Simulating models for inter-polymerase interactions. Average steady-state protein levels from simulations of the DNA molecule with promoters for different polymerases (T7 and E. coli RNA polymerases) transcribing two genes (inset). The two polymerases are expected to interact since the T7 RNA polymerase is ~5 times faster than the E. coli RNA polymerase,. The graph shows different calculated steady-state levels of the two reporter proteins given different models for the interactions between the two polymerases. The (a) 'T7 only' and (b) 'E. coli only' are controls that show expression without E. coli and T7 RNA polymerase, respectively. The 'downstream falloff' model (c) specifies that, upon a collision between two transcribing polymerases, the downstream polymerase will prematurely terminate transcription and release from the DNA. The 'upstream falloff' model (d) describes the opposite situation when the upstream polymerase falls off. Finally, the 'traffic jam' model (e) specifies that the upstream polymerase follows the downstream polymerase at the speed of the downstream polymerase.
Kosuri et al. BMC Bioinformatics 2007 8:480 doi:10.1186/1471-2105-8-480