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

   

Authors:	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.
Article Title:	Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
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. © 2011 by Cold Spring Harbor Laboratory Press.
Journal Title:	Genome Research
Volume:	21
Issue:	2
ISSN:	1088-9051
Publisher:	Cold Spring Harbor Laboratory Press
Date Published:	2011-02-01
Start Page:	203
End Page:	215
Language:	English
DOI:	10.1101/gr.116657.110
PROVIDER:	scopus
PMCID:	PMC3032924
PUBMED:	21177969
DOI/URL:	http://www.scopus.com/inward/record.url?eid=2-s2.0-79551586302&partnerID=40&md5=81f91dafb2d1a2ad98749cbf3966a66d
Notes:	--- - "Export Date: 4 March 2011" - "CODEN: GEREF" - "Source: Scopus"

https://synapse.mskcc.org/synapse/works/has_related_data_chk/3296