2010 Arabidopsis: Genomic Analyses of Arabidopsis miRNAs: Their Roles in Flower Development

2010 拟南芥：拟南芥 miRNA 的基因组分析：它们在花发育中的作用

• 批准号: 0520193
• 负责人: Elliot Meyerowitz
• 金额: --
• 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: 2005
• 资助国家: 美国
• 起止时间: 2005-09-01 至 2009-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0520193&HistoricalAwards=false
• 关键词: 2010; Arabidopsis; Genomic; Analyses; miRNAs

The focus of this 2010 project is to characterize the functions of the Arabidopsis complement of microRNAs (miRNAs), and to identify the gene regulatory networks in which they may participate (in particular during flower development), by using microarray analysis of miRNA expression and other genomic approaches. MicroRNAs are small non-coding RNAs that regulate gene expression in a sequence-specific manner, and they have emerged as a very important class of regulatory molecules in plants and in metazoans. In Arabidopsis, more than 100 miRNAs have already been detected and/or predicted, and the Arabidopsis genome may in fact contain several hundred distinct miRNA loci - a number that demands the development of high-throughput methodologies for their study. The primary objectives of the project are: (1) to revise and, if necessary, extend the computational identification of Arabidopsis microRNAs; (2) to develop a microarray platform for miRNA expression detection; (3) to conduct miRNA expression profiling experiments aimed at understanding the roles of miRNAs during flower development, at gaining experimental evidence for predicted miRNAs, and at identifying miRNA targets; and (4) to develop a method for monitoring miRNA expression and activity in vivo and to use it for studies on miRNAs involved in flower development. miRNA functional insights will be derived from their expression patterns and gene target relationships. Microarray data will be made available through the project's web site and will be submitted to the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/); it will also be posted as supplementary information for any publication that will result from this project. Technical information about the microarrays and protocols and methods for using them will be available in the project's web site (http://2010mirna.caltech.edu/). Once the technology has been developed, it is anticipated that research collaborations with other groups that would benefit from the miRNA microarray platform will be established, and that a certain number of printed microarrays will be made available to the Arabidopsis community.Significance of the project in relation to the overall 2010 Project objectives:This project intends to achieve an accurate description of the Arabidopsis miRNA gene complement. Such a complete list of parts, especially of this important and relatively new class of regulators, is a necessary first step for many of the goals of the 2010 project. Because of their regulatory nature, miRNAs are intrinsic components of gene regulatory networks, and thus the elucidation of those requires miRNA gene characterization much in the same way all other network components (transcription factors, cis-acting elements, target genes) need to be studied. Whole-genome gene expression profiling experiments are showing that the number of genes, including a large number of transcriptional regulators, potentially involved in the processes of flower development is very large. At the same time, initial studies on miRNAs are showing that many of them are expressed in inflorescence and floral tissues. Thus, a comprehensive characterization of an important and large class of regulatory networks in plants (flower development) requires detailed miRNA expression data obtained in parallel with standard gene expression data.Broader impact of the project:The project will generate genome-wide datasets (description of the Arabidopsis miRNA gene complement, atlas of miRNA expression--particularly in relation to flower development--and experimental information on miRNA-target relationships) that will be valuable to many Arabidopsis investigators. The project will also provide deep familiarity with a variety of genomic technologies and approaches to students and post-doctoral fellows. In addition, the new methods developed will be of wide use in the study of gene regulation in plant and animal development.

该2010年项目的重点是表征拟南芥补体（miRNA）的功能，并通过使用miRNA表达和其他其他分析来识别它们可能参与的基因调节网络（尤其是在花朵发育过程中）基因组方法。 microRNA是小的非编码RNA，以序列特异性调节基因表达，并且它们已成为植物和后生动物中非常重要的调节分子类别。 在拟南芥中，已经检测到和/或预测了100多个miRNA，拟南芥基因组实际上可能包含数百个不同的miRNA基因座 - 这一数字需要开发其研究的高通量方法。 该项目的主要目标是：（1）修改，并在必要时扩展拟南芥microRNA的计算识别； （2）开发一个微阵列平台以进行miRNA表达检测； （3）进行miRNA表达谱分析实验，旨在了解miRNA在花朵发育过程中的作用，以获得预测的miRNA的实验证据，并确定miRNA靶标的实验证据； （4）开发一种监测体内miRNA表达和活性的方法，并将其用于研究参与花朵发育的miRNA。 miRNA功能洞察力将从其表达模式和基因靶标关系中得出。 微阵列数据将通过项目的网站提供，并将提交给Gene Expression Omnibus（http://www.ncbi.nlm.nih.gov/geo/）;它也将作为该项目产生的任何出版物的补充信息发布。 有关使用它们的微阵列和协议以及方法的技术信息将在项目网站（http://2010mirna.caltech.edu/）中提供。 一旦开发了该技术，就可以预计将建立与其他将从mirna微阵列平台中受益的团体的研究合作，并且将对拟南芥社区提供一定数量的印刷微阵列。与整个2010年项目目标有关：该项目旨在实现对拟南芥miRNA基因补体的准确描述。 对于2010年项目的许多目标来说，这是这一重要且相对新的监管机构的完整零件列表，特别是相对较新的监管机构。 由于其调节性质，miRNA是基因调节网络的内在组成部分，因此阐明这些组件需要miRNA基因的表征，与所有其他网络组件（转录因子，顺式作用元素，靶基因）相同的方式非常相同。 。 全基因组基因表达分析实验表明，包括大量转录调节剂在内的基因数量可能参与了花朵发育过程。 同时，对miRNA的初步研究表明，其中许多在花序和花卉组织中表达。 因此，对植物中重要和大型调节网络的全面表征（花开发）需要与标准基因表达数据并行获得的详细miRNA表达数据。项目的影响：该项目将生成全基因组数据集（描述）拟南芥miRNA基因补体，miRNA表达的地图集 - 与花朵发育有关，以及有关miRNA-target关系的实验信息），这对许多拟南芥研究者来说都是有价值的。 该项目还将为学生和博士后研究员的各种基因组技术和方法提供深切的熟悉。 此外，开发的新方法将在植物和动物发育中的基因调节研究中广泛使用。