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...

Autosomal dominant polycystic kidney disease (ADPKD) is a common human genetic disease characterized by the formation of multiple fluid-filled cysts in bilateral kidneys. Although mutations in polycystic kidney disease 1 (PKD1) are predominantly responsible for ADPKD, the focal and sporadic property of individual cystogenesis suggests another molecular mechanism such as epigenetic alterations. To determine the epigenomic alterations in ADPKD and their functional relevance, ADPKD and non-ADPKD individuals were analyzed by unbiased methylation profiling genome-wide and compared with their expression data. Intriguingly, PKD1 and other genes related to ion transport and cell adhesion were hypermethylated in gene-body regions, and their expressions were downregulated in ADPKD, implicating epigenetic silencing as the key mechanism underlying cystogenesis. Especially, in patients with ADPKD, PKD1 was hypermethylated in gene-body region and it was associated with recruitment of methyl-CpG-binding domain 2 proteins. Moreover, treatment with DNA methylation inhibitors retarded cyst formation of Madin-Darby Canine Kidney cells, accompanied with the upregulation of Pkd1 expression. These results are consistent with previous studies that knock-down of PKD1 was sufficient for cystogenesis. Therefore, our results reveal a critical role for hypermethylation of PKD1 and cystogenesis-related regulatory genes in cyst development, suggesting epigenetic therapy as a potential treatment for ADPKD.

BackgroundEpigenetic alteration of gene expression is a common event in human cancer. DNA methylation is a well-known epigenetic process, but verifying the exact nature of epigenetic changes associated with cancer remains difficult.MethodsWe profiled the methylome of human gastric cancer tissue at 50-bp resolution using a methylated DNA enrichment technique (methylated CpG island recovery assay) in combination with a genome analyzer and a new normalization algorithm.ResultsWe were able to gain a comprehensive view of promoters with various CpG densities, including CpG Islands (CGIs), transcript bodies, and various repeat classes. We found that gastric cancer was associated with hypermethylation of 5' CGIs and the 5'-end of coding exons as well as hypomethylation of repeat elements, such as short interspersed nuclear elements and the composite element SVA. Hypermethylation of 5' CGIs was significantly correlated with downregulation of associated genes, such as those in the HOX and histone gene families. We also discovered long-range epigenetic silencing (LRES) regions in gastric cancer tissue and identified several hypermethylated genes (MDM2, DYRK2, and LYZ) within these regions. The methylation status of CGIs and gene annotation elements in metastatic lymph nodes was intermediate between normal and cancerous tissue, indicating that methylation of specific genes is gradually increased in cancerous tissue.ConclusionsOur findings will provide valuable data for future analysis of CpG methylation patterns, useful markers for the diagnosis of stomach cancer, as well as a new analysis method for clinical epigenomics investigations.

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