Heritable L1 retrotransposition in the mouse primordial germline and early embryo

Abstract

LINE-1 (L1) retrotransposons are a noted source of genetic diversity and disease in mammals. To expand its genomic footprint, L1 must mobilize in cells that will contribute their genetic material to subsequent generations. Heritable L1 insertions may therefore arise in germ cells and in pluripotent embryonic cells, prior to germline specification, yet the frequency and predominant developmental timing of such events remain unclear. Here, we applied mouse retrotransposon capture sequencing (mRC-seq) and whole-genome sequencing (WGS) to pedigrees of C57BL/6J animals, and uncovered an L1 insertion rate of ≥1 event per eight births. We traced heritable L1 insertions to pluripotent embryonic cells and, strikingly, to early primordial germ cells (PGCs). New L1 insertions bore structural hallmarks of target-site primed reverse transcription (TPRT) and mobilized efficiently in a cultured cell retrotransposition assay. Together, our results highlight the rate and evolutionary impact of heritable L1 retrotransposition and reveal retrotransposition-mediated genomic diversification as a fundamental property of pluripotent embryonic cells in vivo.

L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis

“…S2; Supplemental Table S2). Notably, we subsequently performed 45× WGS on five tumor nodes from the three mice in which these full-length tumor-specific L1 insertions arose, to identify potential 5 ′ truncated L1 insertions that were not detected due to previously described technical difficulties in sequencing the mouse L1 3 ′ end (Richardson et al 2017). As in our previous study, analysis of WGS data did not reveal any additional 5 ′ truncated insertions.…”

“…We isolated 12 HCC tumor nodules and matching tail tissue from 10 Mdr2 −/− mice at age 15 mo (Supplemental Table S1) and performed mouse retrotransposon capture sequencing (mRC-seq) (Richardson et al 2017) on tumor and tail genomic DNA and ∼45× whole-genome sequencing (WGS) on each of five nodules from three animals (Supplemental Table S1). Sequence analysis to identify putative retroelement insertions was performed using the TEBreak bioinformatic pipeline (https://github.com/adamewing/tebreak) and intersected with known nonreference genome TE insertions found in a wide array of mouse strains (Nellaker et al 2012 Table S2).…”

“…2B; Naas et al 1998). Thus, the L1 donor represents one of the most highly active natural L1 T F elements tested in cultured cells to date (Naas et al 1998;Martin et al 2008;Richardson et al 2017).…”

“…Although the vast majority of L1 copies are no longer mobile, 80-100 human L1s and 2000-3000 mouse L1s, per individual, are full-length and retain retrotransposition potential (Goodier et al 2001;Brouha et al 2003). Aside from L1, several retrotransposon families are active in mice, including B1 and B2 SINEs, as well as LTR retrotransposons, such as IAP and ETn elements (Nellaker et al 2012;Richardson et al 2017). In humans, there is one presently active L1 subfamily, L1-Ta, while three mouse L1 subfamilies are known to be recently active: T F , G F , and A.…”

“…In the mammalian germline and early embryo, L1 escapes repression to mobilize and create heritable insertions to ensure its evolutionary success (Kano et al 2009;Faulkner and Garcia-Perez 2017;Richardson et al 2017). More recently, somatic L1 mobilization has been revealed as a characteristic of normal neuronal cells in rodents and humans, and L1 dysregulation has been associated with neurological diseases (Muotri et al 2005(Muotri et al , 2010Baillie et al 2011;Coufal et al 2011;Evrony et al 2012;Upton et al 2015;Erwin et al 2016;Hazen et al 2016).…”