E. coli and Agrobacterium Non-Coding Regulatory RNA Discovery

Prokaryote species express small non-coding RNAs (ncRNAs) to regulate their gene expressions. ncRNAs can be classified into cis- and trans-encoded ncRNAs. cis-ncRNAs can usually be located directly opposing their target genes and they form perfect base-pairings. In contrary, the mechanism at which the trans-ncRNAs regulate their target genes is usually through imperfect base-pairings. Although many ncRNAs for well-known bacteria like E. coli have been identified, the extent and structure of ncRNAs are still largely unanswered for most bacteria. In order to develop a systematic method to identify all ncRNAs in prokaryotes, including both cis- and trans-ncRNAs, we have chosen E. coli and another important biotechnology bacterium Agrobacterium tumefaciens to test our new method. Our method will first conduct a whole-genome thermodynamic analysis to identify all possible imperfect base-pairings between annotated genes and some other genomic sequences. Next we will use a whole-genome tiling microarray to check the actual expression of predicted ncRNAs that are expressed by bacteria grown under various different physiology and nutritional conditions. This presentation focuses on the design and construction of the tiling microarrays based on the NimbleGen platform.

You can fill in the block "Why is this research important or significant to your field of study" by saying that 1) this is of biologically importance, 2) it compliments our understanding of RNA interference in eukaryotes, and 3) it can potentially be developed into new antibiotics to treat dieases or biotechnology methods to control bacteria.