Genome wide application of DNA stability for the annotation of promoter regions

Vetriselvi Rangannan, Manju Bansal
Indian Institute of science, Bangalore, India

Identification and annotation of promoter regions in genomes has drawn significant attention in structural and functional genomics community, due to their important role in controlling gene expression. Prokaryotic as well as eukaryotic promoter sequences exhibit several common sequence and structural features, but very little sequence motif consensus is seen. However, it has been proved that promoter sequences possess certain sequence dependent structural properties, such as lower stability, higher curvature and less bendability, when compared with their neighboring regions. Based on the difference in stability between neighboring upstream and downstream regions in the vicinity of experimentally determined transcription start sites, a promoter prediction algorithm has been developed to identify prokaryotic promoter sequences in whole genomes. Our results prove that while the promoter regions are overall less stable, their average free energy varies compared to other genomic regions, depending on the GC composition of the genomic sequence. In this method the average free energy (E) over known promoter sequences and the difference (D) between E and the average free energy over downstream random sequences (REav) are used to search for promoters in the genomic sequences. Thresholds (E and D) have been generalised for every 5 %GC interval. A protocol that has been successfully applied for microbial promoter identification and their prediction on a large-scale to whole genomic sequences will be presented. High reliability of 70% and 61% for E. coli and B. subtilis respectively, was achieved on carrying out whole genome annotation for proximal promoters in these genomes.