Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

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Abstract

Extensive changes in DNA methylation are common in cancer and may contribute to oncogenesis through transcriptional silencing of tumor-suppressor genes1. Genome-scale studies have yielded important insights into these changes2,3,4,5 but have focused on CpG islands or gene promoters. We used whole-genome bisulfite sequencing (bisulfite-seq) to comprehensively profile a primary human colorectal tumor and adjacent normal colon tissue at single-basepair resolution. Regions of focal hypermethylation in the tumor were located primarily at CpG islands and were concentrated within regions of long-range (>100 kb) hypomethylation. These hypomethylated domains covered nearly half of the genome and coincided with late replication and attachment to the nuclear lamina in human cell lines. We confirmed the confluence of hypermethylation and hypomethylation within these domains in 25 diverse colorectal tumors and matched adjacent tissue. We propose that widespread DNA methylation changes in cancer are linked to silencing programs orchestrated by the three-dimensional organization of chromatin within the nucleus.

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Figure 1: Bisulfite-seq of a colon tumor and adjacent normal mucosa.
Figure 2: Three distinct methylation classes at focal elements.
Figure 3: Focal methylation classes correspond to distinct epigenomic and sequence signatures.
Figure 4: Hypermethylated CGIs fall within long, tumor-specific PMDs.
Figure 5: Properties of PMD boundaries.
Figure 6: Tumor-specific hypermethylation and hypomethylation are correlated and are strongly enriched within PMDs in a diverse set of 25 colon tumors.

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Acknowledgements

We acknowledge generous support of the University of Southern California Epigenome Center by the Kenneth T. and Eileen L. Norris Foundation. We are grateful to S. Hansen for providing DNA replication data. High performance computing support was provided by the University of Southern California High Performance Computing Center (see URLs). We are greatly indebted to Denise Culhane for her superb proofreading skills.

Author information

The project was conceived and the experiments were designed by P.W.L., D.J.W., B.P.B., D.V.D.B. and T.H. The Bisulfite-seq library construction and Genome Analyzer sequencing were performed by D.J.W., J.F.A. and D.V.D.B. The Infinium genotyping and data analysis was performed by B.P.B., motif analysis by H.N. and pipeline automation by B.P.B. and Z.R. Bisulfite-seq data processing and analysis were performed by B.P.B., Z.R. and H.N. Validation samples were collected and analyzed by C.P.E.L., C.M.v.D., R.A.E.M.T., B.P.B., D.J.W. and T.H. The manuscript was prepared by B.P.B. and P.W.L., and the study was supervised by P.W.L.

Correspondence to Peter W Laird.

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Competing interests

P.W.L. is scientific advisory board member and consultant for Epigenomics, AG, which has a commercial interest in DNA methylation biomarkers. The work described in this manuscript was not supported by nor will it benefit Epigenomics, AG.

Supplementary information

Supplementary Text and Figures

Supplementary Note, Supplementary Figures 1–16 (PDF 45448 kb)

Supplementary Tables 1 and 2

Bisulfite-seq summary statistics and Bisulfite-seq detailed statistics by chromosome (XLSX 91 kb)

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Berman, B., Weisenberger, D., Aman, J. et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains. Nat Genet 44, 40–46 (2012) doi:10.1038/ng.969

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