Open Access Highly Accessed Research article

Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana

Wanhui You1, Agata Tyczewska14, Matthew Spencer1, Lucia Daxinger15, Marc W Schmid2, Ueli Grossniklaus2, Stacey A Simon3, Blake C Meyers3, Antonius JM Matzke1 and Marjori Matzke1*

Author Affiliations

1 Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria

2 Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland

3 Department of Plant and Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, USA

4 Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland

5 Epigenetics Laboratory, Queensland Institute of Medical Research, Herston, Brisbane, Queensland, Australia

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BMC Plant Biology 2012, 12:51  doi:10.1186/1471-2229-12-51

Published: 19 April 2012

Abstract

Background

In plants, transposons and non-protein-coding repeats are epigenetically silenced by CG and non-CG methylation. This pattern of methylation is mediated in part by small RNAs and two specialized RNA polymerases, termed Pol IV and Pol V, in a process called RNA-directed DNA methylation. By contrast, many protein-coding genes transcribed by Pol II contain in their gene bodies exclusively CG methylation that is independent of small RNAs and Pol IV/Pol V activities. It is unclear how the different methylation machineries distinguish between transposons and genes. Here we report on a group of atypical genes that display in their coding region a transposon-like methylation pattern, which is associated with gene silencing in sporophytic tissues.

Results

We performed a methylation-sensitive amplification polymorphism analysis to search for targets of RNA-directed DNA methylation in Arabidopsis thaliana and identified several members of a gene family encoding cysteine-rich peptides (CRPs). In leaves, the CRP genes are silent and their coding regions contain dense, transposon-like methylation in CG, CHG and CHH contexts, which depends partly on the Pol IV/Pol V pathway and small RNAs. Methylation in the coding region is reduced, however, in the synergid cells of the female gametophyte, where the CRP genes are specifically expressed. Further demonstrating that expressed CRP genes lack gene body methylation, a CRP4-GFP fusion gene under the control of the constitutive 35 S promoter remains unmethylated in leaves and is transcribed to produce a translatable mRNA. By contrast, a CRP4-GFP fusion gene under the control of a CRP4 promoter fragment acquires CG and non-CG methylation in the CRP coding region in leaves similar to the silent endogenous CRP4 gene.

Conclusions

Unlike CG methylation in gene bodies, which does not dramatically affect Pol II transcription, combined CG and non-CG methylation in CRP coding regions is likely to contribute to gene silencing in leaves because loss of this methylation in synergid cells is associated with CRP gene expression. We discuss this unusual methylation pattern and its alteration in synergid cells as well as the possible retrogene origin and evolutionary significance of CRP genes that are methylated like transposons.