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Abstract

The Affymetrix ATH1 array provides a robust standard tool for transcriptome analysis, but unfortunately doesnot represent all of the transcribed genes inArabidopsis thaliana. Recently, Affymetrix has introduced itsArabidopsis Tiling 1.0R array, which offers whole-genome coverage of the sequenced Col-0 reference strain.Here, we present an approach to exploit this platform for quantitative mRNA expression analysis, and comparethe results with those obtained using ATH1 arrays. We also propose a method for selecting unique tilingprobes for each annotated gene or transcript in the most current genome annotation, TAIR7, generating ChipDefinition Files for the Tiling 1.0R array. As a test case, we compared the transcriptome of wild-type plantswith that of transgenic plants overproducing the heterodimeric E2Fa-DPa transcription factor. We show thatwith the appropriate data pre-processing, the estimated changes per gene for those with significantly differentexpression levels is very similar for the two array types. With the tiling arrays we could identify 368 new E2F-regulated genes, with a large fraction including an E2F motif in the promoter. The latter groups increase thenumber of excellent candidates for new, direct E2F targets by almost twofold, from 181 to 334.