Suzuki O, Koura M, Uchio-Yamada K, Sasaki M. Analysis of the transgene insertion pattern in a transgenic mouse strain using long-read sequencing.
Exp Anim 2020;
69:279-286. [PMID:
32051389 PMCID:
PMC7445054 DOI:
10.1538/expanim.19-0118]
[Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Transgene insertion patterns are critical for the analysis of transgenic animals because
the influence of transgenes may change depending on the insertion pattern (such as copy
numbers and orientations of concatenations) and the insertion position in the genome. We
previously reported a genomic walking strategy to locate transgenes in the genomes of
transgenic mice (Exp. Anim. 53: 103–111, 2004) and to analyze transgene insertion patterns
(Exp. Anim. 55: 65–69, 2006). With such strategies, however, we could not determine the
copy number of transgenes or global genome modification induced by transgene insertion due
to read-length limitation. In this study, we used a long-read sequencer (MinION, Oxford
Nanopore Technologies) to overcome this limitation. We obtained 922,210 reads using MinION
with genomic DNA from a transgenic mouse strain (4C30, Proc. Jpn. Acad. Ser. B. Phys.
Biol. Sci. 87: 550–562, 2011). Among the reads, we found one 21,457-bp read containing the
transgene using a local BLAST search. Nucleotide dot plot analysis revealed that the
transgene was inserted in the genome as a tandem concatemer with an almost entire
construct (15–3,508 of 3,508 bp) and a partial fragment (4–660, 657 bp). Ensembl’s BLAST
search against the C57BL/6N genome revealed a 9,388-bp deletion at the insertion position
in the intron of the Sgcd gene, confirming that mutations such as a large
genomic deletion could occur at the time of transgene insertion. Thus, long-read
sequencers are useful tools for the analysis of transgene insertion patterns.
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