ArticleProceedings of the National Academy of Sciences of the United States of America2003
Strand-biased DNA methylation associated with centromeric regions in Arabidopsis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Homeostasis of DNA Hemi-Methylation in Arabidopsis through Methylation Maintenance, DNA Replication, and Nucleosome Positioning Mechanisms.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Accurate cross-species 5mC detection for Oxford Nanopore sequencing in plants with DeepPlant.Nature communications · 2025Article
- Single-molecule targeted accessibility and methylation sequencing of centromeres, telomeres and rDNAs in Arabidopsis.Nature plants · 2023Article
- Progressive DNA demethylation in epigenetic hybrids between parental plants with and without methylation of the transgene promoter.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Sequence, Chromatin and Evolution of Satellite DNA.International journal of molecular sciences · 2021Review
- Machine learning analyses of methylation profiles uncovers tissue-specific gene expression patterns in wheat.The plant genome · 2020Article
- Molecular Markers Distinguishing T Cell Subtypes With TSDR Strand-Bias Methylation.Frontiers in immunology · 2018Article
- Methylation of microRNA genes regulates gene expression in bisexual flower development in andromonoecious poplar.Journal of experimental botany · 2015Article
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- Genome-wide mapping of DNA methylation in the human malaria parasite Plasmodium falciparum.Cell host & microbe · 2013Article
- Sorting DNA with asymmetry: a new player in gene regulation?Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2013Review
- CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data.Nucleic acids research · 2013Article
- Epigenetic differences between sister chromatids?Annals of the New York Academy of Sciences · 2012Review
- Changes in global gene expression in response to chemical and genetic perturbation of chromatin structure.PloS one · 2011Article
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- Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays.PLoS genetics · 2008Article
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- Permissive transcriptional activity at the centromere through pockets of DNA hypomethylation.PLoS genetics · 2006Article
- Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats.PLoS genetics · 2005Article
- Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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