Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence

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. J., Zamore, P. D., Hannon, G. J., Marra, M. A., Weng, Z. P., Perrimon, N., Lai, E. C. (February 2011) Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Research, 21 (2). pp. 203-215. ISSN 1088-9051

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URL: http://www.ncbi.nlm.nih.gov/pubmed/21177969
DOI: 10.1101/gr.116657.110

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.

Item Type: Paper
Uncontrolled Keywords: EMBRYONIC STEM-CELLS SMALL RNAS CAENORHABDITIS-ELEGANS 3' ADENYLATION BIOGENESIS GENES IDENTIFICATION TRANSCRIPTION EXPRESSION POLYMERASE
Subjects: organism description > animal > insect > Drosophila
bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > argonaute proteins
bioinformatics > genomics and proteomics > annotation > dataset annotation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > miRNA

bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > sRNA
CSHL Authors:
Communities: CSHL labs > Hannon lab
CSHL Cancer Center Shared Resources > Bioinformatics Service
CSHL Cancer Center Shared Resources > DNA Sequencing Service
Depositing User: CSHL Librarian
Date: February 2011
Date Deposited: 20 Oct 2011 15:35
Last Modified: 26 Dec 2014 20:38
PMCID: PMC3032924
Related URLs:
URI: http://repository.cshl.edu/id/eprint/15602

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