A comparative analysis of L1 retrotransposition activities in human genomes suggests an ongoing increase in L1 number despite an evolutionary trend towards lower activity

BACKGROUND: LINE-1 (Long Interspersed Nuclear Elements, L1) retrotransposons are the only autonomously active transposable elements in the human genome. The evolution of L1 retrotransposition rates and its implications for L1 dynamics are poorly understood. Retrotransposition rates are commonly measured in cell culture-based assays, but it is unclear how well these measurements provide insight into L1 population dynamics. This study applied comparative methods to estimate parameters for the evolution of retrotransposition rates, and infer L1 dynamics from these estimates. RESULTS: Our results show that the rates at which new L1s emerge in the human population correlate positively to cell-culture based retrotransposition activities, that there is an evolutionary trend towards lower retrotransposition activity, and that this evolutionary trend is not sufficient to counter-balance the increase in active L1s resulting from continuing retrotransposition. CONCLUSIONS: Together, these findings support a model of the population-level L1 retrotransposition dynamics that is consistent with prior expectations and indicate the remaining gaps in the understanding of L1 dynamics in human genomes.