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

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 heterodimerisation and define a DNA residence time of this complex. Repression of CLOCKBMAL1 is achieved through rhythmic changes to BMAL1CRY1 association and high-affinity interactions between PER2CRY1 which mediates CLOCKBMAL1 displacement from DNA. Finally, stochastic modelling reveals a dual role for PERCRY complexes in which increasing concentrations of PER2CRY1 promotes removal of BMAL1CLOCK from genes consequently enhancing ability to move to new target sites.