Arabidopsis 2010: Functions of Arabidopsis Small RNAs

拟南芥 2010：拟南芥小 RNA 的功能

• 批准号: 0618433
• 负责人: James Carrington
• 金额: --
• 依托单位: Oregon State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-09-01 至 2009-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0618433&HistoricalAwards=false
• 关键词: Arabidopsis; 2010; Functions; Small; RNAs

Major paradigm shifts in understanding gene regulation at the transcriptional and posttranscriptional levels have occurred in recent years through discoveries of RNA-based silencing systems. In plants, these systems form distinct classes of small RNAs (microRNAs, trans-acting siRNA, heterochromatin associated siRNAs, and others) that associate with effector complexes containing ARGONAUTE proteins to suppress or regulate mRNAs, genetic loci or invasive elements. These pathways serve to regulate genes during growth and development, and during stress and antiviral responses. They also interface with chromatin factors to guide heterochromatin formation at loci containing repetitive elements, such as transposons and retroelements. This 2010 Project takes advantage of new technology to examine small RNA pathways at a genome-wide level, and to assign function to biogenesis and effector components, using Arabidopsis thaliana as a central model. This research program is connected to the overall goal of the 2010 Project, "to determine the function of all genes in the model plant Arabidopsis thaliana by the year 2010", by seeking the function of this specific class of RNAs. Data will be made available to the public through the Arabidopsis Small RNA Project database, at http://asrp.cgrb.oregonstate.edu/. The Major Objectives of the project include:1. Analysis of functions, regulation and evolution of several RNA silencing pathways at a genome-wide level. New enabling technology and computation will be used for sequencing-based profiling of A. thaliana small RNAs with a series of silencing-defective mutants, developmental stages, and treatments, as well as with closely related species. This will provide key data to assess the impact, redundancy and evolution of small RNA pathways in plants.2. Identification of small RNAs and small RNA classes that associate with silencing effector proteins in the ARGONAUTE (AGO) family. Associating small RNAs with effectors will provide a genome-wide benchmark to identify AGO specificities and functional redundancies. Broader Impact: The Arabidopsis Small RNA Database will be expanded as a major public resource for plant biology research. The project will engage undergraduates in a front-line research experience. Additionally, an exciting high school outreach module in collaboration with Science Education Partnerships (SEPS) will be developed. This module will be integrated with broader SEPS activities to train teachers and students in new concepts relating to genome-enabled science and gene silencing, using interesting materials generated by this project.This project encompasses all three emphasis or focus areas stated in the 2010 Project Program Description: 1. Benchmarking gene function: Each major objective has a benchmark for gene function or activity. Functional assignments to small RNA biogenesis factors will be made based on quantitative measurements of small RNAs or small RNA classes. Each of the 10 ARGONAUTE protein functions will be benchmarked based on the composition of associated small RNAs. And functions for ta-siRNAs from each TAS gene will be benchmarked in a defined genetic context by detection of phenotypes associated with disruption of tasiRNA interaction sites.2. Developing new genome-wide experimental approaches/tools for analyzing gene function: This proposal integrates new, highly parallel sequencing technology and computation to do non-biased small RNA profiling in a set of small RNA biogenesis mutants and several other plants. This technology allows quantitative, genome-wide surveys of small RNA expression levels. The data will be presented to the community through an established web-based resource that we have managed for nearly four years.3. Exploring exemplary networks and systems: This small RNA profiling technology will also be used to integrate expression of small RNAs and transcriptional activity across the entire genome using tiling arrays. Integrative analyses will illuminate the roles of specific RNA-based silencing pathways during development.

近年来，通过发现基于RNA的沉默系统的发现，在转录和转录后的理解基因调节的主要范式转移发生了。在植物中，这些系统形成了不同类别的小RNA（microRNA，跨作用siRNA，异染色质siRNA等），它们与含有Argonaute蛋白的效应复合物相关联，以抑制或调节mRNA，遗传基因座或侵入性元件。这些途径在生长和发育期间以及压力和抗病毒反应期间调节基因。它们还与染色质因子接触，以指导包含重复元素的基因座（例如转座和恢复元素）的异染色质形成。该2010年的项目利用新技术在全基因组水平上检查小型RNA途径，并使用拟南芥作为中心模型，将功能分配给生物发生和效应子组件。该研究计划与2010年项目的整体目标联系在一起，“通过寻求该特定类别的RNA的功能，以确定模型植物拟南芥中所有基因的功能”。 数据将通过http://asrp.cgrb.oregonstate.edu/ http://asrp.cgrb.oregonstate.edu/向公众提供向公众提供。 该项目的主要目标包括：1。在全基因组水平上的几种RNA沉默途径的功能，调节和演变分析。新的启用技术和计算将用于基于测序的塔利亚纳小rNA，具有一系列沉默缺陷的突变体，发育阶段和处理，以及与密切相关的物种。这将提供关键数据，以评估植物中小RNA途径的影响，冗余和演变2。鉴定小的RNA和小的RNA类，这些类别与Argona（AGO）家族中的沉默效应蛋白相关联。将小型RNA与效应子相关联将提供一个全基因组基准，以识别以前的特异性和功能冗余。更广泛的影响：拟南芥小RNA数据库将作为植物生物学研究的主要公共资源扩展。该项目将参与一线研究经验。此外，将开发与科学教育合作伙伴关系（SEP）合作的令人兴奋的高中外展模块。该模块将使用该项目生成的有趣材料培训有关与基因组科学和基因沉默有关的新概念的教师和学生的广泛活动。本项目涵盖了2010年项目计划中所述的所有三个重点或重点领域的研究：1。基因基因功能：每个主要目标：每个主要目标：每个主要目标都具有基因标记的基因函数或基因功能或活动。基于小RNA或小RNA类别的定量测量，将对小RNA生物发生因子进行功能分配。 10种Argonaute蛋白功能中的每一个都将根据相关的小RNA的组成进行基准测试。来自每个TAS基因的Ta-siRNA的功能将通过检测与tasirna相互作用位点的破坏相关的表型来在确定的遗传环境中进行基准测试。2。开发全基因组全基因组的实验方法/工具来分析基因功能：该建议将新的，高度平行的测序技术和计算集成在一组小的RNA生物发生突变体和其他几种植物中进行无偏见的小RNA分析。该技术允许对小RNA表达水平进行定量的，全基因组的调查。数据将通过我们管理了将近四年的既定基于Web的资源向社区呈现。3。探索示例性网络和系统：这种小的RNA分析技术也将用于使用瓷砖阵列整合整个基因组中小的RNA和转录活性的表达。综合分析将阐明开发过程中基于特定的基于RNA的沉默途径的作用。