Luban Stan, Kihara Daisuke
Department of Computer Science, Markey Center for Structural Biology, West Lafayette, Indiana 47907, USA.
OMICS. 2007 Spring;11(1):58-73. doi: 10.1089/omi.2006.0005.
In recent years, various families of small non-coding RNAs (sRNAs) have been discovered by experimental and computational approaches, both in bacterial and eukaryotic genomes. Although most of them await elucidation of their function, it has been reported that some play important roles in gene regulation. Here we carried out comparative genomics analysis of possible sRNAs that are computationally identified in 30 bacterial genomes from gamma- and alpha-proteobacteria and Deinococcus radiodurans. Identified sRNAs are clustered by a complete-linkage clustering method to see conservation among the organisms. On average, sRNAs are found in approximately 30% of intergenic regions of each genome sequence. Of these, 25.7% are conserved among three or more organisms. Approximately 60% of the conserved sRNAs do not locate in orthologous intergenic regions, implying that sRNAs may be shuffled their positions in genomes. The current study implies that sRNAs may be involved in a more extensive range of functions in bacteria.
近年来，通过实验和计算方法，在细菌和真核生物基因组中发现了各种小非编码RNA（sRNA）家族。尽管它们中的大多数功能尚待阐明，但据报道，有些sRNA在基因调控中发挥着重要作用。在此，我们对通过计算方法在来自γ-和α-变形菌以及耐辐射球菌的30个细菌基因组中鉴定出的可能的sRNA进行了比较基因组学分析。通过完全连锁聚类方法对鉴定出的sRNA进行聚类，以观察不同生物体之间的保守性。平均而言，在每个基因组序列的约30%的基因间区域中发现了sRNA。其中，25.7%在三种或更多生物体中保守。大约60%的保守sRNA不在直系同源基因间区域中定位，这意味着sRNA可能在基因组中改变了它们的位置。当前的研究表明，sRNA可能在细菌中参与更广泛的功能。
