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Berezikov, E., Robine, N., Samsonova, A., Westholm, J.O., Naqvi, A., Hung, J.H., Okamura, K., Dai, Q., Bortolamiol-Becet, D., Martin, R., Zhao, Y., Zamore, P.D., Hannon, G.J., Marra, M.A., Weng, Z., Perrimon, N., Lai, E.C. (2011). Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence.  Genome Res. 21(2): 203--215.
FlyBase ID
FBrf0213080
Publication Type
Research paper
Abstract

Since the initial annotation of miRNAs from cloned short RNAs by the Ambros, Tuschl, and Bartel groups in 2001, more than a hundred studies have sought to identify additional miRNAs in various species. We report here a meta-analysis of short RNA data from Drosophila melanogaster, aggregating published libraries with 76 data sets that we generated for the modENCODE project. In total, we began with more than 1 billion raw reads from 187 libraries comprising diverse developmental stages, specific tissue- and cell-types, mutant conditions, and/or Argonaute immunoprecipitations. We elucidated several features of known miRNA loci, including multiple phased byproducts of cropping and dicing, abundant alternative 5' termini of certain miRNAs, frequent 3' untemplated additions, and potential editing events. We also identified 49 novel genomic locations of miRNA production, and 61 additional candidate loci with limited evidence for miRNA biogenesis. Although these loci broaden the Drosophila miRNA catalog, this work supports the notion that a restricted set of cellular transcripts is competent to be specifically processed by the Drosha/Dicer-1 pathway. Unexpectedly, we detected miRNA production from coding and untranslated regions of mRNAs and found the phenomenon of miRNA production from the antisense strand of known loci to be common. Altogether, this study lays a comprehensive foundation for the study of miRNA diversity and evolution in a complex animal model.

PubMed ID
PubMed Central ID
PMC3032924 (PMC) (EuropePMC)
Related Publication(s)
Personal communication to FlyBase

Lai lab miRNA expression and conservation data for Drosophila.
Mohammed and Lai, 2016.2.8, Lai lab miRNA expression and conservation data for Drosophila. [FBrf0230987]

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Secondary IDs
    Language of Publication
    English
    Additional Languages of Abstract
    Parent Publication
    Publication Type
    Journal
    Abbreviation
    Genome Res.
    Title
    Genome Research
    Publication Year
    1995-
    ISBN/ISSN
    1088-9051
    Data From Reference