Strand-biased DNA methylation associated with centromeric regions in Arabidopsis
- Howard Hughes Medical Institute and Department of Molecular Genetics and Cell Biology, University of Chicago, 1103 East 57th Street, Chicago, IL 60637
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Edited by Elliot M. Meyerowitz, California Institute of Technology, Pasadena, CA (received for review February 17, 2003)
Abstract
The Arabidopsis genome project assembled 15 megabases of heterochromatic sequence, facilitating investigations of heterochromatin assembly, maintenance, and structure. In many species, large quantities of methylcytosine decorate heterochromatin; these modifications are typically maintained by methyltransferases that recognize newly replicated hemimethylated DNA. We assessed the extent and patterns of Arabidopsis heterochromatin methylation by amplifying and sequencing genomic DNA treated with bisulfite, which converts cytosine, but not methylcytosine, to uracil. This survey revealed unexpected asymmetries in methylation patterns, with one helix strand often exhibiting higher levels of methylation. We confirmed these observations both by immunoprecipitating methylated DNA strands and by restriction enzyme digestion of amplified, bisulfite-treated DNA. We also developed a primer-extension assay that can monitor the methylation status of an entire chromosome, demonstrating that strand-specific methylation occurs predominantly in the centromeric regions. Conventional models for methylation maintenance do not explain these unusual patterns; instead, new models that allow for strand specificity are required. The abundance of Arabidopsis strand-specific modifications points to their importance, perhaps as epigenetic signals that mark the heterochromatic regions that confer centromere activity.
Footnotes
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↵ * To whom correspondence should be addressed. E-mail: dpreuss{at}midway.uchicago.edu.
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This paper was submitted directly (Track II) to the PNAS office.
- Copyright © 2003, The National Academy of Sciences
