Comparative genomics of small RNAs in bacterial genomes.

TitleComparative genomics of small RNAs in bacterial genomes.
Publication TypeJournal Article
Year of Publication2007
AuthorsLuban S, Kihara D
JournalOMICS
Volume11
Issue1
Pagination58-73
Date Published2007 Spring
ISSN1536-2310
KeywordsCluster Analysis, Computational Biology, Deinococcus, Escherichia coli, Genetic Linkage, Genome, Bacterial, Genomics, Models, Biological, Models, Genetic, Multigene Family, RNA, Bacterial, RNA, Untranslated
Abstract

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.

DOI10.1089/omi.2006.0005
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/17411396?dopt=Abstract
Alternate TitleOMICS
PubMed ID17411396