The hidden physical codes for modulating the prokaryotic transcription initiation

Promoters contain specific DNA sequences and response regulatory elements, which are close to the adjacent gene’s transcription start site (TSS). And they largely controls the biological activation of the gene. Accurate transcription initiation is an essential step in the elucidation of gene regulation and understanding of the life-cycles. Although many studies have been made in this area, the mechanism of transcriptional regulation is still obscure. In this study, the six physical structural variables based on molecular dynamics (MD) simulations, three rotational descriptors and three translational descriptors, are first introduced to analyze the core promoter regions of the E. coli K12 genome. The specific structural patterns in the promoter region show that this suite of DNA geometric flexibility parameters originating from the three-dimensional structure can describe the transcription initiation of the prokaryotic genome well. Further, the prediction results by using these hidden physical codes also demonstrate that the DNA structural properties are helpful for increasing the in silico prediction of prokaryotic promoters.