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Integration of expressed sequence tag data flanking predicted RNA secondary structures facilitates novel non-coding RNA discovery

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Item Type:Article
Title:Integration of expressed sequence tag data flanking predicted RNA secondary structures facilitates novel non-coding RNA discovery
Creators Name:Krzyzanowski, P.M. and Price, F.D. and Muro, E.M. and Rudnicki, M.A. and Andrade-Navarro, M.A.
Abstract:Many computational methods have been used to predict novel non-coding RNAs (ncRNAs), but none, to our knowledge, have explicitly investigated the impact of integrating existing cDNA-based Expressed Sequence Tag (EST) data that flank structural RNA predictions. To determine whether flanking EST data can assist in microRNA (miRNA) prediction, we identified genomic sites encoding putative miRNAs by combining functional RNA predictions with flanking ESTs data in a model consistent with miRNAs undergoing cleavage during maturation. In both human and mouse genomes, we observed that the inclusion of flanking ESTs adjacent to and not overlapping predicted miRNAs significantly improved the performance of various methods of miRNA prediction, including direct high-throughput sequencing of small RNA libraries. We analyzed the expression of hundreds of miRNAs predicted to be expressed during myogenic differentiation using a customized microarray and identified several known and predicted myogenic miRNA hairpins. Our results indicate that integrating ESTs flanking structural RNA predictions improves the quality of cleaved miRNA predictions and suggest that this strategy can be used to predict other non-coding RNAs undergoing cleavage during maturation.
Keywords:Blotting, Northern, Cell Line, Expressed Sequence Tags, MicroRNAs, Nucleic Acid Conformation, Oligonucleotide Array Sequence Analysis, Untranslated RNA, Animals, Mice
Source:PLoS ONE
ISSN:1932-6203
Publisher:Public Library of Science (U.S.A.)
Volume:6
Number:6
Page Range:e20561
Date:15 June 2011
Official Publication:https://doi.org/10.1371/journal.pone.0020561
PubMed:View item in PubMed

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