Analysis of pleiotropic transcriptional profiles: A case study of DNA gyrase inhibition

Genetic and environmental perturbations often result in complex transcriptional responses involving multiple and regulons. In order to understand the nature of a response, one has to account for the contribution of downstream effects to the formation of a response. Such analysis can be carried out within a statistical framework which the individual effects are independently collected and then combined within a linear model. Here, we the contribution of DNA replication, supercoiling, and repair to the transcriptional response of inhibition of Escherichia coli gyrase. By representing the gyrase inhibition as a true pleiotropic phenomenon, we were able demonstrate that: (1) DNA replication is required for the formation of spatial transcriptional domains; (2) transcriptional response to the gyrase inhibition is coordinated between at least two modules involved in maintenance, relaxation and damage response; (3) the genes whose transcriptional response to the gyrase does not depend on the main relaxation activity of the cell can be classified on the basis of a GC excess in upstream and coding sequences; and (4) relaxation by topoisomerase I dominates the transcriptional followed by the effects of replication and RecA. We functionally tested the effect of the interaction between and repair activities, and found support for the model derived from the microarray data. We conclude that compound transcriptional profiles as a combination of downstream transcriptional effects allows for a more accurate, and meaningful representation of the transcriptional activity of a genome.