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Kojima N, Suda T, Kurinomaru T, Kurita R. Immobilization of DNA with nitrogen mustard-biotin conjugate for global epigenetic analysis. Anal Chim Acta 2018; 1043:107-114. [PMID: 30392657 DOI: 10.1016/j.aca.2018.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 12/01/2022]
Abstract
We report the quantitative analysis of 5-methylcytosine, a representative epigenetic modification in genomic DNA, with an enzyme-linked immunosorbent assay (ELISA). We synthesized a novel hetero-bifunctional linker molecule consisting of nitrogen mustard and biotin to capture DNA on the surface of biosensing devices. The molecule can successfully immobilize genomic DNA on a streptavidin coated 96-well microplate, which was then employed for immunochemical epigenetic assessment. We achieved the sensitive and quantitative detection of 5-mC in genomic DNA samples. The CpG methylation ratios obtained from our system for mouse brain and mouse small intestine genomes were 79% and 82%, respectively. These numbers are in good agreement with the previously reported methylation ratio of 75-85%, which was identified by whole genome bisulfite sequencing. Accordingly, the present technology using our novel bifunctional linker molecule provides a fast, easy, and inexpensive method for epigenetic assessment, without the need for any conventional bisulfite treatment, polymerase chain reaction (PCR), or sequencing.
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Affiliation(s)
- Naoshi Kojima
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB, DAICENTER, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Tomomi Suda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB, DAICENTER, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Takaaki Kurinomaru
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka, 563-8577, Japan
| | - Ryoji Kurita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB, DAICENTER, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
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Garcia-Moreno SA, Plebanek MP, Capel B. Epigenetic regulation of male fate commitment from an initially bipotential system. Mol Cell Endocrinol 2018; 468:19-30. [PMID: 29410272 PMCID: PMC6084468 DOI: 10.1016/j.mce.2018.01.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 12/21/2022]
Abstract
A fundamental goal in biology is to understand how distinct cell types containing the same genetic information arise from a single stem cell throughout development. Sex determination is a key developmental process that requires a unidirectional commitment of an initially bipotential gonad towards either the male or female fate. This makes sex determination a unique model to study cell fate commitment and differentiation in vivo. We have focused this review on the accumulating evidence that epigenetic mechanisms contribute to the bipotential state of the fetal gonad and to the regulation of chromatin accessibility during and immediately downstream of the primary sex-determining switch that establishes the male fate.
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Affiliation(s)
| | | | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.
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Kurinomaru T, Kojima N, Kurita R. An alkylating immobilization linker for immunochemical epigenetic assessment. Chem Commun (Camb) 2018; 53:8308-8311. [PMID: 28686257 DOI: 10.1039/c7cc02883k] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A bifunctional linker molecule containing nitrogen mustard and a cyclic disulfide group has been developed for the covalent immobilization of intact DNA, which allows quantitative analysis of epigenomic modification in immobilized DNA using SPR-based immune sensing.
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Affiliation(s)
- Takaaki Kurinomaru
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
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4
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Herceg Z. Epigenetic Mechanisms as an Interface Between the Environment and Genome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 903:3-15. [PMID: 27343085 DOI: 10.1007/978-1-4899-7678-9_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Recent advances in epigenetics have had tremendous impact on our thinking and understanding of biological phenomena and the impact of environmental stressors on complex diseases, notably cancer. Environmental and lifestyle factors are thought to be implicated in the development of a wide range of human cancers by eliciting epigenetic changes, however, the underlying mechanisms remain poorly understood. Epigenetic mechanisms can be viewed as an interface between the genome and environmental influence, therefore aberrant epigenetic events associated with environmental stressors and factors in the cell microenvironment are likely to play an important role in the onset and progression of different human malignancies. At the cellular level, aberrant epigenetic events influence critical cellular events (such as gene expression, carcinogen detoxification, DNA repair, and cell cycle), which are further modulated by risk factor exposures and thus may define the severity/subtype of cancer. This review summarizes recent progress in our understanding of the epigenetic mechanisms through which environmental stressors and endogenous factors may promote tumor development and progression.
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Affiliation(s)
- Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France.
