Cytosine methylation, a common form of DNA modification that antagonizes transcription, is found at transposons and repeats in vertebrates, plants and fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana genome at high resolution. DNA methylation covers transposons and is present within a large fraction of A. thaliana genes. Methylation within genes is conspicuously biased away from gene ends, suggesting a dependence on RNA polymerase transit. Genic methylation is strongly influenced by transcription: moderately transcribed genes are most likely to be methylated, whereas genes at either extreme are least likely. In turn, transcription is influenced by methylation: short methylated genes are poorly expressed, and loss of methylation in the body of a gene leads to enhanced transcription. Our results indicate that genic transcription and DNA methylation are closely interwoven processes.
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We thank J. Penterman (University of California Berkeley) for providing genomic DNA, R.L. Fischer (University of California Berkeley) for met1-6 seeds, M.E. Figueroa and J. Greally for help with the linear amplification protocol, T.D. Bryson for technical assistance and P. Talbert for comments on the manuscript. D.Z. is a Leukemia and Lymphoma Society Fellow. M.G. is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation.
The authors declare no competing financial interests.
Bisulfite sequencing analysis of Arabidopsis genes. (PDF 274 kb)
Functional annotation of methylated and unmethylated genes. (PDF 437 kb)
Box plots of genic methylation. (PDF 406 kb)
Relationship between DNA methylation and expression in Arabidopsis. (PDF 1189 kb)
Bisulfite sequencing data, methylated vs. unmethylated gene calls and correlation between methylation in wild-type and expression in met1-6. (XLS 1352 kb)
Average transcription levels and lengths of genes in functional categories. (PDF 12 kb)
Methylated genes are preferentially targeted by siRNAs. (PDF 8 kb)
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Zilberman, D., Gehring, M., Tran, R. et al. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39, 61–69 (2007). https://doi.org/10.1038/ng1929
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