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.
The primary objective of this project was to characterize the rice "epigenome" – the reversibly modified states of the genome that influence gene expression and plant phenotype. This is an important topic for study for agricultural and basic science reasons, because epigenetic mechanisms have demonstrated and important roles in plant development, stress responses, transcriptional regulation, and other aspects of plant biology. In addition, rice is an important food crop, providing more than a fifth of all calories consumed by humans worldwide. To conduct this work we built off of and developed novel laboratory and bioinformatics methods for whole-genome chromatin analysis and for the analysis of small RNAs. This project generated a wealth of data including genome-wide measurements of DNA methylation, histone methylation, small RNA and mRNA profiles for rice tissues, treatments, and genotypes, and we made these data available to the public via well-known and easily accessible data repositories and our own project websites. The work led to insights into the rice chromatin modifications, and into the small RNAs that can direct these modifications and have other functions in gene regulation. Thus, we also measured the impact of these chromatin modifications and small RNAs on gene expression. One particularly outstanding example was that while studying levels of DNA methylation in rice plants that were regenerated from tissue-cultured cells, we noticed significant losses of methylation compared to wild type, progenitor plants. The changes were stable over many generations, and altered gene expression of nearby genes. We showed that the rice plants regenerated from tissue culture are epigenetically modified as a result of this growth process. These results suggest a component of the long-known "somaclonal variation," a visible and lasting impact of cell culture on regenerated plants, may be due to epigenetic effects. In addition to these and other published results, to better understand the process by which epigenetic modifications are established and maintained, we characterized a variety of mutants in rice and other comparable plant systems with alterations in genes critical to chromatin remodeling and related small RNA pathways, providing insights into the fundamental processes which direct and reinforce epigenetic processes. The comprehensive genomic resource that we developed for rice is suitable for comparative analyses with other plant genomic data, and the data have tremendous utility to a broad set of plant biologists interested in development, stress responses, epigenetics, and plant genomics.
