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In higher plants (e.g.,  Arabidopsis thaliana ), the core structure of the circadian clock is mostly governed by a repression process with very few direct activators. With a series of simplified models, we studied the underlying mechanism and found that the  Arabidopsis  clock consists of type-2 incoherent feed-forward loops (IFFLs), one of them creating a pulse-like expression in  PRR9/7 . The double-negative feedback loop between  CCA1/LHY  and  PRR5/TOC1  generates a bistable, hysteretic behavior in the  Arabidopsis  circadian clock. We found that the IFFL involving  PRR9/7  breaks the bistability and moves the system forward with a rapid pulse in the daytime, and the evening complex ( EC ) breaks it in the evening. With this illustration, we can intuitively explain the behavior of the clock under mutant conditions. Thus, our results provide new insights into the underlying network structures of the  Arabidopsis  core oscillator.

An incoherent feed-forward loop switches the Arabidopsis clock rapidly between two hysteretic states