LINE-1 (L1) Lineages in the Mouse

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Abstract
Recently, a rapidly amplifying family of mouse LINE-1 (L1) has been identified and named TF. The evolutionary context surrounding the derivation of the TF family was examined through phylogenetic analysis of sequences in the 3′ portion of the repeat. The Mus musculus domesticus TF family was found to be the terminal subfamily of the previously identified L1Md4 lineage. The L1Md4 lineage joins the other prototypical mouse LINE-1 lineage (the L1MdA2 lineage) approximately 1 MYA at about the time of the common ancestor of M. m. domesticus, Mus spicilegus, and Mus spretus. However, the TF family from M. m. domesticus was found to join to the previously reported M. spretus Ms475 and Ms7024 LINE-1 families at just 0.5 MYA, indicating horizontal transfer. The TF family from M. m. domesticus was then found to be even more recently related to LINE-1's from another species, M. spicilegus. A separate spretus A2 lineage was found through a directed search of a PCR library. This lineage, in contrast to the spretus TF lineage, does join domesticus at about 1 MYA, as would be expected in the absence of horizontal transfer. A third major family was also found that splits off from the L1Md4 lineage shortly after its departure from the L1MdA2 lineage. The new family, named the Z family, was found to contain the de novo LINE-1 inserts causing the beige and med mutations. Whether the split with the Z family was before or after the recombination that introduced the F-type promoters and defined the inception of TF as a lineage is unclear. In enumerating copies of the various LINE-1 families, we found that TF 3′ ends were not much more numerous than the reported number of 5′ ends, suggesting that TF may not be subjected to the 90% truncation pattern typical of LINE-1 as a whole.