Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells

Abstract

Cytosine methylation is required for mammalian development and is often perturbed in human cancer. To determine how this epigenetic modification is distributed in the genomes of primary and transformed cells, we used an immunocapturing approach followed by DNA microarray analysis to generate methylation profiles of all human chromosomes at 80-kb resolution and for a large set of CpG islands. In primary cells we identified broad genomic regions of differential methylation with higher levels in gene-rich neighborhoods. Female and male cells had indistinguishable profiles for autosomes but differences on the X chromosome. The inactive X chromosome (Xi) was hypermethylated at only a subset of gene-rich regions and, unexpectedly, overall hypomethylated relative to its active counterpart. The chromosomal methylation profile of transformed cells was similar to that of primary cells. Nevertheless, we detected large genomic segments with hypomethylation in the transformed cell residing in gene-poor areas. Furthermore, analysis of 6,000 CpG islands showed that only a small set of promoters was methylated differentially, suggesting that aberrant methylation of CpG island promoters in malignancy might be less frequent than previously hypothesized.

Surveying the epigenomic landscape, one base at a time

“…Many methods have been put forth with which to probe various aspects of the epigenome (Table 1), but until recently, the resolution of genome-wide methods for epigenome characterization, such as ChIP-chip [8] and MeDIP [9], was on the order of hundreds of base pairs, with the use of hybridization-based read-out technologies and chromatin preparation protocols based on random fragmentation. However, with the advent of massively parallel short-read DNA sequencing and its potential for single base-pair resolution, there has been a renaissance of interest in traditional methods for chromatin characterization, including the use of bisulfite sequencing for mapping DNA methylation [10] and the use of non-specific nucleases, including micrococcal nuclease (MNase) [11], deoxyribonuclease I (DNase I) [12] and exonuclease [13] (Table 1).…”

DNA Methyltransferase 1–Dependent DNA Hypermethylation Constrains Arteriogenesis by Augmenting Shear Stress Set Point

“…DNA is methylated at a cysteine base pair, most often at a CpG dinucleotide (CpG site) 9. Methylation of CpG sites in the promoter region of a gene is commonly associated with repression of gene expression 10, 11, 12. DNA methylation occurs through the activity of DNA methyltransferases (DNMTs), particularly DNMT1 postdevelopment 13, 14, 15.…”

Profils de méthylation de l’ADN dans les cellules normales et cancéreuses

“…C'est pourquoi de nombreux groupes ont tenté de développer de nouvelles méthodes d'analyse à grande échelle. Parmi ces méthodes, nous avons développé MeDIP (methylated DNA immunoprecipitation) dont le principe est que l'ADN est fragmenté par sonication puis immunopré-cipité avec un anticorps qui reconnaît la 5-méthylcytidine [5]. Cette fraction méthylée peut ensuite être hybridée sur n'importe quel type de microarray ( Figure 1A).…”

“…En accord avec les premières études effectuées sur certains locus, il a été montré que la majorité de la méthylation se trouve dans les régions codantes (exons, introns), intergéniques et les éléments répétés [5,7]. La méthylation de l'ADN y joue un rôle de protection de l'intégrité du génome en inhibant l'activation d'éléments mobiles et en maintenant la stabilité du génome.…”

“…Par ailleurs, les cellules cancéreuses présentent des changements de méthylation à plus grande échelle. En comparant les profils de méthylation dans des lignées de cancer du côlon et des cellules non transformées, nous avons identifié des régions de plusieurs méga-bases hypométhylées dans les cellules cancéreuses [5]. De telles régions hypométhylées ont aussi été récemment observées dans les cellules de cancer du sein [14].…”