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Minskaia E, Lacerda JF. Analysis of FOXP3 DNA Methylation Patterns to Identify Functional FOXP3+ T-Cell Subpopulations. Methods Mol Biol 2023; 2559:115-136. [PMID: 36180630 DOI: 10.1007/978-1-0716-2647-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Human regulatory CD4+CD25+FOXP3+ T cells (Tregs) are involved in the suppression of immune responses and play important roles in the maintenance of self-tolerance and immune homeostasis. Abnormal Treg function may result in disease states of varying severity. As FOXP3-expressing Treg cells are phenotypically and functionally heterogeneous, the success of Treg therapies depends on the ability to reliably distinguish subpopulations of T cells bearing a Treg-like phenotype. Methylation of cytosines within CpG dinucleotides is an important epigenetic mechanism involved in regulation (and suppression) of gene expression. On the other hand, demethylation of regulatory DNA sequences, such as promoters and enhancers, is essential for initiation of gene transcription. This protocol shows that bisulfite sequencing (BS) distinguishes methylated and unmethylated cytosines within DNA and reveals the methylation status of individual CpGs in cells within each population, identifying functionally different FOXP3+ subpopulations.
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Affiliation(s)
- Ekaterina Minskaia
- Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
- Infection and Immunity Division, Institute of Immunity and Transplantation, University College London, Royal Free Hospital, London, UK
| | - João F Lacerda
- Instituto de Medicina Molecular - João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal.
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2
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Lountos GT, Cherry S, Tropea JE, Wlodawer A, Miller M. Structural basis for cell type specific DNA binding of C/EBPβ: The case of cell cycle inhibitor p15INK4b promoter. J Struct Biol 2022; 214:107918. [PMID: 36343842 PMCID: PMC9909937 DOI: 10.1016/j.jsb.2022.107918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/22/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
C/EBPβ is a key regulator of numerous cellular processes, but it can also contribute to tumorigenesis and viral diseases. It binds to specific DNA sequences (C/EBP sites) and interacts with other transcription factors to control expression of multiple eukaryotic genes in a tissue and cell-type dependent manner. A body of evidence has established that cell-type-specific regulatory information is contained in the local DNA sequence of the binding motif. In human epithelial cells, C/EBPβ is an essential cofactor for TGFβ signaling in the case of Smad2/3/4 and FoxO-dependent induction of the cell cycle inhibitor, p15INK4b. In the TGFβ-responsive region 2 of the p15INK4b promoter, the Smad binding site is flanked by a C/EBP site, CTTAA•GAAAG, which differs from the canonical, palindromic ATTGC•GCAAT motif. The X-ray crystal structure of C/EBPβ bound to the p15INK4b promoter fragment shows how GCGC-to-AAGA substitution generates changes in the intermolecular interactions in the protein-DNA interface that enhances C/EBPβ binding specificity, limits possible epigenetic regulation of the promoter, and generates a DNA element with a unique pattern of methyl groups in the major groove. Significantly, CT/GA dinucleotides located at the 5'ends of the double stranded element maintain local narrowing of the DNA minor groove width that is necessary for DNA recognition. Our results suggest that C/EBPβ would accept all forms of modified cytosine in the context of the CpT site. This contrasts with the effect on the consensus motif, where C/EBPβ binding is modestly increased by cytosine methylation, but substantially decreased by hydroxymethylation.
