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

California Institute Of Technology, Pasadena CA

Investigators

Abstract

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.