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| Status |
Public on Dec 25, 2011 |
| Title |
Methyl DIP-chip from self-pollinated ddm1 mutant and ddm1 kyp double mutant |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Methylation profiling by genome tiling array
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| Summary |
Methylation of histone H3 lysine 9 (H3K9me) and small RNA are associated with constitutively silent chromatin in diverse eukaryotes including plants. In plants, silent transposons are also marked by cytosine methylation, especially at non-CpG sites. The transposon-specific non-CpG methylation in plants is controlled by small RNA and H3K9me. Although it is often assumed that small RNA directs H3K9me,　interaction between small RNA and H3K9me has not been directly shown in plants. We have previously shown that a mutation in a chromatin remodeling gene DDM1 (decrease in DNA methylation) induces a global decrease as well as local increase of cytosine methylation and accumulation of small RNA in a locus called BONSAI. Here we show that the de novo BONSAI methylation does not depend on RNAi but depends on H3K9me. Notably, in mutant of H3K9 methylase gene KRYPTONITE or H3K9me-dependent DNA methylase gene CHROMOMETHYALSE3, the ddm1-induced de novo cytosine methylation was abolished for all three contexts, CpG, CpHpG, and CpHpH. Furthermore, RNAi mutants showed strong developmental defects when combined with ddm1 mutation. Our results revealed unexpected interactions of epigenetic modifications, which could be conserved among diverse eukaryotes.
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| Overall design |
comparison of DNA methylation between WT, 2G ddm1 (2 replications), 8G ddm1 (2 replications), and 8G ddm1 kyp
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| Contributor(s) |
Sasaki T |
| Citation(s) |
22269081 |
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| Submission date |
Dec 07, 2011 |
| Last update date |
Mar 29, 2012 |
| Contact name |
Taku Sasaki |
| E-mail(s) |
[email protected]
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| Organization name |
Gregor Mendel Institute
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| Street address |
Dr. Bohr-gasse 3
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platforms (3) |
| GPL8080 |
Nimblegen Arabidopsis thaliana Whole Genome Tiling Array (385K) 3 of 3 |
| GPL14974 |
NimbleGen Arabidopsis thaliana Whole Genome Tiling Array 385K (1 of 3) |
| GPL14975 |
NimbleGen Arabidopsis thaliana Whole Genome Tiling Array 385K (2 of 3) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA149817 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE34222_RAW.tar |
279.3 Mb |
(http)(custom) |
TAR (of PAIR) |
| Processed data included within Sample table |
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