201
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Lai HC, Lin YW, Huang THM, Yan P, Huang RL, Wang HC, Liu J, Chan MWY, Chu TY, Sun CA, Chang CC, Yu MH. Identification of novel DNA methylation markers in cervical cancer. Int J Cancer 2008; 123:161-7. [PMID: 18398837 DOI: 10.1002/ijc.23519] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Testing for DNA methylation has potential in cancer screening. Most previous studies of DNA methylation in cervical cancer used a candidate gene approach. The aim our study was to identify novel genes that are methylated in cervical cancers and to test their potential in clinical applications. We did a differential methylation hybridization using a CpG island (CGI) microarray containing 8640 CGI tags to uncover methylated genes in squamous cell carcinomas (SCC) of the uterine cervix. Pooled DNA from cancer tissues and normal cervical swabs were used for comparison. Methylation-specific polymerase chain reaction, bisulfite sequencing and reverse transcription polymerase chain reaction were used to confirm the methylation status in cell lines, normal cervices (n = 45), low-grade lesions (n = 45), high-grade lesions (HSIL; n = 58) and invasive squamous cell carcinomas (SCC; n = 22 from swabs and n = 109 from tissues). Human papillomavirus (HPV) was detected using reverse line blots. We reported 6 genes (SOX1, PAX1, LMX1A, NKX6-1, WT1 and ONECUT1) more frequently methylated in SCC tissues (81.5, 94.4, 89.9, 80.4, 77.8 and 20.4%, respectively) than in their normal controls (2.2, 0, 6.7, 11.9, 11.1 and 0%, respectively; p < 0.0001). Parallel testing of HPV and PAX1 methylation in cervical swabs confers an improved sensitivity than HPV testing alone (80% vs. 66%) without compromising specificity (63% vs. 64%) for HSIL/SCC. Testing PAX1 methylation marker alone, the specificity for HSIL/SCC is 99%. The analysis of these novel DNA methylations may be a promising approach for the screening of cervical cancers.
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Affiliation(s)
- Hung-Cheng Lai
- Department of Obstetrics and Gynecology, Tri-Service General Hospital, Taipei, Taiwan, Republic of China.
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202
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Kaminsky Z, Petronis A, Wang SC, Levine B, Ghaffar O, Floden D, Feinstein A. Epigenetics of personality traits: an illustrative study of identical twins discordant for risk-taking behavior. Twin Res Hum Genet 2008; 11:1-11. [PMID: 18251670 DOI: 10.1375/twin.11.1.1] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
DNA methylation differences between identical twins could account for phenotypic twin discordance of behavioral traits and diseases. High throughput epigenomic microarray profiling can be a strategy of choice for identification of epigenetic differences in phenotypically different monozygotic (MZ) twins. Epigenomic profiling of a pair of MZ twins with quantified measures of psychometric discordance identified several DNA methylation differences, some of which may have developmental and behavioral implications and are consistent with the contrasting psychometric profiles of the twins. In particular, differential methylation of CpG islands proximal to the homeobox DLX1 gene could modulate stress responses and risk taking behavior, and deserve further attention as a potential marker of aversion to danger. The epigenetic difference detected at DLX1 of approximately 1.2 fold change was used to evaluate experimental design issues such as the required numbers of technical replicates. It also enabled us to estimate the power this technique would have to detect a functionally relevant epigenetic difference given a range of 1 to 50 twin pairs. We found that use of epigenomic microarray profiling in a relatively small number (15-25) of phenotypically discordant twin pairs has sufficient power to detect 1.2 fold epigenetic changes.
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Affiliation(s)
- Zachary Kaminsky
- The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
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203
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Allen ND. Temporal and epigenetic regulation of neurodevelopmental plasticity. Philos Trans R Soc Lond B Biol Sci 2008; 363:23-38. [PMID: 17311782 PMCID: PMC2605484 DOI: 10.1098/rstb.2006.2010] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The anticipated therapeutic uses of neural stem cells depend on their ability to retain a certain level of developmental plasticity. In particular, cells must respond to developmental manipulations designed to specify precise neural fates. Studies in vivo and in vitro have shown that the developmental potential of neural progenitor cells changes and becomes progressively restricted with time. For in vitro cultured neural progenitors, it is those derived from embryonic stem cells that exhibit the greatest developmental potential. It is clear that both extrinsic and intrinsic mechanisms determine the developmental potential of neural progenitors and that epigenetic, or chromatin structural, changes regulate and coordinate hierarchical changes in fate-determining gene expression. Here, we review the temporal changes in developmental plasticity of neural progenitor cells and discuss the epigenetic mechanisms that underpin these changes. We propose that understanding the processes of epigenetic programming within the neural lineage is likely to lead to the development of more rationale strategies for cell reprogramming that may be used to expand the developmental potential of otherwise restricted progenitor populations.
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Affiliation(s)
- Nicholas D Allen
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3US, UK.
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204
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Fleury L, Gerus M, Lavigne AC, Richard-Foy H, Bystricky K. Eliminating epigenetic barriers induces transient hormone-regulated gene expression in estrogen receptor negative breast cancer cells. Oncogene 2008; 27:4075-85. [PMID: 18317449 DOI: 10.1038/onc.2008.41] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In breast cancer, approximately one-third of tumors express neither the estrogen receptor (ERalpha) nor estrogen-regulated genes such as the progesterone receptor gene (PR). Our study provides new insights into the mechanism allowing hormone-activated expression of ERalpha target genes silenced in ERalpha-negative mammary tumor cells. In cell lines derived from ERalpha-negative MDA-MB231 cells, stable expression of different levels of ERalpha from a transgene did not result in transcription of PR. A quantitative comparative analysis demonstrates that inhibiting DNA methyltransferases using 5-aza-2'-deoxycytidine or specific disruption of DNMT1 by small interfering RNAs and treatment with the histone-deacetylase inhibitor trichostatin A enabled ERalpha-mediated hormone-dependent expression of endogenous PR. We show that demethylation of a CpG island located in the first exon of PR was a prerequisite for ERalpha binding to these regulatory sequences. Although not a general requirement, DNA demethylation is also necessary for derepression of a subset of ERalpha target genes involved in tumorigenesis. PR transcription did not subsist 4 days after removal of the DNA methyltransferase blocking agents, suggesting that hormone-induced expression of ERalpha target genes in ERalpha-negative tumor cells is transient. Our observations support a model where an epigenetic mark confers stable silencing by precluding ERalpha access to promoters.
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Affiliation(s)
- L Fleury
- Laboratoire de Biologie Moléculaire Eucaryote, Université de Toulouse, Toulouse, France
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205
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Methylation perturbations in retroelements within the genome of a Mus interspecific hybrid correlate with double minute chromosome formation. Genomics 2008; 91:267-73. [DOI: 10.1016/j.ygeno.2007.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Revised: 10/10/2007] [Accepted: 12/05/2007] [Indexed: 12/22/2022]
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206
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Jiang G, Xu L, Song S, Zhu C, Wu Q, Zhang L, Wu L. Effects of long-term low-dose cadmium exposure on genomic DNA methylation in human embryo lung fibroblast cells. Toxicology 2008; 244:49-55. [PMID: 18077075 DOI: 10.1016/j.tox.2007.10.028] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2007] [Revised: 10/26/2007] [Accepted: 10/28/2007] [Indexed: 11/25/2022]
Abstract
Cadmium is a toxic transition metal of continuing occupational and environmental concern. As a well-recognized human carcinogen, its carcinogenic mechanisms are still poorly understood. Cadmium has long been considered a non-genotoxic carcinogen and thought to act through epigenetic mechanisms. In the present study, we tested the effects of long-term low-dose cadmium exposure on DNA methylation in human embryo lung fibroblast (HLF) cells. After 2 months of exposure to 0-1.5 micromol/L cadmium, both the level of genomic DNA methylation and the enzyme activity of DNA methyltransferases (DNMTs) were increased in a concentration-related manner. Moreover, our results showed that cadmium exposure up-regulated the mRNA levels of DNMT1, DNMT3a and DNMT3b at higher concentrations. We further tested the growth dynamics of HLF cells, and observed significantly elevated growth rates, decreased cell population of G0/G1-phase and increased cell population of S-phase at 0.9, 1.2, and 1.5 micromol/L concentrations. Our study indicated that long-term low-dose cadmium exposure could disrupt DNA methylation, which may be one of the possible underlying carcinogenic mechanisms of cadmium.
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Affiliation(s)
- Gaofeng Jiang
- Faculty of Preventive Medicine, Medical College, Wuhan University of Science and Technology, Huangjiahu Campus, Wuhan 430065, Hubei Province, People's Republic of China.
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207
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Kovalchuk O. Epigenetic research sheds new light on the nature of interactions between organisms and their environment. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2008; 49:1-3. [PMID: 18196589 DOI: 10.1002/em.20362] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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208
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Kovalchuk O, Baulch JE. Epigenetic changes and nontargeted radiation effects--is there a link? ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2008; 49:16-25. [PMID: 18172877 DOI: 10.1002/em.20361] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
It is now well accepted that the effects of ionizing radiation (IR) exposure can be noticed far beyond the borders of the directly irradiated tissue. IR can affect neighboring cells in the proximity, giving rise to a bystander effect. IR effects can also span several generations and influence the progeny of exposed parents, leading to transgeneration effects. Bystander and transgeneration IR effects are linked to the phenomenon of the IR-induced genome instability that manifests itself as chromosome aberrations, gene mutations, late cell death, and aneuploidy. While the occurrence of the above-mentioned phenomena is well documented, the exact mechanisms that lead to their development have still to be delineated. Evidence suggests that the IR-induced genome instability, bystander, and transgeneration effects may be epigenetically mediated. The epigenetic changes encompass DNA methylation, histone modification, and RNA-associated silencing. Recent studies demonstrated that IR exposure alters epigenetic parameters in the directly exposed tissues and in the distant bystander tissues. Transgeneration radiation effects were also proposed to be of an epigenetic nature. We will discuss the role of the epigenetic mechanisms in radiation responses, bystander effects, and transgeneration effects.
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Affiliation(s)
- Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Alberta, Canada.
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209
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Manoharan M, Ramachandran K, Soloway MS, Singal R. Epigenetic targets in the diagnosis and treatment of prostate cancer. Int Braz J Urol 2007; 33:11-8. [PMID: 17335593 DOI: 10.1590/s1677-55382007000100003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2006] [Indexed: 11/22/2022] Open
Abstract
Prostate cancer (PC) is one of leading cause of cancer related deaths in men. Various aspects of cancer epigenetics are rapidly evolving and the role of 2 major epigenetic changes including DNA methylation and histone modifications in prostate cancer is being studied widely. The epigenetic changes are early event in the cancer development and are reversible. Novel epigenetic markers are being studied, which have the potential as sensitive diagnostic and prognostic marker. Variety of drugs targeting epigenetic changes are being studied, which can be effective individually or in combination with other conventional drugs in PC treatment. In this review, we discuss epigenetic changes associated with PC and their potential diagnostic and therapeutic applications including future areas of research.
