Induced pluripotent stem cells (iPSCs) can in principle differentiate into any cell of the body, and have revolutionized biomedical research and regenerative medicine. Unlike their human counterparts, mouse iPSCs (miPSCs) are reported to silence transposable elements and prevent transposable element-mediated mutagenesis. Here we apply short-read or Oxford Nanopore Technologies long-read genome sequencing to 38 bulk miPSC lines reprogrammed from 10 parental cell types, and 18 single-cell miPSC clones. While single nucleotide variants and structural variants restricted to miPSCs are rare, we find 83 de novo transposable element insertions, including examples intronic to Brca1 and Dmd. LINE-1 retrotransposons are profoundly hypomethylated in miPSCs, beyond other transposable elements and the genome overall, and harbor alternative protein-coding gene promoters. We show that treatment with the LINE-1 inhibitor lamivudine does not hinder reprogramming and efficiently blocks endogenous retrotransposition, as detected by long-read genome sequencing. These experiments reveal the complete spectrum and potential significance of mutations acquired by miPSCs.
© 2022. The Author(s).

Induced pluripotent stem cells (iPSCs) may differentiate into any cell of the body and as such have revolutionized biomedical research and regenerative medicine. Unlike their human counterparts, mouse iPSCs (miPSCs) are reported to silence transposable elements (TEs) and prevent TE-mediated mutagenesis. Here we applied short- or long-read genome sequencing to 30 bulk miPSC lines reprogrammed from 10 parental cell types, as well as 18 single-cell miPSC clones. While single nucleotide variants and structural variants restricted to miPSCs were rare, we found 55 de novo TE insertions, including examples intronic to Brca1 and Dmd . LINE-1 (L1) retrotransposon families were profoundly hypomethylated in miPSCs, beyond other TEs and the genome overall, and harbored alternative promoters for protein-coding genes. Treatment with the L1 reverse transcriptase inhibitor lamivudine did not hinder reprogramming, pointing to a viable strategy to block retrotransposition. These experiments reveal the complete spectrum and potential significance of mutations acquired by miPSCs.