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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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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).
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pone-0020587-g003: 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).

Mentions: We observed that a number of the genes moderately but significantly upregulated in 5-AC treated seedlings, such as the DMC1 and AtBRCA1 genes had putative or documented roles in DNA repair. We found that these genes were also induced by bleomycin and mitomycin treatment as profiled in AtGenExpress genotoxic stress timecourse dataset (ExpressionSet_ME000326, http://www.arabidopsis.org/servlets/TairObject?type=expression_set&id=1007966782) (Figure S4). These genes were not differentially regulated in the ddm1 mutant, and this suggests that 5-AC treatment may either result in increased DNA damage or double stranded breaks and that this DNA damage results from an aspect of chromatin remodeling not affected in the ddm1 mutant. This is consistent with findings in other systems regarding the effects of 5-AC treatment [19], [23]. Several genes involved in DNA-damage repair were chosen for validation by quantitative reverse-transcriptase PCR (Figure 3). In contrast to other genes with a role in DNA repair, several genes for DNA base excision repair, including REPRESSOR OF SILENCING1 (ROS1) and DEMETER-LIKE3 (DML3), were significantly down-regulated in response to 5-AC treatment as well as in the ddm1 mutant. ROS1 and DML3 encode DNA glycosylases that have been shown to be involved in active de-methylation of targets by base excision repair [24], [25], [26], this may indicate that these genes are negatively regulated by genomic hypomethylation or other effects of 5-AC treatment.


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)

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).
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3108824&req=5

pone-0020587-g003: 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).
Mentions: We observed that a number of the genes moderately but significantly upregulated in 5-AC treated seedlings, such as the DMC1 and AtBRCA1 genes had putative or documented roles in DNA repair. We found that these genes were also induced by bleomycin and mitomycin treatment as profiled in AtGenExpress genotoxic stress timecourse dataset (ExpressionSet_ME000326, http://www.arabidopsis.org/servlets/TairObject?type=expression_set&id=1007966782) (Figure S4). These genes were not differentially regulated in the ddm1 mutant, and this suggests that 5-AC treatment may either result in increased DNA damage or double stranded breaks and that this DNA damage results from an aspect of chromatin remodeling not affected in the ddm1 mutant. This is consistent with findings in other systems regarding the effects of 5-AC treatment [19], [23]. Several genes involved in DNA-damage repair were chosen for validation by quantitative reverse-transcriptase PCR (Figure 3). In contrast to other genes with a role in DNA repair, several genes for DNA base excision repair, including REPRESSOR OF SILENCING1 (ROS1) and DEMETER-LIKE3 (DML3), were significantly down-regulated in response to 5-AC treatment as well as in the ddm1 mutant. ROS1 and DML3 encode DNA glycosylases that have been shown to be involved in active de-methylation of targets by base excision repair [24], [25], [26], this may indicate that these genes are negatively regulated by genomic hypomethylation or other effects of 5-AC treatment.

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