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Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray.


ABSTRACT: 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.

SUBMITTER: Kim H 

PROVIDER: S-EPMC430289 | biostudies-literature | 2003 Mar

REPOSITORIES: biostudies-literature

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Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray.

Kim Heenam H   Snesrud Erik C EC   Haas Brian B   Cheung Foo F   Town Christopher D CD   Quackenbush John J  

Genome research 20030301 3


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 predi  ...[more]

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