Recombination between subtypes creates a mosaic lineage of LINE-1 that is expressed and actively retrotransposing in the mouse genome

Abstract

LINE-1, or L1, elements are retrotransposons that have amplified to high-copy number during the evolution of mammals. L1 appears to amplify in waves, spawning large numbers of progeny such that elements with distinct sequence features dominate the dispersal process in a given window of time. This process generates discrete subfamilies of L1 within mammalian genomes, with the oldest being remnants, or fossils, of earlier waves of amplification. In mice, at least three distinct subfamilies of L1 were distinguished by their unique 5′ ends, A, F and V. These subfamilies amplified at distinct times in the evolution of mice, with A being the youngest and V the oldest; both V and F subfamilies were believed extinct. Recent data established that a variant of the F family, T F, is actively retrotransposing. We demonstrate here that members of the T F subfamily are abundantly expressed in mouse cells and encode the major protein constituent of L1 ribonucleoprotein particles. Although members of the T F subfamily are not as numerous in the genomes of laboratory mice as are members of the older A and F subfamilies, they appear to have been activated some time ago during mouse evolution, in the common ancestor of Mus spretus and Mus domesticus. Phylogenetic analysis demonstrates that this modern, active form of T F-type L1 has a composite evolutionary history, showing evidence of multiple recombinations between distinct L1 variants, including members of the A and F subfamilies.