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Affiliation(s)
- Murugesan Manoharan
- Department of Urology, Miller School of Medicine, University of Miami, Miami, Florida 33101, USA.
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210
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Lu Q, Wu A, Tesmer L, Ray D, Yousif N, Richardson B. Demethylation of CD40LG on the inactive X in T cells from women with lupus. THE JOURNAL OF IMMUNOLOGY 2007; 179:6352-8. [PMID: 17947713 DOI: 10.4049/jimmunol.179.9.6352] [Citation(s) in RCA: 332] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Why systemic lupus erythematosus primarily affects women is unknown. Recent evidence indicates that human lupus is an epigenetic disease characterized by impaired T cell DNA methylation. Women have two X chromosomes; one is inactivated by mechanisms including DNA methylation. We hypothesized that demethylation of sequences on the inactive X may cause gene overexpression uniquely in women, predisposing them to lupus. We therefore compared expression and methylation of CD40LG, a B cell costimulatory molecule encoded on the X chromosome, in experimentally demethylated T cells from men and women and in men and women with lupus. Controls included TNFSF7, a methylation-sensitive autosomal B cell costimulatory molecule known to be demethylated and overexpressed in lupus. Bisulfite sequencing revealed that CD40LG is unmethylated in men, while women have one methylated and one unmethylated gene. 5-Azacytidine, a DNA methyltransferase inhibitor, demethylated CD40LG and doubled its expression on CD4(+) T cells from women but not men, while increasing TNFSF7 expression equally between sexes. Similar studies demonstrated that CD40LG demethylates in CD4(+) T cells from women with lupus, and that women but not men with lupus overexpress CD40LG on CD4(+) T cells, while both overexpress TNFSF7. These studies demonstrate that regulatory sequences on the inactive X chromosome demethylate in T cells from women with lupus, contributing to CD40LG overexpression uniquely in women. Demethylation of CD40LG and perhaps other genes on the inactive X may contribute to the striking female predilection of this disease.
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Affiliation(s)
- Qianjin Lu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, 41011 Hunan, China
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211
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Bonanno C, Shehi E, Adlerstein D, Makrigiorgos GM. MS-FLAG, a Novel Real-Time Signal Generation Method for Methylation-Specific PCR. Clin Chem 2007; 53:2119-27. [DOI: 10.1373/clinchem.2007.094011] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Abstract
Background: Aberrant promoter methylation is a major mechanism for silencing tumor suppressor genes in cancer. Detection of hypermethylation is used as a molecular marker for early cancer diagnosis, as a prognostic index, or to define therapeutic targets for reversion of aberrant methylation. We report on a novel signal generation technology for real-time PCR to detect gene promoter methylation.
Methods: FLAG (fluorescent amplicon generation) is a homogeneous signal generation technology based on the exceptionally thermostable endonuclease PspGI. FLAG provides real-time signal generation during PCR by PspGI-mediated cleavage of quenched fluorophores at the 5′ end of double-stranded PCR products. Methylation-specific PCR (MSP) applied on bisulfite-treated DNA was adapted to a real-time format (methylation-specific FLAG; MS-FLAG) for quantifying methylation in the promoter of CDKN2A (p16), GATA5, and RASSF1. We validated MS-FLAG on plasmids and genomic DNA with known methylation status and applied it to detection of methylation in a limited number of clinical samples. We also conducted bisulfite sequencing on these samples.
Results: Real-time PCR results obtained via MS-FLAG agreed with results obtained via conventional, gel-based MSP. The new technology showed high specificity, sensitivity (2–3 plasmid copies), and selectivity (0.01% of methylated DNA) on control samples. It enabled correct prediction of the methylation status of all 3 gene promoters in 21 lung adenocarcinoma samples, as confirmed by bisulfite sequencing. We also developed a multiplex MS-FLAG assay for GATA5 and RASSF1 promoters.
Conclusion: MS-FLAG provides a new, quantitative, high-throughput method for detecting gene promoter methylation and is a convenient alternative to agarose gel-based MSP for screening methylation. In addition to methylation, FLAG-based real-time signal generation may have broad applications in DNA diagnostics.
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Affiliation(s)
| | | | | | - G Mike Makrigiorgos
- Dana Farber-Brigham and Women’s Cancer Center, Harvard Medical School, Boston, MA
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212
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Feng WH, Kenney SC. Valproic acid enhances the efficacy of chemotherapy in EBV-positive tumors by increasing lytic viral gene expression. Cancer Res 2007; 66:8762-9. [PMID: 16951192 DOI: 10.1158/0008-5472.can-06-1006] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
EBV infection in tumor cells is generally restricted to the latent forms of viral infection. Switching the latent form of viral infection into the lytic form may induce tumor cell death. We have previously reported that certain chemotherapy agents can increase the amount of lytic viral gene expression in EBV-positive tumor cells. In this report, we have explored the potential utility of valproic acid (VPA), an anti-seizure drug that also has strong histone deacetylase inhibitory activity, for activating lytic viral gene expression in EBV-positive tumors. Although VPA treatment alone induced only a modest increase in the level of lytic viral gene expression, it strongly enhanced the ability of chemotherapeutic agents to induce lytic EBV gene expression in EBV-positive epithelial and lymphoid cells in vitro. Furthermore, VPA enhanced cell killing in vitro by chemotherapeutic agents in lymphoblastoid cells and gastric cells (AGS) containing wild-type EBV. In contrast, VPA did not enhance the cytotoxicity of chemotherapy in lymphoblastoid cells containing a lytic-defective (BZLF1-knockout) form of EBV or in EBV-negative AGS cells. Finally, we found that the combination of VPA and chemotherapy was significantly more effective in inhibiting EBV-driven lymphoproliferative disease in severe combined immunodeficient mice than chemotherapy alone. These results suggest that VPA could potentiate the efficacy of chemotherapy for EBV-positive tumors in patients.
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Affiliation(s)
- Wen-Hai Feng
- Department of Medicine and Microbiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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213
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Fan S, Fang F, Zhang X, Zhang MQ. Putative zinc finger protein binding sites are over-represented in the boundaries of methylation-resistant CpG islands in the human genome. PLoS One 2007; 2:e1184. [PMID: 18030324 PMCID: PMC2065907 DOI: 10.1371/journal.pone.0001184] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2007] [Accepted: 10/26/2007] [Indexed: 12/31/2022] Open
Abstract
Background Majority of CpG dinucleotides in mammalian genomes tend to undergo DNA methylation, but most CpG islands are resistant to such epigenetic modification. Understanding about mechanisms that may lead to the methylation resistance of CpG islands is still very poor. Methodology/Principal Findings Using the genome-scale in vivo DNA methylation data from human brain, we investigated the flanking sequence features of methylation-resistant CpG islands, and discovered that there are several over-represented putative Transcription Factor Binding Sites (TFBSs) in methylation-resistant CpG islands, and a specific group of zinc finger protein binding sites are over-represented in boundary regions (∼400 bp) flanking such CpG islands. About 77% of the over-represented putative TFBSs are conserved among human, mouse and rat. We also observed the enrichment of 4 histone methylations in methylation-resistant CpG islands or their boundaries. Conclusions/Significance Our results suggest a possible mechanism that certain putative zinc finger protein binding sites over-represented in the boundary regions of the methylation-resistant CpG islands may block the spreading of methylation into these islands, and those TFBSs over-represented within the islands may both reinforce the methylation blocking and promote transcription. Some histone modifications may also enhance the immunity of the CpG islands against DNA methylation by augmenting these TFs' binding. We speculate that the dynamical equilibrium between methylation spreading and blocking is likely to be responsible for the establishment and maintenance of the relatively stable DNA methylation pattern in human somatic cells.
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Affiliation(s)
- Shicai Fan
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST, Department of Automation, Tsinghua University, Beijing 100084, China
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214
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Tanaka K, Tainaka K, Umemoto T, Nomura A, Okamoto A. An osmium-DNA interstrand complex: application to facile DNA methylation analysis. J Am Chem Soc 2007; 129:14511-7. [PMID: 17963391 DOI: 10.1021/ja076140r] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleic acids often acquire new functions by forming a variety of complexes with metal ions. Osmium, in an oxidized state, also reacts with C5-methylated pyrimidines. However, control of the sequence specificity of osmium complexation with DNA is still immature, and the value of the resulting complexes is unknown. We have designed a bipyridine-attached adenine derivative for sequence-specific osmium complexation. Sequence-specific osmium complexation was achieved by hybridization of a short DNA molecule containing this functional nucleotide to a target DNA sequence and resulted in the formation of a cross-linked structure. The interstrand cross-link clearly distinguished methylated cytosines from unmethylated cytosines and was used to quantify the degree of methylation at a specific cytosine in the genome.
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Affiliation(s)
- Kazuo Tanaka
- Frontier Research System, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-1098, Japan
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215
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Ongenaert M, Van Neste L, De Meyer T, Menschaert G, Bekaert S, Van Criekinge W. PubMeth: a cancer methylation database combining text-mining and expert annotation. Nucleic Acids Res 2007; 36:D842-6. [PMID: 17932060 PMCID: PMC2238841 DOI: 10.1093/nar/gkm788] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Epigenetics, and more specifically DNA methylation is a fast evolving research area. In almost every cancer type, each month new publications confirm the differentiated regulation of specific genes due to methylation and mention the discovery of novel methylation markers. Therefore, it would be extremely useful to have an annotated, reviewed, sorted and summarized overview of all available data. PubMeth is a cancer methylation database that includes genes that are reported to be methylated in various cancer types. A query can be based either on genes (to check in which cancer types the genes are reported as being methylated) or on cancer types (which genes are reported to be methylated in the cancer (sub) types of interest). The database is freely accessible at http://www.pubmeth.org. PubMeth is based on text-mining of Medline/PubMed abstracts, combined with manual reading and annotation of preselected abstracts. The text-mining approach results in increased speed and selectivity (as for instance many different aliases of a gene are searched at once), while the manual screening significantly raises the specificity and quality of the database. The summarized overview of the results is very useful in case more genes or cancer types are searched at the same time.
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Affiliation(s)
- Maté Ongenaert
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Laboratory for Bioinformatics and Computational Genomics, Ghent University, B-9000 Ghent, Belgium.