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Affiliation(s)
- George T Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
| | - Scott Cherry
- Protein Purification Core, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Joseph E Tropea
- Protein Purification Core, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Alexander Wlodawer
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702-1201 USA
| | - Maria Miller
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702-1201 USA
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3
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Shenk CE, O'Donnell KJ, Pokhvisneva I, Kobor MS, Meaney MJ, Bensman HE, Allen EK, Olson AE. Epigenetic Age Acceleration and Risk for Posttraumatic Stress Disorder following Exposure to Substantiated Child Maltreatment. JOURNAL OF CLINICAL CHILD AND ADOLESCENT PSYCHOLOGY : THE OFFICIAL JOURNAL FOR THE SOCIETY OF CLINICAL CHILD AND ADOLESCENT PSYCHOLOGY, AMERICAN PSYCHOLOGICAL ASSOCIATION, DIVISION 53 2022; 51:651-661. [PMID: 33471576 PMCID: PMC8289945 DOI: 10.1080/15374416.2020.1864738] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
OBJECTIVE Child maltreatment is among the strongest predictors of posttraumatic stress disorder (PTSD). However, less than 40% of children who have been maltreated are ever diagnosed with PTSD, suggesting that exposure to child maltreatment alone is insufficient to explain this risk. This study examined whether epigenetic age acceleration, a stress-sensitive biomarker derived from DNA methylation, explains variation in PTSD diagnostic status subsequent to child maltreatment. METHOD Children and adolescents (N = 70; 65.7% female), 8-15 years of age (M = 12.00, SD = 2.37) and exposed to substantiated child maltreatment within the 12 months prior to study entry, were enrolled. Participants provided epithelial cheek cells via buccal swab for genotyping and quantification of epigenetic age acceleration within a case-control design. PTSD diagnostic status was determined using the Child PTSD Symptoms Scale according to the DSM-IV-TR algorithm. RESULTS Epigenetic age acceleration predicted current PTSD status, revealing an effect size magnitude in the moderate range, OR = 2.35, 95% CI: 1.22- 4.51, after adjusting for sample demographics, polygenic risk for PTSD, and lifetime exposure to other childhood adversities. Supplemental analyses demonstrated that epigenetic age acceleration was related to a greater severity of PTSD arousal symptoms (r =.29, p =.015). There were no differential effects for child maltreatment subtype on epigenetic age acceleration or PTSD status. CONCLUSIONS The biological embedding of child maltreatment may explain variation in PTSD diagnostic status and serve as a novel approach for informing selective prevention or precision-based therapeutics for those at risk for PTSD.
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Affiliation(s)
- Chad E Shenk
- Department of Human Development and Family Studies, The Pennsylvania State University
- Department of Pediatrics, The Pennsylvania State University College of Medicine
| | - Kieran J O'Donnell
- The Douglas Hospital Research Centre, Department of Psychiatry, McGill University
- Child and Brain Developmental Program, Canadian Institute for Advanced Research
| | - Irina Pokhvisneva
- The Douglas Hospital Research Centre, Department of Psychiatry, McGill University
| | - Michael S Kobor
- Child and Brain Developmental Program, Canadian Institute for Advanced Research
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia
| | - Michael J Meaney
- The Douglas Hospital Research Centre, Department of Psychiatry, McGill University
- Child and Brain Developmental Program, Canadian Institute for Advanced Research
- Agency for Science, Technology and Research, Singapore Institute of Clinical Sciences
| | - Heather E Bensman
- Department of Pediatrics, The University of Cincinnati College of Medicine
| | - Elizabeth K Allen
- Department of Human Development and Family Studies, The Pennsylvania State University
| | - Anneke E Olson
- Department of Human Development and Family Studies, The Pennsylvania State University
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Vetter VM, Spira D, Banszerus VL, Demuth I. Epigenetic Clock and Leukocyte Telomere Length Are Associated with Vitamin D Status but not with Functional Assessments and Frailty in the Berlin Aging Study II. J Gerontol A Biol Sci Med Sci 2021; 75:2056-2063. [PMID: 32324874 DOI: 10.1093/gerona/glaa101] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Indexed: 12/14/2022] Open
Abstract
DNA methylation (DNAm) age acceleration, a parameter derived via the epigenetic clock, has recently been suggested as a biomarker of aging. We hypothesized that accelerated biological aging, measured by both this new and the established biomarker of aging, relative leukocyte telomere length (rLTL), are associated with vitamin D deficiency. Moreover, we tested for an association between rLTL/DNAm age acceleration and different clinical assessments for functional capacity, including the Fried frailty score. Cross-sectional data of 1,649 participants of the Berlin Aging Study II was available (~50% female, age: 22-37 and 60-84 years). A seven cytosine-phosphate-guanine clock was estimated to calculate the DNAm age acceleration. rLTL was measured by quantitative real-time polymerase chain reaction (PCR). 25-hydroxyvitamin D (25(OH)D) serum levels <25 nmol/L was defined as vitamin D deficiency and <50 nmol/L as vitamin D insufficiency. Vitamin D-sufficient individuals had a 1.4 years lower mean DNAm age acceleration (p < .05, analysis of variance [ANOVA]) and a 0.11 longer rLTL (p < .001, ANOVA) than vitamin D-deficient participants. Likewise, vitamin D-sufficient participants had lower DNAm age acceleration (β = 1.060, p = .001) and longer rLTL (β = -0.070; p < .001) than vitamin D nonsufficient subjects in covariate-adjusted analysis. Neither DNAm age acceleration nor rLTL were significantly associated with the Fried frailty score or the functional assessments. Only the clock drawing test was associated with DNAm age acceleration (subgroup of older men: β = 1.898, p = .002). Whether the analyzed biomarkers of aging can be used to predict an individual's functional capacity or will be associated with frailty in the advanced course of aging, will be clarified by future longitudinal analyses.
