Gene expression in response to genetic and chemical perturbations of chromatin structure

Microarray expression profiling was used to identify genes expressed misexpressed in wild-type Arabidopsis seedlings treated with 5-aza-2’ deoxyctidine (5AC) or trichostatin A (TSA), and in decrease in dna methylation1 (ddm1) mutant seedlings. Overall design: 10 day-old Arabidopsis seedlings (ecotype Ws) were grown in 0.5X MS media (containing 1% sucrose) at 21 C in continuous white light. Media (including 5AC and TSA) were refreshed after 5 days of growth. RNA was extracted using the Qiagen Plant RNeasy kit. Three biological replicates for each treatment and genotype were used.