Uracils at nucleotide position 9–11 are required for the rapid turnover of miR-29 family

Abstract

MicroRNAs are endogenous small RNA molecules that regulate gene expression. Although the biogenesis of microRNAs and their regulation have been thoroughly elucidated, the degradation of microRNAs has not been fully understood. Here by using the pulse–chase approach, we performed the direct measurement of microRNA lifespan. Five representative microRNAs demonstrated a general feature of relatively long lifespan. However, the decay dynamic varies considerably between these individual microRNAs. Mutation analysis of miR-29b sequence revealed that uracils at nucleotide position 9–11 are required for its rapid decay, in that both specific nucleotides and their position are critical. The effect of uracil-rich element on miR-29b decay dynamic occurs in duplex but not in single strand RNA. Moreover, analysis of published data on microRNA expression profile during development reveals that a substantial subset of microRNAs with the uracil-rich sequence tends to be down-regulated compared to those without the sequence. Among them, Northern blotting shows that miR-29c and fruit fly bantam possess a relatively rapid turnover rate. The effect of uracil-rich sequence on microRNA turnover depends on the sequence context. The present work indicates that microRNAs contain sequence information in the middle region besides the sequence element at both ends.

Argonaute proteins regulate microRNA stability: Increased microRNA abundance by Argonaute proteins is due to microRNA stabilization

“…Thus, determination of half-lives was hampered by a lack of appropriate model systems. Only in a single recent publication by Zhang et al let-7a displayed a half-live of less than twelve hours 44 in stark contrast to previous publications and our own experiments. This might be due to the use of perfectly complementary miRNA mimics in very high concentrations that might influence the metabolism of miRNAs (e.g., due to a lack of sufficient Ago proteins) and the thermodynamic stability differs from the natural miRNA sequences used in our study.…”

Brain-specific knockdown of miR-29 results in neuronal cell death and ataxia in mice

“…This is in agreement with our observations from in situ hybridization (Roshan et al 2012) and reports from other groups in HeLa cells (Hwang et al 2007) and in renal medulla of rats. miR-29a transcripts have also been shown to be more stable than miR-29b transcripts (Zhang et al 2011). In vivo, LNA29 effectively down-regulated miR-29a and miR29b in different parts of the brain (Fig.…”

“…The miR-29 family consists of miR-29a, miR-29b-1, miR-29b-2, and miR-29c, of which miR-29c has very low expression, perhaps due to a high turnover rate (Zhang et al 2011;Kriegel et al 2012). The mature sequences of these miRNAs are highly conserved in human, mouse, and rat.…”

The role of miR-29 family members in malignant hematopoiesis

“…Others demonstrated that the differences between miR-29a and miR-29c result in the relatively quicker decay of miR-29c (ref. 24 ).…”