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

这个2010年项目的重点是描述拟南芥microRNAs补体（miRNAs）的功能，并通过miRNA表达的微阵列分析和其他基因组方法确定它们可能参与的基因调控网络（特别是在花发育过程中）。microrna是一种以序列特异性方式调节基因表达的小非编码rna，是植物和后生动物中非常重要的一类调节分子。在拟南芥中，已经检测和/或预测了100多个miRNA，并且拟南芥基因组实际上可能包含数百个不同的miRNA位点-这一数字需要开发高通量的研究方法。该项目的主要目标是：(1)修改并在必要时扩展拟南芥microrna的计算鉴定；(2)开发miRNA表达检测微阵列平台；(3)开展miRNA表达谱实验，了解miRNA在花发育过程中的作用，获得预测miRNA的实验证据，识别miRNA靶点；(4)建立一种监测miRNA在体内表达和活性的方法，并将其用于花发育相关miRNA的研究。miRNA的功能见解将从它们的表达模式和基因靶标关系中得到。微阵列数据将通过该项目的网站提供，并将提交给Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/)；它也将作为补充资料张贴在将由这个项目产生的出版物上。有关微阵列的技术信息以及使用它们的协议和方法将在该项目的网站（http://2010mirna.caltech.edu/）上提供。一旦这项技术被开发出来，预计将与其他团体建立研究合作，从miRNA微阵列平台中受益，并且将向拟南芥社区提供一定数量的印刷微阵列。本项目对2010年项目总体目标的意义：本项目旨在实现拟南芥miRNA基因补体的准确描述。要实现2010年计划的许多目标，这样一份完整的部分清单，尤其是这类重要且相对较新的监管机构，是必要的第一步。由于其调控性质，miRNA是基因调控网络的内在组成部分，因此阐明这些需要miRNA基因的表征，就像研究所有其他网络组成部分（转录因子、顺式作用元件、靶基因）一样。全基因组基因表达谱实验表明，可能参与花发育过程的基因数量非常大，其中包括大量的转录调节因子。同时，对mirna的初步研究表明，其中许多mirna在花序和花组织中表达。因此，要全面表征植物（花发育）中一大类重要的调控网络，需要与标准基因表达数据并行获得详细的miRNA表达数据。该项目的广泛影响：该项目将产生全基因组数据集（拟南芥miRNA基因补体的描述，miRNA表达图谱-特别是与花发育有关的-以及miRNA-靶点关系的实验信息），这对许多拟南芥研究者来说将是有价值的。该项目还将为学生和博士后提供对各种基因组技术和方法的深入了解。此外，这些新方法将广泛应用于植物和动物发育过程中基因调控的研究。

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.