The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Relationship between nucleosome positioning and DNA methylation
Open accessAbstract
Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana using massively parallel sequencing of mononucleosomes. By combining this data with profiles of DNA methylation at single base resolution, we identified 10-base periodicities in the DNA methylation status of nucleosome-bound DNA and found that nucleosomal DNA was more highly methylated than flanking DNA. These results indicate that nucleosome positioning influences DNA methylation patterning throughout the genome and that DNA methyltransferases preferentially target nucleosome-bound DNA. We also observed similar trends in human nucleosomal DNA, indicating that the relationships between nucleosomes and DNA methyltransferases are conserved. Finally, as has been observed in animals, nucleosomes were highly enriched on exons, and preferentially positioned at intron–exon and exon–intron boundaries. RNA polymerase II (Pol II) was also enriched on exons relative to introns, consistent with the hypothesis that nucleosome positioning regulates Pol II processivity. DNA methylation is also enriched on exons, consistent with the targeting of DNA methylation to nucleosomes, and suggesting a role for DNA methylation in exon definition.
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Cites
Conservation and divergence of methylation patterning in plants and animals
Feng, S., Cokus, S. J., Zhang, X., Chen, P.-Y., Bostick, M., Goll, M. G., Hetzel, J., Jain, J., Strauss, S. H., Halpern, M. E., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1002720107 · Cited by 1,285
Self-citationWhole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis
Zhang, X., Clarenz, O., Cokus, S., Bernatavichute, Y. V., Pellegrini, M., Goodrich, J., & Jacobsen, S. E. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050129 · Cited by 767
Self-citationChromatin organization marks exon-intron structure
Schwartz, S., Meshorer, E., & Ast, G. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1659 · Cited by 638
Cited by
Functions of DNA methylation: islands, start sites, gene bodies and beyond
Jones, P. A. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3230 · Cited by 6,061
Function and information content of DNA methylation
Schübeler, D. (2015) · Nature · doi:10.1038/nature14192 · Cited by 2,060
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
Shukla, S., Kavak, E., Gregory, M., Imashimizu, M., Shutinoski, B., Kashlev, M., Oberdoerffer, P., Sandberg, R., & Oberdoerffer, S. (2011) · Nature · doi:10.1038/nature10442 · Cited by 973
Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain
Guo, J. U., Su, Y., Shin, J. H., Shin, J., Li, H., Xie, B., Zhong, C., Hu, S., Le, T., Fan, G., et al. (2014) · Nature Neuroscience · doi:10.1038/nn.3607 · Cited by 714
Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants
Schmitz, R. J., Schultz, M. D., Lewsey, M. G., O’Malley, R. C., Urich, M. A., Libiger, O., Schork, N. J., & Ecker, J. R. (2011) · Science · doi:10.1126/science.1212959 · Cited by 698
Metadata
- Authors
- Chodavarapu, R. K., Feng, S., Bernatavichute, Y. V., Chen, P.-Y., Stroud, H., Yu, Y., Hetzel, J. A., Kuo, F., Kim, J., Cokus, S. J., Casero, D., Bernal, M., Huijser, P., Clark, A. T., Krämer, U., Merchant, S. S., Zhang, X., Jacobsen, S. E., & Pellegrini, M.
- Venue
- Nature
- Published
- 2010-05-30
- Volume
- 466
- Issue
- 7304
- Pages
- 388-392
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2077562677
- Cited by
- 696
- References
- 3
- FWCI
- 32.49
- Type
- journal article
- Language
- en
- Open access
- green
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- Chodavarapu, R. K., Feng, S., Bernatavichute, Y. V., Chen, P.-Y., Stroud, H., Yu, Y., Hetzel, J. A., Kuo, F., Kim, J., Cokus, S. J., Casero, D., Bernal, M., Huijser, P., Clark, A. T., Krämer, U., Merchant, S. S., Zhang, X., Jacobsen, S. E., & Pellegrini, M. (2010). Relationship between nucleosome positioning and DNA methylation. Nature. https://doi.org/10.1038/nature09147
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