A 5′–3′ terminal stem in small non-coding RNAs extends their lifetime

4.5SI and 4.5SH are two non-coding RNAs about 100nt long, synthesized by RNA polymerase III in cells of various rodents including mice, rats, and hamsters. The first RNA is long-lived whereas the half-life of the second is only 20min. We previously found that the 16bp double-stranded structure (stem), formed by 4.5SI RNA termini, contributes essentially to the long lifetime of this RNA (Koval et al., 2012). The rapid decay of 4.5SH RNA seems to be related to the lack of a similar structure in this RNA. The aim of this work was to verify whether the lifetime of any other short-lived non-coding RNA can be prolonged following creation of the double-stranded structure with its terminal regions. Here RNAs transcribed by RNA polymerase III from short interspersed elements (SINEs) B2 and Rhin-1 from the genomes of mouse and horseshoe bat, respectively, were used. Replacement of 16nt at the 3′-terminal region by the sequence complementary to the 5′ end region of B2 and Rhin-1 RNA increased their half-life more than 4 fold. In addition, we demonstrated that shortening of the terminal stem from 16 to 8bp decreased only slightly the 4.5SI RNA lifetime. Finally, we showed that the disruption of an internal (non-terminal) stem in 4.5SI RNA did not accelerate its decay in cells. Possible mechanisms of the small non-coding RNA lifetime extension are discussed. •Long terminal stem significantly prolongs lifetime of short-lived SINE transcripts.•4.5SI RNA with 8bp terminal stem instead of 16bp stem decays quite slowly.•Internal stem did not contribute to 4.5SI RNA lifetime.