Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray

Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray

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Unformatted text preview: 10.1101/gr.552003 Access the most recent version at doi: 2003 13: 327-340 Genome Res. Heenam Kim, Erik C. Snesrud, Brian Haas, Foo Cheung, Christopher D. Town and John Quackenbush Genomic DNA Amplicon Microarray Chromosome 2 Using a Arabidopsis Gene Expression Analyses of References http://www.genome.org/cgi/content/full/13/3/327#otherarticles Article cited in: http://www.genome.org/cgi/content/full/13/3/327#References This article cites 46 articles, 18 of which can be accessed free at: service Email alerting click here top right corner of the article or Receive free email alerts when new articles cite this article - sign up in the box at the Notes http://www.genome.org/subscriptions/ go to: Genome Research To subscribe to 2003 Cold Spring Harbor Laboratory Press on November 28, 2006 www.genome.org Downloaded from Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray Heenam Kim, 1 Erik C. Snesrud, 1 Brian Haas, Foo Cheung, Christopher D. Town, and John Quackenbush 2 The Institute for Genomic Research, Rockville, MD 20850, USA. The gene predictions and accompanying functional assignments resulting from the sequencing and annotation of a genome represent hypotheses that can be tested and used to develop a more complete understanding of the organism and its biology. In the model plant Arabidopsis thaliana , we developed a novel approach to constructing whole-genome microarrays based on PCR amplification of the 3 ends of each predicted gene from genomic DNA, and constructed an array representing more than 94% of the predicted genes and pseudogenes on chromosome 2. With this array, we examined various tissues and physiological conditions, providing expression-based validation for 84% of the gene predictions and providing clues as to the functions of many predicted genes. Further, by examining the distribution of expression along the physical chromosome, we were able to identify a region of repressed transcription that may represent a previously undescribed heterochromatic region. [The sequence data from this study have been submitted to ArrayExpress under accession nos.: For the Array Design, A-TIGR-2. For the three subgroups of experiments: AbioticStress, E-TIGR-2; BioticStress, E-TIGR-3; Tissues, E-TIGR-4.] The sequencing of the whole Arabidopsis genome by an inter- national consortium, Arabidopsis Genome Initiative (AGI), be- gan in 1996. Chromosomes 2 and 4 were published in De- cember 1999 (Lin et al. 1999; Mayer et al. 1999), and the remainder of the genome, chromosomes 1, 3, and 5, was com- pleted and published in the winter of 2000 ( Arabidopsis Ge- nome Initiative 2000; European Union Chromosome 3 Ara- bidopsis Sequencing Consortium 2000; Kazusa DNA Research Institute et al. 2000; Theologis et al. 2000). The goal of a genome project is not the collection of the organisms DNA sequence, but rather the identification of the genes encoded within. Consequently, as the Arabidopsis sequence became available, significant effort was devoted to gene prediction...
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Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray

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