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Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis

Robert K Tran1, Daniel Zilberman12, Cecilia de Bustos3, Renata F Ditt1, Jorja G Henikoff1, Anders M Lindroth4, Jeffrey Delrow1, Tom Boyle1, Samson Kwong1, Terri D Bryson12, Steven E Jacobsen4 and Steven Henikoff12*

Author Affiliations

1 Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA

2 Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA

3 Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, 751 85 Sweden

4 Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA

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Genome Biology 2005, 6:R90  doi:10.1186/gb-2005-6-11-r90

Published: 19 October 2005



DNA methylation occurs at preferred sites in eukaryotes. In Arabidopsis, DNA cytosine methylation is maintained by three subfamilies of methyltransferases with distinct substrate specificities and different modes of action. Targeting of cytosine methylation at selected loci has been found to sometimes involve histone H3 methylation and small interfering (si)RNAs. However, the relationship between different cytosine methylation pathways and their preferred targets is not known.


We used a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related siRNA silencing component (AGO4) in methylating target loci. We found that KYP targets are also CMT3 targets, suggesting that histone methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar proximal distributions that correspond to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome. We find an inverse relationship between element size and loss of methylation in ago4 and drm mutants.


We conclude that the targets of both DNA methylation and histone H3K9 methylation pathways are transposable elements genome-wide, irrespective of element type and position. Our findings also suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to be maintained in a silent state by a chromatin-based mechanism alone. Thus, parallel pathways would be needed to maintain silencing of transposable elements.