Journal Article

A dimeric SINE discovered in shrew mole is structurally similar to primate Alu

Borodulina, Olga, Kosushkin, Sergey, Kramerov, Dmitri, Vassetzky, Nikita

2026

Overview

Background Short interspersed elements (SINEs) are non-autonomous retroelements that are transcribed by RNA polymerase III from an internal promoter. Most SINE families originate from tRNAs, but a few, exclusively within supraprimates (primates, rodents, tree shrews) and, exceptionally, hagfish, derive from the 7SL RNA. These 7SL-derived SINEs all arose after an ~ 183-nt central deletion in the 7SL RNA sequence and are mobilized by LINE1-encoded reverse transcriptase. No 7SL-derived SINE has previously been reported outside these taxa. Results Mining of mole (Talpidae) genomes revealed no mole-specific tRNA-derived SINE in the gracile shrew mole Uropsilus gracilis . Instead, ~ 280 000 copies of a dimeric 7SL RNA-derived SINE, named Urop, populate its genome but not five other talpid species. Three subfamilies (a–c) share two 7SL-derived monomers joined by an A-rich linker. The left monomer and Urop_a right monomer carry the canonical central deletion; Urop_b/c right monomers additionally harbor a 24-nt tandem duplication, paralleling the 29-nt quasi-dimer of murid B1. Monomeric fossils suggest they preceded dimeric Urop formation. Sequence divergence and subfamily analysis date the origin of Urop soon after the Uropsilinae split from other moles. Urop_c, the youngest subfamily, displays a striking excess of extra-long pure poly(A) tails, far exceeding those in young human AluY elements. Conclusions Urop represents a remarkable case of convergent evolution, independently generating an Alu-like dimeric SINE in a distantly related mammal. Its independent origin from 7SL RNA, parallel structural trajectory (monomer → dimer via identical deletion boundaries), and suppression of tRNA-derived SINEs mirror the evolutionary history of primate Alu. The abundance of long intact poly(A) tails in Urop_c suggests unique biochemical controls on tail dynamics and hint at continued retropositional activity. These findings underscore the exceptional evolutionary potential of rare, large-scale deletions within 7SL RNA as a SINE progenitor and raises new questions about poly(A) tail regulation and SINE family dynamics.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: 7SL RNA / Alu / Alu Elements - genetics / Analysis / Animals / Base Sequence / Biological evolution / Biomedical and Life Sciences / Deletion / Dimers / DNA-directed RNA polymerase / Evolution, Molecular / Fossils / Genetic aspects / Genomes / Life Sciences / Moles (Animals) / Moles - genetics / Monkeys & apes / Monomers / Nucleic Acid Conformation / Nucleotide sequence / Polyadenine / Polyadenylation / Primates / Primates - genetics / Retroposon / Retrotransposon / RNA-directed DNA polymerase / Rodents / Short interspersed nucleotide elements / Short Interspersed Nucleotide Elements - genetics / SINE / Transfer RNA / Transposable element / tRNA