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Dyachenko OV, Tarlachkov SV, Marinitch DV, Shevchuk TV, Buryanov YI. Expression of exogenous DNA methyltransferases: application in molecular and cell biology. BIOCHEMISTRY (MOSCOW) 2015; 79:77-87. [PMID: 24794723 DOI: 10.1134/s0006297914020011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
DNA methyltransferases might be used as powerful tools for studies in molecular and cell biology due to their ability to recognize and modify nitrogen bases in specific sequences of the genome. Methylation of the eukaryotic genome using exogenous DNA methyltransferases appears to be a promising approach for studies on chromatin structure. Currently, the development of new methods for targeted methylation of specific genetic loci using DNA methyltransferases fused with DNA-binding proteins is especially interesting. In the present review, expression of exogenous DNA methyltransferase for purposes of in vivo analysis of the functional chromatin structure along with investigation of the functional role of DNA methylation in cell processes are discussed, as well as future prospects for application of DNA methyltransferases in epigenetic therapy and in plant selection.
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Affiliation(s)
- O V Dyachenko
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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6
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Truong M, Yang B, Wagner J, Desotelle J, Jarrard DF. Analysis of promoter non-CG methylation in prostate cancer. Epigenomics 2013; 5:65-71. [PMID: 23414321 DOI: 10.2217/epi.12.67] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND In vertebrates, DNA methylation occurs primarily at CG dinucleotides but recently, non-CG methylation has been found at appreciable levels in embryonic stem cells. MATERIALS & METHODS To assess non-CG methylation in cancer, we compared the extent of non-CG methylation at several biologically important CG islands in prostate cancer and normal cell lines. An assessment of the promoter CG islands EVX1 and FILIP1L demonstrates a fourfold higher rate of non-CG methylation at EVX1 compared with FILIP1L across all cell lines. These loci are densely methylated at CG sites in cancer. RESULTS No significant difference in non-CG methylation was demonstrated between cancer and normal. Treatment of cancer cell lines with 5-azacytidine significantly reduced methylation within EVX1 at CG and CC sites, preferentially. CONCLUSION Non-CG methylation does not correlate with CG methylation at hypermethylated promoter regions in cancer. Furthermore, global inhibition of DNA methyltransferases does not affect all methylated cytosines uniformly.
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Affiliation(s)
- Matthew Truong
- Department of Urology, University of Wisconsin School of Medicine & Public Health, Madison, WI, USA
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Nishino K, Hattori N, Sato S, Arai Y, Tanaka S, Nagy A, Shiota K. Non-CpG methylation occurs in the regulatory region of the Sry gene. J Reprod Dev 2011; 57:586-93. [PMID: 21636956 DOI: 10.1262/jrd.11-033a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Sry (sex determining region on Y chromosome) gene is a master gene for sex determination. We previously reported that the Sry gene has tissue-dependent and differentially methylated regions (T-DMRs) by analyzing the DNA methylation states at CpG sites in the promoter regions. In this study, we found unique non-CpG methylation at the internal cytosine in the 5'-CCTGG-3' pentanucleotide sequence in the Sry T-DMR. This non-CpG methylation was detected in four mouse strains (ICR, BALB/c, DBA2 and C3H), but not in two strains (C57BL/6 and 129S1), suggesting that the CCTGG methylation is tentative and unstable. Interestingly, this CCTGG methylation was associated with demethylation of the CpG sites in the Sry T-DMR in the developmental process. A methylation-mediated promoter assay showed that the CCTGG methylation promotes gene expression. Our finding shows that non-CpG methylation has unique characteristic and is still conserved in mammals.
