Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
Authors
Berezikov, EugeneRobine, 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
Lai, Eric C.
UMass Chan Affiliations
Program in Bioinformatics and Integrative BiologyDepartment of Biochemistry and Molecular Pharmacology
Document Type
Journal ArticlePublication Date
2011-02-01Keywords
AnimalsBase 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
Metadata
Show full item recordAbstract
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.Source
Genome Res. 2011 Feb;21(2):203-15. doi: 10.1101/gr.116657.110. Link to article on publisher's siteDOI
10.1101/gr.116657.110Permanent Link to this Item
http://hdl.handle.net/20.500.14038/25902PubMed ID
21177969Related Resources
Link to article in PubMedRights
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/.ae974a485f413a2113503eed53cd6c53
10.1101/gr.116657.110