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Genome Res. 2014 Sep;24(9):1421-32. doi: 10.1101/gr.163485.113. Epub 2014 Jun 10.

Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer.

Author information

1
Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia; Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia;
2
Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia;
3
Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA; Active Motif, Inc., Carlsbad, California 92008, USA;
4
Epigenetics Research, Cancer Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, New South Wales 2010, Australia; p.jones@med.usc.edu s.clark@garvan.org.au.
5
Departments of Biochemistry and Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90033, USA; Van Andel Research Institute, Grand Rapids, Michigan 49503, USA p.jones@med.usc.edu s.clark@garvan.org.au.

Abstract

It is well established that cancer-associated epigenetic repression occurs concomitant with CpG island hypermethylation and loss of nucleosomes at promoters, but the role of nucleosome occupancy and epigenetic reprogramming at distal regulatory elements in cancer is still poorly understood. Here, we evaluate the scope of global epigenetic alterations at enhancers and insulator elements in prostate and breast cancer cells using simultaneous genome-wide mapping of DNA methylation and nucleosome occupancy (NOMe-seq). We find that the genomic location of nucleosome-depleted regions (NDRs) is mostly cell type specific and preferentially found at enhancers in normal cells. In cancer cells, however, we observe a global reconfiguration of NDRs at distal regulatory elements coupled with a substantial reorganization of the cancer methylome. Aberrant acquisition of nucleosomes at enhancer-associated NDRs is associated with hypermethylation and epigenetic silencing marks, and conversely, loss of nucleosomes with demethylation and epigenetic activation. Remarkably, we show that nucleosomes remain strongly organized and phased at many facultative distal regulatory elements, even in the absence of a NDR as an anchor. Finally, we find that key transcription factor (TF) binding sites also show extensive peripheral nucleosome phasing, suggesting the potential for TFs to organize NDRs genome-wide and contribute to deregulation of cancer epigenomes. Together, our findings suggest that "decommissioning" of NDRs and TFs at distal regulatory elements in cancer cells is accompanied by DNA hypermethylation susceptibility of enhancers and insulator elements, which in turn may contribute to an altered genome-wide architecture and epigenetic deregulation in malignancy.

PMID:
24916973
PMCID:
PMC4158760
DOI:
10.1101/gr.163485.113
[Indexed for MEDLINE]
Free PMC Article

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