Institute for Molecular Bioscience, University of Queensland, St. Lucia QLD 4072, Australia.
BMC Genomics. 2010 Feb 1;11:77. doi: 10.1186/1471-2164-11-77.
The increasing interest in small non-coding RNAs (ncRNAs) such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs) and recent advances in sequencing technology have yielded large numbers of short (18-32 nt) RNA sequences from different organisms, some of which are derived from small nucleolar RNAs (snoRNAs) and transfer RNAs (tRNAs). We observed that these short ncRNAs frequently cover the entire length of annotated snoRNAs or tRNAs, which suggests that other loci specifying similar ncRNAs can be identified by clusters of short RNA sequences.
We combined publicly available datasets of tens of millions of short RNA sequence tags from Drosophila melanogaster, and mapped them to the Drosophila genome. Approximately 6 million perfectly mapping sequence tags were then assembled into 521,302 tag-contigs (TCs) based on tag overlap. Most transposon-derived sequences, exons and annotated miRNAs, tRNAs and snoRNAs are detected by TCs, which show distinct patterns of length and tag-depth for different categories. The typical length and tag-depth of snoRNA-derived TCs was used to predict 7 previously unrecognized box H/ACA and 26 box C/D snoRNA candidates. We also identified one snRNA candidate and 86 loci with a high number of tags that are yet to be annotated, 7 of which have a particular 18mer motif and are located in introns of genes involved in development. A subset of new snoRNA candidates and putative ncRNA candidates was verified by Northern blot.
In this study, we have introduced a new approach to identify new members of known classes of ncRNAs based on the features of TCs corresponding to known ncRNAs. A large number of the identified TCs are yet to be examined experimentally suggesting that many more novel ncRNAs remain to be discovered.
越来越多的人对小非编码 RNA（ncRNA），如 microRNAs（miRNAs）、小干扰 RNA（siRNAs）和 Piwi 相互作用 RNA（piRNAs）感兴趣，测序技术的最新进展也从不同生物中产生了大量短（18-32nt）RNA 序列，其中一些来源于小核仁 RNA（snoRNAs）和转移 RNA（tRNAs）。我们观察到，这些短 ncRNA 经常覆盖注释 snoRNA 或 tRNA 的全长，这表明可以通过短 RNA 序列簇来识别其他指定类似 ncRNA 的基因座。
我们结合了来自黑腹果蝇的数千万个短 RNA 序列标签的公开可用数据集，并将它们映射到果蝇基因组上。大约 600 万个完全匹配的序列标签然后根据标签重叠组装成 521302 个标签串联（TCs）。大多数转座子衍生序列、外显子和注释的 miRNAs、tRNAs 和 snoRNAs 都被 TCs 检测到，它们显示出不同类别的长度和标签深度的不同模式。snoRNA 衍生 TCs 的典型长度和标签深度用于预测 7 个以前未识别的 box H/ACA 和 26 个 box C/D snoRNA 候选物。我们还鉴定了一个 snRNA 候选物和 86 个具有大量标签但尚未注释的基因座，其中 7 个具有特定的 18mer 基序，位于参与发育的基因的内含子中。新 snoRNA 候选物和假定 ncRNA 候选物的一部分通过 Northern blot 进行了验证。
在这项研究中，我们提出了一种新方法，基于对应已知 ncRNA 的 TCs 的特征来识别已知类别的新成员。已识别的 TCs 中有很大一部分尚未进行实验检查，这表明还有更多新的 ncRNA 有待发现。
