DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes

Dvir Aran, Sivan Sabato, Asaf Hellman*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

247 Scopus citations


Background: Abnormal epigenetic marking is well documented in gene promoters of cancer cells, but the study of distal regulatory siteshas lagged behind.We performed a systematic analysis of DNA methylation sites connected with gene expression profilesacross normal and cancerous human genomes. Results: Utilizing methylation and expression data in 58 cell types, we developed a model for methylationexpression relationships in gene promoters and extrapolated it to the genome. We mapped numerous sites at which DNA methylation was associated with expression of distal genes. These sites bind transcription factors in a methylation-dependent manner, and carry the chromatin marks of a particular class of transcriptional enhancers. In contrast to the traditional model of one enhancer site per cell type, we found that single enhancer sites may define gradients of expression levels across many different cell types. Strikingly, the identified sites were drastically altered in cancers: hypomethylated enhancer sites associated with upregulation of cancer-related genes and hypermethylated sites with downregulation. Moreover, the association between enhancer methylation and gene deregulation in cancerwas significantly stronger than the association of promoter methylationwith gene deregulation. Conclusions: Methylation of distal regulatory sites is closely related to gene expression levels across the genome. Single enhancers may modulate ranges of cell-specific transcription levels, from constantlyopen promoters. In contrast to the remote relationships between promoter methylation and gene dysregulation in cancer, altered methylation of enhancer sites is closely related to gene expression profiles of transformed cells.

Original languageAmerican English
Article numberR21
JournalGenome Biology
Issue number3
StatePublished - 12 Mar 2013

Bibliographical note

Funding Information:
We are grateful to Shai Shalev-Shwartz for his helpful advice regarding the development of the machine-learning algorithm. Thanks are also due to Yehudit Bergman, Gadi Glaser, Amir Eden, Benjamin Glaser, Reuven Laskov and Howard Cedar for helpful discussions and comments. This work was supported by the Adams Fellowship Program of the Israel Academy of Sciences and Humanities (to SS), by the I-CORE Program of the Planning and Budgeting Committee and the Israel Science Foundation (Grant No. 41/11 to AH), and by the Israel Science Foundation (Grant No. 887/08to AH).

Publisher Copyright:
© 2013 Aran et al.


  • Cancer
  • DNA methylation
  • Distal control elements
  • Enhancers
  • Epigenomics
  • Gene regulation
  • Gene-enhancer pairing
  • Machine-learning


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