Widespread regulatory activity of vertebrate microRNA* species

Abstract

An obligate intermediate during microRNA (miRNA) biogenesis is an~22-nucleotide RNA duplex, from which the mature miRNA is preferentially incorporated into a silencing complex. Its partner miRNA* species is generally regarded as a passenger RNA, whose regulatory capacity has not been systematically examined in vertebrates. Our bioinformatic analyses demonstrate that a substantial fraction of miRNA* species are stringently conserved over vertebrate evolution, collectively exhibit greatest conservation in their seed regions, and define complementary motifs whose conservation across vertebrate 39-UTR evolution is statistically significant. Functional tests of 22 miRNA expression constructs revealed that a majority could repress both miRNA and miRNA* perfect match reporters, and the ratio of miRNA:miRNA* sensor repression was correlated with the endogenous ratio of miRNA:miRNA* reads. Analysis of microarray data provided transcriptome-wide evidence for the regulation of seedmatched targets for both mature and star strand species of several miRNAs relevant to oncogenesis, including mir-17, mir-34a, and mir-19. Finally, 39-UTR sensor assays and mutagenesis tests confirmed direct repression of five miR-19* targets via star seed sites. Overall, our data demonstrate that miRNA* species have demonstrable impact on vertebrate regulatory networks and should be taken into account in studies of miRNA functions and their contribution to disease states.

Testing hypotheses on the rate of molecular evolution in relation to gene expression using microRNAs

“…The role of miR* is sometimes ambiguous. Some miR* products can be functional (43,44), whereas the rest are unlikely to be so. The remaining two parts of the miRNA precursor, the loop end and the stem extension, are very unlikely to give rise to functional products.…”

Construction of MicroRNA- and MicroRNA*-mediated regulatory networks in plants

“…11,15,48,49 In plants, the specific sorting of miRNA* strands into AGO proteins were also observed, 16 whereas no systemic study on their activities has been performed.…”

The use of high-throughput sequencing methods for plant microRNA research

“…However, recent studies revealed some important biological functions of miRNA*s in both plants and animals. 44,58,[111][112][113][114] Here, based on the results obtained from our sRNA-seq-based bioinformatics analysis, we proposed that certain miRNA*s or isomiR*s could act as anti-miRs to inhibit the cognate miRNAs from binding the target transcripts, thus reducing the activities of the miRNAs. It is based on the following evidences: (1) According to the biogenesis model of the plant miRNAs, after DCL1-mediated 2-step processing, miRNA and its miRNA*, forming as a short RNA duplex, were exported to the cytoplasm for loading into the AGO1 complex.…”