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216
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Malik G, Rojahn E, Ward MD, Gretzer MB, Partin AW, Semmes OJ, Veltri RW. SELDI protein profiling of dunning R-3327 derived cell lines: identification of molecular markers of prostate cancer progression. Prostate 2007; 67:1565-75. [PMID: 17705230 DOI: 10.1002/pros.20646] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND We recently demonstrated the protein expression profiling of Dunning rat tumor cell lines of varying metastatic potential (G (0%), AT-1 ( approximately 20%), and MLL (100%)) using SELDI-TOF-MS. As a parallel effort, we have been pursuing the identification of the protein(s) comprising the individual discriminatory "peaks" and evaluating their utility as potential biomarkers for prostate cancer progression. METHODS To identify the observed SELDI-TOF-MS m/z (mass/charge) values with discriminatory expression between different sublines, we employed a combination of chemical pre-fractionation, liquid chromatography, gel electrophoresis and tandem mass spectroscopy. Identified proteins were then verified by immuno-assay and Western analysis. RESULTS A 17.5 K m/z SELDI-TOF-MS peak was found to retain discriminatory value in each of two separate study-sets with an increased expression in the metastatic MLL line. Sequence identification and subsequent immunoassays verified that Histone H2B is the observed 17.5 K m/z SELDI peak. SELDI-based immuno-assay and Western Blotting revealed that Histone H2B is specifically over-expressed in metastatic MLL lines. CONCLUSIONS SELDI-TOF MS analysis of the Dunning prostate cancer cell lines confirmed the consistent overexpression of a 17.5 K m/z peak in metastatic MLL subline. The 17.5 kDa protein from MLL has been isolated and identified as Histone H2B.
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Affiliation(s)
- Gunjan Malik
- Center for Biomedical Proteomics, Virginia Prostate Center, Eastern Virginia Medical School, Norfolk, Virginia, USA
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217
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Ostler KR, Davis EM, Payne SL, Gosalia BB, Expósito-Céspedes J, Le Beau MM, Godley LA. Cancer cells express aberrant DNMT3B transcripts encoding truncated proteins. Oncogene 2007; 26:5553-63. [PMID: 17353906 PMCID: PMC2435620 DOI: 10.1038/sj.onc.1210351] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 01/17/2007] [Accepted: 01/17/2007] [Indexed: 12/21/2022]
Abstract
Cancer cells display an altered distribution of DNA methylation relative to normal cells. Certain tumor suppressor gene promoters are hypermethylated and transcriptionally inactivated, whereas repetitive DNA is hypomethylated and transcriptionally active. Little is understood about how the abnormal DNA methylation patterns of cancer cells are established and maintained. Here, we identify over 20 DNMT3B transcripts from many cancer cell lines and primary acute leukemia cells that contain aberrant splicing at the 5' end of the gene, encoding truncated proteins lacking the C-terminal catalytic domain. Many of these aberrant transcripts retain intron sequences. Although the aberrant transcripts represent a minority of the DNMT3B transcripts present, Western blot analysis demonstrates truncated DNMT3B isoforms in the nuclear protein extracts of cancer cells. To test if expression of a truncated DNMT3B protein could alter the DNA methylation patterns within cells, we expressed DNMT3B7, the most frequently expressed aberrant transcript, in 293 cells. DNMT3B7-expressing 293 cells have altered gene expression as identified by microarray analysis. Some of these changes in gene expression correlate with altered DNA methylation of corresponding CpG islands. These results suggest that truncated DNMT3B proteins could play a role in the abnormal distribution of DNA methylation found in cancer cells.
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Affiliation(s)
- KR Ostler
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
| | - EM Davis
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
| | - SL Payne
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
| | - BB Gosalia
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
| | - J Expósito-Céspedes
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
| | - MM Le Beau
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
- University of Chicago Cancer Research Center, University of Chicago, Chicago, IL, USA
| | - LA Godley
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
- University of Chicago Cancer Research Center, University of Chicago, Chicago, IL, USA
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218
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Kawaji H, Frith MC, Katayama S, Sandelin A, Kai C, Kawai J, Carninci P, Hayashizaki Y. Dynamic usage of transcription start sites within core promoters. Genome Biol 2007; 7:R118. [PMID: 17156492 PMCID: PMC1794431 DOI: 10.1186/gb-2006-7-12-r118] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 10/26/2006] [Accepted: 12/12/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mammalian promoters do not initiate transcription at single, well defined base pairs, but rather at multiple, alternative start sites spread across a region. We previously characterized the static structures of transcription start site usage within promoters at the base pair level, based on large-scale sequencing of transcript 5' ends. RESULTS In the present study we begin to explore the internal dynamics of mammalian promoters, and demonstrate that start site selection within many mouse core promoters varies among tissues. We also show that this dynamic usage of start sites is associated with CpG islands, broad and multimodal promoter structures, and imprinting. CONCLUSION Our results reveal a new level of biologic complexity within promoters--fine-scale regulation of transcription starting events at the base pair level. These events are likely to be related to epigenetic transcriptional regulation.
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Affiliation(s)
- Hideya Kawaji
- NTT Software Corporation, 209 Yamashita-cho Nakak-ku, Yokohama, Kanagawa, 231-8551, Japan
| | - Martin C Frith
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Institute for Molecular Bioscience, University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072, Australia
| | - Shintaro Katayama
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Albin Sandelin
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- The Bioinformatics Centre, University of Copenhagen, Universitetsparken 15, DK-2100 København Ø, Denmark
| | - Chikatoshi Kai
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Jun Kawai
- The Bioinformatics Centre, University of Copenhagen, Universitetsparken 15, DK-2100 København Ø, Denmark
- Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Piero Carninci
- The Bioinformatics Centre, University of Copenhagen, Universitetsparken 15, DK-2100 København Ø, Denmark
- Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoshihide Hayashizaki
- Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
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Celewicz L, Mayer M, Shetlar MD. The Photochemistry of Thymidylyl-(3′-5′)-5-methyl-2′-deoxycytidine in Aqueous Solution¶. Photochem Photobiol 2007. [DOI: 10.1111/j.1751-1097.2005.tb00201.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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220
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Kim SH, Park J, Choi MC, Kim HP, Park JH, Jung Y, Lee JH, Oh DY, Im SA, Bang YJ, Kim TY. Zinc-fingers and homeoboxes 1 (ZHX1) binds DNA methyltransferase (DNMT) 3B to enhance DNMT3B-mediated transcriptional repression. Biochem Biophys Res Commun 2007; 355:318-23. [PMID: 17303076 DOI: 10.1016/j.bbrc.2007.01.187] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Accepted: 01/26/2007] [Indexed: 11/26/2022]
Abstract
DNA methyltransferases (DNMT) 3B is a de novo DNMT that represses transcription independent of DNMT activity. In order to gain a better insight into DNMT3B-mediated transcriptional repression, we performed a yeast two-hybrid analysis using DNMT3B as a bait. Of the various binding candidates, ZHX1, a member of zinc-finger and homeobox protein, was found to interact with DNMT3B in vivo and in vitro. N-terminal PWWP domain of DNMT3B was required for its interaction with homeobox motifs of ZHX1. ZHX1 contains nuclear localization signal at C-terminal homeobox motif, and both ZHX1 and DNMT3B were co-localized in nucleus. Furthermore, we found that ZHX1 enhanced the transcriptional repression mediated by DNMT3B when DNMT3B is directly targeted to DNA. These results showed for the first the direct linkage between DNMT and zinc-fingers homeoboxes protein, leading to enhanced gene silencing by DNMT3B.
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Affiliation(s)
- Sung-Hak Kim
- National Research Laboratory for Cancer Epigenetics, Cancer Research Institute, Seoul, Republic of Korea
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221
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Pfister S, Schlaeger C, Mendrzyk F, Wittmann A, Benner A, Kulozik A, Scheurlen W, Radlwimmer B, Lichter P. Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma. Nucleic Acids Res 2007; 35:e51. [PMID: 17344319 PMCID: PMC1874664 DOI: 10.1093/nar/gkm094] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Existing microarray-based approaches for screening of DNA methylation are hampered by a number of shortcomings, such as the introduction of bias by DNA copy-number imbalances in the test genome and negligence of tissue-specific methylation patterns. We developed a method designated array-based profiling of reference-independent methylation status (aPRIMES) that allows the detection of direct methylation status rather than relative methylation. Array-PRIMES is based on the differential restriction and competitive hybridization of methylated and unmethylated DNA by methylation-specific and methylation-sensitive restriction enzymes, respectively. We demonstrate the accuracy of aPRIMES in detecting the methylation status of CpG islands for different states of methylation. Application of aPRIMES to the DNA from desmoplastic medulloblastomas of monozygotic twins showed strikingly similar methylation profiles. Additional analysis of 18 sporadic medulloblastomas revealed an overall correlation between highly methylated tumors and poor clinical outcome and identified ZIC2 as a frequently methylated gene in pediatric medulloblastoma.
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Affiliation(s)
- Stefan Pfister
- Department of Molecular Genetics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany, Department of Pediatric Oncology, Hematology & Immunology, University of Heidelberg, Im Neuenheimer Feld 153, 69120 Heidelberg, Germany, Central Unit Biostatistics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and Cnopf'sche Kinderklinik, Nürnberg Children's Hospital, St. Johannis Muehlgasse 19, 90419 Nuernberg, Germany
| | - Christof Schlaeger
- Department of Molecular Genetics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany, Department of Pediatric Oncology, Hematology & Immunology, University of Heidelberg, Im Neuenheimer Feld 153, 69120 Heidelberg, Germany, Central Unit Biostatistics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and Cnopf'sche Kinderklinik, Nürnberg Children's Hospital, St. Johannis Muehlgasse 19, 90419 Nuernberg, Germany
| | - Frank Mendrzyk
- Department of Molecular Genetics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany, Department of Pediatric Oncology, Hematology & Immunology, University of Heidelberg, Im Neuenheimer Feld 153, 69120 Heidelberg, Germany, Central Unit Biostatistics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and Cnopf'sche Kinderklinik, Nürnberg Children's Hospital, St. Johannis Muehlgasse 19, 90419 Nuernberg, Germany
| | - Andrea Wittmann
- Department of Molecular Genetics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany, Department of Pediatric Oncology, Hematology & Immunology, University of Heidelberg, Im Neuenheimer Feld 153, 69120 Heidelberg, Germany, Central Unit Biostatistics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and Cnopf'sche Kinderklinik, Nürnberg Children's Hospital, St. Johannis Muehlgasse 19, 90419 Nuernberg, Germany
| | - Axel Benner
- Department of Molecular Genetics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany, Department of Pediatric Oncology, Hematology & Immunology, University of Heidelberg, Im Neuenheimer Feld 153, 69120 Heidelberg, Germany, Central Unit Biostatistics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and Cnopf'sche Kinderklinik, Nürnberg Children's Hospital, St. Johannis Muehlgasse 19, 90419 Nuernberg, Germany
| | - Andreas Kulozik
- Department of Molecular Genetics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany, Department of Pediatric Oncology, Hematology & Immunology, University of Heidelberg, Im Neuenheimer Feld 153, 69120 Heidelberg, Germany, Central Unit Biostatistics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and Cnopf'sche Kinderklinik, Nürnberg Children's Hospital, St. Johannis Muehlgasse 19, 90419 Nuernberg, Germany
| | - Wolfram Scheurlen
- Department of Molecular Genetics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany, Department of Pediatric Oncology, Hematology & Immunology, University of Heidelberg, Im Neuenheimer Feld 153, 69120 Heidelberg, Germany, Central Unit Biostatistics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and Cnopf'sche Kinderklinik, Nürnberg Children's Hospital, St. Johannis Muehlgasse 19, 90419 Nuernberg, Germany
| | - Bernhard Radlwimmer
- Department of Molecular Genetics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany, Department of Pediatric Oncology, Hematology & Immunology, University of Heidelberg, Im Neuenheimer Feld 153, 69120 Heidelberg, Germany, Central Unit Biostatistics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and Cnopf'sche Kinderklinik, Nürnberg Children's Hospital, St. Johannis Muehlgasse 19, 90419 Nuernberg, Germany
| | - Peter Lichter
- Department of Molecular Genetics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany, Department of Pediatric Oncology, Hematology & Immunology, University of Heidelberg, Im Neuenheimer Feld 153, 69120 Heidelberg, Germany, Central Unit Biostatistics, German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany and Cnopf'sche Kinderklinik, Nürnberg Children's Hospital, St. Johannis Muehlgasse 19, 90419 Nuernberg, Germany
- *To whom correspondence should be addressed. Tel:+49-6221-424619+49-6221-424639
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Witkiewicz A, Raghunath P, Wasik A, Junkins-Hopkins JM, Jones D, Zhang Q, Odum N, Wasik MA. Loss of SHP-1 tyrosine phosphatase expression correlates with the advanced stages of cutaneous T-cell lymphoma. Hum Pathol 2007; 38:462-7. [PMID: 17239936 DOI: 10.1016/j.humpath.2006.09.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Revised: 08/31/2006] [Accepted: 09/07/2006] [Indexed: 11/23/2022]
Abstract
Cutaneous T-cell lymphoma (CTCL) comprises distinct and often progressive stages of skin involvement by patches, plaques, and tumors. We have previously demonstrated that CTCL-derived malignant T-cell lines display loss of a tumor suppressor SHP-1 tyrosine phosphatase because of epigenetic silencing of its gene. The silencing is induced by an activated phosphorylated (p)-STAT3 transcription factor in cooperation with DNA methyltransferase 1 (DNMT1), the key member of the epigenetic gene silencing machinery. To determine at which stage of CTCL the loss of SHP-1 occurs and how it correlates with the expression of (p)-STAT3 and DNMT1, we examined by immunohistochemistry 47 formalin-fixed skin biopsies from various stages of CTCL. Six pairs of the biopsies were obtained before and after CTCL progression at the patch or plaque and tumor stage, respectively. In 5 of these pairs, we identified loss of SHP-1 expression in atypical lymphocytes at the tumor stage; less prominent SHP-1 loss was noted in 3 biopsies from the earlier stage. The SHP-1 loss was also observed in 5 of 6 tumor, 12 of 18 plaque, and only 2 of 11 patch stages in patients with single biopsies. The expression of (p)-STAT3 and DNMT1 could be identified in almost all cases in at least a subset of the lesional cells. Based on these findings, we postulate that expression of (p)-STAT3 and DNMT1 occurs at the early stages of CTCL, and that this expression alone seems insufficient to induce loss of SHP-1 expression. In turn, SHP-1 loss correlates with, and may contribute to, progression of CTCL.
