title: Reexamining microRNA site accessibility in Drosophila: a population genomics study.
abstract: Kertesz et al. (Nature Genetics 2008) described PITA, a miRNA target prediction algorithm based on hybridization energy and site accessibility. In this note, we used a population genomics approach to reexamine their data and found that the PITA algorithm had lower specificity than methods based on evolutionary conservation at comparable levels of sensitivity.We also showed that deeply conserved miRNAs tend to have stronger hybridization energies to their targets than do other miRNAs. Although PITA had higher specificity in predicting targets than a naïve seed-match method, this signal was primarily due to the use of a single cutoff score for all miRNAs and to the observed correlation between conservation and hybridization energy. Overall, our results clarify the accuracy of different miRNA target prediction algorithms in Drosophila and the role of site accessibility in miRNA target prediction.
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, United States of America. kc1111@nyu.edu
authors.forename: Kevin
authors.initials: K
authors.lastname: Chen
authors.forename: Jonas
authors.initials: J
authors.lastname: Maaskola
authors.forename: Mark L
authors.initials: ML
authors.lastname: Siegal
authors.forename: Nikolaus
authors.initials: N
authors.lastname: Rajewsky
mesh_terms: D019943:Amino Acid Substitution; D000818:Animals; D001483:Base Sequence; D004330:Drosophila / Q000235:genetics*; D005828:Genetics, Population; D023281:Genomics; D035683:MicroRNAs / Q000235:genetics*
chemical_list: D035683:MicroRNAs