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Published online May 7, 2007
doi:10.1083/jcb.200607133
The Journal of Cell Biology, Vol. 177, No. 3, 401-411
The Rockefeller University Press, 0021-9525 $30.00
© 2007 Gilbert et al.
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Article

DNA methylation affects nuclear organization, histone modifications, and linker histone binding but not chromatin compaction



Nick Gilbert1,2, Inga Thomson1, Shelagh Boyle1, James Allan3, Bernard Ramsahoye2, and Wendy A. Bickmore1

1 Medical Research Council Human Genetics Unit, Edinburgh EH4 2XU, Scotland, UK
2 The University of Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh EH4 2XR, Scotland, UK
3 Institute of Structural and Molecular Biology, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK

Correspondence to Wendy A. Bickmore: W.Bickmore{at}hgu.mrc.ac.uk

DNA methylation has been implicated in chromatin condensation and nuclear organization, especially at sites of constitutive heterochromatin. How this is mediated has not been clear. In this study, using mutant mouse embryonic stem cells completely lacking in DNA methylation, we show that DNA methylation affects nuclear organization and nucleosome structure but not chromatin compaction. In the absence of DNA methylation, there is increased nuclear clustering of pericentric heterochromatin and extensive changes in primary chromatin structure. Global levels of histone H3 methylation and acetylation are altered, and there is a decrease in the mobility of linker histones. However, the compaction of both bulk chromatin and heterochromatin, as assayed by nuclease digestion and sucrose gradient sedimentation, is unaltered by the loss of DNA methylation. This study shows how the complete loss of a major epigenetic mark can have an impact on unexpected levels of chromatin structure and nuclear organization and provides evidence for a novel link between DNA methylation and linker histones in the regulation of chromatin structure.

Abbreviations used in this paper: ChIP, chromatin immunoprecipitation; ES, embryonic stem; EtBr, ethidium bromide; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; Mnase, micrococcal nuclease; ROI, region of interest; WT, wild type.


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