Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis.

Authors

Leslie O Goodwin, The Jackson LaboratoryFollow
Erik Splinter
Tiffany Leidy-Davis, The Jackson LaboratoryFollow
Rachel Urban, The Jackson LaboratoryFollow
Hao He
Robert E Braun, The Jackson LaboratoryFollow
Elissa J Chesler, The Jackson LaboratoryFollow
Vivek Kumar, The Jackson LaboratoryFollow
Max van Min
Juliet Ndukum, The Jackson LaboratoryFollow
Vivek M. Philip, The Jackson LaboratoryFollow
Laura G Reinholdt, The Jackson LaboratoryFollow
Karen L. Svenson, The Jackson LaboratoryFollow
Jacqueline K White, The Jackson LaboratoryFollow
Michael Sasner, The Jackson LaboratoryFollow
Cathleen Lutz, The Jackson LaboratoryFollow
Stephen A. Murray, The Jackson LaboratoryFollow

Document Type

Article

Publication Date

3-1-2019

Keywords

JMG, JGM

JAX Source

Genome Res 2019 Mar; 29(3):494-505.

Volume

29

Issue

3

First Page

494

Last Page

505

ISSN

1549-5469

PMID

30659012

DOI

https://doi.org/10.1101/gr.233866.117

Grant

CA034196,OD011185,HG006332,OD011190,OD010921,OD023222

Abstract

Transgenesis has been a mainstay of mouse genetics for over 30 yr, providing numerous models of human disease and critical genetic tools in widespread use today. Generated through the random integration of DNA fragments into the host genome, transgenesis can lead to insertional mutagenesis if a coding gene or an essential element is disrupted, and there is evidence that larger scale structural variation can accompany the integration. The insertion sites of only a tiny fraction of the thousands of transgenic lines in existence have been discovered and reported, due in part to limitations in the discovery tools. Targeted locus amplification (TLA) provides a robust and efficient means to identify both the insertion site and content of transgenes through deep sequencing of genomic loci linked to specific known transgene cassettes. Here, we report the first large-scale analysis of transgene insertion sites from 40 highly used transgenic mouse lines. We show that the transgenes disrupt the coding sequence of endogenous genes in half of the lines, frequently involving large deletions and/or structural variations at the insertion site. Furthermore, we identify a number of unexpected sequences in some of the transgenes, including undocumented cassettes and contaminating DNA fragments. We demonstrate that these transgene insertions can have phenotypic consequences, which could confound certain experiments, emphasizing the need for careful attention to control strategies. Together, these data show that transgenic alleles display a high rate of potentially confounding genetic events and highlight the need for careful characterization of each line to assure interpretable and reproducible experiments.

Comments

The authors thank Brianna Caddle and Larry Bechtel for their technical assistance in isolating spleen cells and Kevin Peterson for his helpful and thoughtful comments on the manuscript.

Recommended Citation

Goodwin L, Splinter E, Leidy-Davis T, Urban R, He H, Braun R, Chesler E, Kumar V, van Min M, Ndukum J, Philip VM, Reinholdt L, Svenson KL, White J, Sasner M, Lutz C, Murray SA. Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis. Genome Res 2019 Mar; 29(3):494-505.