mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts.
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.
Hammell
Molly
M
Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Suite 306, Worcester, Massachusetts 01605, USA.
Long
Dang
D
Zhang
Liang
L
Lee
Andrew
A
Carmack
C Steven
CS
Han
Min
M
Ding
Ye
Y
Ambros
Victor
V
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*
C504319:AIN-1 protein, C elegans; D002352:Carrier Proteins; D035683:MicroRNAs; D012333:RNA, Messenger; D012261:Ribonucleoproteins