Transcription profiling of Arabidopsis dms4-1, drd1-1 and drd1-6 mutant seedlings against wild-type to identify targets of IWR1-like transcription factor

ABSTRACT: We identified in a forward genetic screen a novel factor required for RNA-directed DNA methylation (IWR1-like transcription factor). The aim of the study was to identify natural targets of this factor and to compare it to targets of drd1 another major key factor required for the RNA silencing process in plants. We performed transcriptome analysis to identify targets of this factor. For this we used whole plants at seedling stage, isolated total RNA and then used the standard Affymetrix pipeline/chemistry. The mutated transcription factor, dms4-1 was compared to its respective wildtype (EDT, Col-O background). For microarray analysis THREE biological replicates were run.

For transcriptome comparison we analyzed another factor required for the process RNA-directed DNA methylation in plants, drd1 also identified in a forward genetic screen and previously characterized in depth (Kanno et al. Current Biology, 14, 801-805, (2004), Huettel et al. EMBO J. 25, 2828-2836 (2006)). For transcriptome analysis two alleles of drd1 (drd1-1 and drd1-6) with two biological replicates each was compared to the respective wildtype DT, which served as starting material in this forward genetic screen (DT, Col-0 background). For drd1 mutants and DT wildtype analysis 10 day old seedlings were used as starting matieral while for dms4-1 and EDT 3 week old seedlings were analyzed.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Bruno Huettel 

PROVIDER: E-MEXP-2251 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress