Identification of novel small RNAs using comparative genomics and microarrays
Identification of novel small RNAs using comparative genomics and microarrays
复制标题
DOI：
10.1101/gad.901001
复制
发表时间：
2001-07-01
影响因子：
10.5
通讯作者：
Gottesman, S
中科院分区：
文献类型：
--
作者：
Wassarman, KM;Repoila, F;Gottesman, S
在原核细胞和真核细胞中已经鉴定出具有多种调控功能的小RNA。然而，通过序列检查来鉴定小RNA仍然是困难的。我们使用的高度保守的小RNA密切相关的细菌物种之间，以及高密度寡核苷酸探针阵列检测到的转录本的分析，预测大肠杆菌基因组的基因间区域的新的小RNA基因的存在。通过北方分析证实了23种不同的新RNA种类的存在。其中，6个被预测为编码短ORF，而17个可能是新的功能性小RNA。我们发现许多这些小RNA与RNA结合蛋白Hfq相互作用，这表明Hfq蛋白在促进小RNA功能方面具有全局作用。这里使用的方法应该允许在其他生物体中识别小RNA。
A burgeoning list of small RNAs with a variety of regulatory functions has been identified in both prokaryotic and eukaryotic cells. However, it remains difficult to identify small RNAs by sequence inspection. We used the high conservation of small RNAs among closely related bacterial species, as well as analysis of transcripts detected by high-density oligonucleotide probe arrays, to predict the presence of novel small RNA genes in the intergenic regions of the Escherichia coli genome. The existence of 23 distinct new RNA species was confirmed by Northern analysis. Of these, six are predicted to encode short ORFs, whereas 17 are likely to be novel functional small RNAs. We discovered that many of these small RNAs interact with the RNA-binding protein Hfq, pointing to a global role of the Hfq protein in facilitating small RNA function. The approaches used here should allow identification of small RNAs in other organisms.