Epigenetics of gene expression in human hepatoma cells: expression profiling the response to inhibition of DNA methylation and histone deacetylation

<p>Abstract</p> <p>Background</p> <p>DNA methylation and histone deacetylation are epigenetic mechanisms that play major roles in eukaryotic gene regulation. We hypothesize that many genes in the human hepatoma cell line HepG2 are regulated by DNA methylation and histon...

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Main Authors: Edenberg Howard J, Dannenberg Luke O
Format: Article
Language:English
Published: BMC 2006-07-01
Series:BMC Genomics
Online Access:http://www.biomedcentral.com/1471-2164/7/181
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spelling doaj-d9d1d1b35c0f4fb1b7fb3e16af1012bd2020-11-25T00:21:03ZengBMCBMC Genomics1471-21642006-07-017118110.1186/1471-2164-7-181Epigenetics of gene expression in human hepatoma cells: expression profiling the response to inhibition of DNA methylation and histone deacetylationEdenberg Howard JDannenberg Luke O<p>Abstract</p> <p>Background</p> <p>DNA methylation and histone deacetylation are epigenetic mechanisms that play major roles in eukaryotic gene regulation. We hypothesize that many genes in the human hepatoma cell line HepG2 are regulated by DNA methylation and histone deacetylation. Treatment with 5-aza-2'-deoxycytidine (5-aza-dC) to inhibit DNA methylation with and/or Trichostatin A (TSA) to inhibit histone deacetylation should allow us to identify genes that are regulated epigenetically in hepatoma cells.</p> <p>Results</p> <p>5-aza-dC had a much larger effect on gene expression in HepG2 cells than did TSA, as measured using Affymetrix<sup>® </sup>HG-U133 Plus 2.0 microarrays. The expression of 1504 probe sets was affected by 5-aza-dC (at p < 0.01), 535 probe sets by TSA, and 1929 probe sets by the combination of 5-aza-dC and TSA. 5-aza-dC treatment turned on the expression of 211 probe sets that were not detectably expressed in its absence. Expression of imprinted genes regulated by DNA methylation, such as <it>H19 </it>and <it>NNAT</it>, was turned on or greatly increased in response to 5-aza-dC. Genes involved in liver processes such as xenobiotic metabolism (<it>CYP3A4</it>, <it>CYP3A5</it>, and <it>CYP3A7</it>) and steroid biosynthesis (<it>CYP17A1 </it>and <it>CYP19A1</it>), and genes encoding CCAAT element-binding proteins (C/EBPα, C/EBPβ, and C/EBPγ) were affected by 5-aza-dC or the combination. Many of the genes that fall within these groups are also expressed in the developing fetal liver and adult liver. Quantitative real-time RT-PCR assays confirmed selected gene expression changes seen in microarray analyses.</p> <p>Conclusion</p> <p>Epigenetics play a role in regulating the expression of several genes involved in essential liver processes such as xenobiotic metabolism and steroid biosynthesis in HepG2 cells. Many genes whose expression is normally silenced in these hepatoma cells were re-expressed by 5-aza-dC treatment. DNA methylation may be a factor in restricting the expression of fetal genes during liver development and in shutting down expression in hepatoma cells.</p> http://www.biomedcentral.com/1471-2164/7/181
collection DOAJ
language English
format Article
sources DOAJ
author Edenberg Howard J
Dannenberg Luke O
spellingShingle Edenberg Howard J
Dannenberg Luke O
Epigenetics of gene expression in human hepatoma cells: expression profiling the response to inhibition of DNA methylation and histone deacetylation
BMC Genomics
author_facet Edenberg Howard J
Dannenberg Luke O
author_sort Edenberg Howard J
title Epigenetics of gene expression in human hepatoma cells: expression profiling the response to inhibition of DNA methylation and histone deacetylation
title_short Epigenetics of gene expression in human hepatoma cells: expression profiling the response to inhibition of DNA methylation and histone deacetylation
title_full Epigenetics of gene expression in human hepatoma cells: expression profiling the response to inhibition of DNA methylation and histone deacetylation
title_fullStr Epigenetics of gene expression in human hepatoma cells: expression profiling the response to inhibition of DNA methylation and histone deacetylation
title_full_unstemmed Epigenetics of gene expression in human hepatoma cells: expression profiling the response to inhibition of DNA methylation and histone deacetylation
title_sort epigenetics of gene expression in human hepatoma cells: expression profiling the response to inhibition of dna methylation and histone deacetylation
publisher BMC
series BMC Genomics
issn 1471-2164
publishDate 2006-07-01
description <p>Abstract</p> <p>Background</p> <p>DNA methylation and histone deacetylation are epigenetic mechanisms that play major roles in eukaryotic gene regulation. We hypothesize that many genes in the human hepatoma cell line HepG2 are regulated by DNA methylation and histone deacetylation. Treatment with 5-aza-2'-deoxycytidine (5-aza-dC) to inhibit DNA methylation with and/or Trichostatin A (TSA) to inhibit histone deacetylation should allow us to identify genes that are regulated epigenetically in hepatoma cells.</p> <p>Results</p> <p>5-aza-dC had a much larger effect on gene expression in HepG2 cells than did TSA, as measured using Affymetrix<sup>® </sup>HG-U133 Plus 2.0 microarrays. The expression of 1504 probe sets was affected by 5-aza-dC (at p < 0.01), 535 probe sets by TSA, and 1929 probe sets by the combination of 5-aza-dC and TSA. 5-aza-dC treatment turned on the expression of 211 probe sets that were not detectably expressed in its absence. Expression of imprinted genes regulated by DNA methylation, such as <it>H19 </it>and <it>NNAT</it>, was turned on or greatly increased in response to 5-aza-dC. Genes involved in liver processes such as xenobiotic metabolism (<it>CYP3A4</it>, <it>CYP3A5</it>, and <it>CYP3A7</it>) and steroid biosynthesis (<it>CYP17A1 </it>and <it>CYP19A1</it>), and genes encoding CCAAT element-binding proteins (C/EBPα, C/EBPβ, and C/EBPγ) were affected by 5-aza-dC or the combination. Many of the genes that fall within these groups are also expressed in the developing fetal liver and adult liver. Quantitative real-time RT-PCR assays confirmed selected gene expression changes seen in microarray analyses.</p> <p>Conclusion</p> <p>Epigenetics play a role in regulating the expression of several genes involved in essential liver processes such as xenobiotic metabolism and steroid biosynthesis in HepG2 cells. Many genes whose expression is normally silenced in these hepatoma cells were re-expressed by 5-aza-dC treatment. DNA methylation may be a factor in restricting the expression of fetal genes during liver development and in shutting down expression in hepatoma cells.</p>
url http://www.biomedcentral.com/1471-2164/7/181
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