Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli.
Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli.
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DOI：
10.1093/nar/gki256
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发表时间：
2005
影响因子：
14.9
通讯作者：
Storz G
中科院分区：
文献类型：
--
作者：
Kawano M;Reynolds AA;Miranda-Rios J;Storz G
越来越多的证据表明，小的非编码RNA是重要的调控分子。计算和实验搜索导致大肠杆菌中的1060个小RNA基因的鉴定。然而，这些研究大多集中在基因间区域，并假设小RNA是>50 nt。因此，先前的筛选遗漏了在蛋白质编码基因的反义链上编码的小RNA和<50 nt的小RNA。为了鉴定额外的小RNA，我们进行了基于克隆的筛选，重点是30-65 nt的RNA。在该筛选中，我们鉴定了对应于rRNA、tRNA和已知小RNA片段的RNA种类。一些小RNA也对应于5′和3′非翻译区（UTR）和mRNA的内部片段。4个3′-UTR衍生的RNA高度丰富，2个显示出与相应mRNA不同的表达模式，表明3′-UTR衍生的小RNA具有独立的功能。我们还检测到三个以前未识别的RNA编码的基因间区域和RNA的长直接重复和hok/sok元件。此外，我们还鉴定了一些小RNA，它们与蛋白质编码基因表达相反，并且可以与mRNA的5′或3′末端进行完全互补的碱基配对。
Evidence is accumulating that small, noncoding RNAs are important regulatory molecules. Computational and experimental searches have led to the identification of ∼60 small RNA genes in Escherichia coli. However, most of these studies focused on the intergenic regions and assumed that small RNAs were >50 nt. Thus, the previous screens missed small RNAs encoded on the antisense strand of protein-coding genes and small RNAs of <50 nt. To identify additional small RNAs, we carried out a cloning-based screen focused on RNAs of 30–65 nt. In this screen, we identified RNA species corresponding to fragments of rRNAs, tRNAs and known small RNAs. Several of the small RNAs also corresponded to 5′- and 3′-untranslated regions (UTRs) and internal fragments of mRNAs. Four of the 3′-UTR-derived RNAs were highly abundant and two showed expression patterns that differed from the corresponding mRNAs, suggesting independent functions for the 3′-UTR-derived small RNAs. We also detected three previously unidentified RNAs encoded in intergenic regions and RNAs from the long direct repeat and hok/sok elements. In addition, we identified a few small RNAs that are expressed opposite protein-coding genes and could base pair with 5′ or 3′ ends of the mRNAs with perfect complementarity.
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