Aberrant de novo methylation of the p16INK4A CpG island is initiated post gene silencing in association with chromatin remodeling and mimics nucleosome positioning

Cancer Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia.
Human Molecular Genetics (Impact Factor: 6.39). 06/2009; 18(16):3098-109. DOI: 10.1093/hmg/ddp251
Source: PubMed


Changes in the epigenetic landscape are widespread in neoplasia, with de novo methylation and histone repressive marks commonly enriched in CpG island associated promoter regions. DNA hypermethylation
and histone repression correlate with gene silencing, however, the dynamics of this process are still largely unclear. The
tumour suppressor gene p16INK4A is inactivated in association with CpG island methylation during neoplastic progression in a variety of cancers, including
breast cancer. Here, we investigated the temporal progression of DNA methylation and histone remodelling in the p16INK4A CpG island in primary human mammary epithelial cell (HMEC) strains during selection, as a model for early breast cancer.
Silencing of p16INK4A has been previously shown to be necessary before HMECs can escape from selection. Here, we demonstrate that gene silencing
occurs prior to de novo methylation and histone remodelling. An increase in DNA methylation was associated with a rapid loss of both histone H3K27
trimethylation and H3K9 acetylation and a gradual gain of H3K9 dimethylation. Interestingly, we found that regional-specific
‘seeding’ methylation occurs early after post-selection and that the de novo methylation pattern observed in HMECs correlates with the apparent footprint of nucleosomes across the p16INK4A CpG island. Our results demonstrate for the first time that p16INK4A gene silencing is a precursor to epigenetic suppression and that subsequent de novo methylation initially occurs in nucleosome-free regions across the p16INK4A CpG island and this is associated with a dynamic change in histone modifications.

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Available from: Sue Clark, Jan 06, 2016
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    • "Aberrant p16 methylation is an early event in carcinogenesis and has been shown to significantly increase the risk of malignant transformation of epithelial dysplasia in the stomach, oral cavity and other organs in many studies [15]–[17]. Although p16 methylation is one of the well-studied epigenetic events [18]–[20], most of studies employed in vitro cell culture system. The methylation is not often detectable in tissue samples, especially in the radiation-induced carcinogenesis. "
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    ABSTRACT: DNA methylation is an important part of epigenetics. In this study, we examined the methylation state of two CpG islands in the promoter of the p16 gene in radiation-induced thymic lymphoma samples. The mRNA and protein levels of P16 were significantly reduced in radiation-induced thymic lymphoma tissue samples. Twenty-three CpG sites of the CpG islands in the p16 promoter region were detected, and the methylation percentages of -71, -63, -239, -29, -38, -40, -23, 46 CpG sites were significantly higher in radiation-induced thymic lymphoma tissue samples than those in matched non-irradiated thymus tissue samples. This study provides new evidence for the methylation state of p16 in the radiation-induced thymic lymphoma samples, which suggests that the methylation of these CpG sites in the p16 promoter may reduce its expression in the thymic lymphoma after irradiation.
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    • "More recently, opposing functional histone methylation, catalysed by MLL1 and DDB1-CUL4 complex for H3 lysine 4 trimethylation (H3K4me3) and Polycomb complex for H3 lysine 27 trimethylation (H3K27me3), was reported to mark transcriptional activation or repression of p16 INK4a , respectively (Itahana et al, 2003; Bracken et al, 2007; Dietrich et al, 2007; Agherbi et al, 2009). In addition, histone positioning at p16 INK4a promoter was demonstrated to be differentially associated with its transcriptional outcome (Fatemi et al, 2005; Hinshelwood et al, 2009), suggesting that chromatin remodelling would actively participate in senescence progress through de-condensation of p16 INK4a promoter. Mammalian FOXA1, as a member of TF family characterized by B100 amino acid Forkhead DNA-binding domain (DBD), is implicated in endodermic and reproductive organogenesis of liver, pancreas, lung, prostate, and mammary gland ( "
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    ABSTRACT: Mechanisms governing the transcription of p16(INK4a), one of the master regulators of cellular senescence, have been extensively studied. However, little is known about chromatin dynamics taking place at its promoter and distal enhancer. Here, we report that Forkhead box A1 protein (FOXA1) is significantly upregulated in both replicative and oncogene-induced senescence, and in turn activates transcription of p16(INK4a) through multiple mechanisms. In addition to acting as a classic sequence-specific transcriptional activator, FOXA1 binding leads to a decrease in nucleosome density at the p16(INK4a) promoter in senescent fibroblasts. Moreover, FOXA1, itself a direct target of Polycomb-mediated repression, antagonizes Polycomb function at the p16(INK4a) locus. Finally, a systematic survey of putative FOXA1 binding sites in the p16(INK4a) genomic region revealed an ∼150 kb distal element that could loop back to the promoter and potentiate p16(INK4a) expression. Overall, our findings establish several mechanisms by which FOXA1 controls p16(INK4a) expression during cellular senescence.
    Full-text · Article · Feb 2013 · The EMBO Journal
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    • "Nucleosome positioning is tightly controlled and maintained in cells by several factors, including DNA sequence, ATP-dependent chromatin remodelers and nucleosome modifications (8,9). In cancer, significant changes in nucleosome positioning result in aberrant compaction of chromatin structure and, hence, altered gene expression signatures (10,11). This can often be explained by malfunctioning of chromatin remodeling complexes, such as the SWI/SNF (SWItch/Sucrose NonFermentable) complex, which are frequently found to be mutated in cancer (4,5,8,12). "
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    ABSTRACT: DNA methylation inhibitors such as 5-aza-2'-deoxycytidine (5-Aza-CdR) are currently used for the treatment of myelodysplastic syndrome. Although global DNA demethylation has been observed after treatment, it is unclear to what extent demethylation induces changes in nucleosome occupancy, a key determinant of gene expression. We use the colorectal cancer cell line HCT116 as a model to address this question and determine that <2% of regions demethylated by 5-Aza-CdR treatment assume an open configuration. Consolidating our findings, we detect nucleosome retention at sites of global DNA methylation loss in DKO1, an HCT116-derived non-tumorigenic cell-line engineered for DNA methyltransferase disruption. Notably, regions that are open in both HCT116 cells after treatment and in DKO1 cells include promoters belonging to tumor suppressors and genes under-expressed in colorectal cancers. Our results indicate that only a minority of demethylated promoters are associated with nucleosome remodeling, and these could potentially be the epigenetic drivers causing the loss of tumorigenicity. Furthermore, we show that the chromatin opening induced by the histone deacetylase inhibitor suberoylanilide hydroxamic acid has strikingly distinct targets compared with those of 5-Aza-CdR, providing a mechanistic explanation for the importance of combinatorial therapy in eliciting maximal de-repression of the cancer epigenome.
    Full-text · Article · Feb 2013 · Nucleic Acids Research
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