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

Cancer Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia.
Human Molecular Genetics (Impact Factor: 6.68). 06/2009; 18(16):3098-109. DOI: 10.1093/hmg/ddp251
Source: PubMed

ABSTRACT 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 p16(INK4A) 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 p16(INK4A) CpG island in primary human mammary epithelial cell (HMEC) strains during selection, as a model for early breast cancer. Silencing of p16(INK4A) 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 p16(INK4A) CpG island. Our results demonstrate for the first time that p16(INK4A) gene silencing is a precursor to epigenetic suppression and that subsequent de novo methylation initially occurs in nucleosome-free regions across the p16(INK4A) CpG island and this is associated with a dynamic change in histone modifications.

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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.
    The EMBO Journal 02/2013; 32(6). DOI:10.1038/emboj.2013.35 · 10.75 Impact Factor
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    • "Epigenetic mechanisms regulate genomic output in normal tissue and are implicated in reprogramming (Maherali et al., 2007; Rideout et al., 2001). The roles of DNA methylation and histone modifications have been extensively studied in promoter regulation, whereas the significance of nucleosome occupancy is increasingly being recognized (Hinshelwood et al., 2009; Kelly et al., 2010; Lin et al., 2007; Wolff et al., 2010; You et al., 2011). "
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    ABSTRACT: Key regulatory genes, suppressed by Polycomb and H3K27me3, become active during normal differentiation and induced reprogramming. Using the well-characterized enhancer/promoter pair of MYOD1 as a model, we have identified a critical role for enhancers in reprogramming. We observed an unexpected nucleosome-depleted region (NDR) at the H3K4me1-enriched enhancer at which transcriptional regulators initially bind, leading to subsequent changes in the chromatin at the cognate promoter. Exogenous Myod1 activates its own transcription by binding first at the enhancer, leading to an NDR and transcription-permissive chromatin at the associated MYOD1 promoter. Exogenous OCT4 also binds first to the permissive MYOD1 enhancer but has a different effect on the cognate promoter, where the monovalent H3K27me3 marks are converted to the bivalent state characteristic of stem cells. Genome-wide, a high percentage of Polycomb targets are associated with putative enhancers in permissive states, suggesting that they may provide a widespread avenue for the initiation of cell-fate reprogramming.
    Cell 12/2011; 147(6):1283-94. DOI:10.1016/j.cell.2011.10.040 · 33.12 Impact Factor
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