Changes in global gene expression in response to chemical and genetic perturbation of chromatin structure

Abstract

DNA methylation is important for controlling gene expression in all eukaryotes. Microarray analysis of mutant and chemically-treated Arabidopsis thaliana seedlings with reduced DNA methylation revealed an altered gene expression profile after treatment with the DNA methylation inhibitor 5-aza-2' deoxycytidine (5-AC), which included the upregulation of expression of many transposable elements. DNA damage-response genes were also coordinately upregulated by 5-AC treatment. In the ddm1 mutant, more specific changes in gene expression were observed, in particular for genes predicted to encode transposable elements in centromeric and pericentromeric locations. These results confirm that DDM1 has a very specific role in maintaining transcriptional silence of transposable elements, while chemical inhibitors of DNA methylation can affect gene expression at a global level.

Figure 1. Transposable element genes are upregulated in the ddm1 mutant and after 5-AC treatment.

Log expression differences (5-AC/Ws or ddm1/Ws) for 240 probesets annotated as transposable elements that were present on the microarray.

Figure 2. Genes misregulated in ddm1 are not evenly distributed in the Arabidopsis genome.

A. log₁₀ fold-difference values (5-AC/Ws) and (ddm1/Ws) are plotted by transcription start site for 5 Arabidopsis chromosomes. B. log₁₀ fold-difference values for 5-AC treated and ddm1 seedlings for chloroplast and mitochondrial genes.

Figure 3. DNA damage repair genes are upregulated after 5-AC treatment.

Quantitative RT-PCR expression ratios (5-AC and ddm1 normalized to Ws untreated control) for genes associated with repair of DNA damage or chromatin structure. Error bars indicate 95% confidence interval. AtBRCA1, ARABIDOPSIS THALIANA BREAST CANCER SUSCEPTIBILITY1 (At4g21070); DMC1, DISRUPTION OF MEIOTIC CONTROL1 (At3g22880); ROS1, REPRESSOR OF SILENCING1 (At2g36490); MSH4, MUTS HOMOLOG4 (At4g17380).