title: MicroRNA-target binding structures mimic microRNA duplex structures in humans.
abstract: Traditionally, researchers match a microRNA guide strand to mRNA sequences using sequence comparisons to predict its potential target genes. However, many of the predictions can be false positives due to limitations in sequence comparison alone. In this work, we consider the association of two related RNA structures that share a common guide strand: the microRNA duplex and the microRNA-target binding structure. We have analyzed thousands of such structure pairs and found many of them share high structural similarity. Therefore, we conclude that when predicting microRNA target genes, considering just the microRNA guide strand matches to gene sequences may not be sufficient--the microRNA duplex structure formed by the guide strand and its companion passenger strand must also be considered. We have developed software to translate RNA binding structure into encoded representations, and we have also created novel automatic comparison methods utilizing such encoded representations to determine RNA structure similarity. Our software and methods can be utilized in the other RNA secondary structure comparisons as well.
authors.affiliation: Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America.
authors.forename: Xi
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland, United States of America.
authors.forename: Lu
authors.initials: L
authors.lastname: Shen
authors.affiliation: Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, United States of America ; Department of Computer Science, Iowa State University, Ames, Iowa, United States of America.
authors.forename: Hui-Hsien
authors.initials: HH
authors.lastname: Chou
mesh_terms: D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D019143:Evolution, Molecular; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry* / Q000145:classification; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012333:RNA, Messenger / Q000737:chemistry* / Q000145:classification; D012984:Software
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger