Understanding the Rice Epigenome: From Genes to Genomes

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PI: Blake Meyers (Univ. Delaware)CoPIs: Steven Jacobsen (UCLA; subawardee), Matteo Pelligrini (UCLA; subawardee), Guo-Liang Wang (Ohio State Univ.; subawardee)The goal of this project is to apply novel methods to understand the rice epigenome, with the fundamental objective of transferring the extensive knowledge about plant epigenetics to rice, perhaps the world's most important food crop. One recently proposed and updated definition of epigenetics states that it is "the structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states." (Nature 447, 396-398). Epigenetic mechanisms have a demonstrated and important role in plant development, stress responses, and transcriptional regulation. The data generated by this project will include genome-wide measurements of DNA methylation, histone methylation, small RNA and mRNA profiles for a comparative set of rice tissues and genotypes. These data will enable functional and genomic studies of rice chromatin modifications, small RNAs that can direct these modifications, and their impact on gene expression. To enhance these studies and as a long-term resource, one aspect of the project is the development and characterization of mutants in rice genes critical to chromatin remodeling. The research will utilize novel laboratory and bioinformatics methods for whole-genome chromatin analysis and for the deep sequencing of small RNAs. The project will develop a comprehensive genomic resource for rice, suitable for comparative analyses with other plant genomic data. More broadly, these data have an important impact by allowing the experimental characterization of chromatin modifications and epigenetic processes in rice, an agriculturally and scientifically important plant species that also serves as a model for other cereal crops. The data, mutants and particularly the sequencing-based methods that are developed will have tremendous utility to a broad set of plant biologists interested in development, stress responses, epigenetics, and plant genomics. The project will also include a novel education and outreach component focused on a proposal exchange system that can be used broadly by plant genetics and genomics courses at universities to build writing, communication, and critical thinking skills among graduate students. Finally, the project will build on existing websites to facilitate public use of these data and to assist in analyses of the rice genome and epigenome. The data will be accessible through our websites http://mpss.udel.edu/rice or http://epigenomics.mcdb.ucla.edu, and biological materials available through USDA-approved stock centers.