Extensive feedback between gene expression state and the cellular environment yields tangled hierarchies . This lack of strictly hierarchical control mechanisms poses a challenge to developmental biologists: the outcome of interaction networks with extensive feedbacks is not intuitive and must be analyzed with analytical tools. Here, I propose a combination of experimental and theoretical approaches to study control mechanisms of plant architecture and their emergent properties. The plant hormone auxin appears to be a major player in developmental patterning and architecture. We and others have shown previously that auxin distribution patterns can self-organize and elaborate different architectures by principles of self-organization. We have discovered that the PLETHORA transcription factors, which form instructive gradients during root development, are involved in early embryo and shoot development as well, and that they constitute a principal component of plant development. Excitingly, PLETHORA genes are regulated by auxin accumulation but they feed back on the most important actors that determine auxin distribution, the PIN proteins. The dynamics of this PLETHORA-PIN loop can display emergent properties that may explain the majority of principal patterning events that determine root and shoot specification as well as branching. Here, I propose to investigate this feedback system in detail using (1) molecular genetic approaches, (2) computer modelling and (3) functional genomics approaches. The projected outcomes are a deep understanding of major control mechanisms for tissue pattern and organismal architecture and general insights into genetic information encoding using tangled hierarchies.
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