Oncotarget

Research Papers:

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

Su-Jin Baek _, Mirang Kim, Dong-Hyuck Bae, Jeong-Hwan Kim, Hee-Jin Kim, Myoung-Eun Han, Sae-Ock Oh, Yong Sung Kim and Seon-Young Kim

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Oncotarget. 2016; 7:25620-25631. https://doi.org/10.18632/oncotarget.8239

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Abstract

Su-Jin Baek1,2, Mirang Kim1,3, Dong-Hyuck Bae1,3, Jeong-Hwan Kim3, Hee-Jin Kim1,3, Myoung-Eun Han4, Sae-Ock Oh4, Yong Sung Kim1,3, Seon-Young Kim1,2

1Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea

2Genomic Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea

3Epigenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea

4Departments of Anatomy and Surgery, School of Medicine, Pusan National University, Busan, Republic of Korea

Correspondence to:

Seon-Young Kim, email: [email protected]

Keywords: gastric cancer, DNA methylation, enhancer, promoter, lncRNAs

Received: December 02, 2015     Accepted: March 10, 2016     Published: March 21, 2016

ABSTRACT

Abnormal DNA methylation is an epigenetic mechanism that promotes gastric carcinogenesis. While the abnormal methylation at promoter regions has been characterized for many genes, the function of DNA methylation marks at distal regulatory regions in gastric cancer remains poorly described. Here, we performed RNA-seq, MBD-seq, and H3K27ac ChIP-seq on gastric tissues and cell lines to understand the epigenetic changes in the distal as well as the proximal regulatory regions. In total, 257,651 significant DMRs (Differentially methylated regions) were identified in gastric cancer, and the majority of these DMRs were located in the intergenic, intronic, and non-coding RNA regions. We identified the aberrant expression of many genes and lncRNAs due to changes in DNA methylation. Furthermore, we profiled the molecular subtype-specific methylation patterns in gastric cancer to characterize subtype-specific regulators that undergo DNA methylation changes. Our findings provide insights for understanding methylation changes at distal regulatory regions and reveal novel epigenetic targets in gastric cancer.


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