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223
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Abstract
Aberrant gene methylation plays an important role in human tumorigenesis, including thyroid tumorigenesis. Many tumor suppressor genes are aberrantly methylated in thyroid cancer, and some even in benign thyroid tumors, suggesting a role of this epigenetic event in early thyroid tumorigenesis. Methylation of some of these genes tends to occur in certain types of thyroid cancer and is related to specific signaling pathways. For example, methylation of PTEN and RASSF1A genes occurs mostly in follicular thyroid cancer, and its tumorigenic role may be related to the phosphatidylinositol 3-kinase/Akt signaling pathway, whereas methylation of genes for tissue inhibitor of metalloproteinase-3, SLC5A8, and death-associated protein kinase occurs in papillary thyroid cancer and is related to the BRAF/MAPK kinase/MAPK pathway. Methylation of thyroid-specific genes, such as those for sodium/iodide symporter and thyroid-stimulating hormone receptor, is also common in thyroid cancer. Although its tumorigenic role is not clear, methylation, and hence silencing, of these thyroid-specific genes is a cause for the failure of clinical radioiodine treatment of thyroid cancer. Unlike gene methylation, histone modifications have been relatively poorly investigated in thyroid tumors. Future studies need to emphasize the mechanistic aspects of these two types of epigenetic alterations to uncover new molecular mechanisms in thyroid tumorigenesis and to provide novel therapeutic targets for thyroid cancer.
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Affiliation(s)
- Mingzhao Xing
- Division of Endocrinology and Metabolism, The Johns Hopkins University School of Medicine, 1830 East Monument Street, Suite 333, Baltimore, MD 21287, USA.
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224
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Feng CZ, Zhu XJ, Dai ZM, Liu FQ, Xiang JH, Yang WJ. Identification of a novel DNA methyltransferase 2 from the brine shrimp, Artemia franciscana. Comp Biochem Physiol B Biochem Mol Biol 2007; 147:191-8. [PMID: 17400496 DOI: 10.1016/j.cbpb.2007.01.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 01/07/2007] [Accepted: 01/11/2007] [Indexed: 01/16/2023]
Abstract
DNA methyltransferase 2 (Dnmt2) is a dual-specificity DNA methyltransferase, which contains a weak DNA methyltransferase and novel tRNA methyltransferase activity. However, its biological function is still enigmatic. To elucidate the expression profiles of Dnmt2 in Artemia franciscana, we isolated the gene encoding a Dnmt2 from A. franciscana and named it as AfDnmt2. The cDNA of AfDnmt2 contained a 1140-bp open reading frame that encoded a putative Dnmt2 protein of 379 amino acids exhibiting 32% approximately 39% identities with other known Dnmt2 homologs. This is the first report of a DNA methyltransferase gene in Crustacean. By using semi-quantitative RT-PCR, AfDnmt2 was found to be expressed through all developmental stages and its expression increased during resumption of diapause cysts development. Southern blot analysis indicated the presence of multiple copies of AfDnmt2 genes in A. franciscana.
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Affiliation(s)
- Chen-Zhuo Feng
- Institute of Cell Biology and Genetics, College of Life Sciences, Zhejiang University, Zijingang Campus, Hangzhou, Zhejiang 310058, PR China
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225
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Asagiri M, Takayanagi H. The molecular understanding of osteoclast differentiation. Bone 2007; 40:251-64. [PMID: 17098490 DOI: 10.1016/j.bone.2006.09.023] [Citation(s) in RCA: 1029] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Revised: 09/01/2006] [Accepted: 09/06/2006] [Indexed: 12/12/2022]
Abstract
Osteoclasts are multinucleated cells of monocyte/macrophage origin that degrade bone matrix. The differentiation of osteoclasts is dependent on a tumor necrosis factor (TNF) family cytokine, receptor activator of nuclear factor (NF)-kappaB ligand (RANKL), as well as macrophage colony-stimulating factor (M-CSF). Congenital lack of osteoclasts causes osteopetrosis, investigation of which has provided insights into the essential molecules for osteoclastogenesis, including TNF receptor-associated factor (TRAF) 6, NF-kappaB and c-Fos. In addition, genome-wide screening techniques have shed light on an additional set of gene products such as nuclear factor of activated T cells (NFAT) c1. Here we summarize the efforts to understand the sequential molecular events induced by RANKL during osteoclast differentiation. RANKL binds to its receptor RANK, which recruits adaptor molecules such as TRAF6. TRAF6 activates NF-kappaB, which is important for the initial induction of NFATc1. NFATc1 is activated by calcium signaling and binds to its own promoter, thus switching on an autoregulatory loop. An activator protein (AP)-1 complex containing c-Fos is required for the autoamplification of NFATc1, enabling the robust induction of NFATc1. Finally, NFATc1 cooperates with other transcriptional partners to activate osteoclast-specific genes. NFATc1 autoregulation is controlled by an epigenetic mechanism, which has profound implications for an understanding of the general mechanism of irreversible cell fate determination. From the clinical point of view, RANKL signaling pathway has promise as a strategy for suppressing the excessive osteoclast formation characteristic of a variety of bone diseases.
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Affiliation(s)
- Masataka Asagiri
- Department of Cell Signaling, Graduate School, Tokyo Medical and Dental University, Yushima 1-5-45, Tokyo 113-8549, Japan
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226
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Babinger P, Völkl R, Cakstina I, Maftei A, Schmitt R. Maintenance DNA methyltransferase (Met1) and silencing of CpG-methylated foreign DNA in Volvox carteri. PLANT MOLECULAR BIOLOGY 2007; 63:325-36. [PMID: 17033890 DOI: 10.1007/s11103-006-9091-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2006] [Accepted: 09/10/2006] [Indexed: 05/12/2023]
Abstract
DNA methylation plays an important role in the gene-silencing network of higher eukaryotes. We have analyzed the 21.5-kb maintenance methyltransferase (M-MTase) gene, met1, of the multicellular green alga Volvox carteri. The met1 transcript was detected only during the period when DNA replication and cell division are taking place. It encodes a 238 kDa protein containing eight C-terminal activity domains typical of M-MTases, plus upstream DNA-binding domains including the ProDom domain PD003757, which experimental analyses in animal systems have indicated is required for targeting the enzyme to DNA-replication foci. Several insertions of unknown function make Volvox Met1 the largest known member of the Met1/Dnmt1 family. Here we also show that several endogenous transposon families are CpG-methylated in Volvox, which we think causes them to be inactive. This view is supported by the observation that an in vitro CpG-methylated gene introduced into Volvox was maintained in the methylated and silent state over >100 generations. Thus, we believe that Met1 recognizes and perpetuates the in vitro methylation signal, and that the silencing machinery is then able to transduce such a methylation-only signal into a stable heterochromatic (and silent) state.
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Affiliation(s)
- P Babinger
- Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, 93040 Regensburg, Germany.
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227
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Growth of the protozoan parasite Entamoeba histolytica in 5-azacytidine has limited effects on parasite gene expression. BMC Genomics 2007; 8:7. [PMID: 17207281 PMCID: PMC1779778 DOI: 10.1186/1471-2164-8-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2006] [Accepted: 01/05/2007] [Indexed: 12/28/2022] Open
Abstract
Background In higher eukaryotes DNA methylation regulates important biological functions including silencing of gene expression and protection from adverse effects of retrotransposons. In the protozoan parasite Entamoeba histolytica, a DNA methyltransferase has been identified and treatment with 5-azacytidine (5-AzaC), a potent inhibitor of DNA methyltransferase, has been reported to attenuate parasite virulence. However, the overall extent of DNA methylation and its subsequent effects on global gene expression in this parasite are currently unknown. Results In order to identify the genome-wide effects of DNA methylation in E. histolytica, we used a short oligonucleotide microarray representing 9,435 genes (~95% of all annotated amebic genes) and compared the expression profile of E. histolytica HM-1:IMSS parasites with those treated with 23 μM 5-AzaC for up to one week. Overall, 2.1% of genes tested were transcriptionally modulated under these conditions. 68 genes were upregulated and 131 genes down regulated (2-fold change; p-value < 0.05). Sodium-bisulfite treatment and sequencing of genes indicated that there were at least two subsets of genes with genomic DNA methylation in E. histolytica: (i) genes that were endogenously silenced by genomic DNA methylation and for which 5-AzaC treatment induced transcriptional de-repression, and (ii) genes that have genomic DNA methylation, but which were not endogenously silenced by the methylation. We identified among the genes down regulated by 5-AzaC treatment a cysteine proteinase (2.m00545) and lysozyme (52.m00148) both of which have known roles in amebic pathogenesis. Decreased expression of these genes in the 5-AzaC treated E. histolytica may account in part for the parasites reduced cytolytic abilities. Conclusion This work represents the first genome-wide analysis of DNA-methylation in Entamoeba histolytica and indicates that DNA methylation has relatively limited effects on gene expression in this parasite.
