Hagfish genome reveals parallel evolution of 7SL RNA-derived SINEs.

Background: Short interspersed elements (SINEs) are ubiquitous components of eukaryotic genomes. SINEs are composite transposable elements that are mobilized by non-long terminal repeat (non-LTR) retrotransposons, also called long interspersed elements (LINEs). The 3' part of SINEs usually originated from that of counterpart non-LTR retrotransposons. The 5' part of SINEs mostly originated from small RNA genes. SINE1 is a group of SINEs whose 5' part originated from 7SL RNA, and is represented by primate and murine . Well-defined SINE1 has been found only from Euarchontoglires, a group of mammals, in contrast to the wide distribution of SINE2, which has a tRNA-derived sequence, from animals to plants to protists. Both and are mobilized by -type non-LTR retrotransposons, which are the only lineage of autonomous non-LTR retrotransposons active in these mammalian lineages.

Results: Here a new lineage of SINE1 is characterized from the seashore hagfish genome. This SINE1 family, designated -, is young, and is transposed by -type non-LTR retrotransposon, not -type. Comparison with other SINE families from hagfish indicated the birth of - through chimera formation of a 7SL RNA-derived sequence and an older tRNA-derived SINE family. It reveals parallel evolution of SINE1 in two vertebrate lineages with different autonomous non-LTR retrotransposon partners. The comparison between two SINE1 lineages supports that the RNA secondary structure of the domain of 7SL RNA is required for the efficient retrotransposition.

Conclusions: The hagfish SINE1 is the first evident SINE1 family found outside of Euarchontoglires. Independent evolution of SINE1 with similar RNA secondary structure originated in 7SL RNA indicates the functional importance of 7SL RNA-derived sequence in the proliferation of SINEs.