title: mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts.
abstract: Target prediction for animal microRNAs (miRNAs) has been hindered by the small number of verified targets available to evaluate the accuracy of predicted miRNA-target interactions. Recently, a dataset of 3,404 miRNA-associated mRNA transcripts was identified by immunoprecipitation of the RNA-induced silencing complex components AIN-1 and AIN-2. Our analysis of this AIN-IP dataset revealed enrichment for defining characteristics of functional miRNA-target interactions, including structural accessibility of target sequences, total free energy of miRNA-target hybridization and topology of base-pairing to the 5' seed region of the miRNA. We used these enriched characteristics as the basis for a quantitative miRNA target prediction method, miRNA targets by weighting immunoprecipitation-enriched parameters (mirWIP), which optimizes sensitivity to verified miRNA-target interactions and specificity to the AIN-IP dataset. MirWIP can be used to capture all known conserved miRNA-mRNA target relationships in Caenorhabditis elegans at a lower false-positive rate than can the current standard methods.
authors.affiliation: Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Suite 306, Worcester, Massachusetts 01605, USA.
authors.forename: Molly
authors.initials: M
authors.lastname: Hammell
authors.forename: Dang
authors.initials: D
authors.lastname: Long
authors.forename: Liang
authors.initials: L
authors.lastname: Zhang
authors.forename: Andrew
authors.initials: A
authors.lastname: Lee
authors.forename: C Steven
authors.initials: CS
authors.lastname: Carmack
authors.forename: Min
authors.initials: M
authors.lastname: Han
authors.forename: Ye
authors.initials: Y
authors.lastname: Ding
authors.forename: Victor
authors.initials: V
authors.lastname: Ambros
mesh_terms: D000818:Animals; D001665:Binding Sites; D017173:Caenorhabditis elegans / Q000235:genetics*; D002352:Carrier Proteins / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics*; D012261:Ribonucleoproteins / Q000235:genetics*
chemical_list: C504319:AIN-1 protein, C elegans; D002352:Carrier Proteins; D035683:MicroRNAs; D012333:RNA, Messenger; D012261:Ribonucleoproteins