title: Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes.
abstract: The Affymetrix ATH1 array provides a robust standard tool for transcriptome analysis, but unfortunately does not represent all of the transcribed genes in Arabidopsis thaliana. Recently, Affymetrix has introduced its Arabidopsis 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 compare the results with those obtained using ATH1 arrays. We also propose a method for selecting unique tiling probes for each annotated gene or transcript in the most current genome annotation, TAIR7, generating Chip Definition Files for the Tiling 1.0R array. As a test case, we compared the transcriptome of wild-type plants with that of transgenic plants overproducing the heterodimeric E2Fa-DPa transcription factor. We show that with the appropriate data pre-processing, the estimated changes per gene for those with significantly different expression 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 the number of excellent candidates for new, direct E2F targets by almost twofold, from 181 to 334.
authors.affiliation: Department of Plant Systems Biology, VIB, Technologiepark 927, Ghent, Belgium.
authors.forename: Naïra
authors.initials: N
authors.lastname: Naouar
authors.forename: Klaas
authors.initials: K
authors.lastname: Vandepoele
authors.forename: Tim
authors.initials: T
authors.lastname: Lammens
authors.forename: Tineke
authors.initials: T
authors.lastname: Casneuf
authors.forename: Georg
authors.initials: G
authors.lastname: Zeller
authors.forename: Paul
authors.initials: P
authors.lastname: van Hummelen
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.forename: Gunnar
authors.initials: G
authors.lastname: Rätsch
authors.forename: Dirk
authors.initials: D
authors.lastname: Inzé
authors.forename: Martin
authors.initials: M
authors.lastname: Kuiper
authors.forename: Lieven
authors.initials: L
authors.lastname: De Veylder
authors.forename: Marnik
authors.initials: M
authors.lastname: Vuylsteke