The Samuel Roberts Noble Foundation is awarded a grant to investigate how genome scale transcriptional regulatory networks control gene expression. The project will address diversity and complexity of gene regulation in plant systems and key regulatory elements, including transcription factors, microRNAs (miRNAs), trans-acting small interfering RNAs (ta-siRNAs), and emergent regulatory elements. Using systems bioinformatics approaches to decipher plant transcriptional regulatory networks, specific aims include: 1) developing graphical models to model and simulate plant transcriptional regulatory networks; 2) developing novel computational algorithms to infer large-scale gene regulatory networks (GRNs) from high throughput functional genomics data in model plants; 3) constructing Arabidopsis Gene Regulation Networks (AGRN) focusing on hormone-related regulatory networks; 4) constructing legume gene regulatory networks (LGRN) involved in regulation of nodulation in three model legumes: Medicago truncatula, Lotus japonicus, and Glycine max; and 5) developing integrated web systems to host AGRN and LGRN along with supportive genome-scale data, and network discovery, search and curation tools as plug-ins of popular Cytoscape-based open-source network visualization software linked to AGRN and LGRN web services.
Integrating these systems will not only fulfill the needs of the plant biology research community and plant breeders, but will ultimately lead to the development of better engineered economically important crops, e.g. forage legumes. The proposed work is trans-disciplinary and requires the application of genomics, computational biology, and bioinformatics to the classical disciplines of genetics, molecular and cell biology, and plant physiology. By providing a single training ground at the Noble Foundation, this project will empower postdoctoral fellows, visiting scientists, students, and technical staff to acquire many of the research skills that are essential for cutting-edge biological research. A strong student outreach program will be harnessed to maximize teaching and learning outcomes for this project.
