From Stem Cells To Differentiated Tissue: Identifying System Components and Network Connections In The Arabidopsis Root

Understanding organ development from a systems biology perspective first requires identification of the system’s constituent components, followed by establishment of the connections between those components. The inherent difficulties in this effort are compounded in multicellular organisms, where development encompasses diverse processes that occur with spatial and temporal specificity. To identify the molecular mechanisms that underlie the developmental progression from stem cells to differentiated tissues, we exploit the simple structure and organization of the Arabidopsis root. Using methods we developed for high throughput isolation of marked cell populations, we have profiled each of the major system components: transcripts, small RNAs, proteins and metabolites at cell type-specific resolution. Because root development is affected by environmental stimuli, we have expanded the transcriptional profiling to include roots grown under abiotic and biotic stress conditions. Additionally, we have identified a periodic transcriptional network that establishes the position of branches along the root’s longitudinal axis.  With the identification of many different system components, we are working towards forming networks that function in distinct cell types and developmental stages in the root.