TY  - JOUR
A1  - Berezikov, Eugene
A1  - Robine, Nicolas
A1  - Samsonova, Anastasia
A1  - Westholm, Jakub O.
A1  - Naqvi, Ammar
A1  - Hung, Jui-Hung
A1  - Okamura, Katsutomo
A1  - Dai, Qi
A1  - Bortolamiol-Becet, Diane
A1  - Martin, Raquel
A1  - Zhao, Yongjun
A1  - Zamore, Phillip D.
A1  - Hannon, Gregory J.
A1  - Marra, Marco A.
A1  - Weng, Zhiping
A1  - Perrimon, Norbert
A1  - Lai, Eric C.
T1  - Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
Y1  - 2011/02/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 203 
EP  - 215 
DO  - 10.1101/gr.116657.110 
VL  - 21 
IS  - 2 
UR  - http://genome.cshlp.org/content/21/2/203.abstract 
N2  - 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. 
ER  -