Tissue-specific variation in DNA methylation levels along human chromosome 1. Homo sapiens

DNA methylation is a major epigenetic modification important for regulating gene expression and suppressing spurious transcription. Most methods to scan the genome in different tissues for differentially methylated sites have focused on the methylation of CpGs in CpG islands, which are concentrations of CpGs often associated with gene promoters. Here, we use a methylation-profiling strategy that is predominantly responsive to methylation differences outside of CpG islands. The method compares the yield from two samples of size-selected fragments generated by a methylation-sensitive restriction enzyme. We profile eight different normal tissues relative to spleen for each of two human donors using a custom array of genomic clones covering the euchromatic portion of human chromosome 1 and representing 8% of the human genome. We observe gross regional differences in methylation states across chromosome 1 between tissues from the same individual, with the most striking differences detected in the comparison of cerebellum and spleen. Profiles of the same tissue from different donors are strikingly similar, as are the profiles of different lobes of the brain. Using DNMT1-deficient cells as a test case, we show that much finer-scale fluctuations in relative fragment yield can be detected when the methylation profiling is performed using a high-resolution oligomer array for chromosome 1. The varied patterns of methylation differences detected between tissues by this method reinforce the potential functional significance of regional differences in methylation levels outside of CpG islands. Overall design: DNA digested with methylation-sensitive restriction enzyme (HpaII) and size-selected. Eleven human tissue types studied, most from two human individuals, each in triplicate, and one cell line. Two control hybrizations consisting of DNA prepared independently from the same tissue.