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Affiliation(s)
- Koichiro Nishino
- Laboratory of Cellular Biochemistry, Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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Fuso A, Ferraguti G, Grandoni F, Ruggeri R, Scarpa S, Strom R, Lucarelli M. Early demethylation of non-CpG, CpC-rich, elements in the myogenin 5'-flanking region: a priming effect on the spreading of active demethylation. Cell Cycle 2010; 9:3965-76. [PMID: 20935518 DOI: 10.4161/cc.9.19.13193] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The dynamic changes and structural patterns of DNA methylation of genes without CpG islands are poorly characterized. The relevance of CpG to the non-CpG methylation equilibrium in transcriptional repression is unknown. In this work, we analyzed the DNA methylation pattern of the 5'-flanking of the myogenin gene, a positive regulator of muscle differentiation with no CpG island and low CpG density, in both C2C12 muscle satellite cells and embryonic muscle. Embryonic brain was studied as a non-expressing tissue. High levels of both CpG and non-CpG methylation were observed in non-expressing experimental conditions. Both CpG and non-CpG methylation rapidly dropped during muscle differentiation and myogenin transcriptional activation, with an active demethylation dynamics. Non-CpG demethylation occurred more rapidly than CpG demethylation. Demethylation spread from initially highly methylated short CpC-rich elements to a virtually unmethylated status. These short elements have a high CpC content and density, share some motifs and largely coincide with putative recognition sequences of some differentiation-related transcription factors. Our findings point to a dynamically controlled equilibrium between CpG and non-CpG active demethylation in the transcriptional control of tissue-specific genes. The short CpC-rich elements are new structural features of the methylation machinery, whose functions may include priming the complete demethylation of a transcriptionally crucial DNA region.
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Affiliation(s)
- Andrea Fuso
- Department of Surgery P. Valdoni, Sapienza University of Rome, Italy
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Dyachenko OV, Schevchuk TV, Kretzner L, Buryanov YI, Smith SS. Human non-CG methylation: are human stem cells plant-like? Epigenetics 2010; 5:569-72. [PMID: 20647766 DOI: 10.4161/epi.5.7.12702] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Non-CG methylation is well characterized in plants, where it appears to play a role in gene silencing and genomic imprinting. Although strong evidence for the presence of non-CG methylation in animals has been available for some time, both its origin and function remain elusive. In this review we discuss available evidence on non-CG methylation in animals in light of evidence suggesting that the human stem cell methylome contains significant levels of methylation outside the CG site.
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Affiliation(s)
- Olga V Dyachenko
- Pushchino Branch, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia
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10
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Dyachenko OV, Shevchuk TV, Buryanov YI. Structural and functional features of the 5-methylcytosine distribution in the eukaryotic genome. Mol Biol 2010. [DOI: 10.1134/s0026893310020019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Cruickshank MN, Besant P, Ulgiati D. The impact of histone post-translational modifications on developmental gene regulation. Amino Acids 2010; 39:1087-105. [PMID: 20204433 DOI: 10.1007/s00726-010-0530-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 02/12/2010] [Indexed: 02/06/2023]
Abstract
Eukaryotic genomic DNA is orderly compacted to fit into the nucleus and to inhibit accessibility of specific sequences. DNA is manipulated in many different ways by bound RNA and proteins within the composite material known as chromatin. All of the biological processes that require access to genomic DNA (such as replication, recombination and transcription) therefore are dependent on the precise characteristics of chromatin in eukaryotes. This distinction underlies a fundamental property of eukaryotic versus prokaryotic gene regulation such that chromatin structure must be regulated to precisely repress or relieve repression of particular regions of the genome in an appropriate spatio-temporal manner. As well as playing a key role in structuring genomic DNA, histones are subject to site-specific modifications that can influence the organization of chromatin structure. This review examines the molecular processes regulating site-specific histone acetylation, methylation and phosphorylation with an emphasis on how these processes underpin differentiation-regulated transcription.
