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

Hudson K, Luo S, Hagemann N, Preuss D - PLoS ONE (2011)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Howard Hughes Medical Institute, Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, United States of America.

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.

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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.
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pone-0020587-g002: 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.

Mentions: To determine if gene expression changes resulting from changes in DNA methylation and chromatin structure were randomly distributed throughout the genome, average expression change for all the genes called present on the array was plotted against the chromosomal position of the genes obtained from AGI annotations. Figure 2 shows that genes up- or down-regulated after 5-AC treatment appear to be distributed evenly throughout the genome, and change in expression by up to 100-fold. In contrast, in the ddm1 mutant, relatively few genes changed dramatically in expression. The genes for which expression was altered were almost all up regulated, and these genes were located primarily in centromeric and pericentromeric regions. We also examined expression changes for genes encoded by subcellular organelle genomes (mitochondrion and chloroplast). We found that genes in the chloroplast were reduced in expression after 5-AC treatment (Figure 2B). Expression of genes in the mitochondrial genome (although there were fewer mitochondrial genes than chloroplast genes on the array) did not change significantly in response to 5-AC treatment, and the magnitude of change in expression levels of both plastid and mitochondrial genes was small in the ddm1 mutant, as is expected from the nuclear localization of DDM1 and its role in nuclear chromatin remodeling.


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

Hudson K, Luo S, Hagemann N, Preuss D - PLoS ONE (2011)

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.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3108824&req=5

pone-0020587-g002: 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.
Mentions: To determine if gene expression changes resulting from changes in DNA methylation and chromatin structure were randomly distributed throughout the genome, average expression change for all the genes called present on the array was plotted against the chromosomal position of the genes obtained from AGI annotations. Figure 2 shows that genes up- or down-regulated after 5-AC treatment appear to be distributed evenly throughout the genome, and change in expression by up to 100-fold. In contrast, in the ddm1 mutant, relatively few genes changed dramatically in expression. The genes for which expression was altered were almost all up regulated, and these genes were located primarily in centromeric and pericentromeric regions. We also examined expression changes for genes encoded by subcellular organelle genomes (mitochondrion and chloroplast). We found that genes in the chloroplast were reduced in expression after 5-AC treatment (Figure 2B). Expression of genes in the mitochondrial genome (although there were fewer mitochondrial genes than chloroplast genes on the array) did not change significantly in response to 5-AC treatment, and the magnitude of change in expression levels of both plastid and mitochondrial genes was small in the ddm1 mutant, as is expected from the nuclear localization of DDM1 and its role in nuclear chromatin remodeling.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Howard Hughes Medical Institute, Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, United States of America.

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.

Show MeSH
Related in: MedlinePlus