Kim Sneppen

This visit was instrumental in the completion of an existing project, studying protein roadblocking of DNA transcription in bacteria. Genomic DNA is bound by many proteins that could potentially impede elongation of RNA polymerase (RNAP), but the factors determining the magnitude of transcriptional roadblocking in vivo are poorly understood. We have been combining systematic experiments (in Ian Dodd’s laboratory) and mathematical modelling (a collaboration between Kim Sneppen and Sandeep Krishna) to analyse how roadblocking by the lac repressor (LacI) in E. coli cells is affected by promoter firing rate, the concentration and affinity of the roadblocker protein, the transcription-coupled repair protein Mfd, and promoter-roadblock spacing. In this visit we were able to build models of RNAP traffic and LacI roadblocking, and combine them with experiments to make specific predictions that will lead to further experiments. In the spring of 2014 we submitted a manuscript on this work to Nucelic Acids Research where it is currently under a second round of reviewing after revisions