Identifying Chromatin-level Mechanisms that Regulate Responses to Phosphorus- and Iron-deficiencies in Rice

Pi：Aaron P.Smith(路易斯安那州立大学农业与机械学院)Co-Pi：Niranjan Baisakh(路易斯安那州立大学农业中心)大米是一种主要作物，养活了全球20多亿人。用于种植水稻的农地往往含有次优营养水平。磷(P)和铁(Fe)这两种重要营养物质的低效性通常会限制作物的产量，而过量的铁会对在淹水条件下生长的水稻造成毒害。由于这些生长限制，植物通过涉及大量基因的全基因组转录调控网络来调节对磷和铁水平波动的复杂反应。DNA存在于细胞核中，包裹在组蛋白周围形成称为核小体的结构。核小体是染色质的基本单位，染色质是一种流体的高阶组装，由许多重塑复合体修饰。尽管染色质结构在控制基因表达方面起着重要作用，但有关染色质水平调控植物营养动态平衡的机制还不是很清楚。以前的工作已经表明，磷和铁之间的相互作用影响缺乏诱导的应激反应的开始。该项目的目标是确定染色质水平的机制，以调节水稻对磷和铁的吸收、同化和利用。该项目的四个具体目标是：1)确定水稻幼苗在磷和/或铁缺乏下的生理和转录变化；2)确定与营养缺乏有关的水稻基因组核小体定位的变化；3)研究组蛋白变异体在调节水稻全基因组基因表达中的作用；以及4)表征营养缺乏期间水稻P和Fe稳态基因中存在的组蛋白翻译后修饰。通过将染色质结构的三个关键成分(即核小体定位、组蛋白变体定位和组蛋白修饰)与基因表达谱相关联，将揭示调控磷和铁缺乏反应的调控机制。确定这些染色质水平的机制将为开发养分利用效率更高的作物提供机会，显著改善美国和全球农业。在该项目期间产生的所有序列数据将通过基因表达综合数据库(GEO：http://www.ncbi.nlm.nih.gov/geo/).This)向公众提供，该项目将有助于研究生和本科生的教育。研究人员拥有不同种族和性别的研究小组，并将通过路易斯安那州立大学提供的项目(包括博士前学者研究所和诺伊斯老虎研究实习)指导学生，继续促进代表性不足的群体参与研究。其他计划的活动包括通过一年一度的超级科学星期六活动进行K-12推广，以及在夏季对地区高中的师生对进行为期两周的动手研究培训。

PI: Aaron P. Smith (Louisiana State University & Agricultural and Mechanical College)Co-PI: Niranjan Baisakh (Louisiana State University Agricultural Center)Rice is a staple crop that feeds more than two billion people worldwide. Agricultural lands used for growing rice frequently contain sub-optimal nutrient levels. Low availability of two important nutrients, phosphorus (P) and iron (Fe), commonly limits crop productivity, whereas excess Fe can cause toxicity in rice grown under flooding conditions. Because of these growth restraints, plants modulate complex responses to fluctuating P and Fe levels via genome-wide transcriptional regulatory networks that involve numerous genes. DNA is found in the nucleus wrapped around histone proteins into structures known as nucleosomes. Nucleosomes are the basic unit of chromatin, which is a fluid, higher-order assembly that is modified by many remodeling complexes. Although chromatin structure plays a substantial role in controlling gene expression, the chromatin-level mechanisms involved in regulating nutrient homeostasis in plants are not well understood. Previous work has shown that the interaction between P and Fe influences the onset of deficiency-induced stress responses. The goal of this project is to identify chromatin-level mechanisms that regulate the uptake, assimilation, and utilization of P and Fe in rice. The four specific aims of the project are to: 1) determine the physiological and transcriptional changes in rice seedlings under P and/or Fe deficiency; 2) identify nutrient deficiency-dependent changes in nucleosome positioning across the rice genome; 3) examine the role of the H2A.Z histone variant in regulating gene expression in rice genome-wide; and 4) characterize the histone post-translational modifications present at rice P and Fe homeostasis genes during nutrient deficiency. By correlating three key components of chromatin structure (i.e. nucleosome positioning, histone variant localization, and histone modifications) with gene expression profiles, the regulatory mechanisms that modulate P and Fe deficiency responses will be revealed. Identifying these chromatin-level mechanisms will provide opportunities for developing crops with improved nutrient use-efficiency, significantly improving U.S. and global agriculture. All sequence data generated during this project will be made available to the public through the Gene Expression Omnibus database (GEO:http://www.ncbi.nlm.nih.gov/geo/).This project will contribute to the education of graduate and undergraduate students. The investigators have research groups diverse in ethnicity and gender, and will continue to foster involvement of underrepresented groups in research by mentoring students through programs available through LSU, including the Pre-doctoral Scholars Institute and Noyce Tigers Research Internship. Other planned activities include K-12 outreach through the annual Super Science Saturday event, and training of student-teacher pairs from area high schools in hands-on research for two weeks during the summer.