A Dimeric SINE Discovered in Shrew Mole is Structurally Similar to Primate Alu

Abstract

Families of Short Interspersed Elements (SINEs) originate from tRNA, 5S rRNA, and 7SL RNA molecules in the genomes of multicellular organisms. Families of 7SL RNA-derived SINEs are very rare; however, they have been best studied in primates and rodents. The rodent B1 SINE is a monomeric element, whereas the primate Alu is composed of two 7SL RNA-derived monomers.We found that in contrast to other members of the family Talpidae (moles), which possess a tRNA-derived Tal SINE, the shrew mole Uropsilus gracilis contains 280,000 genomic copies of the previously unknown 7SL RNA-derived Urop SINE. Like Alu, Urop consists of two monomers connected by an A-rich linker. The origin of the Urop monomers, like that of the Alu and B1 monomers, was mediated by several essentially identical events - a long central deletion in the 7SL RNA, dimerization, and/or internal duplication. Urop copies can be divided into three subfamilies (a, b, and c), the latter being the most numerous and recent. Urop_c has more copies with poly(A) tails longer than 50 compared to other L1-mobilized SINEs. Urop and Alu illustrate an independent emergence in the evolutionary history of highly similar SINEs.