A systems-driven experimental approach reveals the complex regulatory distribution of p53 by circadian factors

Unlike single-cell organisms with self-contained timekeeping systems, multicellular organisms partition their oscillators among different cell types and depend on more complex molecular networks to sense signals and coordinate effective responses. We found that the core circadian clock protein Period 2 (Per2) directly interacts with the checkpoint regulatory component p53, promoting its stabilization and controlling p53 transcriptional activity. Remarkably, circadian phases of Per2 and p53 are anti-phase in the cytoplasm and in-phase in the nucleus, posing new questions about the extent to which Per2 association modulates p53 distribution. Therefore, we focused our efforts on investigating what simulated conditions better relate to the experimental data using mathematical models. Specifically, the model predicted that the phase of the Per2:p53 interaction strongly depends on the binding mechanisms between Per2 and p53 mediated by ubiquitin, as determined by evolving the interaction types between Per2 and p53 in the model during the fitting process. As a result, the ubiquitilation state of p53 impacts Per2 binding and subcellular distribution. All predictions were confirmed experimentally.