An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites

An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites Differential cytosine methylation of genes and transposons is important for maintaining integrity of plant genomes. In Arabidopsis, transposons are heavily methylated at both CG and non‐CG sites, whereas the non‐CG methylation is rarely found in active genes. Our previous genetic analysis suggested that a jmjC domain‐containing protein IBM1 (increase in BONSAI methylation 1) prevents ectopic deposition of non‐CG methylation, and this process is necessary for normal Arabidopsis development. Here, we directly determined the genomic targets of IBM1 through high‐resolution genome‐wide analysis of DNA methylation. The ibm1 mutation induced extensive hyper‐methylation in thousands of genes. Transposons were unaffected. Notably, long transcribed genes were most severely affected. Methylation of genes is limited to CG sites in wild type, but CHG sites were also methylated in the ibm1 mutant. The ibm1‐induced hyper‐methylation did not depend on previously characterized components of the RNAi‐based DNA methylation machinery. Our results suggest novel transcription‐coupled mechanisms to direct genic methylation not only at CG but also at CHG sites. IBM1 prevents the CHG methylation in genes, but not in transposons. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png The EMBO Journal Wiley

An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites

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Publisher
Wiley
Copyright
Copyright © 2013 Wiley Periodicals, Inc
ISSN
0261-4189
eISSN
1460-2075
D.O.I.
10.1038/emboj.2009.59
Publisher site
See Article on Publisher Site

Abstract

Differential cytosine methylation of genes and transposons is important for maintaining integrity of plant genomes. In Arabidopsis, transposons are heavily methylated at both CG and non‐CG sites, whereas the non‐CG methylation is rarely found in active genes. Our previous genetic analysis suggested that a jmjC domain‐containing protein IBM1 (increase in BONSAI methylation 1) prevents ectopic deposition of non‐CG methylation, and this process is necessary for normal Arabidopsis development. Here, we directly determined the genomic targets of IBM1 through high‐resolution genome‐wide analysis of DNA methylation. The ibm1 mutation induced extensive hyper‐methylation in thousands of genes. Transposons were unaffected. Notably, long transcribed genes were most severely affected. Methylation of genes is limited to CG sites in wild type, but CHG sites were also methylated in the ibm1 mutant. The ibm1‐induced hyper‐methylation did not depend on previously characterized components of the RNAi‐based DNA methylation machinery. Our results suggest novel transcription‐coupled mechanisms to direct genic methylation not only at CG but also at CHG sites. IBM1 prevents the CHG methylation in genes, but not in transposons.

Journal

The EMBO JournalWiley

Published: Apr 22, 2009

References

  • DNA methylation and epigenetics
    Bender, Bender
  • Arabidopsis MET1 cytosine methyltransferase mutants
    Kankel, Kankel; Ramsey, Ramsey; Stokes, Stokes; Flowers, Flowers; Haag, Haag; Jeddeloh, Jeddeloh; Riddle, Riddle; Verbsky, Verbsky; Richards, Richards
  • Role of CG and non‐CG methylation in immobilization of transposons in Arabidopsis
    Kato, Kato; Miura, Miura; Bender, Bender; Jacobsen, Jacobsen; Kakutani, Kakutani
  • Comparative analysis of jmjC‐domain‐containing proteins reveals the potential histone demethylases in Arabidopsis and rice
    Lu, Lu; Li, Li; Cui, Cui; Liu, Liu; Wang, Wang; Cao, Cao
  • An Arabidopsis SET domain protein is required for maintenance but not establishment of DNA methylation
    Malagnac, Malagnac; Bartee, Bartee; Bender, Bender
  • Mechanisms of epigenetic inheritance
    Martin, Martin; Zhang, Zhang
  • Targets of RNA‐directed DNA methylation
    Matzke, Matzke; Kanno, Kanno; Huettel, Huettel; Daxinger, Daxinger; Matzke, Matzke
  • Heritable epigenetic mutation of a transposon‐flanked Arabidopsis gene due to lack of the chromatin‐remodeling factor DDM1
    Saze, Saze; Kakutani, Kakutani

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