PI: Erich Grotewold (The Ohio State University (OSU)) coPIs: John Gray (University of Toledo (UT),OH; subawardee) and Ramana Davuluri (The Ohio State University (OSU)) Collaborator: Daniel Janies (The Ohio State University (OSU))
An emerging theme in plant systems biology is establishing the architecture of regulatory networks and linking system components to agronomic traits. The goal of this project is to provide a concerted effort to perform comparative transcriptional genomics across several grass crops (maize, sorghum, sugarcane and rice), combining the development of experimental tools and bioinformatic resources to discover and display regulatory motifs. The Grass Regulatory Information Service (GRASSIUS, www.grassius.org/) will be implemented as a public web resource that integrates sequence and expression information on transcription factors (TFs), their DNA-binding properties, TF binding sites in the genome, the genes that TFs target for regulation and the regulatory motifs in which they participate. A method for the in vivo identification of direct targets for TFs, which should be applicable even in the absence of a complete genome sequence, will be developed and applied towards the identification of direct targets for a small subset of maize, rice, sorghum and sugarcane TFs. Together with the generation of a large centralized collection of plasmids harboring open reading frames for several TFs and antibodies to a subset of them, this project will facilitate the community-wide identification of protein-DNA interactions, essential for establishing the grass regulatory map. The experimental and computational integration of regulatory motifs with QTLs will provide an accelerated translation of findings derived from these studies to issues of agronomic relevance.
Benefiting from the increasing amount of genome sequence available, this proposal integrates genetics, molecular biology, biochemistry, statistics, bioinformatics and computer sciences in establishing the architecture of the regulatory networks that control plant gene expression, in a pioneering effort to launch the comparative transcriptional genomics field to important grass crops. The interdisciplinary nature of this project provides a unique opportunity for training at various levels (undergraduate, graduate and post-doctoral) across several disciplines, training that will be complemented by the application of tools and resources developed here into the classroom at UT and OSU, in the existing OSU Functional Genomics Training Workshop, and through the development of a new workshop in Plant Regulatory Networks. The expansion of ongoing collaborations with international leaders in the field of grass genomics will further enhance the educational impact of this proposal, by offering students and postdocs an opportunity to advance their research abroad in areas of actual need, but for which modest research is ongoing nationally (e.g., sugarcane research). Finally, the development of Web-accessible public databases will continue to ensure that the findings derived from this project will have the broadest possible dissemination.
An emerging theme in plant systems biology is to establish the architecture of regulatory networks and linking system components to agronomic traits. This project provided key initial steps towards this goal. It involved the generation of a pilot collection of transcription factor open reading frames (ORF) from maize, sorghum and rice in recombination-ready vectors. The development of the this collection resulted in the development of the "Fostering the Integration of Research and Undergraduate Education (FIRE)" training initiative at the University of Toledo, OH (http://grassius.org/outreach.html). We developed GRASSIUS (http://grassius.org) as a public knowledgebase web resource that integrates information for comparative regulatory genomics across the grasses, initially maize, sorghum, sugarcane and rice, later expanded to include Brachypodium. We coordinated the naming of grass TFs, and provided GRASSIUS as a clearinghouse for TF nomenclature issues. We also generated or acquired several antibodies against maize TFs and identified direct target genes for several of them (e.g., P1, KN1, MYB31, MYB42), and identified genes directly regulated by them using a combination of ChIP (chromatin immunoprecipitation), ChIP coupled with second generation sequencing (ChIP-Seq) and genome-wide mRNA profiling (RNA-Seq), providing a first glimpse of the emerging properties of a maize gene regulatory network. All the information generated was uploaded into the GRASSIUS public database. Besides the training of numerous undergraduate students, Ph.D. students and postdocs in cutting-edge technologies, this project also funded the two-week lond Practical Summer Workshop in Functional Genomics (https://caps.osu.edu/pfg-workshop) during the summers of 2010 and 2012, in which 18-20 reserachers each year from the USA and around the world interacted with top-notch speakers and got involved in advanced genetic and molecular biology techniques.
