title: Large-scale screens of miRNA-mRNA interactions unveiled that the 3'UTR of a gene is targeted by multiple miRNAs.
abstract: Animal microRNA (miRNA) target prediction is still a challenge, although many prediction programs have been exploited. MiRNAs exert their function through partially binding the messenger RNAs (mRNAs; likely at 3' untranslated regions [3'UTRs]), which makes it possible to detect the miRNA-mRNA interactions in vitro by co-transfection of miRNA and a luciferase reporter gene containing the target mRNA fragment into mammalian cells under a dual-luciferase assay system. Here, we constructed a human miRNA expression library and used a dual-luciferase assay system to perform large-scale screens of interactions between miRNAs and the 3'UTRs of seven genes, which included more than 3,000 interactions with triplicate experiments for each interaction. The screening results showed that the 3'UTR of one gene can be targeted by multiple miRNAs. Among the prediction algorithms, a Bayesian phylogenetic miRNA target identification algorithm and a support vector machine (SVM) presented a relatively better performance (27% for EIMMo and 24.7% for miRDB) against the average precision (17.3%) of the nine prediction programs used here. Additionally, we noticed that a relatively high conservation level was shown at the miRNA 3' end targeted regions, as well as the 5' end (seed region) binding sites.
authors.affiliation: State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Zhou
authors.forename: Weiyi
authors.initials: W
authors.lastname: Xu
authors.forename: Xueling
authors.initials: X
authors.lastname: Peng
authors.forename: Zhenhua
authors.initials: Z
authors.lastname: Luo
authors.forename: Qinghe
authors.initials: Q
authors.lastname: Xing
authors.forename: Xulin
authors.initials: X
authors.lastname: Chen
authors.forename: Chengqian
authors.initials: C
authors.lastname: Hou
authors.forename: Weihong
authors.initials: W
authors.lastname: Liang
authors.forename: Jianwen
authors.initials: J
authors.lastname: Zhou
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Wu
authors.forename: Zhou
authors.initials: Z
authors.lastname: Songyang
authors.forename: Songshan
authors.initials: S
authors.lastname: Jiang
mesh_terms: D020413:3' Untranslated Regions; D001483:Base Sequence; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D002460:Cell Line; D017124:Conserved Sequence; D004843:Epistasis, Genetic; D015870:Gene Expression; D015723:Gene Library; D055106:Genome-Wide Association Study; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D008840:Microfilament Proteins / Q000235:genetics / Q000378:metabolism; D009154:Mutation; D034622:RNA Interference / Q000502:physiology*; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D015203:Reproducibility of Results; D000089804:Shelterin Complex; D034501:Telomere-Binding Proteins / Q000235:genetics / Q000378:metabolism; D035341:Telomeric Repeat Binding Protein 2 / Q000235:genetics / Q000378:metabolism; D025521:Tumor Suppressor Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D020413:3' Untranslated Regions; D051792:Basic Helix-Loop-Helix Proteins; D002352:Carrier Proteins; D035683:MicroRNAs; D008840:Microfilament Proteins; D012333:RNA, Messenger; D000089804:Shelterin Complex; D034501:Telomere-Binding Proteins; D035341:Telomeric Repeat Binding Protein 2; D025521:Tumor Suppressor Proteins; C502658:FSCN1 protein, human; C079440:MXI1 protein, human; C440849:POT1 protein, human