Arabidopsis 2010: Next Generation Cellular Resolution Profiling of the Transcriptome and Epigenome

拟南芥 2010：转录组和表观基因组的下一代细胞分辨率分析

• 批准号: 0929349
• 负责人: Elliot Meyerowitz
• 金额: $ 64万
• 依托单位: California Institute of Technology
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-12-15 至 2011-11-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0929349&HistoricalAwards=false
• 关键词: Arabidopsis; 2010; Next; Generation; Cellular

The purpose of the project is to develop and apply methods to sequence translating messenger RNA from specific cell types. An important deficit in current experiments that obtain the list of active genes in plant tissue is that the tissue used comes from a mixture of different cell types, for example, it uses whole flowers or whole seedlings, each of which is made up of many different types of cells. The resulting data on active genes is useful, but is information on the activity of genes from many cells that have different collections of active genes. As cell-type-specific data are necessary to infer gene regulatory networks, current types of data are inadequate to understand a complex organ like a leaf, shoot, or flower. The research will use developing flowers as a system, will adapt existing methods and develop new methods to isolate cell-type specific RNA, and to perform detailed sequencing of the RNA from individual cell types of the developing flower. The result will be a set of tested methods that allow researchers to isolate messenger RNA from single cell types found in complex tissues, and therefore to record patterns and changing patterns of gene activity from each of the single cell types found in developing organs.Broader ImpactsThe broader impacts of the project are in three areas. First, the completion of the proposed research will result in new technologies for the entire plant science community to study RNA and gene activity at cellular resolution in virtually any cell type, which is expected to be crucial for the understanding of various questions from development to energy capture and response to the environment. All the methods and lines generated through this project, which will enable cell-type specific analysis in other laboratories, including those of young and starting researchers who would have to spend considerable time to make such lines, will be made freely available to the research community. Second, by being partly established within the environment of a much larger group of undergraduate students, graduate students, postdoctoral fellows and technical staff that are engaged in different research projects on Arabidopsis and animal development (the Meyerowitz laboratory and the personnel of the Caltech Jacobs Center for Genetics and Genomics), the project will provide familiarity with a variety of genomic technologies and approaches to a substantial pool of future independent investigators. This pool will include undergraduate summer researchers and students from underrepresented minorities recruited through established programs at Caltech. Finally, public outreach and training activities will include provision of the materials generated (especially images) for the "Grounding in Botany" program, a collaboration between the Meyerowitz lab and the Huntington Botanical Gardens, in which laboratory exercises using plants are developed by teachers for high school classrooms; and for a program in which graduate students and postdoctoral scholars from Caltech spend up to six weeks at the Exploratorium in San Francisco, teaching high school and elementary science teachers in a summer teacher training program.

该项目的目的是开发和应用从特定细胞类型中翻译信使RNA的方法。目前获得植物组织中活性基因列表的实验中的一个重要缺陷是，所使用的组织来自不同细胞类型的混合物，例如，它使用整个花或整个幼苗，每一个都由许多不同类型的细胞组成。所得到的关于活性基因的数据是有用的，但是是关于来自具有不同活性基因集合的许多细胞的基因活性的信息。 由于细胞类型特异性数据对于推断基因调控网络是必要的，因此目前的数据类型不足以理解复杂的器官，如叶，芽或花。 该研究将使用发育中的花作为一个系统，将调整现有的方法并开发新的方法来分离细胞类型特异性RNA，并对发育中花的单个细胞类型的RNA进行详细测序。 其结果将是一套经过测试的方法，使研究人员能够从复杂组织中发现的单细胞类型中分离信使RNA，从而记录发育器官中发现的每种单细胞类型的基因活性模式和变化模式。首先，拟议研究的完成将为整个植物科学界提供新技术，以研究几乎任何细胞类型中细胞分辨率的RNA和基因活性，预计这对理解从发育到能量捕获和对环境的反应等各种问题至关重要。 通过该项目产生的所有方法和细胞系将免费提供给研究界，这将使其他实验室能够进行细胞类型特异性分析，包括那些必须花费大量时间才能建立此类细胞系的年轻和刚起步的研究人员。其次，部分建立在由从事拟南芥和动物发育不同研究项目的本科生、研究生、博士后研究员和技术人员组成的更大群体的环境中（Meyerowitz实验室和加州理工学院雅各布遗传学和基因组学中心的工作人员），该项目将使大量未来的独立调查人员熟悉各种基因组技术和方法。 该人才库将包括本科夏季研究人员和通过加州理工学院既定项目招募的代表性不足的少数民族学生。 最后，公共宣传和培训活动将包括提供所产生的材料（特别是图像）为“植物学基础”计划，迈耶罗维茨实验室和亨廷顿植物园之间的合作，其中使用植物的实验室练习是由教师为高中教室开发的;加州理工学院的研究生和博士后学者在旧金山弗朗西斯科的探索馆学习长达六周的课程，在暑期教师培训项目中教授高中和小学科学教师。