Induced pluripotent stem cells (iPSCs) are derived by reprogramming somatic cells and have the capacity to generate cells corresponding to all three germ layers. Because of their similarities to embryonic stem cells, iPSCs are a prospective tool to study developmental biology, and for biomedical applications, making characterisation of potential genomic abnormalities in these cells very important.
Long interspersed element 1 (L1 or LINE-1) retrotransposons are mobile genetic elements that comprise 17% of the human genome and 18% of the mouse genome. ~3000 L1 copies are potentially active in mice and can act as insertional mutagens. Previous reports (Wissing et al., Hum Mol Genet, 2012; Klawitter et al., Nat Commun, 2016) have demonstrated that human iPSCs support L1 retrotransposition. By contrast, an analysis (Quinlan et al., Cell Stem Cell, 2011) of 3 mouse iPSC (miPSC) lines did not identify any reprogramming-associated L1 insertions, leading to a broad conclusion of retroelement stability in miPSCs.
To address this discrepancy, we performed 30x WGS upon 27 miPSC lines derived by bulk expansion and mouse retrotransposon-capture sequencing (mRC-seq) and WGS on 18 miPSC lines derived by clonal expansion including matched controls. Our analysis revealed 33 de novo retrotransposon insertions that are absent from the reference genome. Each insertion was validated by PCR and 32 were present in only one miPSC line, consistent with mobilisation during reprogramming. These results demonstrate that reprogramming can lead to L1 mobilisation in miPSCs, potentially affecting genome stability.