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Affiliation(s)
- Mark N Cruickshank
- Biochemistry and Molecular Biology, School of Biomedical, Biomolecular and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
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12
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Sotgia S, Zinellu A, Pisanu E, Murgia L, Pinna GA, Gaspa L, Deiana L, Carru C. A hydrophilic interaction ultraperformance liquid chromatography (HILIC–UPLC) method for genomic DNA methylation assessment by UV detection. Anal Bioanal Chem 2010; 396:2937-41. [DOI: 10.1007/s00216-010-3565-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 02/05/2010] [Accepted: 02/10/2010] [Indexed: 01/30/2023]
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13
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Brena RM, Plass C. Bio-COBRA: absolute quantification of DNA methylation in electrofluidics chips. Methods Mol Biol 2009; 507:257-69. [PMID: 18987820 DOI: 10.1007/978-1-59745-522-0_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
DNA methylation is the best-studied epigenetic modification, and in mammals it describes the conversion of cytosine to 5-methylcytosine in the context of CpG dinucleotides. In recent years, it has become evident that epigenetic mechanisms are severely disrupted in human neoplasia, and evidence suggests that alterations of DNA methylation patterns may be an integral mechanism in the etiology of other diseases such as bipolar disorder and schizophrenia. The main effect of altered DNA methylation is the disruption of normal patterns of gene expression through genomic instability and hypermethylation of CpG islands, which together could lead to uncontrolled cell proliferation. DNA methylation can be reversed through pharmacological intervention via the systemic administration of DNA methylation inhibitors. Thus, the ability to accurately quantify DNA methylation levels in genomic sequences is a prerequisite to assess not only treatment efficacy, but also the effect of the DNA methylation inhibitors on bystander tissues. Several methods are currently available for the analysis of DNA methylation. Nonetheless, accurate and reproducible quantification of DNA methylation remains challenging. Here, we describe Bio-COBRA, a modified protocol for combined bisulfite restriction analysis (COBRA) that incorporates an electrophoresis step in microfluidics chips. Microfluidics technology involves the handling of small amounts of liquid in miniaturized systems. Bio-COBRA provides a platform for the rapid and quantitative assessment of DNA methylation patterns in large sample sets. Its sensitivity and reproducibility also make it an excellent tool for the analysis of DNA methylation in clinical samples.
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Affiliation(s)
- Romulo Martin Brena
- Division of Human Cancer Genetics, The Ohio State University, Columbus, OH, USA
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14
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Sotgia S, Carru C, Franconi F, Fiori PB, Manca S, Pettinato S, Magliona S, Ginanneschi R, Deiana L, Zinellu A. Rapid quantification of total genomic DNA methylation degree by short-end injection capillary zone electrophoresis. J Chromatogr A 2008; 1185:145-50. [DOI: 10.1016/j.chroma.2008.01.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 01/09/2008] [Accepted: 01/15/2008] [Indexed: 11/29/2022]
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Brena RM, Auer H, Kornacker K, Plass C. Quantification of DNA methylation in electrofluidics chips (Bio-COBRA). Nat Protoc 2007; 1:52-8. [PMID: 17406211 DOI: 10.1038/nprot.2006.8] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alterations of normal gene expression patterns are a hallmark of human cancers. It is now clear that the dysregulation of epigenetic modifications of the DNA and surrounding histones contributes to aberrant gene silencing, thus being major participants not only in the progression but also the initiation of the disease phenotype. The best-studied epigenetic modification is DNA methylation, which converts cytosine to 5-methylcytosine. Aberrant hypermethylation of the promoter is frequently observed in cancer and is generally associated with gene silencing. Currently, accurate and reproducible quantification of DNA methylation remains challenging. Here, we describe Bio-COBRA, a modified protocol for Combined Bisulfite Restriction Analysis (COBRA), that incorporates an electrophoresis step in microfluidics chips. Microfluidics technology involves the handling of small amounts of liquid in miniaturized systems. In the life sciences, microfluidics usually entails the scaling down of at least one application, such as electrophoresis, to chip format, which often results in increased efficiency and reliability. Bio-COBRA provides a platform for the rapid and quantitative assessment of DNA methylation patterns in large sample sets. Its sensitivity and reproducibility also makes it a tool for the analysis of DNA methylation in clinical samples. The Bio-COBRA assay can be performed on 12 samples in less than 1 h. If the protocol is started at the DNA isolation step, however, approximately 48 h would be required to complete the entire procedure.
