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| Status |
Public on Apr 17, 2013 |
| Title |
DDM1 and RdDM are the major regulators of transposon DNA methylation in Arabidopsis |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Eukaryotic DNA methylation is found in silent transposable elements and active genes. Nucleosome remodelers of the DDM1/Lsh family are thought to be specifically required to maintain transposon methylation, but the reason for this is unknown. Here, we find that a chromatin gradient that extends from the most heterochromatic transposons to euchromatic genes determines the requirement of DDM1 for methylation maintenance in all sequence contexts. We also show that small RNA-directed DNA methylation (RdDM) is inhibited by heterochromatin and absolutely requires the nucleosome remodeler DRD1. DDM1 and RdDM independently mediate nearly all transposon methylation, which is catalyzed by the methyltransferases MET1 (CG), CMT3 (CHG), DRM2 (CHH) and CMT2 (CHH), and collaborate to repress transposition and regulate the methylation and expression of genes. Our results indicate that the Arabidopsis genome is defined by a heterochromatic continuum that governs the access of DNA methyltransferases and potentially all DNA binding proteins.
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| |
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| Overall design |
Examination of DNA methylation, transcription and nucleosomes in Arabidopsis wild-type and/or ddm1, RdDM and DNA methylase mutants.
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| |
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| Contributor(s) |
Zemach A, Hsieh P, Coleman-Derr D, Thao K, Harmer SL, Zilberman D |
| Citation(s) |
23540698 |
| |
| Submission date |
Oct 03, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Toshiro Nishimura |
| E-mail(s) |
tnish@berkeley.edu
|
| Phone |
5106429550
|
| Organization name |
University of California at Berkeley
|
| Department |
Plant and Microbial Biology
|
| Lab |
Daniel Zilberman
|
| Street address |
211 Koshland Hall
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platforms (3) |
| GPL9302 |
Illumina Genome Analyzer II (Arabidopsis thaliana) |
| GPL11221 |
Illumina Genome Analyzer IIx (Arabidopsis thaliana) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
|
| Samples (33)
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| Relations |
| BioProject |
PRJNA176484 |
| SRA |
SRP015983 |
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