Diffusion, dimensionality and noise in transcriptional regulation

TL;DR

This paper investigates how one-dimensional sliding of proteins along DNA influences the noise in transcriptional regulation, revealing that the expected reduction in noise due to sliding is largely offset by increased temporal correlations.

Contribution

It demonstrates that, contrary to prior assumptions, DNA sliding has minimal impact on the fundamental limits of transcriptional precision due to correlation effects.

Findings

Sliding along DNA has little effect on noise reduction in regulation.

Temporal correlations in 1D diffusion offset benefits of sliding.

Physical limits to transcriptional precision are not significantly improved by sliding.

Abstract

The precision of biochemical signaling is limited by randomness in the diffusive arrival of molecules at their targets. For proteins binding to the specific sites on the DNA and regulating transcription, the ability of the proteins to diffuse in one dimension by sliding along the length of the DNA, in addition to their diffusion in bulk solution, would seem to generate a larger target for DNA binding, consequently reducing the noise in the occupancy of the regulatory site. Here we show that this effect is largely cancelled by the enhanced temporal correlations in one dimensional diffusion. With realistic parameters, sliding along DNA has surprisingly little effect on the physical limits to the precision of transcriptional regulation.