| Abstract Detail
Monday Morning Plenary Session Genomics meets Biodiversity Ecker, Joseph R. [1]. Discovery of Functional Elements in the Arabidopsis Genome. COMPLETE genome sequences are now available for several plant species and many more are on the way. In order to carryout functional analysis using this information, accurate determination of gene structures and complete gene inventories will be essential. Computational gene prediction methods are improving but alone are inadequate for new gene discovery and accurate annotation of genomes, in particular for certain gene classes such as non-coding RNA genes. New approaches are required to identify the entire complement of transcription units (protein coding and non-coding), and their associated regulatory elements (e.g. TF/chromatin binding locations and sites of DNA methylation). We are pursuing empirical approaches to decode this information using the genome sequence of the reference plant Arabidopsis, enabling more rapid assessment of the biological functions of the ~30,000 predicted genes. Unbiased mapping of the transcription units is being carried out using third-generation Affymetrix whole genome tiling arrays (WGA) containing the entire Arabidopsis genome on a single array (6.4 million oligos). The high-resolution transcription unit location information is being used to guide the construction of a complete, expression-ready, gene inventory: “the plant ORFeome”. We have also begun to utilize WGAs as a universal data-gathering platform for capturing a variety of types of genome-scale information, including the chromosomal locations of DNA methylation sites (and identification of the methylases that target these sites), chromatin/transcription factor binding sites and for discovery of genome-wide allelic variations among geographically isolated Arabidopsis accessions. When coupled with transcriptome mapping data, these unbiased sets of genome-wide regulatory information will begin to allow the construction of an integrated set of cellular/molecular connectivity maps for Arabidopsis.
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Related Links:
Salk Institute Genomic Analysis Laboratory
1 - The Salk Institute for Biological Studies, Plant Biology and Genomic Analysis Laboratories, 10010 N. Torrey Pines Road, La Lolla, CA, 92037, USA
Keywords:
Arabidopsis.
Session: SOL02-2
Location: Ballroom ABCD/Monona Terrace
Date: Monday, July 24th, 2006
Time: 8:30 AM
Abstract ID:397 |
