Hypoxia is a microenvironmental pathophysiologic factor commonly associated with tumors and tissue inflammation. We previously reported that hypoxia repressed IL-1 beta-induced monocyte chemoattractant protein-1 (MCP-1) expression. The purpose of this study was to investigate the mechanisms involved in the repression of MCP-1 expression under hypoxia. Treatment of HeLa cells with 5-aza-dC, an inhibitor of DNA methylation, abolished the repression of IL-1 beta-induced MCP-1 expression by hypoxia. A detailed study of the methylation of CpGs sites using bisulfite-sequencing PCR and 5-methylcytosine immunoprecipitation showed that hypoxia induced DNA methylation in both the enhancer and promoter regions of MCP-1in IL-1 beta-treated cells. Next, we analyzed histone methylation within the MCP-1 promoter and enhancer regions. The level of H3K9 di-methylation, a mark of gene repression, in both promoter and enhancer regions was increased by hypoxia in IL-1 beta-treated cells. Our findings suggest that changes in the methylation status of CpGs, as well as histone 3 methylation, may represent a critical event in transcriptional repression of IL-1 beta-induced MCP-1 expression by hypoxia. Therefore, DNA methylation is associated with not only epigenetic gene silencing, but also with transient transcriptional repression. (C) 2011 Elsevier Inc. All rights reserved.