of I-SceI-mediated transgenesis and further understanding the mechanisms underlying this transgenic method.en_US
SponsorThis work was funded by the U.S. NIH (R01GM114105, R01DE029802 and R03DE022813 to SW). Illumina NGS was performed by Marshall University Genomics Core Facility and supported by NIH grant P20GM103434.en_US
CitationJian Wang, Congyu Lu, Shuo Wei, Whole-genome sequencing identifies I-SceI-mediated transgene integration sites in Xenopus tropicalis snai2: eGFP line, G3 Genes | Genomes | Genetics, 2022;, jkac037, https://doi.org/10.1093/g3journal/jkac037en_US
ISSN2160-1836
URLhttps://udspace.udel.edu/handle/19716/30738
Languageen_USen_US
PublisherG3: Genes | Genomes | Geneticsen_US
Keywordswhole-genome sequencingen_US
Keywordstransgenesisen_US
KeywordsI-SceIen_US
KeywordsXenopus tropicalisen_US
Keywordssnai2: eGFP lineen_US
TitleWhole-genome sequencing identifies I-SceI-mediated transgene integration sites in Xenopus tropicalis snai2: eGFP lineen_US
TypeArticleen_US
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