Widespread regulatory activity of vertebrate microRNA* species

Shiuan Yang, Michael D. Phillips, Doron Betel, Ping Mu, Andrea Ventura, Adam C. Siepel, Kevin C. Chen, Eric C. Lai

Research output: Contribution to journalArticle

232 Citations (Scopus)

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 3′-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, 3′-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. Published by Cold Spring Harbor Laboratory Press.

Original languageEnglish (US)
Pages (from-to)312-326
Number of pages15
JournalRNA
Volume17
Issue number2
DOIs
StatePublished - Feb 1 2011
Externally publishedYes

Fingerprint

MicroRNAs
Vertebrates
3' Untranslated Regions
Seeds
RNA
Microarray Analysis
Computational Biology
Transcriptome
Mutagenesis
Carcinogenesis
Nucleotides

Keywords

  • 3′UTR
  • microRNA
  • Post-transcriptional repression

ASJC Scopus subject areas

  • Molecular Biology

Cite this

Yang, S., Phillips, M. D., Betel, D., Mu, P., Ventura, A., Siepel, A. C., ... Lai, E. C. (2011). Widespread regulatory activity of vertebrate microRNA* species. RNA, 17(2), 312-326. https://doi.org/10.1261/rna.2537911

Widespread regulatory activity of vertebrate microRNA* species. / Yang, Shiuan; Phillips, Michael D.; Betel, Doron; Mu, Ping; Ventura, Andrea; Siepel, Adam C.; Chen, Kevin C.; Lai, Eric C.

In: RNA, Vol. 17, No. 2, 01.02.2011, p. 312-326.

Research output: Contribution to journalArticle

Yang, S, Phillips, MD, Betel, D, Mu, P, Ventura, A, Siepel, AC, Chen, KC & Lai, EC 2011, 'Widespread regulatory activity of vertebrate microRNA* species', RNA, vol. 17, no. 2, pp. 312-326. https://doi.org/10.1261/rna.2537911
Yang S, Phillips MD, Betel D, Mu P, Ventura A, Siepel AC et al. Widespread regulatory activity of vertebrate microRNA* species. RNA. 2011 Feb 1;17(2):312-326. https://doi.org/10.1261/rna.2537911
Yang, Shiuan ; Phillips, Michael D. ; Betel, Doron ; Mu, Ping ; Ventura, Andrea ; Siepel, Adam C. ; Chen, Kevin C. ; Lai, Eric C. / Widespread regulatory activity of vertebrate microRNA* species. In: RNA. 2011 ; Vol. 17, No. 2. pp. 312-326.
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