RESEARCH-PGR: Transcriptional Control of the Maize Genome

研究-PGR：玉米基因组的转录控制

• 批准号: 1546781
• 负责人: Jay Hollick
• 金额: $ 99.39万
• 依托单位: Ohio State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-08-15 至 2022-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1546781&HistoricalAwards=false
• 关键词: RESEARCH; PGR; Transcriptional; Control; Maize

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.

该项目定义了玉米基因组中编码的信息的段落，从而使选择，解密和编辑对当前和未来的玉米改善策略至关重要。一种新颖的技术用于界定细胞机读取并转录为瞬态指令的基因组序列的开始和末端。这些机器的三种类型在所有生物体中都从根本上转录，但是植物还有另外两种类型的类型，这些类型被转录为“暗物质”。在某种程度上，这些“暗物质”指令通过帮助指导对适当成长和最佳健康所需的遗传蓝图进行协调读取来影响经济利益的特征。尽管这些“暗物质”区域代表了全球植物品种中最大的遗传变异来源，但它们的功能仍然很少了解。该项目的目的是通过评估干扰各种玉米品种中这些“暗物质”区域的转录机制的影响来破译其中一些功能。该项目生成的公开信息，分析工具和材料将显着提高现有资源的实用性，并为植物生物学和遗传学中的新发现提供重要参考。这些活动将整合本科和研究生级别的年轻科学家的培训，并与美国化学学会合作，为经济劣势的高中学生提供研究经验。此外，将通过拟南芥生物资源中心的现有外展计划生成教学的教育材料，并提供基本和先进的遗传概念。Gene表达在转录和转录后级别受到控制；然而，每个人对RNA丰度的贡献通常是未知的。在植物中，这些对照的可遗传变化可能会受到与POL II相关的RNA聚合酶（RNAP）复合物的作用的影响。这些RNAP中至少有五个是在草中发现的，但是它们的功能意义仍然不清楚。该项目定义了玉米的新生转录景观，确定了转录后控制的潜在病例，并使用突变分析来了解这些与POL II相关的RNAP复合物如何影响基因表达。具体而言，该项目将1）优化用于全局跑步测序的协议，并生成参考新生的转录组数据集以实现新颖的基因组注释； 2）使用特定的突变体和比较RNA分析来区分由于RNA指导的DNA甲基化与RNAP IV竞争的基因调节，并允许推断单个RNA稳定性； 3）确定在没有RNAP IV与对转录行为类似于参数敏感的rNAP IV的情况下可以改变调节的特征； 4）使用突变分析评估RNAP IV将环境感知转化为可遗传转录控制的变化的假设。项目成果将提供重要的社区资源，以了解产生和维持农作物物种表观基因组多样性的核系统。该项目产生的所有数据都将立即提供，并集成到现有的数据库框架中，并通过培训和外展机会促进，以增强对真核遗传学和作物物种的基因组生物学的了解。