Systematic Curation of miRBase Annotation Using Integrated Small RNA High-Throughput Sequencing Data for C. elegans and Drosophila.
Systematic Curation of miRBase Annotation Using Integrated Small RNA High-Throughput Sequencing Data for C. elegans and Drosophila.
复制标题
使用集成的小型RNA高通量测序数据对秀丽隐杆线虫和果蝇的积分注释进行系统策划。
DOI：
10.3389/fgene.2011.00025
复制
发表时间：
2011
影响因子：
3.7
通讯作者：
Liu XS
中科院分区：
文献类型：
--
作者：
Wang X;Liu XS
微小RNA（microRNAs，miRNAs）是一类20-23个核苷酸的小分子RNA，在动物和植物中转录后调节基因表达。通过miRNA数据库（miRBase）对miRNA进行注释在很大程度上依赖于计算方法。因此，许多miRBase条目缺乏实验验证，并且经常观察到miRBase注释与实际miRNA序列之间的差异。在这项研究中，我们整合了秀丽隐杆线虫和黑腹果蝇的小RNA测序（smRNA-seq）数据集，并设计了一个分析管道，结合详细的手动检查，在miRBase中系统地管理miRNA注释。我们的分析揭示了19个（17.0%）和51个（31.3%）具有可检测的smRNA-seq读段的miRNAs条目在C中具有成熟序列差异。elegans和D. melanogaster分别。这些差异经常发生在保守的miRNA家族中，其成熟序列是根据其在其他物种中的同源对应物预测的，或者是其前体miRNA（pre-miRNA）发夹产生丰富的多种miRNA同种型或变体的miRNA。我们的分析表明，虽然果蝇pre-miRNAs，平均而言，除了它们的5′和3′变体异构体外，还产生不到60%准确的成熟miRNAs读段，但C.秀丽隐杆线虫的比例更高，超过90%。基于修改后的miRNA序列，我们分析了保守性较高（MC）和保守性较低（LC）的miRNA的表达模式，发现MC miRNA通常在多个发育阶段共表达，而LC miRNA往往在更少的发育阶段特异性表达。阶段。
MicroRNAs (miRNAs) are a class of 20–23 nucleotide small RNAs that regulate gene expression post-transcriptionally in animals and plants. Annotation of miRNAs by the miRNA database (miRBase) has largely relied on computational approaches. As a result, many miRBase entries lack experimental validation, and discrepancies between miRBase annotation and actual miRNA sequences are often observed. In this study, we integrated the small RNA sequencing (smRNA-seq) datasets in Caenorhabditis elegans and Drosophila melanogaster and devised an analytical pipeline coupled with detailed manual inspection to curate miRNA annotation systematically in miRBase. Our analysis reveals 19 (17.0%) and 51 (31.3%) miRNAs entries with detectable smRNA-seq reads have mature sequence discrepancies in C. elegans and D. melanogaster, respectively. These discrepancies frequently occur either for conserved miRNA families whose mature sequences were predicted according to their homologous counterparts in other species or for miRNAs whose precursor miRNA (pre-miRNA) hairpins produce an abundance of multiple miRNA isoforms or variants. Our analysis shows that while Drosophila pre-miRNAs, on average, produce less than 60% accurate mature miRNA reads in addition to their 5′ and 3′ variant isoforms, the precision of miRNA processing in C. elegans is much higher, at over 90%. Based on the revised miRNA sequences, we analyzed expression patterns of the more conserved (MC) and less conserved (LC) miRNAs and found that, whereas MC miRNAs are often co-expressed at multiple developmental stages, LC miRNAs tend to be expressed specifically at fewer stages.