Cargando…

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

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 simult...

Descripción completa

Detalles Bibliográficos
Autores principales: Tsai, Yi-Chien, Chiao, Chun-Hui, Chang, Ian Yi-Feng, Chen, Dow-Tien, Liu, Tze-Tze, Hua, Kate, Chang, Chuan-Hsiung, Hsu, Ming-Ta
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Molecular Diversity Preservation International (MDPI) 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3757401/
https://www.ncbi.nlm.nih.gov/pubmed/24212793
http://dx.doi.org/10.3390/cancers3021996
_version_ 1782282205268017152
author Tsai, Yi-Chien
Chiao, Chun-Hui
Chang, Ian Yi-Feng
Chen, Dow-Tien
Liu, Tze-Tze
Hua, Kate
Chang, Chuan-Hsiung
Hsu, Ming-Ta
author_facet Tsai, Yi-Chien
Chiao, Chun-Hui
Chang, Ian Yi-Feng
Chen, Dow-Tien
Liu, Tze-Tze
Hua, Kate
Chang, Chuan-Hsiung
Hsu, Ming-Ta
author_sort Tsai, Yi-Chien
collection PubMed
description 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).
format Online
Article
Text
id pubmed-3757401
institution National Center for Biotechnology Information
language English
publishDate 2011
publisher Molecular Diversity Preservation International (MDPI)
record_format MEDLINE/PubMed
spelling pubmed-37574012013-09-04 Common Altered Epigenomic Domains in Cancer Cells: Characterization and Subtle Variations Tsai, Yi-Chien Chiao, Chun-Hui Chang, Ian Yi-Feng Chen, Dow-Tien Liu, Tze-Tze Hua, Kate Chang, Chuan-Hsiung Hsu, Ming-Ta Cancers (Basel) Article 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). Molecular Diversity Preservation International (MDPI) 2011-04-18 /pmc/articles/PMC3757401/ /pubmed/24212793 http://dx.doi.org/10.3390/cancers3021996 Text en © 2011 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Article
Tsai, Yi-Chien
Chiao, Chun-Hui
Chang, Ian Yi-Feng
Chen, Dow-Tien
Liu, Tze-Tze
Hua, Kate
Chang, Chuan-Hsiung
Hsu, Ming-Ta
Common Altered Epigenomic Domains in Cancer Cells: Characterization and Subtle Variations
title Common Altered Epigenomic Domains in Cancer Cells: Characterization and Subtle Variations
title_full Common Altered Epigenomic Domains in Cancer Cells: Characterization and Subtle Variations
title_fullStr Common Altered Epigenomic Domains in Cancer Cells: Characterization and Subtle Variations
title_full_unstemmed Common Altered Epigenomic Domains in Cancer Cells: Characterization and Subtle Variations
title_short Common Altered Epigenomic Domains in Cancer Cells: Characterization and Subtle Variations
title_sort common altered epigenomic domains in cancer cells: characterization and subtle variations
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3757401/
https://www.ncbi.nlm.nih.gov/pubmed/24212793
http://dx.doi.org/10.3390/cancers3021996
work_keys_str_mv AT tsaiyichien commonalteredepigenomicdomainsincancercellscharacterizationandsubtlevariations
AT chiaochunhui commonalteredepigenomicdomainsincancercellscharacterizationandsubtlevariations
AT changianyifeng commonalteredepigenomicdomainsincancercellscharacterizationandsubtlevariations
AT chendowtien commonalteredepigenomicdomainsincancercellscharacterizationandsubtlevariations
AT liutzetze commonalteredepigenomicdomainsincancercellscharacterizationandsubtlevariations
AT huakate commonalteredepigenomicdomainsincancercellscharacterizationandsubtlevariations
AT changchuanhsiung commonalteredepigenomicdomainsincancercellscharacterizationandsubtlevariations
AT hsumingta commonalteredepigenomicdomainsincancercellscharacterizationandsubtlevariations