Poster Presentation Society for Molecular Biology and Evolution Conference 2016

Identification of polymorphic L1 insertions in mice (#689)

Patricia Gerdes 1 , Sandra R. Richardson 1 , Geoffrey J. Faulkner 1 2
  1. Mater Research Institute - University of Queensland, Woolloongabba, QLD, Australia
  2. School of Biomedical Sciences, University of Queensland, St. Lucia, QLD, Australia

Long interspersed element 1 (L1 or LINE-1) retrotransposons are mobile genetic elements that comprise 17% of the human and 18% of the mouse genome. L1 mobilizes, or retrotransposes, via the reverse transcription and integration of an RNA intermediate. In mice, ~3000 copies per individual are potentially active and belong to three subfamilies (TF, GF and A), whereas the human genome harbours only ~80-100 potentially active copies. L1 mobilization has to occur in the germline or pluripotent cells of the early embryo prior to germline specification to be transmissible and have an ongoing impact on genome evolution. Importantly, L1 insertions contribute to genomic diversity thereby creating variation among individuals of a species but insertions within and proximal to genes can disrupt gene function and cause genetic disease.

Here, we used mouse retrotransposon capture sequencing (mRC-seq) to identify endogenous retrotransposition events in pedigrees of C57BL/6J mice. We identified 35 polymorphic insertions  including L1 TF and GF subfamilies as well as  B1 and B2 short interspersed elements (SINEs) that appeared throughout our pedigrees but were absent from the reference genome. 18/35 polymorphic insertions were varying in presence among our animals. 7 out of these 18 insertions were validated by PCR and fully characterized identifying target site duplications (TSDs) and other structural hallmarks of target-site primed reverse transcription (TPRT). In addition, 3’ transductions on two polymorphic L1 insertions allows identification of the progenitor L1 element. Two L1 insertions differentially present within our mouse pedigrees inserted into introns of genes, allowing the opportunity to study the functional impact of retroelement polymorphisms in mammals. Together, these studies will elucidate the ways in which retrotransposon activity can impact the genomic landscape of a species.