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Affiliation(s)
- Romulo M Brena
- Department of Molecular Genetics, The Ohio State University, 420 West 12th Ave, Room 435, Columbus, Ohio 43210, USA
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Brena RM, Auer H, Kornacker K, Hackanson B, Raval A, Byrd JC, Plass C. Accurate quantification of DNA methylation using combined bisulfite restriction analysis coupled with the Agilent 2100 Bioanalyzer platform. Nucleic Acids Res 2006; 34:e17. [PMID: 16464820 PMCID: PMC1361623 DOI: 10.1093/nar/gnj017] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
DNA methylation is the best-studied epigenetic modification and describes the conversion of cytosine to 5-methylcytosine. The importance of this phenomenon is that aberrant promoter hypermethylation is a common occurrence in cancer and is frequently associated with gene silencing. Various techniques are currently available for the analysis of DNA methylation. However, accurate and reproducible quantification of DNA methylation remains challenging. In this report, we describe Bio-COBRA (combined bisulfite restriction analysis coupled with the Agilent 2100 Bioanalyzer platform), as a novel approach to quantitative DNA methylation analysis. The combination of a well-established method, COBRA, which interrogates DNA methylation via the restriction enzyme analysis of PCR-amplified bisulfite treated DNAs, with the Bioanalyzer platform allows for the rapid and quantitative assessment of DNA methylation patterns in large sample sets. The sensitivity and reproducibility of Bio-COBRA make it a valuable tool for the analysis of DNA methylation in clinical samples, which could aid in the development of diagnostic and prognostic parameters with respect to disease detection and management.
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Affiliation(s)
- Romulo Martin Brena
- Department of Molecular Genetics, The Ohio State UniversityColumbus, OH, USA
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State UniversityColumbus, OH, USA
| | - Herbert Auer
- Columbus Children's Research InstituteColumbus, OH, USA
| | - Karl Kornacker
- Division of Sensory Biophysics, The Ohio State UniversityColumbus, OH, USA
| | - Björn Hackanson
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State UniversityColumbus, OH, USA
- Department of Hematology, University of Freiburg Medical CenterFreiburg, Germany
| | - Aparna Raval
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State UniversityColumbus, OH, USA
| | - John C. Byrd
- Department of Medicine and the Comprehensive Cancer Center, Divisions of Hematology-Oncology, The Ohio State UniversityColumbus, OH, USA
| | - Christoph Plass
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State UniversityColumbus, OH, USA
- To whom correspondence should be addressed at Division of Human Cancer Genetics, Medical Research Facility Room 464A, 420 West 12th Avenue, Columbus, OH 43210, USA. Tel: +1 614 292 6505; Fax: +1 614 688 4761;
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Brena RM, Huang THM, Plass C. Quantitative assessment of DNA methylation: potential applications for disease diagnosis, classification, and prognosis in clinical settings. J Mol Med (Berl) 2006; 84:365-77. [PMID: 16416310 DOI: 10.1007/s00109-005-0034-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Accepted: 11/29/2005] [Indexed: 12/31/2022]
Abstract
Deregulation of the epigenome is now recognized as a major mechanism involved in the development and progression of human diseases such as cancer. As opposed to the irreversible nature of genetic events, which introduce changes in the primary DNA sequence, epigenetic modifications are reversible and leave the original DNA sequence intact. There is now evidence that the epigenetic landscape in humans undergoes modifications as the result of normal aging, with older individuals exhibiting higher levels of promoter hypermethylation compared to younger ones. Thus, it has been proposed that the higher incidence of certain disease in older individuals might be, in part, a consequence of an inherent change in the control and regulation of the epigenome. These observations are of remarkable clinical significance since the aberrant epigenetic changes characteristic of disease provide a unique platform for the development of new therapeutic approaches. In this review, we address the significance of DNA methylation changes that result or lead to disease, occur with aging, or may be the result of environmental exposure. We provide a detailed description of quantitative techniques currently available for the detection and analysis of DNA methylation and provide a comprehensive framework that may allow for the incorporation of protocols which include DNA methylation as a tool for disease diagnosis and classification, which could lead to the tailoring of therapeutic approaches designed to individual patient needs.
