Department of Biochemistry and Molecular Pharmacology; Program in Bioinformatics and Integrative Biology
Animals; Base Sequence; Cell Line; Computational Biology; Drosophila melanogaster; Female; Gene Expression Regulation; Male; MicroRNAs; Molecular Sequence Annotation; RNA Editing; RNA, Antisense; RNA, Messenger; Ribonuclease III; Sequence Alignment
Bioinformatics | Computational Biology | Genetics and Genomics | Systems Biology
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.
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Freely available online through the Genome Research Open Access option. This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported License), as described at http://creativecommons.org/licenses/by-nc/3.0/.
DOI of Published Version
Genome Res. 2011 Feb;21(2):203-15. doi: 10.1101/gr.116657.110. Link to article on publisher's site
Berezikov, Eugene; Robine, Nicolas; Samsonova, Anastasia; Westholm, Jakub Orzechowski; Naqvi, Ammar; Hung, Jui-Hung; Okamura, Katsutomo; Dai, Qi; Bortolamiol-Becet, Diane; Martin, Raquel; Zhao, Yongjun; Zamore, Phillip D.; Hannon, Gregory J.; Marra, Marco A.; Weng, Zhiping; Perrimon, Norbert; and Lai, Eric C., "Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence" (2011). Program in Bioinformatics and Integrative Biology Publications and Presentations. 44.