title: Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery.
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.
authors: Laboratory for Novel sequencing technology, Functional and Medical Genomics, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.
authors: Na
authors: N
authors: Li
authors: Xintian
authors: X
authors: You
authors: Tao
authors: T
authors: Chen
authors: Sebastian D
authors: SD
authors: Mackowiak
authors: Marc R
authors: MR
authors: Friedländer
authors: Martina
authors: M
authors: Weigt
authors: Hang
authors: H
authors: Du
authors: Andreas
authors: A
authors: Gogol-Döring
authors: Zisong
authors: Z
authors: Chang
authors: Christoph
authors: C
authors: Dieterich
authors: Yuhui
authors: Y
authors: Hu
authors: Wei
authors: W
authors: Chen
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics / Q000378:metabolism; D002460:Cell Line; D051379:Mice; D035683:MicroRNAs / Q000737:chemistry / Q000378:metabolism*; D017393:RNA Editing; D012322:RNA Precursors / Q000737:chemistry / Q000378:metabolism*; D012323:RNA Processing, Post-Transcriptional; D017423:Sequence Analysis, RNA; D012984:Software; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors
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