Traffic phenomenon in the genome

Inside cells, multiple RNA polymerases transcribe a gene at the same time, indicating the presence of RNA polymerase “traffic”, like that of vehicles on the road. When a car stops on a single-lane road, the trailing cars pile up, creating a traffic jam. However, it remains poorly understood what happens when an RNA polymerase pauses while there are multiple RNA polymerases traveling on a DNA template. There are three scenarios, which are not mutually exclusive: (1) hard-sphere interactions between RNA polymerases, similar to a pile-up of cars behind (examined in Kim and Jacobs-Wagner, Biophys J 2018), (2) RNA polymerases pushing the paused one upon collision (Epshtein and Nudler, Science 2003), and (3) dissociation of RNA polymerases (pre-mature termination) upon collision. We aim to accurately characterize the traffic pattern of RNA polymerases and understand the underlying mechanism governing the creation and resolution of the traffic phenomenon.

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