Family C of Short Interspersed Elements in the Genomes of Lagomorphs: Structure, Evolution, Transcription and Transcript Polyadenylation
Abstract
Short Interspersed Elements (SINEs) are eukaryotic non-autonomous retrotransposons that rely on RNA polymerase III (pol III) for transcription. A subset of mammalian SINEs—designated T+ SINEs—harbors a canonical polyadenylation signal (AATAAA), a pol III terminator, and an A-rich tail at their 3′ end, thereby acquiring the unusual ability to undergo AAUAAA-dependent polyadenylation. Here, we delineate the genomic architecture, evolutionary history, and polyadenylation behavior of the C SINE family in Lagomorpha. Comprehensive bioinformatics searches identified 1.2–1.6 million C copies distributed across Leporidae (hares and rabbits) and Ochotonidae (pikas) genomes. Phylogenetic reconstruction resolved two diverged leporid subfamilies, C1 and C2, with C1 predating C2 and comprising five-fold more copies. Only C1 qualifies as a T+ SINE, retaining functional or rudimentary AATAAA motifs and pol III terminators. In contrast, C2 is absent from pika genomes, yet remains retrotranspositionally competent in hares and rabbits. Lineage-specific analyses further reveal episodic activity of certain C1 variants throughout the last 10 million years of pika evolution. Functional assays in transfected HeLa cells demonstrate that AATAAA and an upstream polypyrimidine tract constitute the minimal cis-determinant for efficient C1 transcript polyadenylation. Finally, transcriptome profiling of pre-implantation rabbit embryos indicates that pol III-driven SINE C transcription is activated at the 16-cell stage.