SY-STEM

Systems biology of stem cell function in Arabidopsis thaliana

Introduction

In plants, stem cells continue to be totipotent throughout the plant’s life, as is evident from the capacity of plants to be propagated from small pieces of tissue or indeed from single cells. This capacity is fulfilled by the Shoot Apical Meristems (SAMs) : small populations of dividing, undifferentiated cells that generate organs at the tips of stems and branches throughout the life of the plant. Indeed they define the number, type and position of lateral organs that caracterise plant architecture, allowing plants to adapt their development to their environment. The underlying question is how such a little structure can last and can give rise to all organs throughout plant’s life?

Significant progress has been made in this field during the last few years, although this has been largely focused on the analysis of individual analysis but its complexity and lack of completeness is such that an integrated view of meristem function is not yet possible; partially because several approaches have been lacking, in particular the systematic application of functional genomics and modeling technologies.

SY-STEM project

SY-STEM is clearly inter- and multi-disciplinary, and will build new bridges between biology, mathematics, statistics and computer modeling. It will use genetic, molecular and cellular approaches, imaging techniques, as well as large-scale genomic techniques to generate sets of data describing SAMs regulations and organ initiation in the model plant Arabidopsis thaliana. Therefore, adapted mathematical and informatics approaches are required to integrate the growing body of knowledge in such a way that it can advance the level of understanding in the field by computational modeling of the apical meristem.

Main outlines

1. An important aim of the project, therefore, is to identify the largest possible sets of genes expressed in the different domains of the meristem and the early forming organs, that To define stem cell identity.
2. In parallel, we will study meristem cell characteristics in situ and in vivo including the dynamics of stem cells, generation times, expansion rates, differentiation patterns and clonal relationships.
3. The data coming from both approaches will be integrated using the computing and modelling platform. The aim here is to generate two types of models. One is a network model, representing the complexity of the expression data. The other is a virtual meristem reflecting a selected number of spatial aspects. Both models will be interconnected. They will therefore help to formulate new hypotheses.
4. Typical examples of hypotheses that will come from the modelling approach are: potential links between transcription factors and downstream targets, potential targets of hormones, links between cellular parameters and expression patterns. A major aim of the project will be to test at least some of these hypotheses. The data coming from these experiments will again feed into the models, which should become progressively more refined.

Acknowledgement

SY-STEM is a Research Training Network (RTN) within the MARIE CURIE ACTIONS of the EU.