Genome-Wide Conservation Profiling and Size Distribution Analysis of Intergenic Sequences in Prokaryotes Provide Insights to Refine sRNA Searches

­­­­            Interest in the search of small RNAs (sRNAs) in bacteria have significantly increased in recent years due to the important regulatory functions that they are now known to be capable of exerting [1]. Development of high-throughput methods (e.g. next-generation sequencing) and more sophisticated computational algorithms has allowed rapid identification of potential sRNA targets in a way that includes complete genome coverage [2-5]. However, given their varying size (50-500nts) and their potential genomic locations in the 5' and 3' untranslated regions as well as in intergenic regions [6], identification and validation of true functionally-active sRNAs have been challenging.

In this study, we analyzed the distribution of profiled sRNAs in 10 different bacteria species using existing transcriptome data. All the intergenic regions were analyzed by WU-BLAST to examine conservation levels relative to other species within or outside their genus. We categorized all members of this bacterial set into different classes according to the conservation patterns that we observed. We will discuss our observations of the correlations between conservation of intergenic regions and sRNA abundance. We also analyzed the size distribution of all intergenic regions in each organism. We will discuss the latter results as well as their implications for refining the discovery and validation of sRNAs in prokaryotes using combined computational and experimental methods. 

1.               Gottesman S, Storz G, Robertson MP, Joyce GF, Gold L, et al. (2011) Bacterial Small RNA Regulators : Versatile Roles and Rapidly Evolving Variations. Cold Spring Harb Perspect Biol: ;3:a003798 1.

2.               Gelderman G, Contreras LM (2013) Discovery of Posttranscriptional Regulatory RNAs Using Next Generation Sequencing Technologies. In: Alper HS, editor. Systems Metabolic Engineering: Methods and Protocols. Totowa, NJ: Humana Press, Vol. 985. pp. 269-295.

3.               Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.

4.               Storz G, Vogel J, Wassarman KM (2011) Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 43: 880-891.

5.               Livny J (2012) Bioinformatic Discovery of Bacterial Regulatory RNAs Using SIPHT. In: Keiler KC, editor. Bacterial Regulatory RNA: Methods and Protocols. Totowa, NJ: Humana Press, Vol. 905. pp. 3-14.

6.               Kawano M, Reynolds AA, Miranda-Rios J, Storz G (2005) Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Res 33: 1040-1050.