Open AccessIntegrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer
Author(s) -
SuJin Baek,
Mirang Kim,
Donghyuck Bae,
JeongHwan Kim,
HeeJin Kim,
MyoungEun Han,
SaeOck Oh,
YongSung Kim,
SeonYoung Kim
Publication year - 2016
Publication title -
oncotarget
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.373
H-Index - 127
ISSN - 1949-2553
DOI - 10.18632/oncotarget.8239
Subject(s) - dna methylation , epigenetics , epigenomics , carcinogenesis , epigenome , cancer , methylation , biology , cancer research , cpg site , promoter , enhancer , genetics , gene , gene expression
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.