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

这个2010年项目的重点是通过使用miRNA表达的微阵列分析和其他基因组方法来表征拟南芥microRNA（miRNA）互补序列的功能，并确定它们可能参与的基因调控网络（特别是在花发育期间）。MicroRNA是一类以序列特异性方式调控基因表达的小分子非编码RNA，在植物和后生动物中已成为一类非常重要的调控分子。 在拟南芥中，已经检测和/或预测了100多种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方法来进行研究。 本项目的主要目标是：（1）修改并在必要时扩展拟南芥microRNA的计算机鉴定;（2）开发用于miRNA表达检测的微阵列平台;（3）进行miRNA表达谱实验，旨在了解miRNAs在花发育过程中的作用，为预测的miRNAs获得实验证据，并确定miRNAs靶点;（4）研究miRNAs在花发育过程中的作用。以及（4）开发一种体内监测miRNA表达和活性的方法，并将其用于参与花发育的miRNA的研究。 miRNA的功能见解将来自其表达模式和基因靶点关系。 微阵列数据将通过该项目的网站提供，并将提交给基因表达综合网站（http：//www.ncbi.nlm.nih.gov/geo/）;它也将作为补充资料张贴在该项目产生的任何出版物上。 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，预计将建立与其他小组的研究合作，这些小组将从miRNA微阵列平台中受益，并且一定数量的打印微阵列将提供给拟南芥社区。该项目的意义与2010年项目的总体目标：该项目旨在实现拟南芥miRNA基因互补序列的准确描述。 这样一份完整的部分清单，特别是这一重要和相对较新的监管机构类别的清单，是实现2010年项目许多目标的必要的第一步。 由于它们的调控性质，miRNA是基因调控网络的内在组成部分，因此这些的阐明需要miRNA基因表征，就像需要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，包括大量转录调节因子在内的基因数量非常庞大，可能参与花发育过程。 与此同时，对miRNAs的初步研究表明，它们中的许多在花序和花组织中表达。 因此，一个重要的和大类的调控网络在植物（花发育）的全面表征需要详细的miRNA表达数据与标准的基因表达数据并行获得。该项目的更广泛的影响：该项目将产生全基因组数据集（拟南芥miRNA基因互补的描述，miRNA表达图谱-特别是在花发育-和miRNA靶关系的实验信息），这将是有价值的许多拟南芥研究人员。 该项目还将为学生和博士后研究员提供对各种基因组技术和方法的深入了解。 此外，开发的新方法将广泛用于植物和动物发育中的基因调控研究。

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.