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Affiliation(s)
- Romulo Martin Brena
- Division of Human Cancer Genetics, Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
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18
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Shevchuk T, Kretzner L, Munson K, Axume J, Clark J, Dyachenko OV, Caudill M, Buryanov Y, Smith SS. Transgene-induced CCWGG methylation does not alter CG methylation patterning in human kidney cells. Nucleic Acids Res 2005; 33:6124-36. [PMID: 16246913 PMCID: PMC1266073 DOI: 10.1093/nar/gki920] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2005] [Revised: 09/09/2005] [Accepted: 10/05/2005] [Indexed: 12/21/2022] Open
Abstract
Several reports suggest that C(m)CWGG methylation tends not to co-exist with (m)CG methylation in human cells. We have asked whether or not methylation at CCWGG sites can influence CG methylation. DNA from cells expressing an M.EcoRII-GFP fusion was actively methylated at CCWGG sites. CG methylation as measured by R.HpaII/R.MspI ratios was unchanged in cells expressing the transgene. Cloned representatives of C(m)CWGG methylated DNA often contained, or were adjacent to an ALU repeat, suggesting that M.EcoRII-GFP actively methylated gene-rich R-band DNA. The transgenic methyltransferase applied C(m)CWGG methylation to a representative human promoter that was heavily methylated at CG dinucleotides (the SERPINB5 promoter) and to a representative promoter that was essentially unmethylated at CG dinucleotides (the APC promoter). In each case, the CG methylation pattern remained in its original state, unchanged by the presence of neighboring C(m)CWGG sites. Q-PCR measurements showed that RNA expression from the APC gene was not significantly altered by the presence of C(m)CWGG in its promoter. Kinetic studies suggested that an adjacent C(m)CWGG methylation site influences neither the maintenance nor the de novo methylation activities of purified human Dnmt1. We conclude that C(m)CWGG methylation does not exert a significant effect on CG methylation in human kidney cells.
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Affiliation(s)
- Taras Shevchuk
- City of Hope National Medical Center and Beckman Research Institute1500 E. Duarte Road, Duarte, CA 91010, USA
- Laboratory of Plant Biotechnology, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesPushchino, Moscow Region 142290, Russia
| | - Leo Kretzner
- City of Hope National Medical Center and Beckman Research Institute1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Kristofer Munson
- City of Hope National Medical Center and Beckman Research Institute1500 E. Duarte Road, Duarte, CA 91010, USA
| | - John Axume
- Department of Human Nutrition and Food Science, College of Agriculture, California State Polytechnic University3801 West Temple Avenue, Pomona, CA 91768, USA
| | - Jarrod Clark
- City of Hope National Medical Center and Beckman Research Institute1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Olga V. Dyachenko
- Laboratory of Plant Biotechnology, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesPushchino, Moscow Region 142290, Russia
| | - Marie Caudill
- Department of Human Nutrition and Food Science, College of Agriculture, California State Polytechnic University3801 West Temple Avenue, Pomona, CA 91768, USA
| | - Yaroslav Buryanov
- Laboratory of Plant Biotechnology, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesPushchino, Moscow Region 142290, Russia
| | - Steven S. Smith
- City of Hope National Medical Center and Beckman Research Institute1500 E. Duarte Road, Duarte, CA 91010, USA
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Krüger DH, Reuter M. Reliable detection of DNA cytosine methylation at CpNpG sites using the engineered restriction enzyme EcoRII-C. Biotechniques 2005; 38:855-6. [PMID: 16018543 DOI: 10.2144/05386bm01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Detlev H Krüger
- Institute of Virology, Humboldt University, Charité Medical School, Berlin, Germany.
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Aniello F, Villano G, Corrado M, Locascio A, Russo MT, D'Aniello S, Francone M, Fucci L, Branno M. Structural organization of the sea urchin DNA (cytosine-5)-methyltransferase gene and characterization of five alternative spliced transcripts. Gene 2003; 302:1-9. [PMID: 12527191 DOI: 10.1016/s0378-1119(02)01138-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Sea urchin DNA (cytosine-5)-methyltransferase (Dnmt1) that is responsible for maintenance of DNA methylation patterns clearly shares similarity with various Dnmt1s identified in vertebrates. In this study, we determined the structure of the sea urchin Dnmt1 gene by screening a genomic library of the sea urchin Paracentrotus lividus with the complementary DNA (cDNA) as probe. Analysis of the positive clones demonstrated that the Dnmt1 gene consists of 34 exons and 33 introns spanning a distance of 35 kb. All exon-intron junction sequences agree with the GT/AG consensus with the exception of the 3' acceptor site of intron 8 where CT replaces AG consensus. The differences in the total number of exons between sea urchin and mouse genes reside mainly in the N-terminal region of the protein (exons 5-7 of the sea urchin, exons 5-12 of the mouse) where there is very low similarity in the amino acid sequence. By reverse transcription-polymerase chain reaction using oligonucleotides spanning different regions of the cDNA we carried out a comprehensive analysis of alternative splicing of the Dnmt1 messenger RNA (mRNA) in sea urchin embryos at different stages of development. We demonstrated the presence of at least five alternative spliced mRNAs that are regulated during development and are translated in truncated or deleted proteins.
