Epigenetic alterations caused by viral oncoproteins are strong initiation factors for cancer development, but their mechanisms are largely unknown. To identify the epigenetic effects of viral hepatitis B virus X (HBx) that lead to hepatocellular carcinoma (HCC), we profiled the DNA methylomes of normal and HBx transgenic mouse liver. Intriguingly, severe hypomethylation of intragenic CpG islands (CGIs) was observed in HBx liver before the full development of HCC. Normally, these CGIs were highly methylated (mCGIs) by the DNMT3L complex and marked with epigenetic signatures associated with active expression, such as H3K36me3. Hypomethylation of mCGI was caused by the downregulation of Dnmt3L and Dnmt3a due to HBx bound to their promoters, along with HDAC1. These events lead to the downregulation of many developmental regulators that could facilitate tumorigenesis. Here we provide an intriguing epigenetic regulation mediated by mCGI that is required for cell differentiation and describe a previously unidentified epigenetic role for HBx in promoting HCC development.DNA methylation | methylated CpG island | viral protein H epatocellular carcinoma (HCC) is one of the most dangerous cancers that threaten many people, especially those with hepatitis B or C virus (HBV or HCV) (1-3). However, the exact mechanisms underlying HCC are not clear because there are multiple factors, including chronic inflammation (4), genetic alteration caused by viral integration into the host genome (5), and the oncogenic actions of viral proteins (6). Although many studies have previously demonstrated that these factors, alone or in combination with other factors, are able to initiate tumorigenesis (1), the oncogenic potential of viral protein in cancer development is one of the most interesting exogenic factors that facilitates tumorigenesis, in particular, through the epigenetic regulation of infected cells (7).Epigenetic alterations in cancer cells are now regarded as one of the most important factors driving cancer initiation. Abnormal DNA methylation is the most frequently found change in many cancers and is believed to control associated gene expression without altering the DNA sequence itself (8). The transcriptional silencing of tumor suppressor genes associated with the hypermethylation of promoter regions is a typical epigenetic change in many cancers (9). The DNA hypomethylation in repeat sequences and transposable elements is known to induce chromosomal instability and mutation events (10) that lead to cancer development and progression (11). In addition, various types of cancer cells exhibit abnormal expression levels of DNA methyltransferase (DNMT) families, which probably causes global changes in DNA methylation (12).In mammalian cells, large clusters of CpG dinucleotides known as CpG islands (CGIs) appear to act as a key epigenetic element regulating gene expression. Most CGIs are found at the 5′ end of transcripts and behave as functional promoters (13).Some unmethylated intragenic and intergenic CGIs contain distinct epige...