The genomic landscape of DNA methylation across human tissues and colon cancer.

摘要

DNA methylation (DNAm) is a heritable modification of DNA, occurring at CpG dinucleotides in mammals, central to numerous cellular processes including imprinting, regulation of transcription, and genomic stability. While a great deal is known about DNAm and its disregulation in human disease at the single gene level, relatively little is known at the genomic level, mainly because of limitations in technology.;The development of the Illumina GoldenGate methylation platform enabled examination of DNAm beyond single genes by measuring 1,505 CpG sites in 807 genes. Illumina analysis of human cerebrum, cerebellum, and pons tissues, revealed DNAm signatures clearly distinguish the three brain regions from one another. We identified statistically significant differences in DNAm ( P 0.004) at 156 loci, with 58% being located outside of CpG islands (CGI). Thus, genomic patterns of DNAm may contribute to functional specialization and may occur outside of CGIs.;Comprehensive analysis of the methylome requires a highly sensitive and quantitative method capable of measuring a much larger number of CpG sites than is possible on the Illumina platform. Thus, we compared the specificity of three high-throughput microarray approaches: (1) MeDIP; (2) the HELP assay; and (3) McrBC fractionation. We found substantial limitations for each including genomic coverage, fragment size, and CpG density biases. Therefore, we developed a new approach, termed C&barbelow;omprehensive H&barbelow;igh-throughput A&barbelow;rrays for R&barbelow;elative M&barbelow;ethylation (CHARM); it is highly quantitative, sensitive, and is not restricted to CpG-dense regions of the genome. Thus, CHARM offers substantial advantages to the study of human disease.;Most studies of cancer focus on CpG-dense CGIs and gene promoters, however, we used CHARM to examine the colon cancer methylome. Surprisingly, CHARM analysis revealed: (1) 67% of altered DNAm in cancer does not occur in promoters or CGIs but occurs up to 2 kb distant, termed "CpG island shores"; (2) methylation at CGI shores is highly conserved and associated with transcription; (3) most aberrant DNAm in cancer is located where DNAm normally distinguishes tissues from one another. These findings provide new diagnostic and therapeutic targets for cancer and support including lower CpG density regions in future studies of human disease.