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Affiliation(s)
- Francesco Aniello
- Department of Genetics, General and Molecular Biology, University of Naples Federico II, via Mezzocannone 8, 80134, Naples, Italy
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Cao X, Jacobsen SE. Locus-specific control of asymmetric and CpNpG methylation by the DRM and CMT3 methyltransferase genes. Proc Natl Acad Sci U S A 2002; 99 Suppl 4:16491-8. [PMID: 12151602 PMCID: PMC139913 DOI: 10.1073/pnas.162371599] [Citation(s) in RCA: 415] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many plant, animal, and fungal genomes contain cytosine DNA methylation in asymmetric sequence contexts (CpHpH, H = A, T, C). Although the enzymes responsible for this methylation are unknown, it has been assumed that asymmetric methylation is maintained by the persistent activity of de novo methyltransferases (enzymes capable of methylating previously unmodified DNA). We recently reported that the DOMAINS REARRANGED METHYLASE (DRM) genes are required for de novo DNA methylation in Arabidopsis thaliana because drm1 drm2 double mutants lack the de novo methylation normally associated with transgene silencing. In this study, we have used bisulfite sequencing and Southern blot analysis to examine the role of the DRM loci in the maintenance of asymmetric methylation. At some loci, drm1 drm2 double mutants eliminated all asymmetric methylation. However, at the SUPERMAN locus, asymmetric methylation was only completely abolished in drm1 drm2 chromomethylase 3 (cmt3) triple mutant plants. drm1 drm2 double mutants also showed a strong reduction of CpNpG (n = A, T, C, or G) methylation at some loci, but not at others. The drm1 drm2 cmt3 triple mutant plants did not affect CpG methylation at any locus tested, suggesting that the primary CpG methylases are encoded by the MET1 class of genes. Although neither the drm1 drm2 double mutants nor the cmt3 single mutants show morphological defects, drm1 drm2 cmt3 triple mutant plants show pleiotropic effects on plant development. Our results suggest that the DRM and CMT3 genes act in a partially redundant and locus-specific manner to control asymmetric and CpNpG methylation.
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Affiliation(s)
- Xiaofeng Cao
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles 90095-1606, USA
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22
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French SW, Dawson DW, Miner MD, Doerr JR, Malone CS, Wall R, Teitell MA. DNA methylation profiling: a new tool for evaluating hematologic malignancies. Clin Immunol 2002; 103:217-30. [PMID: 12173296 DOI: 10.1006/clim.2002.5186] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Samuel W French
- Department of Pathology and Laboratory Medicine, UCLA School of Medicine, 675 Charles E. Young Dr. South, MRL 4-760, Los Angeles, CA 90095-1732, USA
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23
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Franchina M, Kay PH. Novel nucleotide substitutions within the coding region of DNMT2 are in strong linkage disequilibrium in Caucasians and Japanese. Hum Hered 2002; 52:210-6. [PMID: 11713417 DOI: 10.1159/000053378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Investigations into mechanims by which cytosine methylation may be genetically controlled have led to the identification of single nucleotide polymorphisms within the coding region of DNMT2 that are conserved in different ethnic groups. The DNMT2 I allele includes a G at nucleotide position 104 of exon 2 and a C at position 50 of exon 4. The alternative allele, DNMT2 II, includes an A and T, respectively, at these positions. G was never found in the absence of C and vice versa and A was never found in the absence of T and vice versa. The gene products of DNMT2 I and DNMT2 II differ by the inclusion of a histidine or tyrosine residue at the position specified by codon 101. This amino acid substitution alters the amino acid composition of a conserved methylating enzyme motif shown to be involved in S-adenosylmethionine binding in M.HhaI, a bacterial methyltransferase that is almost identical to DNMT2 in size and structure. Demonstration of strong linkage disequilibrium between the nucleotide substitutions associated with each DNMT2 allele provides valuable tools for the investigation of molecular genetic mechanisms of evolution and speciation.
