2010 Project Summary

Summary of the Project

A current challenge in Arabidopsis functional genomics is to organize individual genes into networks that depict their functional relationships in biological processes. At present, we have only a rudimentary understanding of Arabidopsis gene networks, due in part to the dearth of suitable model gene networks to use as paradigms for network construction and analysis. In this project, we use a systems-based approach to construct and analyze the relatively simple gene network that controls root epidermal cell differentiation. This is an exceptional system because root epidermal cells are developmentally simple, easy to observe and manipulate, and amenable to sophisticated genetic and molecular dissection. Most importantly, a framework of gene interactions has already been established, which provides a biological foundation for network modeling. This research utilizes an interdisciplinary collaboration between a molecular developmental geneticist (Schiefelbein) and a systems biologist (Woolf). In preliminary work, a robust cell-specific transcript profiling method has been used to define a set of genes involved in root epidermal cell differentiation. These genes are being assembled into a probabilistic model network by systematically perturbing specific genes (nodes) and defining independence relationships from microarray-based expression data using Bayesian network analysis. This network will then be refined by resolving uncertain parts of the network and by testing specific relationships using biological experiments. Further, the network will be extended to incorporate the effects of hormonal and environmental factors. This work is expected to provide a paradigm for future efforts in gene network construction in Arabidopsis.

Broader Impacts of the Project

This project will generate broader impacts in several areas. First, it will help provide training for the next generation of plant systems biologists through a rich interdisciplinary research experience for the undergraduates, graduate students, and postdoctoral fellows. Also, this project will be part of a summer research program for high school students from across the country, with a special emphasis on underrepresented minorities. The PIs will also incorporate this research into a formal course in biotechnology for graduate and undergraduate students at the University of Michigan. Further, the project results are expected to have a major impact on the Arabidopsis community, by generating novel computational and experimental approaches for network construction, by uncovering fundamental features of plant gene network structure and circuitry, by defining specific gene regulatory relationships that may be used to build new networks, and by providing a foundational network for researchers in the root epidermis field. To facilitate the international dissemination of the project findings, a project website will be developed and frequently updated with a description of the project, a list of genes under study, and the resources generated (including access information for plant materials and computational resources). In the long term, this project will improve our understanding of plant gene regulatory mechanisms to enable the rationale design of biological and synthetic networks for plant improvement.