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| Status |
Public on Feb 18, 2013 |
| Title |
Genome-wide analysis of the cytosine methylation profile in Arabidopsis thaliana crown galls |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Methylation profiling by genome tiling array
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| Summary |
Integration of the bacterial T-DNA into the plant genome by virulent agrobacteria causes crown gall development on many plant species. Plant tumor development shares fundamental similarities with mammalian cancer progression despite obvious differences in initiation of tumor development. For neoplastic growth in mammals, DNA methylation changes are known to be essential. The role of epigenetic modifications for plant tumor development is addressed here. Genome-wide comparison of methylation profiles of Arabidopsis crown galls and tumor-free tissue revealed 2,876 annotated genes that were affected by differential methylation. Thereof, 1,822 genes were hit by hypermethylated regions and 1,100 genes overlapped with hypomethylated regions (sum of hyper-and hypomethylated genes is higher than the number of affected genes because one gene may contain several differentially methylated regions [DMRs]). DMRs found to be methylated only in tumor-free tissue covered 275 kb of the genome, whereas those methylated only in crown galls total to 560 kb. Contrary to the globally hypermethylated tumor genome, promoter regions of protein coding genes appeared to be rather hypomethylated. In contrast, mammalian cancer cells are associated with global hypomethylation and local hypermethylation of gene promoters. In summary, while aberrant DNA methylation in mammals increases malignacy of the cancer phenotype, our results indicate that methylation events in the plant genome rather confine tumor growth.
All 15,431 mCIP-enriched regions reported in the paper are contained in the supplementary BED files.
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| Overall design |
mCIP of gDNA from crown galls vs. mCIP of gDNA from inflorescence stalks (3 biol. replicates each)
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| Contributor(s) |
Gohlke J, Scholz CJ, Deeken R |
| Citation(s) |
23408907 |
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| Submission date |
May 01, 2012 |
| Last update date |
May 09, 2017 |
| Contact name |
Claus Juergen Scholz |
| Organization name |
University Hospital Würzburg
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| Department |
Core Unit SysMed
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| Street address |
Josef-Schneider-Str. 2
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| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
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| Platforms (1) |
| GPL10977 |
[At35b_MR] Affymetrix Arabidopsis Tiling 1.0R Array |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA162677 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE37680_K2_K3_K4_smoothed.bedGraph.gz |
36.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE37680_RAW.tar |
578.4 Mb |
(http)(custom) |
TAR (of BEDGRAPH, CEL) |
| GSE37680_T2_T3_T4_smoothed.bedGraph.gz |
36.5 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE37680_hypermethylated_regions.bed.gz |
11.0 Kb |
(ftp)(http) |
BED |
| GSE37680_hypomethylated_regions.bed.gz |
5.8 Kb |
(ftp)(http) |
BED |
| GSE37680_unchanged_regions.bed.gz |
107.7 Kb |
(ftp)(http) |
BED |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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