Nature Genetics
- 38, 1378 - 1385 (2006)
Published online: 29 October 2006; | doi:10.1038/ng1909
DNA methylation profiling of human chromosomes 6, 20 and 22Florian Eckhardt1, Joern Lewin1, Rene Cortese1, Vardhman K Rakyan2, John Attwood2, Matthias Burger1, John Burton2, Tony V Cox2, Rob Davies2, Thomas A Down2, Carolina Haefliger1, Roger Horton2, Kevin Howe2, David K Jackson2, Jan Kunde1, 3, Christoph Koenig1, Jennifer Liddle2, David Niblett2, Thomas Otto1, Roger Pettett2, Stefanie Seemann1, Christian Thompson1, Tony West2, Jane Rogers2, Alex Olek1, Kurt Berlin1 & Stephan Beck21
Epigenomics AG, Kleine Präsidentstrasse 1, 10178 Berlin, Germany. 2
Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK. 3
Present address: Schering AG, Müllerstr. 178, 13342 Berlin, Germany.
Correspondence should be addressed to Florian Eckhardt florian.eckhardt@epigenomics.com or Stephan Beck beck@sanger.ac.uk DNA methylation is the most stable type of epigenetic modification modulating the transcriptional plasticity of mammalian genomes. Using bisulfite DNA sequencing, we report high-resolution methylation profiles of human chromosomes 6, 20 and 22, providing a resource of about 1.9 million CpG methylation values derived from 12 different tissues. Analysis of six annotation categories showed that evolutionarily conserved regions are the predominant sites for differential DNA methylation and that a core region surrounding the transcriptional start site is an informative surrogate for promoter methylation. We find that 17% of the 873 analyzed genes are differentially methylated in their 5' UTRs and that about one-third of the differentially methylated 5' UTRs are inversely correlated with transcription. Despite the fact that our study controlled for factors reported to affect DNA methylation such as sex and age, we did not find any significant attributable effects. Our data suggest DNA methylation to be ontogenetically more stable than previously thought.
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