Understanding the Rice Epigenome: From Genes to Genomes

PI：布莱克·迈耶斯(大学科皮斯：史蒂文·雅各布森(加州大学洛杉矶分校；获奖者)，马泰奥·佩里格里尼(加州大学洛杉矶分校；获奖者)，王国良(俄亥俄州立大学；获奖者)这个项目的目标是应用新的方法来理解水稻表观基因组，基本目标是将植物表观遗传学的广泛知识转移到水稻上，水稻可能是世界上最重要的粮食作物。最近提出并更新的表观遗传学定义称，表观遗传学是“染色体区域的结构性适应，以便登记、发出信号或使改变的活动状态永久化。”(自然447,396-398)。表观遗传机制在植物发育、逆境反应和转录调控中发挥着重要的作用。该项目产生的数据将包括对DNA甲基化、组蛋白甲基化、小RNA和mRNA图谱的全基因组测量，以比较一组水稻组织和基因类型。这些数据将使水稻染色质修饰的功能和基因组研究成为可能，可以指导这些修饰的小RNA，以及它们对基因表达的影响。为了加强这些研究，作为一个长期的资源，该项目的一个方面是开发和鉴定对染色质重塑至关重要的水稻基因突变。这项研究将利用新的实验室和生物信息学方法进行全基因组染色质分析和小RNA的深度测序。该项目将开发一个全面的水稻基因组资源，适合与其他植物基因组数据进行比较分析。更广泛地说，这些数据通过对水稻染色质修饰和表观遗传过程的实验表征产生了重要影响，水稻是一种在农业和科学上具有重要意义的植物物种，也是其他谷类作物的模型。所开发的数据、突变体，特别是基于测序的方法，将对对发育、胁迫反应、表观遗传学和植物基因组学感兴趣的广泛的植物生物学家具有巨大的实用价值。该项目还将包括一个新的教育和推广部分，重点是一个提案交换系统，该系统可被大学的植物遗传学和基因组学课程广泛使用，以培养研究生的写作、沟通和批判性思维技能。最后，该项目将建立在现有网站的基础上，以便利公众使用这些数据，并协助分析水稻基因组和表观基因组。这些数据将通过我们的网站http://mpss.udel.edu/rice或http://epigenomics.mcdb.ucla.edu，以及美国农业部批准的库存中心提供的生物材料获得。

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.