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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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Related in: MedlinePlus

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.
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pone-0020587-g001: 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.

Mentions: Since it is known that both DNA methylation and DDM1 are involved in silencing transposable elements and pseudogenes, we examined the responses of these two classes of genes. Figure 1 shows the fold induction in response to 5-AC treatment or in the ddm1 mutant for all of the genes (240) annotated by the Arabidopsis Genome Initiative (AGI, see Methods) as “transposable elements” and called “present” in this study by the MAS Version 5.0 software (Affymetrix). In both ddm1 mutants and 5-AC treated seedlings, many transposable elements were upregulated by 100-fold or more. The Affymetrix ATH1 microarray contains probes for 113 genes that are annotated as “pseudogenes”. Of the 33 probes called present in this experiment annotated as pseudogenes, only two of these genes change significantly in expression in either the ddm1 mutant or as a result of treatment with 5-AC (not shown). This is consistent with the role for cytosine methylation and DDM1 in specifically maintaining transcriptional silencing of transposable elements, and indicates that other factors may contribute to the maintenance of transcriptional silencing for pseudogene sequences.


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)

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.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0020587-g001: 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.
Mentions: Since it is known that both DNA methylation and DDM1 are involved in silencing transposable elements and pseudogenes, we examined the responses of these two classes of genes. Figure 1 shows the fold induction in response to 5-AC treatment or in the ddm1 mutant for all of the genes (240) annotated by the Arabidopsis Genome Initiative (AGI, see Methods) as “transposable elements” and called “present” in this study by the MAS Version 5.0 software (Affymetrix). In both ddm1 mutants and 5-AC treated seedlings, many transposable elements were upregulated by 100-fold or more. The Affymetrix ATH1 microarray contains probes for 113 genes that are annotated as “pseudogenes”. Of the 33 probes called present in this experiment annotated as pseudogenes, only two of these genes change significantly in expression in either the ddm1 mutant or as a result of treatment with 5-AC (not shown). This is consistent with the role for cytosine methylation and DDM1 in specifically maintaining transcriptional silencing of transposable elements, and indicates that other factors may contribute to the maintenance of transcriptional silencing for pseudogene sequences.

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