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228
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Venturelli S, Armeanu S, Pathil A, Hsieh CJ, Weiss TS, Vonthein R, Wehrmann M, Gregor M, Lauer UM, Bitzer M. Epigenetic combination therapy as a tumor-selective treatment approach for hepatocellular carcinoma. Cancer 2007; 109:2132-41. [PMID: 17407132 DOI: 10.1002/cncr.22652] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Innovative epigenetic therapeutics comprise histone deacetylase inhibitors (HDAC-I) and demethylating agents (DA). It was recently found that HDAC-I compounds exhibit profound therapeutic activities against hepatocellular carcinoma (HCC). A comprehensive preclinical investigation was performed on the potential of a combined HDAC-I/DA epigenetic regimen for the highly chemotherapy-resistant HCC entity. METHODS Human HCC-derived cell lines or primary human hepatocytes (PHH) were treated with HDAC-I compound suberoylanilide hydroxamic acid (SAHA) or DA compound 5-aza-2'-deoxycytidine (5-aza-dC) or both and examined for cellular damage, proliferation, histone acetylation pattern, and DNA methylation. In vivo activities were investigated in a xenograft hepatoma model. RESULTS Monotherapeutic application of SAHA or 5-aza-dC was found to induce substantial antiproliferative effects in HCC-derived cells, strongly enhanced by combined SAHA and 5-aza-dC treatment. PHH from different human donors did not exhibit any relevant cellular damage even when applying high doses of the combination regimen, whereas HCC-derived cell lines showed a dose-dependent damage. In vivo testing demonstrated a statistical significant inhibition of hepatoma cell growth for the combined treatment regime. CONCLUSIONS Because the combined HDAC-I/DA epigenetic approach was found to produce significant antitumor effects in HCC model systems and did not impair cellular integrity of untransformed hepatocytes, this combination therapy is now considered for further investigation in clinical trials.
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Affiliation(s)
- Sascha Venturelli
- Department of Internal Medicine I, Medical University Clinic, Tubingen, Germany
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229
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Olave IA, Doneanu C, Fang X, Stamatoyannopoulos G, Li Q. Purification and identification of proteins that bind to the hereditary persistence of fetal hemoglobin -198 mutation in the gamma-globin gene promoter. J Biol Chem 2006; 282:853-62. [PMID: 17114178 PMCID: PMC2819221 DOI: 10.1074/jbc.m610404200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Expression of the gamma-globin gene is silenced in adult humans. However, certain point mutations in the gamma-globin gene promoter are capable of maintaining expression of this gene during adult erythropoiesis, a condition called non-deletion hereditary persistence of fetal hemoglobin (HPFH). Among these, the British form of HPFH carrying a T-->C point mutation at position -198 of the Agamma-globin gene promoter results in 4-10% fetal hemoglobin in heterozygotes. In this study, we used nuclear extracts from murine erythroleukemia cells to purify a protein complex that binds the HPFH -198 gamma-globin gene promoter. Members of this protein complex were identified by mass spectrometry and include DNMT1, the transcriptional coactivator p52, the protein SNEV, and RAP74 (the largest subunit of the general transcription factor IIF). Sp1, which was previously considered responsible for HPFH -198 gamma-globin gene activation, was not identified. The potential role of these proteins in the reactivation and/or maintenance of gamma-globin gene expression in the adult transcriptional environment is discussed.
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MESH Headings
- Adult
- Animals
- Antibody Specificity
- Blotting, Western
- Cell Fractionation
- Cell Line, Tumor
- Chromatography, Affinity
- DNA (Cytosine-5-)-Methyltransferase 1
- DNA (Cytosine-5-)-Methyltransferases/immunology
- DNA (Cytosine-5-)-Methyltransferases/isolation & purification
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- Fetal Hemoglobin/genetics
- Gene Expression Regulation, Developmental
- Globins/genetics
- Humans
- Leukemia, Erythroblastic, Acute
- Mass Spectrometry
- Mice
- Mice, Transgenic
- Nuclear Matrix-Associated Proteins/immunology
- Nuclear Matrix-Associated Proteins/isolation & purification
- Nuclear Matrix-Associated Proteins/metabolism
- Point Mutation
- Promoter Regions, Genetic/physiology
- Sp1 Transcription Factor/immunology
- Sp1 Transcription Factor/isolation & purification
- Sp1 Transcription Factor/metabolism
- Transcription Factors/immunology
- Transcription Factors/isolation & purification
- Transcription Factors/metabolism
- Transcription Factors, TFII/immunology
- Transcription Factors, TFII/isolation & purification
- Transcription Factors, TFII/metabolism
- Transcriptional Activation
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Affiliation(s)
- Ivan A. Olave
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195
| | - Catalin Doneanu
- Mass Spectrometry Center, Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195
| | - Xiangdong Fang
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195
| | - George Stamatoyannopoulos
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195
| | - Qiliang Li
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195
- To whom correspondence should be addressed: Div. of Medical Genetics, University of Washington, P. O. Box 357720, Seattle, WA 98195. Tel.: 206-616-4526; Fax: 206-616-4527;
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Zhong S, Fields CR, Su N, Pan YX, Robertson KD. Pharmacologic inhibition of epigenetic modifications, coupled with gene expression profiling, reveals novel targets of aberrant DNA methylation and histone deacetylation in lung cancer. Oncogene 2006; 26:2621-34. [PMID: 17043644 DOI: 10.1038/sj.onc.1210041] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Lung cancer is the leading cause of cancer-related deaths in the United States due, in large part, to the lack of early detection methods. Lung cancer arises from a complex series of genetic and epigenetic changes leading to uncontrolled cell growth and metastasis. Unlike genetic changes, epigenetic changes, such as DNA methylation and histone acetylation, are reversible with currently available pharmaceuticals and are early events in lung tumorigenesis detectable by non-invasive methods. In order to better understand how epigenetic changes contribute to lung cancer, and to identify new disease biomarkers, we combined pharmacologic inhibition of DNA methylation and histone deacetylation in non-small cell lung cancer (NSCLC) cell lines, with genome-wide expression profiling. Of the more than 200 genes upregulated by these treatments, three of these, neuronatin, metallothionein 3 and cystatin E/M, were frequently hypermethylated and transcriptionally downregulated in NSCLC cell lines and tumors. Interestingly, four other genes, cylindromatosis, CD9, activating transcription factor 3 and oxytocin receptor, were dominantly regulated by histone deacetylation and were also frequently downregulated in lung tumors. The majority of these genes also suppressed NSCLC growth in culture when ectopically expressed. This study therefore reveals new putative NSCLC growth regulatory genes and epigenetic disease biomarkers that may enhance early detection strategies and serve as therapeutic targets.
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MESH Headings
- Acetylation
- Adenocarcinoma/drug therapy
- Adenocarcinoma/genetics
- Adenocarcinoma/pathology
- Azacitidine/analogs & derivatives
- Azacitidine/pharmacology
- Biomarkers, Tumor
- Carcinoma, Large Cell/drug therapy
- Carcinoma, Large Cell/genetics
- Carcinoma, Large Cell/pathology
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/pathology
- Chromatin Immunoprecipitation
- Colony-Forming Units Assay
- DNA Methylation/drug effects
- Enzyme Inhibitors/pharmacology
- Epigenesis, Genetic/drug effects
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Histone Deacetylase Inhibitors
- Humans
- Hydroxamic Acids/pharmacology
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Oligonucleotide Array Sequence Analysis
- Reverse Transcriptase Polymerase Chain Reaction
- Tumor Cells, Cultured
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Affiliation(s)
- S Zhong
- Department of Biochemistry & Molecular Biology, UF-Shands Cancer Center Program in Cancer Genetics, Epigenetics and Tumor Virology and Genetics Institute, College of Medicine, University of Florida, Gainesville, FL, USA
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231
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Zhang Q, Wang HY, Woetmann A, Raghunath PN, Odum N, Wasik MA. STAT3 induces transcription of the DNA methyltransferase 1 gene (DNMT1) in malignant T lymphocytes. Blood 2006; 108:1058-64. [PMID: 16861352 PMCID: PMC1895864 DOI: 10.1182/blood-2005-08-007377] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In this study, we demonstrated that STAT3, a well-characterized transcription factor expressed in continuously activated oncogenic form in the large spectrum of cancer types, induces in malignant T lymphocytes the expression of DNMT1, the key effector of epigenetic gene silencing. STAT3 binds in vitro to 2 STAT3 SIE/GAS-binding sites identified in promoter 1 and enhancer 1 of the DNMT1 gene. STAT3 also binds to the promoter 1 region and induces its activity in vivo. Treatment of the malignant T lymphocytes with STAT3 siRNA abrogates expression of DNMT1, inhibits cell growth, and induces programmed cell death. In turn, inhibition of DNMT1 by a small molecule inhibitor, 5-aza-2-deoxy-cytidine, and 2 DNMT1 antisense DNA oligonucleotides inhibits the phosphorylation of STAT3. These data indicate that STAT3 may in part transform cells by fostering epigenetic silencing of tumor-suppressor genes. They also indicate that by inducing DNMT1, STAT3 facilitates its own persistent activation in malignant T cells. Finally, these data provide further rationale for therapeutically targeting STAT3 in T-cell lymphomas and, possibly, other malignancies.
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Affiliation(s)
- Qian Zhang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Medical Center, 7.103 Founders, Philadelphia, 19104, USA.
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232
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Kameda T, Smuga-Otto K, Thomson JA. A severe de novo methylation of episomal vectors by human ES cells. Biochem Biophys Res Commun 2006; 349:1269-77. [PMID: 16973130 DOI: 10.1016/j.bbrc.2006.08.175] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Accepted: 08/29/2006] [Indexed: 11/29/2022]
Abstract
Episomal vectors can allow efficient genetic modification of cells and have the potential advantage of avoiding chromosomal position of integration effects. Here we explore the use of an Epstein-Barr virus-based episomal vector with human embryonic stem (ES) cells, and find high initial transfection rates, but a rapid loss of reporter gene expression. Similar to mouse ES cells, human ES cells express high levels of the de novo DNA methyltransferases, and we detected dramatic CpG methylation and minor non-CpG methylation on the episomes recovered from the human ES cells 7 days after the transfection, which was not present on the same episome recovered from 293 cells. Interestingly, the oriP region of the episomes was relatively excluded from this methylation. These findings define some of the limitations of using episomal vectors with human ES cells and offer a unique platform for analyzing epigenetic gene silencing in human ES cells.
