Identification and characterization of SINEs and LINEs from the horn shark

Abstract

We have isolated and characterized short interspersed repetitive elements (SINEs) and long interspersed repetitive elements (LINEs) from the horn shark (Heterodontus francisci). These SINEs, HF SINEs, were very similar to members of the HE1 SINE family, tRNA-derived SINE, and widespread SINE in higher elasmobranches. Each HF SINE includes a 5′ conserved region preceded by a 5′-end tRNA-related region and followed by a variable region and a 3′ tail region derived from the 3′ untranslated region (UTR) of the HF LINE that encodes a functional reverse transcriptase. The HF LINEs, which are also similar to members of the HER1 LINE family, encoded an amino acid sequence similar to that encoded by the CR1 LINE family, and they contained a strongly conserved 3′-tail region in the 3′ untranslated region. This tail region of the HF LINE was almost identical to that of the HF SINE. Conservation of the secondary structures of the tail regions and of the nucleotide sequences between the HF SINEs and HF LINEs supports the belief that SINEs utilize the enzymatic machinery for retropositioning of LINEs through the recognition of higher-order structures of the conserved 3′-tail region.