title: Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer.
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.
authors.affiliation: Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea.|Genomic Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
authors.forename: Su-Jin
authors.initials: SJ
authors.lastname: Baek
authors.affiliation: Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea.|Epigenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
authors.forename: Mirang
authors.initials: M
authors.lastname: Kim
authors.affiliation: Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea.|Epigenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
authors.forename: Dong-Hyuck
authors.initials: DH
authors.lastname: Bae
authors.affiliation: Epigenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
authors.forename: Jeong-Hwan
authors.initials: JH
authors.lastname: Kim
authors.affiliation: Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea.|Epigenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
authors.forename: Hee-Jin
authors.initials: HJ
authors.lastname: Kim
authors.affiliation: Departments of Anatomy and Surgery, School of Medicine, Pusan National University, Busan, Republic of Korea.
authors.forename: Myoung-Eun
authors.initials: ME
authors.lastname: Han
authors.affiliation: Departments of Anatomy and Surgery, School of Medicine, Pusan National University, Busan, Republic of Korea.
authors.forename: Sae-Ock
authors.initials: SO
authors.lastname: Oh
authors.affiliation: Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea.|Epigenome Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
authors.forename: Yong Sung
authors.initials: YS
authors.lastname: Kim
authors.affiliation: Department of Functional Genomics, University of Science and Technology, Daejeon, Republic of Korea.|Genomic Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
authors.forename: Seon-Young
authors.initials: SY
authors.lastname: Kim
mesh_terms: D019175:DNA Methylation / Q000235:genetics*; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D057890:Epigenomics; D006801:Humans; D011401:Promoter Regions, Genetic / Q000235:genetics*; D013274:Stomach Neoplasms / Q000235:genetics*
keywords: DNA methylation; enhancer; gastric cancer; lncRNAs; promoter