E. coli and Agrobacterium non-coding regulatory RNA discovery

In recent years non-coding regulatory RNAs were discovered to have far more important biological functions than previously thought. The most prominent examples are small interference RNAs and micro RNAs in eukaryote cells that collectively defined the RNA interference pathway and its many applications in biotechnologies, genetics and medicines. Although similar non-coding regulatory RNAs are postulated to exist in prokaryote cells as well, only a small number of these RNAs have been discovered so far, and those discoveries are limited to well-known bacteria like the E. coli. For most bacteria their non-coding regulatory RNAs have not been discovered. The rate-limiting factor in this discovery is the fact that trans-acting regulatory RNAs in prokaryotes only partial base-pair with their target genes, in contrast to the cis-acting regulatory RNAs which can usually be found on the opposite DNA strands of their target genes. We present a novel method that can identify trans-acting non-coding regulatory RNAs in prokaryotes using a whole-genome thermodynamic analysis approach with the software PICKY. Subsequently, both cis-and trans-acting non-coding regulatory RNAs can be validated using a whole-genome tiling microarray to detect expressed RNAs in prokaryotes.