Title

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network

Authors

Authors

J. L. Li; J. Mazar; C. C. Zhong; G. J. Faulkner; S. S. Govindarajan; Z. Zhang; M. E. Dinger; G. Meredith; C. Adams; S. J. Zhang; J. S. Mattick; A. Ray;R. J. Perera

Comments

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Abbreviated Journal Title

Cancer Res.

Keywords

HUMAN CANCER-CELLS; MALIGNANT-MELANOMA; DNA METHYLATION; TUMOR; SUPPRESSORS; CUTANEOUS MELANOMA; EPIGENETIC INACTIVATION; TRANSCRIPTION; FACTOR; MICRORNA EXPRESSION; BREAST-CANCER; LINES; Multidisciplinary Sciences

Abstract

Metastatic melanoma is a malignant cancer with generally poor prognosis, with no targeted chemotherapy. To identify epigenetic changes related to melanoma, we have determined genome-wide methylated CpG island distributions by next-generation sequencing. Melanoma chromosomes tend to be differentially methylated over short CpG island tracts. CpG islands in the upstream regulatory regions of many coding and noncoding RNA genes, including, for example, TERC, which encodes the telomerase RNA, exhibit extensive hypermethylation, whereas several repeated elements, such as LINE 2, and several LTR elements, are hypomethylated in advanced stage melanoma cell lines. By using CpG island demethylation profiles, and by integrating these data with RNA-seq data obtained from melanoma cells, we have identified a co-expression network of differentially methylated genes with significance for cancer related functions. Focused assays of melanoma patient tissue samples for CpG island methylation near the noncoding RNA gene SNORD-10 demonstrated high specificity.

Journal Title

Scientific Reports

Volume

Sci Rep

Publication Date

1-1-2013

Document Type

Article

Language

English

First Page

12

WOS Identifier

3

ISSN

2045-2322

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