Transcriptomics,Genomics

Dataset Information

364

DDM1 and RdDM are the major regulators of transposon DNA methylation in Arabidopsis


ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Daniel Zilberman   Devin Coleman-Derr  Assaf Zemach  Ka Thao  Ping-Hung Hsieh  Stacey L Harmer  Toshiro Nishimura 

PROVIDER: E-GEOD-41302 | ArrayExpress | 2013-04-17

SECONDARY ACCESSION(S): GSE41302SRP015983PRJNA176484

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin.

Zemach Assaf A   Kim M Yvonne MY   Hsieh Ping-Hung PH   Coleman-Derr Devin D   Eshed-Williams Leor L   Thao Ka K   Harmer Stacey L SL   Zilberman Daniel D  

Cell 20130301 1


Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation of transposable elements, but the reason for this is unknown. How DDM1 interacts with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM), which is thought to mediate plant asymmetric methylation through DRM enzymes, is also unclear. Here, we show that most asymmetric methylation is facilitated by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find that heterochromati  ...[more]

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