Omics Science Center, RIKEN Yokohama Institute, Tsurumi, Yokohama 230-0045, Japan.
Genome Res. 2010 Feb;20(2):257-64. doi: 10.1101/gr.095273.109. Epub 2010 Jan 5.
MicroRNAs (miRNAs) are short (20-23 nt) RNAs that are sequence-specific mediators of transcriptional and post-transcriptional regulation of gene expression. Modern high-throughput technologies enable deep sequencing of such RNA species on an unprecedented scale. We find that the analysis of small RNA deep-sequencing libraries can be affected by cross-mapping, in which RNA sequences originating from one locus are inadvertently mapped to another. Similar to cross-hybridization on microarrays, cross-mapping is prevalent among miRNAs, as they tend to occur in families, are similar or derived from repeat or structural RNAs, or are post-transcriptionally modified. Here, we develop a strategy to correct for cross-mapping, and apply it to the analysis of RNA editing in mature miRNAs. In contrast to previous reports, our analysis suggests that RNA editing in mature miRNAs is rare in animals.
MicroRNAs (miRNAs) 是短链 (20-23nt) RNA，能够特异性地调节基因转录和转录后表达。现代高通量技术使我们能够以前所未有的规模对这些 RNA 进行深度测序。我们发现，小 RNA 深度测序文库的分析可能受到跨映射的影响，其中来自一个基因座的 RNA 序列被错误地映射到另一个基因座。与微阵列上的交叉杂交类似，跨映射在 miRNA 中很常见，因为它们往往存在于家族中，或者与重复或结构 RNA 相似或源自重复或结构 RNA，或者是转录后修饰的。在这里，我们开发了一种纠正跨映射的策略，并将其应用于成熟 miRNA 中的 RNA 编辑分析。与之前的报告相比，我们的分析表明，在动物中，成熟 miRNA 中的 RNA 编辑很少见。
