Conserved MicroRNA Characteristics in Mammals

Abstract

Short hairpin RNAs (shRNAs) and short interfering RNAs (siRNAs) probably enter different stages of the microRNA (miRNA) pathway for depletion of mRNA and suppression of protein translation. Primary and secondary structural characteristics that are shared between endogenous primary miRNA transcripts (pri-miRNAs) may contribute toward efficient biogenesis and potent silencing. This study investigates known miRNA transcripts for characteristics that are conserved between miRNAs and that distinguish them from random hairpins with similar lengths. The primary structure is conserved, as demonstrated by a significant presence or absence of certain bases at specific positions in the miRNA precursors and their flanking regions. The secondary structure is also conserved between miRNAs, as internal loops and bulges commonly appear in specific positions in the miRNA stem. The conservation of base-pairing continues past the mature duplex and 13 bases into the primary stem, with no detectable conservation of secondary structure beyond this region. Based on these observations, we have designed a hairpin construct that incorporates the most important characteristics present in endogenous miRNAs. Preliminary experiments suggest that this construct may rescue the efficacy of shRNA triggers that cannot be used with a miR-30-based hairpin, and vice versa.

Abnormal microRNA-16 locus with synteny to human 13q14 linked to CLL in NZB mice

“…The flanking region, containing the mutation, may be important for proper tertiary structure of the stem-loop in the pre-mir. 35 This is consistent with the finding reported by others of decreased miR-16 in some patients with CLL. 33 One possible outcome of decreased miR-16 is a failure to properly reduce target gene expression.…”

Structures of MicroRNA Precursors

“…pri-miR-607. However, in the majority of the analyzed structures (62.6%) the SD junction was located 9-13 nt below the Drosha cleavage site which is in rough agreement with the consensus structure proposed by Han et al [9] and confirmed by Saetrom et al [28]. This region was shorter in 13% of the analyzed precursors and longer in 19.5% of the precursors ( Fig.…”

Epigenetics and MicroRNAs

“…Most known animal miRNAs have a hairpin with a ϳ33 base pair stem flanked by a single-stranded region, and current models suggest that DGCR8 recognize this characteristic structure and guides Drosha to cleave the hairpin about 11 nts from the singlestranded region (33). Drosha or other unknown co-factors may, however, also recognize some of the miRNA hairpin's key features and thereby contribute to cleavage specificity (34,35). Second, the carrier protein Exportin-5 and Ran GTPase transport pre-miRNA from the nucleus to the cytoplasm (36 -38).…”