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Affiliation(s)
- Takashi Kameda
- The Genome Center of Wisconsin, University of Wisconsin-Madison, 53706, USA
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233
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Soma T, Kaganoi J, Kawabe A, Kondo K, Imamura M, Shimada Y. Nicotine induces the fragile histidine triad methylation in human esophageal squamous epithelial cells. Int J Cancer 2006; 119:1023-7. [PMID: 16570269 DOI: 10.1002/ijc.21948] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The fragile histidine triad (FHIT) gene has been proposed to have an important role in very early carcinogenesis. Methylation of the FHIT gene is associated with transcriptional inactivation in esophageal squamous cell carcinoma, and FHIT inactivation has been linked to smoking-related carcinogenesis. In this study, we confirmed methylation of the FHIT gene in human esophageal squamous epithelial cells (HEECs) and examined whether nicotine induced alteration of FHIT. Methylation status in the promoter region of the FHIT gene and p16(INK4A) gene was determined by methylation-specific PCR in HEECs exposed to nicotine under various conditions. Methylation status of the FHIT gene was confirmed by DNA-sequencing analysis. Protein expression of Fhit and the DNA methyltransferases (DNMTs) DNMT1 and DNMT3a were assessed by immunoblot analysis. In the absence of nicotine, methylation of the FHIT gene and attenuation of Fhit protein were not detected in HEECs. Nicotine induced the methylation of FHIT gene and attenuated Fhit protein in association with increased expression of DNMT3a. Reexpression of Fhit protein in HEECs was found after cessation of moderate- to long-term exposure to nicotine. Our results show that nicotine induces methylation of the FHIT gene followed by loss of Fhit protein expression in HEECs. Continuous smoking may thus increase the risk of esophageal cancer.
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Affiliation(s)
- Toshiya Soma
- Department of Surgery and Surgical Basic Science, Kyoto University, Sakyo-ku, Japan
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234
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Majumder S, Ghoshal K, Datta J, Smith DS, Bai S, Jacob ST. Role of DNA methyltransferases in regulation of human ribosomal RNA gene transcription. J Biol Chem 2006; 281:22062-22072a. [PMID: 16735507 PMCID: PMC2243234 DOI: 10.1074/jbc.m601155200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We have previously demonstrated that the expression of human ribosomal RNA genes (rDNA) in normal and cancer cells is differentially regulated by methylation of the promoter CpG islands. Furthermore, we showed that the methyl CpG-binding protein MBD2 plays a selective role in the methylation-mediated block in rDNA expression. Here, we analyzed the role of three functional mammalian DNA methyltransferases (DNMTs) in regulating the rDNA promoters activity. Immunofluorescence analysis and biochemical fractionation showed that all three DNMTs (DNMT1, DNMT3A, and DNMT3B) are associated with the inactive rDNA in the nucleolus. Although DNMTs associate with both methylated and unmethylated rDNA promoters, DNMT1 preferentially associates with the methylated genes. The rDNA primary transcript level was significantly elevated in DNMT1-/- or DNMT3B-/- human colon carcinoma (HCT116) cells. Southern blot analysis demonstrated a moderate level of rDNA promoter hypomethylation in DNMT1-/- cells and a dramatic loss of rDNA promoter methylation in double knockout cells. Transient overexpression of DNMT1 or DNMT3B suppressed the luciferase expression from both methylated and unmethylated pHrD-IRES-Luc, a reporter plasmid where the rDNA promoter drives luciferase expression. DNMT1-mediated suppression of the unmethylated promoter involves de novo methylation of the promoter, whereas histone deacetylase 2 cooperates with DNMT1 to inhibit the methylated rDNA promoter. Unlike DNMT1, both the wild type and catalytically inactive DNMT3B mutant can suppress rDNA promoter irrespective of its methylation status. DNMT3B-mediated suppression of the rDNA promoter also involves histone deacetylation. Treatment of HCT116 cells with Decitabine (a DNMT inhibitor) or trichostatin A (a histone deacetylase inhibitor) up-regulated endogenous rDNA expression. These inhibitors synergistically activated methylated pHrD-IRES-Luc, whereas they exhibited additive effects on the unmethylated promoter. These results demonstrate localization of DNMTs with the inactive rDNA in the nucleolus, the specific role of DNMT1 and DNMT3B in rDNA expression and the differential regulation of rDNA expression from the methylated and unmethylated rDNA promoters.
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Affiliation(s)
- Sarmila Majumder
- Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, Ohio 43210.
| | - Kalpana Ghoshal
- Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, Ohio 43210
| | - Jharna Datta
- Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, Ohio 43210
| | - David Spencer Smith
- Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, Ohio 43210
| | - Shoumei Bai
- Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, Ohio 43210
| | - Samson T Jacob
- Department of Molecular and Cellular Biochemistry, College of Medicine, Ohio State University, Columbus, Ohio 43210.
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235
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Fung WT, Sze KH, Lee KF, Shaw PC. Functional studies of the small subunit of EcoHK31I DNA methyltransferase. Biol Chem 2006; 387:507-13. [PMID: 16740121 DOI: 10.1515/bc.2006.066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
EcoHK31I DNA methyltransferase recognizes the sequence 5'-YGGCCR-3' and adds a methyl group to the fifth position of the internal cytosine to protect the DNA from cleavage by its cognate endonuclease. M.EcoHK31I is composed of polypeptides alpha and beta. Polypeptide beta only contains the conserved IX motif of the C5-MTase family, and provides a unique example to show that this motif alone may be dislocated to another polypeptide. By electromobility shift assay, we found that the alpha/beta complex recognizes specific oligonucleotide substrates. Polypeptide alpha formed aggregates with DNA, while polypeptide beta alone did not bind DNA. Therefore, polypeptide beta assists in the proper binding of polypeptide alpha to DNA substrate. The complex of polypeptide alpha and a polypeptide beta variant with an N-terminal deletion of 41 amino acids showed a 16-fold reduction in methylation activity. Further deletion resulted in an inactive methyltransferase. The dissociation equilibrium constant (Kd) of the alpha/beta complex was 56.4 nM, while the Kd value for the alpha/deltaN46-polypeptide beta complex was increased approximately 95-fold, caused by a drastic decrease in dissociate rate constant (kd) and an increase in the association rate constant (ka). This indicates that the N-terminal region of polypeptide beta takes part in subunit interaction, while the C-terminal region is involved in DNA binding.
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Affiliation(s)
- Wai-To Fung
- Department of Biochemistry and Centre for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, NT, Hong Kong, China
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236
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Grayson DR, Chen Y, Costa E, Dong E, Guidotti A, Kundakovic M, Sharma RP. The human reelin gene: Transcription factors (+), repressors (−) and the methylation switch (+/−) in schizophrenia. Pharmacol Ther 2006; 111:272-86. [PMID: 16574235 DOI: 10.1016/j.pharmthera.2005.01.007] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2005] [Accepted: 01/27/2005] [Indexed: 01/01/2023]
Abstract
A recent report suggests that the down-regulation of reelin and glutamic acid decarboxylase (GAD(67)) mRNAs represents 2 of the more consistent findings thus far described in post-mortem material from schizophrenia (SZ) patients [reviewed in. Neurochemical markers for schizophrenia, bipolar disorder amd major depression in postmortem brains. Biol Psychiatry 57, 252-260]. To study mechanisms responsible for this down-regulation, we have analyzed the promoter of the human reelin gene. Collectively, our studies suggest that SZ is characterized by a gamma-amino butyric acid (GABA)-ergic neuron pathology presumably mediated by promoter hypermethylation facilitated by the over-expression of the methylating enzyme DNA methyltransferase (Dnmt) 1. Using transient expression assays, promoter deletions and co-transfection assays with various transcription factors, we have shown a clear synergistic action that is a critical component of the mechanism of the trans-activation process. Equally important is the observation that the reelin promoter is more heavily methylated in brain regions in patients diagnosed with SZ as compared to non-psychiatric control subjects [Grayson, D. R., Jia, X., Chen, Y., Sharma, R. P., Mitchell, C. P., & Guidotti, A., et al. (2005). Reelin promoter hypermethylation in schizophrenia. Proc Natl Acad Sci U S A 102, 9341-9346]. The combination of studies in cell lines and in animal models of SZ, coupled with data obtained from post-mortem human material provides compelling evidence that aberrant methylation may be part of a core dysfunction in this psychiatric disease. More interestingly, the hypermethylation concept provides a coherent mechanism that establishes a plausible link between the epigenetic misregulation of multiple genes that are affected in SZ and that collectively contribute to the associated symptomatology.
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Affiliation(s)
- Dennis R Grayson
- Department of Psychiatry, The Psychiatric Institute, College of Medicine, University of Illinois at Chicago, 1601 W. Taylor St., 60612, USA.
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237
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Park JH, Roeder RG. GAS41 is required for repression of the p53 tumor suppressor pathway during normal cellular proliferation. Mol Cell Biol 2006; 26:4006-16. [PMID: 16705155 PMCID: PMC1489109 DOI: 10.1128/mcb.02185-05] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
GAS41 is a common subunit of the TIP60 and SRCAP complexes and is essential for cell growth and viability. Here, we report that GAS41 is required for repression of the p53 tumor suppressor pathway during normal cellular proliferation. Either GAS41 small interfering RNA-mediated knockdown of GAS41 expression or specific interruptions of the carboxy-terminal coiled-coil motif of the GAS41 protein activate the p53 tumor suppressor pathway, as evidenced by p53 up-regulation, p53 serine-15 phosphorylation, and p21 transcriptional activation. Activation of the p53 pathway does not result from changes in TIP60 complex assembly or TIP60 coactivator functions for p53, since a TIP60 complex containing a coiled-coil mutant of GAS41 retains the same composition and histone acetyltransferase activity as its wild-type counterpart and since mutant GAS41 does not compromise ectopic p53-dependent transcriptional activation in a reporter gene assay. Finally, we demonstrate that GAS41 is prebound to the promoters of two p53 tumor suppressor pathway genes (p21 and p14ARF) in normal unstressed cells but is dissociated from both promoters in response to stress signals that activate p53. Our data suggest that GAS41 plays a role in repressing the p53 tumor suppressor pathway during the normal cell cycle by a TIP60-independent mechanism.
