A computational study of bacterial gene regulation and adaptation ...

Chapter 1: Global regulators of bacterial transcription initiationbinding intensities than H and C together (PW = 4.5 x 10 -9 ) indicating a preference againstbinding to low-AT genes. These data clearly indicate differential binding of these three factorsto the three sets of genes.In sum, it is notable that the greatest selective preference towards binding to H genes is shownby H-NS, which is recognised as a major global repressor of transcription (McGovern et al.1994): among all H-NS targets in RegulonDB, 70% are repressed by this factor. Comparison(A)Stationary phase response(B)gyrAB coexpression!log pvalue x direction of response!15 !10 !5 0 5 10 15Pearson correlation coefficientwith gyrA and gyrB!1.0 !0.5 0.0 0.5 1.0L C HL C H(C)hupAB coexpression(D)Gyrase bindingPearson correlation coefficientwith hupA and hupB!1.0 !0.5 0.0 0.5 1.0Gyrase ChIP!chip intensity ratio(log scale)!1.0 !0.5 0.0 0.5 1.0L C HL C HFigure 1.5. Supercoiling and AT content. For each of the three classes of lead genes in our study, (A)Distribution of the p-value for differential gene expression in stationary phase against mid-log phase.Each p-value is represented as its negative logarithm (base 10), multiplied by +1 if the gene isupregulated in stationary phase and -1 if it is downregulated. (B) Distribution of Pearson correlationcoefficients with gyrA and gyrB. (C) Distribution of Pearson correlation coefficients with hupA andhupB. (D) Distribution of ChIP-chip binding intensities for DNA gyrase from Jeong et al. 2004.39