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| Status |
Public on Apr 02, 2007 |
| Title |
DNA demethylation in the Arabidopsis genome |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Methylation profiling by genome tiling array
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| Summary |
Cytosine DNA methylation is considered to be a stable epigenetic mark, but active demethylation has been observed in both plants and animals. In Arabidopsis thaliana, DNA glycosylases of the DEMETER (DME) family remove methylcytosines from DNA. Demethylation by DME is necessary for genomic imprinting and demethylation by a related protein, REPRESSOR OF SILENCING1, which prevents gene silencing in a transgenic background. However, the extent and function of demethylation by DEMETER-LIKE (DML) proteins in WT plants is not known. Using genome-tiling microarrays, we mapped DNA methylation in mutant and WT plants and identified 179 loci actively demethylated by DML enzymes. Mutations in DML genes lead to locus-specific DNA hypermethylation. Reintroducing WT DML genes restores most loci to the normal pattern of methylation, although at some loci, hypermethylated epialleles persist. Of loci demethylated by DML enzymes, >80% are near or overlap genes. Genic demethylation by DML enzymes primarily occurs at the 5' and 3' ends, a pattern opposite to the overall distribution of WT DNA methylation. Our results show that demethylation by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis genome to protect genes from potentially deleterious methylation.
Keywords: whole genome profiling, DNA methylation, demethylase
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| Overall design |
Both experiments were done using two channels per chip. The two microarray experiments compared immunoprecipitated, methylated DNA to control genomic DNA.
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| Contributor(s) |
Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL |
| Citation(s) |
17409185 |
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| Submission date |
Mar 22, 2007 |
| Last update date |
Mar 16, 2012 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
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| Phone |
206-667-4850
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| Organization name |
Fred Hutchinson Cancer Research Center
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| Department |
Basic Sciences
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| Lab |
Henikoff
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| Street address |
1100 Fairview AV N, A1-162
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
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| Platforms (1) |
| GPL3371 |
FHCRC Arabidopsis Tiling Array |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA98063 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE7336_RAW.tar |
8.8 Mb |
(http)(custom) |
TAR (of GFF) |
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