Quantification of protein abundance and interaction defines a mechanism for operation of the circadian clock

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 heterodimerisation 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.

Automated summary

This study develops a quantitative model to explain how a finite pool of BMAL1 protein regulates gene expression at thousands of target sites over daily time scales. By tracking dynamic changes in endogenous labeled proteins in tissues, the researchers determine the contribution of multiple rhythmic processes in coordinating BMAL1 DNA binding. The results also reveal the role of nuclear BMAL1 concentration in determining CLOCK and the mechanism of repression of CLOCK:BMAL1 through interactions with PER2:CRY1 and BMAL1:CRY1.