Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs
Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs
复制标题
DOI：
10.1104/pp.010501
复制
发表时间：
2001-11-01
期刊：
影响因子：
7.4
通讯作者：
Green, PJ
中科院分区：
文献类型：
--
作者：
MacIntosh, GC;Wilkerson, C;Green, PJ
拟南芥基因组的测序已经导致了数以千计的新的推定基因的基础上预测的蛋白质编码的鉴定。编码tRNA、核糖体RNA和小核仁RNA的基因也被注释;然而，一类潜在的重要基因在很大程度上逃脱了以前的注释工作。这些基因对应于缺乏显著开放阅读框的RNA，并编码RNA作为其最终产物。越来越多的证据表明，这种“非编码RNA”（ncRNA）可以在广泛的细胞过程中发挥关键作用，包括染色体沉默，转录调控，发育控制和应激反应。大约15个假定的拟南芥ncRNA已在文献中报道或已被注释。虽然有几个在其他植物物种中有同源物，但除了信号识别颗粒RNA外，所有似乎都是植物特异性的。相反，没有一个从酵母或动物系统中报道的ncRNA在拟南芥或其他植物中具有同源物。为了鉴定可能编码ncRNA的其他基因，我们使用计算工具从对应于20，000个表达序列标签克隆的基因中筛选蛋白质编码基因。使用这种策略，我们确定了19个克隆的ncRNA的特征，9个假定的肽编码RNA的开放阅读框架小于100个氨基酸，和11个不能区分这两个类别。同样，这些克隆中没有一个在植物界之外具有同源物，这表明大多数拟南芥ncRNA可能是植物特异性的。这些数据表明，ncRNA代表了拟南芥基因组学的一个重要和欠发达的方面，值得进一步研究。
Sequencing of the Arabidopsis genome has led to the identification of thousands of new putative genes based on the predicted proteins they encode. Genes encoding tRNAs, ribosomal RNAs, and small nucleolar RNAs have also been annotated; however, a potentially important class of genes has largely escaped previous annotation efforts. These genes correspond to RNAs that lack significant open reading frames and encode RNA as their final product. Accumulating evidence indicates that such "non-coding RNAs" (ncRNAs) can play critical roles in a wide range of cellular processes, including chromosomal silencing, transcriptional regulation, developmental control, and responses to stress. Approximately 15 putative Arabidopsis ncRNAs have been reported in the literature or have been annotated. Although several have homologs in other plant species, all appear to be plant specific, with the exception of signal recognition particle RNA. Conversely, none of the ncRNAs reported from yeast or animal systems have homologs in Arabidopsis or other plants. To identify additional genes that are likely to encode ncRNAs, we used computational tools to filter protein-coding genes from genes corresponding to 20,000 expressed sequence tag clones. Using this strategy, we identified 19 clones with characteristics of ncRNAs, nine putative peptide-coding RNAs with open reading frames smaller than 100 amino acids, and 11 that could not be differentiated between the two categories. Again, none of these clones had homologs outside the plant kingdom, suggesting that most Arabidopsis ncRNAs are likely plant specific. These data indicate that ncRNAs represent a significant and underdeveloped aspect of Arabidopsis genomics that deserves further study.