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Affiliation(s)
- Jeong Hyeon Park
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10021, USA
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238
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Lavelle D, Vaitkus K, Hankewych M, Singh M, DeSimone J. Effect of 5-aza-2'-deoxycytidine (Dacogen) on covalent histone modifications of chromatin associated with the epsilon-, gamma-, and beta-globin promoters in Papio anubis. Exp Hematol 2006; 34:339-47. [PMID: 16543068 DOI: 10.1016/j.exphem.2005.12.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2005] [Revised: 12/07/2005] [Accepted: 12/09/2005] [Indexed: 11/21/2022]
Abstract
OBJECTIVE Treatment with the DNA demethylating drug 5-aza-2'-deoxycytidine (Dacogen; DAC) increased fetal hemoglobin and F cells to therapeutically significant levels in patients with sickle cell disease. To gain more insight into the mechanism of action of this drug and to increase our understanding of the relationship between DNA methylation and chromatin structure, we have determined the effect of DAC on covalent histone modifications of chromatin associated with the epsilon, gamma-, and beta-globin promoters in purified bone marrow erythroid cells of four baboons (P. anubis) pre- and posttreatment. RESULTS Fetal hemoglobin increased from 6.45%+/-1.75% in pretreatment samples to 62.1%+/-7.94% following DAC. DNA methylation of three CpG sites within the epsilon-globin promoter and 5 CpG sites within the gamma-globin promoter decreased more than 50% following DAC treatment. Levels of RNA polymerase II, acetyl-histone H3, acetyl-histone H4, dimethyl-histone H3 (lys4), dimethyl-histone H3 (lys36), and dimethyl-histone H3 (lys79) associated with the epsilon-, gamma-, and beta-globin promoters were determined by chromatin immunoprecipitation of formaldehyde-fixed chromatin followed by real-time PCR. Dacogen treatment increased the association of RNA polymerase II, acetyl-histone H3, and acetyl-histone H4 with the gamma-globin promoter but did not significantly affect the association of dimethyl-histone H3 (lys4), dimethyl-histone H3 (lys36), and dimethyl-histone H3 (lys79) with the epsilon-, gamma-, and beta-globin gene promoters. CONCLUSION These experiments illustrate the usefulness of the baboon model to investigate the mechanism of pharmacologic reactivation of fetal hemoglobin synthesis at the molecular level.
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Affiliation(s)
- Donald Lavelle
- Jesse Brown VA Medical Center and Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA.
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239
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Weller RL, Rajski SR. Design, synthesis, and preliminary biological evaluation of a DNA methyltransferase-directed alkylating agent. Chembiochem 2006; 7:243-5. [PMID: 16365907 DOI: 10.1002/cbic.200500362] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Rachel L Weller
- University of Wisconsin-Madison, Department of Chemistry, Madison, WI 53706, USA
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240
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Feng YQ, Desprat R, Fu H, Olivier E, Lin CM, Lobell A, Gowda SN, Aladjem MI, Bouhassira EE. DNA methylation supports intrinsic epigenetic memory in mammalian cells. PLoS Genet 2006; 2:e65. [PMID: 16683039 PMCID: PMC1449906 DOI: 10.1371/journal.pgen.0020065] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Accepted: 03/17/2006] [Indexed: 12/31/2022] Open
Abstract
We have investigated the role of DNA methylation in the initiation and maintenance of silenced chromatin in somatic mammalian cells. We found that a mutated transgene, in which all the CpG dinucleotides have been eliminated, underwent transcriptional silencing to the same extent as the unmodified transgene. These observations demonstrate that DNA methylation is not required for silencing. The silenced CpG-free transgene exhibited all the features of heterochromatin, including silencing of transcriptional activity, delayed DNA replication, lack of histone H3 and H4 acetylation, lack of H3-K4 methylation, and enrichment in tri-methyl-H3-K9. In contrast, when we tested for transgene reactivation using a Cre recombinase-mediated inversion assay, we observed a marked difference between a CpG-free and an unmodified transgene: the CpG-free transgene resumed transcription and did not exhibit markers of heterochromatin whereas the unmodified transgene remained silenced. These data indicate that methylation of CpG residues conferred epigenetic memory in this system. These results also suggest that replication delay, lack of histone H3 and H4 acetylation, H3-K4 methylation, and enrichment in tri-methyl-H3-K9 are not sufficient to confer epigenetic memory. We propose that DNA methylation within transgenes serves as an intrinsic epigenetic memory to permanently silence transgenes and prevent their reactivation.
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Affiliation(s)
- Yong-Qing Feng
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
| | - Romain Desprat
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
| | - Haiqing Fu
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Emmanuel Olivier
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
| | - Chii Mei Lin
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Amanda Lobell
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
| | - Shilpa N Gowda
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Mirit I Aladjem
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Eric E Bouhassira
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
- * To whom correspondence should be addressed. E-mail:
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241
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Aouacheria A, Navratil V, Barthelaix A, Mouchiroud D, Gautier C. Bioinformatic screening of human ESTs for differentially expressed genes in normal and tumor tissues. BMC Genomics 2006; 7:94. [PMID: 16640784 PMCID: PMC1459866 DOI: 10.1186/1471-2164-7-94] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Accepted: 04/26/2006] [Indexed: 11/24/2022] Open
Abstract
Background Owing to the explosion of information generated by human genomics, analysis of publicly available databases can help identify potential candidate genes relevant to the cancerous phenotype. The aim of this study was to scan for such genes by whole-genome in silico subtraction using Expressed Sequence Tag (EST) data. Methods Genes differentially expressed in normal versus tumor tissues were identified using a computer-based differential display strategy. Bcl-xL, an anti-apoptotic member of the Bcl-2 family, was selected for confirmation by western blot analysis. Results Our genome-wide expression analysis identified a set of genes whose differential expression may be attributed to the genetic alterations associated with tumor formation and malignant growth. We propose complete lists of genes that may serve as targets for projects seeking novel candidates for cancer diagnosis and therapy. Our validation result showed increased protein levels of Bcl-xL in two different liver cancer specimens compared to normal liver. Notably, our EST-based data mining procedure indicated that most of the changes in gene expression observed in cancer cells corresponded to gene inactivation patterns. Chromosomes and chromosomal regions most frequently associated with aberrant expression changes in cancer libraries were also determined. Conclusion Through the description of several candidates (including genes encoding extracellular matrix and ribosomal components, cytoskeletal proteins, apoptotic regulators, and novel tissue-specific biomarkers), our study illustrates the utility of in silico transcriptomics to identify tumor cell signatures, tumor-related genes and chromosomal regions frequently associated with aberrant expression in cancer.
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Affiliation(s)
- Abdel Aouacheria
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université Claude Bernard Lyon 1, 69622 Villeurbanne Cedex, France
- Current address: Apoptosis and Oncogenesis Laboratory, IBCP, UMR 5086 CNRS-UCBL, IFR 128, Lyon, France
| | - Vincent Navratil
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université Claude Bernard Lyon 1, 69622 Villeurbanne Cedex, France
| | | | - Dominique Mouchiroud
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université Claude Bernard Lyon 1, 69622 Villeurbanne Cedex, France
| | - Christian Gautier
- Laboratoire de Biométrie et Biologie Evolutive, CNRS UMR 5558, Université Claude Bernard Lyon 1, 69622 Villeurbanne Cedex, France
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242
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Suzuki M, Yamada T, Kihara-Negishi F, Sakurai T, Hara E, Tenen DG, Hozumi N, Oikawa T. Site-specific DNA methylation by a complex of PU.1 and Dnmt3a/b. Oncogene 2006; 25:2477-88. [PMID: 16331260 DOI: 10.1038/sj.onc.1209272] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2005] [Revised: 10/06/2005] [Accepted: 10/20/2005] [Indexed: 11/09/2022]
Abstract
The Ets transcription factor PU.1 is a hematopoietic master regulator essential for the development of myeloid and B-cell lineages. As we previously reported, PU.1 sometimes represses transcription on forming a complex with mSin3A-histone deacetyl transferase-MeCP2. Here, we show an interaction between PU.1 and DNA methyltransferases, DNA methyltransferase (Dnmt)3a and Dnmt3b (Dnmt3s). Glutathione-S-transferase pulldown assay revealed that PU.1 directly interacted with the ATRX domain of Dnmt3s through the ETS domain. Dnmt3s repressed the transcriptional activity of PU.1 on a reporter construct with trimerized PU.1-binding sites. The repression was recovered by addition of 5-aza-deoxycitidine, a DNA methyltransferase inhibitor, but not trichostatin A, a histone deacetylase inhibitor. Bisulfite sequence analysis revealed that several CpG sites in the promoter region neighboring the PU.1-binding sites were methylated when Dnmt3s were coexpressed with PU.1. We also showed that the CpG sites in the p16(INK4A) promoter were methylated by overexpression of PU.1 in NIH3T3 cells, accompanied by a downregulation of p16(INK4A) gene expression. These results suggest that PU.1 may downregulate its target genes through an epigenetic modification such as DNA methylation.
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Affiliation(s)
- M Suzuki
- Department of Cell Genetics, Sasaki Institute, Tokyo, Japan
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243
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Fong CW, Chua MS, McKie AB, Ling SHM, Mason V, Li R, Yusoff P, Lo TL, Leung HY, So SKS, Guy GR. Sprouty 2, an inhibitor of mitogen-activated protein kinase signaling, is down-regulated in hepatocellular carcinoma. Cancer Res 2006; 66:2048-58. [PMID: 16489004 DOI: 10.1158/0008-5472.can-05-1072] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Sprouty proteins are increasingly being recognized to be deregulated in various types of cancers. This deregulation is often associated with aberrant signaling of receptor tyrosine kinases and its downstream effectors, leading to the mitogen-activated protein kinase (MAPK) signaling pathway. In human hepatocellular carcinoma, where the MAPK activity is enhanced via multiple hepatocarcinogenic factors, we observed a consistent reduced expression of the sprouty 2 (Spry2) transcript and protein in malignant hepatocytes compared with normal or cirrhotic hepatocytes. The expression pattern of Spry2 in hepatocellular carcinoma resembles that of several potential tumor markers of hepatocellular carcinoma and also that of several angiogenic factors and growth factor receptors. In contrast to previous studies of Spry2 down-regulation in other cancers, we have ruled out loss of heterozygosity or the methylation of promoter sites, two common mechanisms responsible for the silencing of genes with tumor suppressor properties. Functionally, we show that Spry2 inhibits both extracellular signal-regulated kinase signaling as well as proliferation in hepatocellular carcinoma cell lines, whereas knocking down Spry2 levels in NIH3T3 cells causes mild transformation. Our study clearly indicates a role for Spry2 in hepatocellular carcinoma, and an understanding of the regulatory controls of its expression could provide new means of regulating the angiogenic switch in this hypervascular tumor, thereby potentially controlling tumor growth.
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MESH Headings
- Adaptor Proteins, Signal Transducing
- Animals
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Cell Line, Tumor
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- DNA Methylation
- Down-Regulation
- Fibroblast Growth Factors/pharmacology
- Gene Expression Profiling
- Genes, Tumor Suppressor
- Hepatocyte Growth Factor/pharmacology
- Humans
- Intracellular Signaling Peptides and Proteins
- Liver Cirrhosis/genetics
- Liver Cirrhosis/metabolism
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Loss of Heterozygosity
- MAP Kinase Signaling System/physiology
- Membrane Proteins
- Mice
- Mitogen-Activated Protein Kinases/antagonists & inhibitors
- NIH 3T3 Cells
- Promoter Regions, Genetic
- Protein Serine-Threonine Kinases
- Proteins/genetics
- Proteins/metabolism
- Proteins/physiology
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
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Affiliation(s)
- Chee Wai Fong
- Signal Transduction Laboratory, Institute of Molecular and Cell Biology, Proteos, Singapore
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244
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Abstract
The 14-3-3sigma gene is a direct target of the p53 tumor suppressor and its product inhibits cell cycle progression. Recently, a proteomic analysis revealed that 14-3-3sigma regulates additional cellular processes relevant to carcinogenesis, as migration and MAP-kinase signalling. The expression of 14-3-3sigma is down-regulated by CpG methylation in several types of human cancer, among them prostate, lung, breast and several types of skin cancer. The epigenetic inactivation of 14-3-3sigma occurs at an early stage of tumor development and may allow evasion from senescence and promote genomic instability. In the future the detection of CpG methylation of 14-3-3sigma may be used for diagnostic and prognostic purposes.
