S184: Deciphering the regulatory codes in microbial genomes

Over the past decade or so, dramatic developments in our ability to experimentally determine the contents and functions of genomes have taken place. In particular, high-throughput technologies are now inspiring a new understanding of the bacterial genome on a global scale. In prokaryotes, whole-transcriptome studies have not been performed until recently owing to the general view that microbial gene structures are simple, as well as technical difficulties in enriching for mRNAs that lack poly(A) tails. In the work presented here, a method has been developed for the genome-wide determination of transcriptional start site (TSS) using massive sequencing platform and 5’triphosphorylated mRNA capturing method. In addition, high-density tiling arrays have been used to perform location analysis for three classes of DNA-binding proteins in E. coli. The proteins examined include RNA polymerase complex, broad-acting transcription factors, and nucleoid-associated proteins. These high-throughput data sets were then integrated to fully elucidate the E. coli transcriptome architecture. This systems approach is now revolutionizing our understanding of the complexity, plasticity and regulation of microbial transcriptomes, and sheds light on the synthetic biology applications such as novel biological circuit design.