title: 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 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.
authors.affiliation: Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA.
authors.forename: Jr-Shiuan
authors.initials: JS
authors.lastname: Yang
authors.forename: Michael D
authors.initials: MD
authors.lastname: Phillips
authors.forename: Doron
authors.initials: D
authors.lastname: Betel
authors.forename: Ping
authors.initials: P
authors.lastname: Mu
authors.forename: Andrea
authors.initials: A
authors.lastname: Ventura
authors.forename: Adam C
authors.initials: AC
authors.lastname: Siepel
authors.forename: Kevin C
authors.initials: KC
authors.lastname: Chen
authors.forename: Eric C
authors.initials: EC
authors.lastname: Lai
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D000818:Animals; D001483:Base Sequence; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D016415:Sequence Alignment; D013045:Species Specificity; D014714:Vertebrates / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions; D035683:MicroRNAs