Gene expression analyses of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray.
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.
Kim
Heenam
H
The Institute for Genomic Research, Rockville, MD 20850, USA.
Snesrud
Erik C
EC
Haas
Brian
B
Cheung
Foo
F
Town
Christopher D
CD
Quackenbush
John
J
D017360:Arabidopsis / Q000235:genetics* / Q000382:microbiology / Q000502:physiology; D001424:Bacterial Infections / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics*; D003080:Cold Temperature; D018744:DNA, Plant / Q000235:genetics*; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant / Q000502:physiology; D018390:Gene Targeting / Q000379:methods; D017343:Genes, Plant / Q000502:physiology; D006358:Hot Temperature; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009928:Organ Specificity / Q000235:genetics; D010935:Plant Diseases / Q000382:microbiology; D018514:Plant Structures / Q000235:genetics / Q000382:microbiology / Q000502:physiology; D012492:Salts
D018744:DNA, Plant; D012492:Salts