RESEARCH-PGR: Transcriptional Control of the Maize Genome

该项目定义了编码在玉米基因组中的信息通道，从而使选择、破译和编辑成为可能，这对当前和未来的玉米改良战略至关重要。一种新的技术被用来划定基因组序列的开始和结束，细胞机器读取并转录成瞬时指令。这三种类型的机器转录所有有机体中根本不同的片段，但植物还有两种类型的转录被称为“暗物质”的神秘区域。在某种程度上，这些“暗物质”指令通过帮助引导对正常生长和最佳健康所必需的基因蓝图的协调阅读，影响经济利益的特征。尽管这些“暗物质”区域是世界范围内植物品种遗传变异的最大来源，但它们的功能仍然知之甚少。该项目旨在通过评估干扰不同玉米品种中这些“暗物质”区域的转录机制的效果来破译其中的一些功能。该项目产生的公开信息、分析工具和材料将显著提高现有资源的利用率，并为植物生物学和遗传学的新发现提供必要的参考。这些活动将整合对本科生和研究生的年轻科学家的培训，并与美国化学学会合作，为经济上处于不利地位的高中生提供研究经验。此外，还将编写教授基本和高级遗传概念的教育材料，并通过拟南芥生物资源中心现有的推广计划提供。基因表达在转录和转录后水平上受到控制；然而，每种材料对RNA丰度的贡献往往是未知的。在植物中，这些调控的可遗传变化可以受到PolII相关核糖核酸聚合酶(RNAP)复合体作用(S)的影响。这些RNAP中至少有5个是在草中发现的，但其功能意义尚不清楚(S)。该项目定义了玉米新生的转录图景，确定了协同或转录后调控的潜在情况，并使用突变分析来了解这些与POL II相关的RNAP复合体如何影响基因表达。具体地说，该项目将1)优化全球连续测序的协议，并生成参考的新生转录组数据集，以进行新的基因组注释；2)使用特定的突变体和比较RNA谱来区分由RNA指导的DNA甲基化引起的基因调控与RNAP IV竞争引起的基因调控，并推断单个RNA的稳定性；3)找出在没有RNAP IV的情况下调控发生遗传变化的特征，以分类其转录行为类似于易受突变影响的表位基因的等位基因；以及4)利用突变分析来评估RNAP IV将环境感知转化为可遗传转录控制的变化的假设。项目成果将为理解产生和维持作物物种表观基因组多样性的核系统提供重要的社区资源。该项目产生的所有数据将立即提供，纳入现有的数据库框架，并通过培训和外联机会加以推广，以增强对真核遗传学和作物物种基因组生物学的了解。

This project defines the passages of information encoded in the maize genome thus enabling the selection, deciphering, and editing, essential to current and future corn improvement strategies. A novel technique is used to delimit the beginning and ends of genome sequences that cellular machines read and transcribe into transient instructions. Three types of these machines transcribe fundamentally different passages in all organisms, but plants have two additional types that transcribe enigmatic regions referred to as "dark matter". In some manner, these "dark matter" instructions impact traits of economic interest by helping guide the coordinate reading of the genetic blueprint necessary for proper growth and optimal health. Although these "dark matter" regions represent the single largest source of genetic variation in worldwide plant varieties, their functions remains poorly understood. This project aims to decipher some of these functions by evaluating the effects of interfering with the transcription machinery dedicated to these "dark matter" regions in diverse maize varieties. The publicly available information, analytical tools, and materials generated by this project will significantly elevate the utility of existing resources and provide an essential reference for novel discoveries in plant biology and genetics. The activities will integrate the training of young scientists at both undergraduate and graduate levels and, in collaboration with the American Chemical Society, provide research experiences for high school students of economic disadvantage. Additionally, educational materials for teaching both basic and advanced genetic concepts will be generated and made available through an existing outreach program of the Arabidopsis Biological Resource Center.Gene expression is controlled at transcriptional and post-transcriptional levels; yet the contribution of each to RNA abundance is often unknown. In plants, heritable changes to these controls can be impacted by action(s) of Pol II-related RNA polymerase (RNAP) complexes. At least five of these RNAPs are found in grasses but their functional significance(s) remains unclear. This project defines the nascent transcriptional landscape of maize, identifies potential cases of co- or post-transcriptional control, and uses mutant analyses to understand how these Pol II-related RNAP complexes affect gene expression. Specifically, this project will 1) optimize protocols for global run-on sequencing and generate reference nascent transcriptome datasets to enable novel genome annotations; 2) use specific mutants and comparative RNA profiling to differentiate gene regulation due to RNA-directed DNA methylation versus RNAP IV competitions and to allow individual RNA stabilities to be inferred; 3) identify features where regulation is heritably altered in the absence of RNAP IV to catalog epialleles whose transcriptional behaviors resemble those susceptible to paramutation; and 4) use mutant analyses to evaluate the hypothesis that RNAP IV translates environmental perception into changes in heritable transcriptional control. Project outcomes will provide important community resources to understand the nuclear systems that generate and maintain epigenome diversity in a crop species. All data generated from this project will be made immediately available, integrated into existing database frameworks, and promoted through training and outreach opportunities to empower a greater understanding of eukaryotic genetics and the genome biology of crop species.