Birth of protein-coding exons by ancient domestication of LINE-1 retrotransposon

Transposons, occasionally domesticated as novel host protein-coding genes, are responsible for the lineage-specific functions in vertebrates. LINE-1 (L1) is one of the most active transposons in the vertebrate genomes. Despite its abundance, few examples of L1 co-option for vertebrate proteins have been reported. Here, we describe protein isoforms, in which the L1 retrotransposons are incorporated into host genes as protein-coding exons by alternative splicing. L1 ORF1 protein (ORF1p) is an RNA-binding protein that binds to L1 RNA and is required for retrotransposition by acting as an RNA chaperone. We identified a splicing variant of myosin light chain 4 (MYL4) containing an L1 ORF1–derived exon and encoding a transposon fusion protein of L1 ORF1p and MYL4, which we call “Lyosin” in this study. Molecular evolutionary analysis revealed that the Lyosin isoform was acquired before the divergence of Sauropsida (reptiles and birds) during the Paleozoic era. The amino acid sequence of Lyosin had undergone purifying selection although it was lost in some lineages, including the Neognathae birds and snakes. The Lyosin transcript was expressed in the testes of four reptilian species, suggesting that its function is different from that of the canonical MYL4 transcript expressed in the heart. Furthermore, comprehensive sequence searches revealed other splicing isoforms fused to the L1 ORF1 in three genes in vertebrates. Our findings suggest the involvement of L1 for the birth of lineage-specific proteins and implicate the previously unrecognized adaptive functions of L1 ORF1p.