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Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery

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Item Type:Article
Title:Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery
Creators Name:Li, N. and You, X. and Chen, T. and Mackowiak, S.D. and Friedlaender, M.R. and Weigt, M. and Du, H. and Gogol-Doering, A. and Chang, Z. and Dieterich, C. and Hu, Y. and Chen, W.
Abstract:MicroRNAs (miRNAs) constitute an important class of small regulatory RNAs that are derived from distinct hairpin precursors (pre-miRNAs). In contrast to mature miRNAs, which have been characterized in numerous genome-wide studies of different organisms, research on global profiling of pre-miRNAs is limited. Here, using massive parallel sequencing, we have performed global characterization of both mouse mature and precursor miRNAs. In total, 87 369 704 and 252 003 sequencing reads derived from 887 mature and 281 precursor miRNAs were obtained, respectively. Our analysis revealed new aspects of miRNA/pre-miRNA processing and modification, including eight Ago2-cleaved pre-miRNAs, eight new instances of miRNA editing and exclusively 5' tailed mirtrons. Furthermore, based on the sequences of both mature and precursor miRNAs, we developed a miRNA discovery pipeline, miRGrep, which does not rely on the availability of genome reference sequences. In addition to 239 known mouse pre-miRNAs, miRGrep predicted 41 novel ones with high confidence. Similar as known ones, the mature miRNAs derived from most of these novel loci showed both reduced abundance following Dicer knockdown and the binding with Argonaute2. Evaluation on data sets obtained from Caenorhabditis elegans and Caenorhabditis sp.11 demonstrated that miRGrep could be widely used for miRNA discovery in metazoans, especially in those without genome reference sequences.
Keywords:Caenorhabditis elegans, Cell Line, MicroRNAs, Post-Transcriptional RNA Processing, RNA Editing, RNA Precursors, RNA Sequence Analysis, Software, Transcriptome, Animals, Mice
Source:Nucleic Acids Research
ISSN:0305-1048
Publisher:Oxford University Press (U.K.)
Volume:41
Number:6
Page Range:3619-3634
Date:8 February 2013
Official Publication:https://doi.org/10.1093/nar/gkt072
PubMed:View item in PubMed

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