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ARS Home » Midwest Area » West Lafayette, Indiana » Crop Production and Pest Control Research » Research » Publications at this Location » Publication #258857

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

item Hudson, Karen

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/6/2011
Publication Date: 6/3/2011
Citation: Hudson, K.A., Luo, S., Hagemann, N., Preuss, D. 2011. Changes in global gene expression in response to chemical and genetic perturbation of chromatin structure. Website:

Interpretive Summary: Expression of plant genes is affected not only by information encoded in the DNA sequence, but by information encoded in modifications of the DNA bases (cytosine methylation) or of the histone proteins that DNA strands surround (histone acetylation). In this work, expression of 22,000 genes was monitored for plants receiving chemical treatments to alter cytosine methylation or histone acetylation, as well as in a mutant called decrease in DNA methylation1 (ddm1) which shows increased expression of genes located in normally silent regions of the genome as a result of the loss of cytosine methylation. This experiment provided evidence that DDM1 is required for silencing genes located in heterochromatin, while the chemical treatments resulted in changes in gene expression in any location in the genome. This basic finding from the model plant Arabidopsis thaliana is relevant to and understanding of how the expression of genes is controlled by the local chromatin environment across plant species.

Technical Abstract: DNA methylation and histone acetylation are important for controlling gene expression in all eukaryotes. Microarray analysis revealed an altered gene expression profile after treatment with the DNA methylation inhibitor 5-aza-2’ deoxyctidine (5-AC), which included the upregulation of many transposable elements and pseudogenes. DNA damage genes were 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. DDM1 has a very specific role in maintaining transcriptional silence of transposable elements, while chemical inhibitors of DNA methylation or histone acetylation inhibitors can affect the expression at a global level.