Widespread regulatory activity of vertebrate microRNA* species
- Jr-Shiuan Yang1,2,
- Michael D. Phillips3,
- Doron Betel4,
- Ping Mu5,
- Andrea Ventura5,
- Adam C. Siepel3,
- Kevin C. Chen6 and
- Eric C. Lai1
- 1Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
- 2Molecular Biology Program, Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
- 3Tri-Institutional Program in Computational Biology and Medicine, Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853, USA
- 4Computational Biology Center, Sloan-Kettering Institute, New York, New York 10065, USA
- 5Cancer Biology and Genetics Program, Sloan-Kettering Institute, New York, New York 10065, USA
- 6BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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 seed-matched 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.
Keywords
Footnotes
-
Reprint requests to: Kevin C. Chen, BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, 227 Life Sciences Building, 145 Bevier Road, Piscataway, NJ 08854, USA; e-mail: kcchen{at}biology.rutgers.edu; fax: (732) 445-1147; or Eric C. Lai, Department of Developmental Biology, Sloan-Kettering Institute, 1017 Rockefeller Research Laboratories, 1275 York Avenue, Box 252, New York, NY 10065, USA; e-mail: laie{at}mskcc.org; fax: (212) 717-3604.
-
Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.2537911.
- Received November 9, 2010.
- Accepted November 22, 2010.
- Copyright © 2011 RNA Society