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和机械学院）共同PI：Niranjan Baisakh（路易斯安那州立大学农业中心）水稻是一种主要作物，养活了全世界20多亿人。用于种植水稻的农田经常含有次优营养水平。两种重要的营养物质，磷（P）和铁（Fe）的低可用性通常会限制作物的生产力，而过量的铁会导致水稻在洪水条件下生长的毒性。由于这些生长限制，植物通过涉及众多基因的全基因组转录调控网络来调节对P和Fe水平波动的复杂反应。在细胞核中发现的DNA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，高阶组装体，被许多重塑复合物修饰。虽然染色质结构在控制基因表达中起着重要的作用，但参与调节植物营养稳态的染色质水平机制还不清楚。以前的工作表明，磷和铁之间的相互作用影响的发病不足引起的压力反应。本项目的目标是确定染色质水平的机制，调节吸收，同化和利用的磷和铁在水稻。该项目的四个具体目标是：1）确定缺磷和/或缺铁条件下水稻幼苗的生理和转录变化; 2）确定营养缺乏依赖的水稻基因组核小体定位变化; 3）研究H2 A. Z组蛋白变体在水稻全基因组基因表达调控中的作用;以及4）表征在营养缺乏期间存在于水稻P和Fe稳态基因的组蛋白翻译后修饰。通过将染色质结构的三个关键组成部分（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，将揭示调节P和Fe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具有改善的养分利用效率的作物提供机会，从而显著改善美国和全球农业。该项目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/）向公众提供。该项目将有助于研究生和本科生的教育。调查人员有不同的种族和性别的研究小组，并将继续促进参与研究的代表性不足的群体通过辅导学生通过计划可通过路易斯安那州立大学，包括博士前学者研究所和诺伊斯老虎研究实习。其他计划中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外展，以及在夏季对地区高中的师生进行为期两周的实践研究培训。

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.