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Affiliation(s)
- Dmitri Lodygin
- Molecular Oncology, Independent Max-Planck Research Group, Max-Planck-Institute of Biochemistry, Martinsried, Munich, Germany
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245
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Koturbash I, Rugo RE, Hendricks CA, Loree J, Thibault B, Kutanzi K, Pogribny I, Yanch JC, Engelward BP, Kovalchuk O. Irradiation induces DNA damage and modulates epigenetic effectors in distant bystander tissue in vivo. Oncogene 2006; 25:4267-75. [PMID: 16532033 DOI: 10.1038/sj.onc.1209467] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Irradiated cells induce chromosomal instability in unirradiated bystander cells in vitro. Although bystander effects are thought to be linked to radiation-induced secondary cancers, almost no studies have evaluated bystander effects in vivo. Furthermore, it has been proposed that epigenetic changes mediate bystander effects, but few studies have evaluated epigenetic factors in bystander tissues in vivo. Here, we describe studies in which mice were unilaterally exposed to X-irradiation and the levels of DNA damage, DNA methylation and protein expression were evaluated in irradiated and bystander cutaneous tissue. The data show that X-ray exposure to one side of the animal body induces DNA strand breaks and causes an increase in the levels of Rad51 in unexposed bystander tissue. In terms of epigenetic changes, unilateral radiation suppresses global methylation in directly irradiated tissue, but not in bystander tissue at given time-points studied. Intriguingly, however, we observed a significant reduction in the levels of the de novo DNA methyltransferases DNMT3a and 3b and a concurrent increase in the levels of the maintenance DNA methyltransferase DNMT1 in bystander tissues. Furthermore, the levels of two methyl-binding proteins known to be involved in transcriptional silencing, MeCP2 and MBD2, were also increased in bystander tissue. Together, these results show that irradiation induces DNA damage in bystander tissue more than a centimeter away from directly irradiated tissues, and suggests that epigenetic transcriptional regulation may be involved in the etiology of radiation-induced bystander effects.
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Affiliation(s)
- I Koturbash
- Department of Biological Sciences, University of Lethbridge, Alberta, Canada
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246
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Lavelle D, Vaitkus K, Hankewych M, Singh M, DeSimone J. Developmental changes in DNA methylation and covalent histone modifications of chromatin associated with the ε-, γ-, and β-globin gene promoters in Papio anubis. Blood Cells Mol Dis 2006; 36:269-78. [PMID: 16527500 DOI: 10.1016/j.bcmd.2006.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2005] [Revised: 12/27/2005] [Accepted: 01/03/2006] [Indexed: 11/22/2022]
Abstract
The baboon is a suitable and relevant animal model to study the mechanism of human globin gene switching. This investigation addresses the role of DNA methylation and histone coding in globin gene switching in the baboon, Papio anubis. Bisulfite sequencing and chromatin immunoprecipitation studies were performed in erythroid cells purified from fetuses of varying gestational ages and from adult bone marrow to analyze the manner that changes in DNA methylation of the epsilon-, gamma-, and beta-globin promoters and association of ac-H3, ac-H4, H3-dimeK4, H3-dimeK36, and H3-dimeK79 with the epsilon-, gamma-, and beta-globin promoters occur during development. Changes in DNA methylation of the epsilon- and gamma-globin gene promoters during transitional stages of globin gene switching were consistent with the stochastic model of methylation and a role of DNA methylation in gene silencing. Enrichment of ac-H3, ac-H4, and pol II at the promoters of developmentally active genes was observed, while the pattern of distribution of H3-dimeK4 and H3-dimeK79 suggests that these modifications are found near both currently and formerly active promoters. Enrichment of H3-dimeK36 at the silenced epsilon-globin gene promoter was observed. These studies demonstrate that coordinated epigenetic modifications in the chromatin structure of the beta-like globin gene promoters accompany the highly regulated changes in expression patterns of these genes during development.
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Affiliation(s)
- Donald Lavelle
- Jesse Brown VA Medical Center and Department of Medicine, University of Illinois, MP151C, 820 S. Damen Ave., Chicago, IL 60612, USA.
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247
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Brero A, Leonhardt H, Cardoso MC. Replication and Translation of Epigenetic Information. Curr Top Microbiol Immunol 2006; 301:21-44. [PMID: 16570844 DOI: 10.1007/3-540-31390-7_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Most cells in multicellular organisms contain identical genetic information but differ in their epigenetic information. The latter is encoded at the molecular level by post-replicative methylation of certain DNA bases (in mammals 5-methyl cytosine at CpG sites) and multiple histone modifications in chromatin. In addition, higher-order chromatin structures are generated during differentiation, which might impact on genome expression and stability. The epigenetic information needs to be "translated" in order to define specific cell types with specific sets of active and inactive genes, collectively called the epigenome. Once established, the epigenome needs to be "replicated" at each cell division cycle, i.e., both genetic and epigenetic information have to be faithfully duplicated, which implies a tight coordination between the DNA replication machinery and epigenetic regulators. In this review, we focus on the molecules and mechanisms responsible for the replication and translation of DNA methylation in mammals as one of the central epigenetic marks.
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Affiliation(s)
- A Brero
- Max Delbrück Center for Molecular Medicine, FVK, Berlin, Germany
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248
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Harony H, Bernes S, Siman-Tov R, Ankri S. DNA methylation and targeting of LINE retrotransposons in Entamoeba histolytica and Entamoeba invadens. Mol Biochem Parasitol 2006; 147:55-63. [PMID: 16530279 DOI: 10.1016/j.molbiopara.2006.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Revised: 01/25/2006] [Accepted: 02/03/2006] [Indexed: 10/25/2022]
Abstract
In this study, we have isolated by affinity chromatography, using anti-m5C antibody as a ligand, a DNA encoding reverse transcriptase of LINE retrotransposon (RT LINE) in both Entamoeba invadens and Entamoeba histolytica. RT LINE transcripts were detected in E. histolytica but were absent from E. invadens. The methylation status of genomic copies of E. invadens RT LINE was confirmed by bisulfite analysis. In contrast, all the genomic copies of the E. histolytica RT LINE analyzed in this study were not methylated. Many of these genomic copies diverge from the RT LINE isolated by m5C affinity chromatography by a number of mutations that includes conversion of C to T and G to A. These mutations are reminiscent of the conversion of C to T (and G to A on the complementary DNA strand) that occurred during primate evolution in Alu elements following accelerated deamination of methylated cytosines. E. invadens and E. histolytica RT LINEs isolated by affinity chromatography were cloned in a pEhAct Neo vector, amplified in E. coli GM2163 (dam-dcm) and transformed into E. histolytica. Bisulfite analysis of transfected amoeba showed the presence of m5C in E. invadens RT LINE replicated in E. histolytica, but not in E. histolytica RT LINE or in the neomycine phosphotransferase gene, which is also carried by the pEhAct Neo vector. These results suggest the existence of a specific mechanism based on DNA methylation that controls retrotransposons in these parasites.
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Affiliation(s)
- Hala Harony
- Department of Molecular Microbiology, The Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, P.O. Box 9649, 31096 Haifa, Israel
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249
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Rodenhiser D, Mann M. Epigenetics and human disease: translating basic biology into clinical applications. CMAJ 2006; 174:341-8. [PMID: 16446478 PMCID: PMC1373719 DOI: 10.1503/cmaj.050774] [Citation(s) in RCA: 270] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Epigenetics refers to the study of heritable changes in gene expression that occur without a change in DNA sequence. Research has shown that epigenetic mechanisms provide an "extra" layer of transcriptional control that regulates how genes are expressed. These mechanisms are critical components in the normal development and growth of cells. Epigenetic abnormalities have been found to be causative factors in cancer, genetic disorders and pediatric syndromes as well as contributing factors in autoimmune diseases and aging. In this review, we examine the basic principles of epigenetic mechanisms and their contribution to human health as well as the clinical consequences of epigenetic errors. In addition, we address the use of epigenetic pathways in new approaches to diagnosis and targeted treatments across the clinical spectrum.
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Affiliation(s)
- David Rodenhiser
- EpiGenWestern Research Group, Children's Health Research Institute, London, Ont.
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250
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Pogribny I, Koturbash I, Tryndyak V, Hudson D, Stevenson SML, Sedelnikova O, Bonner W, Kovalchuk O. Fractionated low-dose radiation exposure leads to accumulation of DNA damage and profound alterations in DNA and histone methylation in the murine thymus. Mol Cancer Res 2006; 3:553-61. [PMID: 16254189 DOI: 10.1158/1541-7786.mcr-05-0074] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Thymus, an important component of hematopoietic tissue, is a well-documented "target" of radiation carcinogenesis. Both acute and fractionated irradiation result in a high risk of leukemia and thymic lymphoma. However, the exact mechanisms underlying radiation-induced predisposition to leukemia and lymphoma are still unknown, and the contributions of genetic and epigenetic mechanisms in particular have yet to be defined. Global DNA hypomethylation is a well-known characteristic of cancer cells. Recent studies have also shown that tumor cells undergo prominent changes in histone methylation, particularly a substantial loss of trimethylation of histone H4-Lys20 and demethylation of genomic DNA. These losses are considered a universal marker of malignant transformation. In the present study, we investigated the effect of low-dose radiation exposure on the accumulation of DNA lesions and alterations of DNA methylation and histone H4-Lys20 trimethylation in the thymus tissue using an in vivo murine model. For the first time, we show that fractionated whole-body application of 0.5 Gy X-ray leads to decrease in histone H4-Lys20 trimethylation in the thymus. The loss of histone H4-Lys20 trimethylation was accompanied by a significant decrease in global DNA methylation as well as the accumulation of DNA damage as monitored by persistence of histone gammaH2AX foci in the thymus tissue of mice exposed to fractionated irradiation. Altered DNA methylation was associated with reduced expression of maintenance (DNMT1) and, to a lesser extent, de novo DNA methyltransferase DNMT3a in exposed animals. Expression of another de novo DNA methyltransferase DNMT3b was decreased only in males. Irradiation also resulted in approximately 20% reduction in the levels of methyl-binding proteins MeCP2 and MBD2. Our results show the involvement of epigenetic alterations in radiation-induced responses in vivo. These changes may play a role in genome destabilization that ultimately leads to cancer.
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Affiliation(s)
- Igor Pogribny
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, Arkansas, USA
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