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Global Expression Studies of the Arabidopsis Genome

PI Name: Joseph R. Ecker
PI Institution: The Salk Institute for Biological Studies
PI Email: ecker@salk.edu
PI Phone Number: 858 453-4100 x1752
Co-PI Names: Athanasios Theologis, PGEC, UC Berkeley (theo@nature.berkeley.edu)
Ronald W. Davis, Stanford University (dbowe@sequence.stanford.edu)

Plants to be Studied: Principal: Arabidopsis

Project Objectives:

  • 1.Sequencing and annotation of 8,000 full-length Arabidopsis cDNAs.
  • 2. Construction of 8,000 sequenced validated Open Reading Frame (ORF) clones in a universal recombination cloning vector
  • 3. Experimental identification of all of the expressed Arabidopsis genes utilizing whole genome tiling arrays and RNAs from many different plant treatment conditions and tissues/cell types
  • 4. By-products of our approach to experimentally determine all of the expressed Arabidopsis genes are 1) the development of whole genome tiling chips and the software to read and analysis these arrays .and 2) an experimentally derived gene expression/polymorphism detection chip.

Experimental Approaches:

  • 1.Carry out a pilot project using custom designed Affymetrix genome tiling arrays to determine optimal number/spacing of oligonucleotide probes to detect transcription units in a complex multicellular organism
  • 2.Experimental determination of the Arabidopsis transcription units by hybridization of a wide variety of mRNA populations to the genome-wide tiling chips
  • 3.Construction, and sequencing of full-length cDNAs and ORFeome clones

Information/Materials to be generated:

  • 1. 8,000 full length cDNAs- scheduled (release dates: yr. 1- 300; yr. 2, 3,000; yr. 3. 4,700)
  • 2. 8,000 sequence-validated ORFs cloned into a universal recombination vector
  • 3 A set of Affymetrix tiling chips that cover the entire Arabidopsis genome
  • 4. An experimentally derived Affymetrix gene expression/polymorphism chip- (public release by September 30, 2002)

Contact Information for Deliverables:

  • 1. sequence information/ expression data: Joe Ecker/Sakis Theologis/Ron Davis
  • 2. cDNA/ORF clones: Sakis Theologis/Joe Ecker/Ron Davis
  • 3. Affymetrix: tiling and expression chips: Ron Davis/Sakis Theologis/Joe Ecker

Addresses (Web or Email) for Project Information:

Informatics Contact Person:

    Name: Huaming Chen Email: hchen@salk.edu

Practical Applications of Research:

    * The discovery of new expressed genes that currently are not among the ESTs
    * Development of an inexpensive and high fidelity Affymetrix expression chip
    * Provide experimentally verification of the computationally derived genome annotation
    * Construction of the Arabidopsis Open Reading Frame clones (ORFeome project)
    * Eliminate the need for construction of Arabidopsis cDNA libraries
    * Our SSP custom Affymetrix arrays will also be useful for genome-wide identification of polymorphisms from any Arabidopsis accession

Utility of the SSP/RIKEN ORF clones for future Arabidopsis (2010) research:

    * creation of gain of function mutations for all genes
    * biochemical characterization of the entire proteome
    * structural characterization of the proteome (X-ray Crystallographic, NMR studies)
    * construction of an Arabidopsis protein chip
    * complementation of mutations (E coli, yeast, plant, etc)
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