title: Concordant and discordant regulation of target genes by miR-31 and its isoforms.
abstract: It has been shown that imprecise cleavage of a primary or precursor RNA by Drosha or Dicer, respectively, may yield a group of microRNA (miRNA) variants designated as "isomiR". Variations in the relative abundance of isoforms for a given miRNA among different species and different cell types beg the question whether these isomiRs might regulate target genes differentially. We compared the capacity of three miR-31 isoforms (miR-31-H, miR-31-P, and miR-31-M), which differ only slightly in their 5'- and/or 3'-end sequences, to regulate several known targets and a predicted target, Dicer. Notably, we found isomiR-31s displayed concordant and discordant regulation of 6 known target genes. Furthermore, we validated a predicted target gene, Dicer, to be a novel target of miR-31 but only miR-31-P could directly repress Dicer expression in both MCF-7 breast cancer cells and A549 lung cancer cells, resulting in their enhanced sensitivity to cisplatin, a known attribute of Dicer knockdown. This was further supported by reporter assay using full length 3'-untranslated region (UTR) of Dicer. Our findings not only revealed Dicer to be a direct target of miR-31, but also demonstrated that isomiRs displayed similar and disparate regulation of target genes in cell-based systems. Coupled with the variations in the distribution of isomiRs among different cells or conditions, our findings support the possibility of fine-tuning gene expression by miRNAs.
authors.affiliation: Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan.
authors.forename: Yu-Tzu
authors.initials: YT
authors.lastname: Chan
authors.forename: You-Chin
authors.initials: YC
authors.lastname: Lin
authors.forename: Ruey-Jen
authors.initials: RJ
authors.lastname: Lin
authors.forename: Huan-Hsien
authors.initials: HH
authors.lastname: Kuo
authors.forename: Wai-Cheng
authors.initials: WC
authors.lastname: Thang
authors.forename: Kuo-Ping
authors.initials: KP
authors.lastname: Chiu
authors.forename: Alice L
authors.initials: AL
authors.lastname: Yu
mesh_terms: D020413:3' Untranslated Regions; D002945:Cisplatin / Q000494:pharmacology; D053487:DEAD-box RNA Helicases / Q000235:genetics*; D019008:Drug Resistance, Neoplasm; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008156:Luciferases; D061986:MCF-7 Cells; D035683:MicroRNAs / Q000378:metabolism*; D009841:Oligonucleotides / Q000235:genetics; D010957:Plasmids; D020033:Protein Isoforms / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D043244:Ribonuclease III / Q000235:genetics*
chemical_list: D020413:3' Untranslated Regions; C534612:MIRN31 microRNA, human; D035683:MicroRNAs; D009841:Oligonucleotides; D020033:Protein Isoforms; D012333:RNA, Messenger; D008156:Luciferases; C408087:DICER1 protein, human; D043244:Ribonuclease III; D053487:DEAD-box RNA Helicases; D002945:Cisplatin