PID-APOLO locus in Arabidopsis thaliana: quantitative modelling for inferring operational principles

The development of living organisms is driven by the orchestrated expression of proteins and hormones which allow cell differentiation and thus organ formation. In plants, this role is mainly driven by the hormone auxin, which is produced at the single-cell level and actively transported across tissues, i.e., by the action of dedicated carriers. Among the carriers, PINs are known to mediate the outgoing flux of auxin and display polarization patterns across tissues. PIN polarity and therefore auxin transport is determined by the expression level of a protein kinase called Pinoid, encoded in the gene PID which is the neighbouring gene of APOLO, a long non-coding RNA presumably leading to changes in local epigenetic status. The transcription of APOLO drives the state of the PID-APOLO locus, switching it on or off therefore acting as a signed differentiator circuit, which turns on via auxin stimulus and then spontaneously recloses in about 24 hours, even though the auxin stimulus is still there. Although the past decades have seen extensive work on this subject, it is not known yet what ensures the loop closure, whether there is a role for basal transcription to maintain the closed loop or the observed basal level is ensured by a mixture of open and closed loops which undergo a specific dynamics of opening and closing.  To answer these questions, we will use theoretical modelling based on dynamical systems and ordinary differential equations combined with inference methods to quantitatively understand single-cell data produced using APOLO overexpressors and RNAi knockdowns produced in the Crespi’s team at the Institut des Sciences du Végétal in Gif-sur-Yvette, France.