Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming.

ABSTRACT: Hepatocellular carcinomas (HCC) exhibit distinct promoter hypermethylation patterns, but the epigenetic regulation and function of transcriptional enhancers remain unclear. Here, our affinity- and bisulfite-based whole-genome sequencing analyses reveal global enhancer hypomethylation in human HCCs. Integrative epigenomic characterization further pinpoints a recurrent hypomethylated enhancer of CCAAT/enhancer-binding protein-beta (C/EBP?) which correlates with C/EBP? over-expression and poorer prognosis of patients. Demethylation of C/EBP? enhancer reactivates a self-reinforcing enhancer-target loop via direct transcriptional up-regulation of enhancer RNA. Conversely, deletion of this enhancer via CRISPR/Cas9 reduces C/EBP? expression and its genome-wide co-occupancy with BRD4 at H3K27ac-marked enhancers and super-enhancers, leading to drastic suppression of driver oncogenes and HCC tumorigenicity. Hepatitis B X protein transgenic mouse model of HCC recapitulates this paradigm, as C/ebp? enhancer hypomethylation associates with oncogenic activation in early tumorigenesis. These results support a causal link between aberrant enhancer hypomethylation and C/EBP? over-expression, thereby contributing to hepatocarcinogenesis through global transcriptional reprogramming.

SUBMITTER: Xiong L 

PROVIDER: S-EPMC6338783 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature