Genome-wide analysis in bacteria show small RNA enrichment for long and conserved intergenic regions

by CH Tsai, R. Liao, B. Chou, M. Palumbo, and LM Contreras

Journal of Bacteriology 2014  pii: JB.02359-14

Interest in finding small RNAs (sRNAs) in bacteria has significantly increased in recent years due to their regulatory functions. Development of high-throughput methods and more sophisticated computational algorithms has allowed rapid identification of sRNA candidates in different species. However, given their varying sizes (50-500nts) and their potential genomic locations in the 5′ and 3′ untranslated regions as well as in intergenic regions, identification and validation of true sRNAs have been challenging. In addition, the evolution of bacterial sRNAs across different species continues to be puzzling given that they can exert similar functions with varying sequences and structures. In this study, we analyzed the enrichment patterns of sRNAs in thirteen well-annotated bacterial species using existing transcriptome and experimental data. All intergenic regions were analyzed by WU-BLAST to examine conservation levels relative to species within or outside their genus. In total, more than 900 validated bacterial sRNAs and 23000 intergenic regions were analyzed. The results indicate that sRNAs are enriched in intergenic regions, which are longer and more conserved relative to the average intergenic regions in the corresponding bacterial genome. We also found that sRNA coding regions have different conservation levels relative to their flanking regions. This work provides a way to analyze how non-coding RNAs are distributed in bacterial genomes and also shows conserved features of intergenic regions that encode sRNAs. These results also provide insight into the functions of regions surrounding sRNAs and into optimization of RNA search algorithms.

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