Quantification of protein abundance and interaction defines a mechanism for operation of the circadian clock
- University of Manchester, United Kingdom
- Medical Research Council, United Kingdom
- University of California, Santa Cruz, United States
Abstract
The mammalian circadian clock exerts control of daily gene expression through cycles of DNA binding. Here we develop a quantitative model of how a finite pool of BMAL1 protein can regulate thousands of target sites over daily time scales. We used quantitative imaging to track dynamic changes in endogenous labelled proteins across peripheral tissues and the SCN. We determine the contribution of multiple rhythmic processes coordinating BMAL1 DNA binding, including cycling molecular abundance, binding affinities and repression. We find nuclear BMAL1 concentration determines corresponding CLOCK through heterodimerization and define a DNA residence time of this complex. Repression of CLOCK:BMAL1 is achieved through rhythmic changes to BMAL1:CRY1 association and high affinity interactions between PER2:CRY1 which mediates CLOCK:BMAL1 displacement from DNA. Finally, stochastic modelling reveals a dual role for PER:CRY complexes in which increasing concentrations of PER2:CRY1 promotes removal of BMAL1:CLOCK from genes consequently enhancing ability to move to new target sites.
Data availability
Modelling and analtyical code has been made publicly available via GitHub. The FCS analysis software is at https://github.com/LoudonLab/FcsAnalysisPipeline and the modeling link is https://github.com/LoudonLab/CLOCK-BMAL1-DNA-Binding.Source Data files have been provided for all FCS measurements and FRAP measurements in Figures 1, 2, 3 ,4, and 6.
Article and author information
Author details
Funding
Biotechnology and Biological Sciences Research Council (BB/P017347/1)
- James S Bagnall
- Nicola Begley
- Andrew SI Loudon
Biotechnology and Biological Sciences Research Council (BB/P017355/1)
- Nicola J Smyllie
- Michael H Hastings
Medical Research Council (MC_U105170643)
- Michael H Hastings
National Institutes of Health (GM107069)
- Carrie L Partch
National Institutes of Health (GM141849)
- Carrie L Partch
Wellcome Trust (107851/Z/15/Z)
- Andrew SI Loudon
Wellcome Trust (216416/Z/19/Z)
- Alex Ashton Koch
University of California
- Jennifer L Fribourgh
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: All experimental procedures were carried out in accordance with the Animals (Scientific Procedures) Act of 1986, UK (License number PP7901495).
Copyright
© 2022, Koch et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Quantification of protein abundance and interaction defines a mechanism for operation of the circadian clock
eLife 11:e73976.
https://doi.org/10.7554/eLife.73976
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