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Affiliation(s)
- M Franchina
- Department of Pathology, The University of Western Australia, Perth, Australia
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Franchina M, Hooper J, Kay PH. Five novel alternatively spliced transcripts of DNA (cytosine-5) methyltransferase 2 in human peripheral blood leukocytes. Int J Biochem Cell Biol 2001; 33:1104-15. [PMID: 11551826 DOI: 10.1016/s1357-2725(01)00074-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Alternative splicing of RNA molecules transcribed from DNA (cytosine-5) methyltransferases has been proposed as a mechanism by which methylation is able to effect diverse biological processes in higher eukaryotes. This study has investigated transcriptional versatility of DNA (cytosine-5) methyltransferase 2, which may methylate cytosine residues within 5'-CCTGG-3' pentanucleotides in regions of the human genome devoid of 5'-CG-3' methylation. Five novel splice variants of DNA (cytosine-5) methyltransferase 2 were identified in the peripheral blood leukocytes of healthy subjects following cloning and sequencing of RT-PCR products amplified using gene specific oligodeoxyribonucleotide primers. The generation of some of these splice variants may be influenced by the formation of secondary structures within pre-mRNA due to the repetition of sequences flanking alternatively spliced exons in a reverse and complementary orientation on the same strand. These findings enable novel approaches to investigate the role of RNA secondary structures in alternative splicing. The DNA (cytosine-5) methyltransferase 2 splice variants are generated in all the major cell types of peripheral blood, as well as in neoplastic lymphoid cells indicating that they are unlikely to generate proteins involved in control of the cell cycle or cellular differentiation. Interestingly, the gene products generated by some splice variants completely or partially lack highly conserved amino acid motifs shown to be important for the catalysis of cytosine methylation. The possibility cannot be excluded, therefore, that alternative splicing of DNA (cytosine-5) methyltransferase 2 pre-mRNA may generate protein isoforms which have different methylating capabilities or which are involved in biological processes other than the catalysis of cytosine methylation.
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Affiliation(s)
- M Franchina
- Molecular Pathology Laboratory, Department of Pathology, The University of Western Australia, WA 6907, Nedlands, Australia
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25
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Malone CS, Miner MD, Doerr JR, Jackson JP, Jacobsen SE, Wall R, Teitell M. CmC(A/T)GG DNA methylation in mature B cell lymphoma gene silencing. Proc Natl Acad Sci U S A 2001; 98:10404-9. [PMID: 11504918 PMCID: PMC56973 DOI: 10.1073/pnas.181206898] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA methylation has been linked to gene silencing in cancer. Primary effusion lymphoma (PEL) and myeloma are lymphoid malignancies that arise from terminally differentiated B cells. Interestingly, PEL do not express immunoglobulins or most B lineage-specific genes. The B cell-specific B29 (Igbeta/CD79b) gene is silenced in PEL and some myelomas but is expressed in other normal and malignant B cells. B29 expression was reactivated in PEL by demethylating and histone deacetylase inhibiting treatments. Bisulfite sequencing revealed two types of DNA methylation in silenced B29 promoters: at conventional CpG and at CC(A/T)GG B29 promoter sites. The pattern of methylated CpG ((m)CpG) and C(m)C(A/T)GG B29 promoter methylation observed was similar to that recently reported for epigenetic silencing of an integrated retrovirus. Methylation of C(m)C(A/T)GG sites in the B29 promoter significantly repressed in vivo transcriptional activity. Also, methylation of a central conserved C(m)CTGG B29 promoter site blocked the binding of early B cell factor. This methylated motif formed DNA-protein complexes with nuclear extracts from all cell types examined. Therefore, C(m)C(A/T)GG methylation may represent an important type of epigenetic marker on mammalian DNA that impacts transcription by altering DNA-protein complex formation.
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Affiliation(s)
- C S Malone
- Department of Microbiology and Immunology, Jonsson Comprehensive Cancer Center, University of California, Center for the Health Sciences, Los Angeles, CA 90095, USA
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Lorincz MC, Groudine M. C(m)C(a/t)GG methylation: a new epigenetic mark in mammalian DNA? Proc Natl Acad Sci U S A 2001; 98:10034-6. [PMID: 11526227 PMCID: PMC56909 DOI: 10.1073/pnas.201392598] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- M C Lorincz
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
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