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Cell Syst. 2018 Apr 25;6(4):409-423.e11. doi: 10.1016/j.cels.2018.01.012. Epub 2018 Feb 14.

Frequency Modulation of Transcriptional Bursting Enables Sensitive and Rapid Gene Regulation.

Author information

1
Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, Heidelberg University, 69120 Heidelberg, Germany.
2
Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany.
3
Biochemistry Center, Heidelberg University, 69120 Heidelberg, Germany. Electronic address: michael.brunner@bzh.uni-heidelberg.de.
4
Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Bioquant Center, Heidelberg University, 69120 Heidelberg, Germany. Electronic address: t.hoefer@dkfz.de.

Abstract

Gene regulation is a complex non-equilibrium process. Here, we show that quantitating the temporal regulation of key gene states (transcriptionally inactive, active, and refractory) provides a parsimonious framework for analyzing gene regulation. Our theory makes two non-intuitive predictions. First, for transcription factors (TFs) that regulate transcription burst frequency, as opposed to amplitude or duration, weak TF binding is sufficient to elicit strong transcriptional responses. Second, refractoriness of a gene after a transcription burst enables rapid responses to stimuli. We validate both predictions experimentally by exploiting the natural, optogenetic-like responsiveness of the Neurospora GATA-type TF White Collar Complex (WCC) to blue light. Further, we demonstrate that differential regulation of WCC target genes is caused by different gene activation rates, not different TF occupancy, and that these rates are tuned by both the core promoter and the distance between TF-binding site and core promoter. In total, our work demonstrates the relevance of a kinetic, non-equilibrium framework for understanding transcriptional regulation.

KEYWORDS:

chromatin looping; frequency modulation; mathematical modeling; model identification; non-equilibrium gene regulation; refractoriness; transcription factor; transcriptional bursting

PMID:
29454937
DOI:
10.1016/j.cels.2018.01.012
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