Dynamic methylation of an L1 transduction family during reprogramming and neurodifferentiation

The retrotransposon LINE-1 (L1) is a significant source of endogenous mutagenesis in humans. In each individual genome, a handful of retrotransposition-competent L1s (RC-L1s) can generate new heritable L1 insertions in the early embryo, primordial germline, and in germ cells. L1 retrotransposition can also occur in the neuronal lineage and cause somatic mosaicism. Although DNA methylation mediates L1 promoter repression, the temporal pattern of methylation applied to individual RC-L1s during neurogenesis is unclear. Here, we identified a L1 insertion in a human induced pluripotent stem cell (hiPSC) line via retrotransposon capture sequencing (RC-seq). The L1 insertion was full-length and carried 5' and 3' transductions. The corresponding donor RC-L1 was part of a large and recently active L1 transduction family and was highly mobile in a cultured cell L1 retrotransposition reporter assay. Notably, we observed distinct and dynamic DNA methylation profiles for the L1 and members of its extended transduction family during neuronal differentiation. These experiments reveal how a L1 insertion in a pluripotent stem cell is rapidly recognized and repressed, albeit incompletely, by the host genome during neurodifferentiation, whilst retaining potential for further retrotransposition.