Research Papers:

Genome-wide methylome and chromatin interactome identify abnormal enhancer to be risk factor of breast cancer

Yuan Wang, Da-Peng Hao, Jing-Jing Li, Li Wang and Li-Jun Di _

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Oncotarget. 2017; 8:44705-44719. https://doi.org/10.18632/oncotarget.18348

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Yuan Wang1, Da-Peng Hao1, Jing-Jing Li1, Li Wang2 and Li-Jun Di1

1Cancer Center, Faculty of Health Sciences, University of Macau, Macau, China

2Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau, China

Correspondence to:

Li-Jun Di, email: [email protected]

Keywords: enhancer methylation, breast cancer, chromatin interaction, polII ChIA-PET, gene regulation

Received: April 09, 2017     Accepted: May 15, 2017     Published: June 02, 2017


Enhancer is critical cis regulatory elements in gene expression. To understand whether and how the aberrant enhancer activation may contribute to cancer risk, the differentially methylated enhancers (eDMRs) in normal and malignant breast tissues were identified and analyzed. By incorporating genome-wide chromatin interaction, integrated analysis of eDMRs and target gene expression identified 1,272 enhancer-promoter pairs. Surprisingly, two functionally distinct groups of genes were identified in these pairs, one showing better correlation to enhancer methylation (eRGs) and the other showing better correlation to promoter methylation (pRGs), and the former group is functionally enriched with cancer related genes. Moreover, enhancer methylation based clustering of breast cancer samples is capable of discriminating basal breast cancer from other subtypes. By correlating enhancer methylation status to patient survival, 345 enhancers show the impact on the disease outcome and the majority of their target genes are important regulators of cell survival pathways including known cancer related genes. Together, these results suggest reactivation of enhancers in cancer cells has the add-on effect and contributes to cancer risk in combination.

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PII: 18348