Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators.

Karapetyan, Sargis

Buchler, Nicolas E

United States

2016-01-11T23:41:38Z

2015-12

Genetic oscillators, such as circadian clocks, are constantly perturbed by molecular noise arising from the small number of molecules involved in gene regulation. One of the strongest sources of stochasticity is the binary noise that arises from the binding of a regulatory protein to a promoter in the chromosomal DNA. In this study, we focus on two minimal oscillators based on activator titration and repressor titration to understand the key parameters that are important for oscillations and for overcoming binary noise. We show that the rate of unbinding from the DNA, despite traditionally being considered a fast parameter, needs to be slow to broaden the space of oscillatory solutions. The addition of multiple, independent DNA binding sites further expands the oscillatory parameter space for the repressor-titration oscillator and lengthens the period of both oscillators. This effect is a combination of increased effective delay of the unbinding kinetics due to multiple binding sites and increased promoter ultrasensitivity that is specific for repression. We then use stochastic simulation to show that multiple binding sites increase the coherence of oscillations by mitigating the binary noise. Slow values of DNA unbinding rate are also effective in alleviating molecular noise due to the increased distance from the bifurcation point. Our work demonstrates how the number of DNA binding sites and slow unbinding kinetics, which are often omitted in biophysical models of gene circuits, can have a significant impact on the temporal and stochastic dynamics of genetic oscillators.

http://www.ncbi.nlm.nih.gov/pubmed/26764732

1550-2376

https://hdl.handle.net/10161/11506

eng

American Physical Society (APS)

Phys Rev E Stat Nonlin Soft Matter Phys

10.1103/PhysRevE.92.062712

Binding Sites

Circadian Clocks

DNA

Kinetics

Models, Genetic

Stochastic Processes

Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators.

Journal article

Buchler, Nicolas E|0000-0003-3940-3432

http://www.ncbi.nlm.nih.gov/pubmed/26764732

062712

6

Biology

Duke

Physics

Trinity College of Arts & Sciences

Published

92