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Journal Article

The origin of short transcriptional pauses

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Depken,  Martin
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

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Grill,  Stephan W
Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society;

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Citation

Depken, M., Galburt, E. A., & Grill, S. W. (2009). The origin of short transcriptional pauses. Biophysical Journal, 96(6), 2189-2193.


Cite as: https://hdl.handle.net/21.11116/0000-0001-0DA0-C
Abstract
RNA polymerases are protein molecular machines that transcribe genetic information from DNA into RNA. The elongation of the RNA molecule is frequently interrupted by pauses, the detailed nature of which remains controversial. Here we ask whether backtracking, the central mechanism behind long pauses, could also be responsible for short pauses normally attributed to the ubiquitous pause state. To this end, we model backtracking as a force-biased random walk, giving rise to a broad distribution of pause durations as observed in experiments. Importantly, we find that this single mechanism naturally generates two populations of pauses that are distinct both in duration and trajectory: long-time pauses with the expected behavior of diffusive backtracks, and a new class of short-time backtracks with characteristics similar to those of the ubiquitous pause. These characteristics include an apparent force insensitivity and immobility of the polymerase. Based on these results and a quantitative comparison to published pause trajectories measured with optical tweezers, we suggest that a significant fraction of short pauses are simply due to backtracking.