Properties of the gene regulatory network for the formation of new lateral roots in plants – NewRoot

The development of new organs relies on the precise regulation of cell division, cell fate commitment and cell differentiation by gene regulatory networks. Emergent properties of these genetic systems can generate tissue functional patterning in a robust and plastic fashion, possibly integrating endogenous or environmental cues. Many genes involved in this process were identified by classical genetics experiments in various model organisms. However, how these multiple factors act together to coordinate the functional patterning of new organs often remains poorly understood due to the difficulty of investigating complex genetic systems behaviour in developing organisms. The NEWROOT project aims to address this issue in the favourable context of lateral root development in Arabidopsis thaliana. Indeed throughout their lifetime plants repeatedly generate new lateral roots in which a new stem cell niche is created, allowing subsequent indeterminate growth of the new organ. Additionally our team recently contributed to develop innovative tools allowing precise investigation of live lateral root primordium functional patterning (Goh et al., Development 2016) as well as the inference of a large 250-gene regulatory network operating during that process, in which a number of interactions have already been experimentally validated (Lavenus et al., Plant Cell 2015).
The aim of this project is to uncover and analyse the gene regulatory network controlling lateral root organogenesis using a systems biology approach combining experimental biology and modelling. First, the inferred topology of the 250-gene network will be thoroughly analysed in order to identify master regulator genes and overrepresented structural motives. The dynamic behaviour of this system will be simulated using a specifically dedicated algorithm currently being developed in our team. Interesting predicted properties will be supported by experimental validations of critical genetic interactions (transactivation assays, mutant phenotypes) and characterization of gene expression domains using fluorescent reporter constructs and live confocal imaging of developing primordia. Two mutually inhibitory subnetworks have already been unravelled. One contains genes functionally related to the primordium boundary cell fate and interestingly involves a putative coordinated upregulation of the very long chain fatty acid biosynthesis pathway by the transcription factor PUCHI, which will be fully characterized. Importantly the second subnetwork involves some genes both expressed in the centre of the primordium and whose function is related to root meristem patterning and stem cell niche organization. We will explore the topological and dynamical properties of this circuit in order to identify the key genetic switches that drive central cells to a stem cell identity. These analyses will again be confirmed by virtually and experimentally manipulating the functional patterning of new root meristems.
This work will provide a global understanding of the genetic regulation of lateral root organogenesis and especially of root primordium functional patterning in plants. Importantly it will possibly shed light on new patterning mechanisms operating in this experimental system characterized by high plasticity of cell identities, de novo stem cell niche formation, and tight regulation of cell fates across tissues in which cell walls prevent any migration. Additionally this knowledge will highlight new master genes or association of genes that may be targeted by plant breeding programs in order to create crop varieties with more efficient root systems.