Abstract (NSF IOS-1125620)

Systems Approaches to Identify Gene Regulatory Networks in the Grasses

Establishing the architecture of gene regulatory networks and linking system components to agronomic traits is an emerging theme in plant systems biology. This project provides the first concerted effort to comprehensively dissect the gene regulatory networks that target the metabolism of maize phenolic compounds, including phenylpropanoids, lignins, flavonoids and hydroxamic acids, all of fundamental agricultural importance. This study combines the discovery of novel transcription factors (TFs) that control maize phenolic accumulation, with the identification of their interaction partners and of direct target genes for individual and combinations of TFs. The investigation of allelic TF preference to gene regulation will provide insights that will be applicable to grasses irrespective of ploidy level. The evolutionary conservation/divergence of identified TF-DNA complexes will be evaluated in other grasses, providing an unparalleled understanding of how evolution impacted plant gene regulatory systems, and resulting in knowledge directly applicable to cereal breeding. Together with the generation of a comprehensive and centralized maize transcription factor ORFeome collection and antibodies to several regulatory proteins, these studies will significantly advance our understanding of the regulation and evolution of one of the most important plant metabolic pathways in plants. The resources generated will be useful in accelerating the study of the regulation of other important metabolic and developmental pathways in maize and other grasses. The deployment of the data here generated through the Web-accessible knowledge base GRASSIUS (grassius.org) will continue to ensure that the findings derived from this project will have the broadest possible dissemination. This project integrates genetics, molecular biology, biochemistry, mathematics, and bioinformatics for the comparative transcriptional genomics of phenolic compounds in grass crops. Its interdisciplinary nature provides unique opportunities for the training of students and postdocs across several disciplines.



Abstract (NSF DBI - 0701405)

The Grass Regulome Initiative: Integrating Control of Gene Expression and Agronomic Traits Across the Grasses

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, http://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.

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Education and Outreach

Foster the Integration of Research with Education (F.I.R.E.): This effort is a component of GRASSIUS and NSF Plant Genome Project that involves the undergraduate students enrolled in BIOL 3020 Molecular Genetics Laboratory at University of Toledo. Students use up-to-date Gateway ® cloning technology to clone PCR amplified open reading frames of corn TFs into the pENTR/D-TOPO vector. They annotate the clones with the aid of VectorNTI Advantage ® software and they write individualized lab reports for each clone. Select students have opportunities to continue this work as undergraduate honors projects in Dr.John Gray's laboratory.
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