E-GEOD-41302 - DDM1 and RdDM are the major regulators of transposon DNA methylation in Arabidopsis

Released on 17 April 2013, last updated on 11 March 2016
Arabidopsis thaliana
Samples (33)
Protocols (7)
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. Examination of DNA methylation, transcription and nucleosomes in Arabidopsis wild-type and/or ddm1, RdDM and DNA methylase mutants.
Experiment types
MNase-seq, methylation profiling by high throughput sequencing, RNA-seq of coding RNA 
Toshiro Nishimura <tnish@berkeley.edu>, Assaf Zemach, Daniel Zilberman, Devin Coleman-Derr, Ka Thao, Ping-Hung Hsieh, Stacey L Harmer
The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin. Zemach A, Kim MY, Hsieh PH, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. , Europe PMC 23540698
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-41302.idf.txt
Sample and data relationshipE-GEOD-41302.sdrf.txt
Processed data (59)Click to browse processed data