Next Article in Journal
EGFR-Targeting as a Biological Therapy: Understanding Nimotuzumab’s Clinical Effects
Previous Article in Journal
Essential Gene Pathways for Glioblastoma Stem Cells: Clinical Implications for Prevention of Tumor Recurrence
Previous Article in Special Issue
Epigenetics of Estrogen Receptor Signaling: Role in Hormonal Cancer Progression and Therapy
Article Menu

Export Article

Open AccessArticle
Cancers 2011, 3(2), 1996-2013; doi:10.3390/cancers3021996

Common Altered Epigenomic Domains in Cancer Cells: Characterization and Subtle Variations

Institute of Molecular Biology and Biochemistry, National Yang Ming University, No.155, Sec.2, Linong Street, Taipei, 112 Taiwan
VGH-YM Genome Center, National Yang Ming University, No.155, Sec.2, Linong Street, Taipei, 112 Taiwan
Institute of Biomedical Informatics, National Yang Ming University, No.155, Sec.2, Linong Street, Taipei, 112 Taiwan
These authors contribute equally to this work.
Author to whom correspondence should be addressed.
Received: 9 February 2011 / Revised: 22 March 2011 / Accepted: 1 April 2011 / Published: 18 April 2011
(This article belongs to the Special Issue Epigenetics of Cancer Progression)
View Full-Text   |   Download PDF [1593 KB, uploaded 18 April 2011]   |  


We have previously identified large megabase-sized hypomethylated zones in the genome of the breast cancer cell line MCF-7 using the TspRI-ExoIII technique. In this report, we used a more convenient high throughput method for mapping the hypomethylated zones in a number of human tumor genomes simultaneously. The method was validated by the bisulfite sequencing of 39 randomly chosen sites in a demethylated domain and by bisulfite genome-wide sequencing of the MCF-7 genome. This showed that the genomes of the various tumor cell lines, as well as some primary tumors, exhibit common hypomethylated domains. Interestingly, these hypomethylated domains are correlated with low CpG density distribution genome-wide, together with the histone H3K27Me3 landscape. Furthermore, they are inversely correlated with the H3K9Ac landscape and gene expression as measured in MCF-7 cells. Treatment with drugs resulted in en-bloc changes to the methylation domains. A close examination of the methylation domains found differences between non-invasive and invasive tumors with respect to tumorigenesis related genes. Taken together these results suggest that the human genome is organized in epigenomic domains that contain various different types of genes and imply that there are cis- and trans-regulators that control these domain-wide epigenetic changes and hence gene expression in the human genome. The hypomethylated domains are located in gene deserts that contain mainly tissue-specific genes and therefore we hypothesize that tumor cells keep these regions demethylated and silenced in order to save energy and resources and allow higher levels of cell proliferation and better survival (a thrifty tumor genome hypothesis). View Full-Text
Keywords: epigenetic; DNA methylation; histone modification; cancer epigenetic; DNA methylation; histone modification; cancer

This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Tsai, Y.-C.; Chiao, C.-H.; Chang, I.-F.; Chen, D.-T.; Liu, T.-T.; Hua, K.; Chang, C.-H.; Hsu, M.-T. Common Altered Epigenomic Domains in Cancer Cells: Characterization and Subtle Variations. Cancers 2011, 3, 1996-2013.

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics



[Return to top]
Cancers EISSN 2072-6694 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top