Access

Article

Nature Genetics 38, 1378–1385 (1 December 2006) | doi:10.1038/ng1909

DNA methylation profiling of human chromosomes 6, 20 and 22

Florian Eckhardt , Joern Lewin , Rene Cortese , Vardhman K Rakyan , John Attwood , Matthias Burger , John Burton , Tony V Cox , Rob Davies , Thomas A Down , Carolina Haefliger , Roger Horton , Kevin Howe , David K Jackson , Jan Kunde , Christoph Koenig , Jennifer Liddle , David Niblett , Thomas Otto , Roger Pettett , Stefanie Seemann , Christian Thompson , Tony West , Jane Rogers , Alex Olek , Kurt Berlin & Stephan Beck

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|[prime]| UTRs and that about one-third of the differentially methylated 5|[prime]| 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.