Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
复制标题
DOI：
10.1101/gr.116657.110
复制
发表时间：
2011-02-01
期刊：
影响因子：
7
通讯作者：
Lai, Eric C.
中科院分区：
文献类型：
--
作者：
Berezikov, Eugene;Robine, Nicolas;Lai, Eric C.
自2001年，Ambros，Tuschl和Bartel组从克隆短RNA的MiRNA初始注释以来，一百多项研究试图鉴定各种物种中的其他miRNA。我们在这里报告了来自果蝇果蝇（Drosophila Melanogaster）的简短RNA数据的荟萃分析，该数据汇总了已发表的库，其中76个数据集我们为Modencode Project生成。总的来说，我们从187个文库中的原始读取超过10亿读，其中包括各种发育阶段，特定的组织和细胞类型，突变体条件和/或Argonaute免疫沉淀。我们阐明了已知的miRNA基因座的几个特征，包括多个裁剪和dicing的分阶段副产品，某些miRNA的丰富替代5'末端，频繁的3'未塑料添加和潜在的编辑事件。我们还鉴定了49个新型miRNA产生基因组位置，还有61个其他候选基因座，具有有限的miRNA生物发生证据。尽管这些基因座扩大了果蝇miRNA目录，但这项工作支持以下观点：限制的一组细胞转录本具有由drosha/dicer-1途径专门处理的限制。出乎意料的是，我们从mRNA的编码和未翻译区域中检测到miRNA产生，发现MiRNA产生的现象是从已知基因座的反义链中产生的，很常见。总的来说，这项研究为复杂动物模型中miRNA多样性和进化的研究奠定了全面的基础。
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.