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Affiliation(s)
- Valentin Max Vetter
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Lipid Clinic at the Interdisciplinary Metabolism Center, Germany
| | - Dominik Spira
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Lipid Clinic at the Interdisciplinary Metabolism Center, Germany
| | - Verena Laura Banszerus
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Lipid Clinic at the Interdisciplinary Metabolism Center, Germany
| | - Ilja Demuth
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Lipid Clinic at the Interdisciplinary Metabolism Center, Germany.,Charité - Universitätsmedizin Berlin, BCRT - Berlin Institute of Health Center for Regenerative Therapies, Germany
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Costantino S, Libby P, Kishore R, Tardif JC, El-Osta A, Paneni F. Epigenetics and precision medicine in cardiovascular patients: from basic concepts to the clinical arena. Eur Heart J 2018; 39:4150-4158. [PMID: 29069341 PMCID: PMC6293269 DOI: 10.1093/eurheartj/ehx568] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/04/2017] [Accepted: 09/22/2017] [Indexed: 12/11/2022] Open
Abstract
Cardiovascular diseases (CVDs) remain the leading cause of mortality worldwide and also inflict major burdens on morbidity, quality of life, and societal costs. Considering that CVD preventive medications improve vascular outcomes in less than half of patients (often relative risk reductions range from 12% to 20% compared with placebo), precision medicine offers an attractive approach to refine the targeting of CVD medications to responsive individuals in a population and thus allocate resources more wisely and effectively. New tools furnished by advances in basic science and translational medicine could help achieve this goal. This approach could reach beyond the practitioners 'eyeball' assessment or venerable markers derived from the physical examination and standard laboratory evaluation. Advances in genetics have identified novel pathways and targets that operate in numerous diseases, paving the way for 'precision medicine'. Yet the inherited genome determines only part of an individual's risk profile. Indeed, standard genomic approaches do not take into account the world of regulation of gene expression by modifications of the 'epi'genome. Epigenetic modifications defined as 'heritable changes to the genome that do not involve changes in DNA sequence' have emerged as a new layer of biological regulation in CVD and could advance individualized risk assessment as well as devising and deploying tailored therapies. This review, therefore, aims to acquaint the cardiovascular community with the rapidly advancing and evolving field of epigenetics and its implications in cardiovascular precision medicine.
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Affiliation(s)
- Sarah Costantino
- Center for Molecular Cardiology, University of Zürich, Wagistrasse 12, Schlieren, Zurich, Switzerland
| | - Peter Libby
- Brigham and Women’s Hospital, Division of Cardiovascular Medicine, Boston, MA, USA
| | - Raj Kishore
- Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, MERB-953, 3500 N Broad Street, Philadelphia, PA, USA
- Department of Pharmacology, Temple University, Philadelphia, PA, USA
| | - Jean-Claude Tardif
- Montreal Health Innovations Coordinating Center (MHICC), Montreal, Canada
- Montreal Heart Institute, Université de Montréal, Montreal, Canada
| | - Assam El-Osta
- Central Clinical School, Faculty of Medicine, Monash University, Victoria, Australia
- Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR
| | - Francesco Paneni
- Center for Molecular Cardiology, University of Zürich, Wagistrasse 12, Schlieren, Zurich, Switzerland
- University Heart Center, Cardiology, University Hospital Zürich, Zürich, Switzerland
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Avin BA, Umbricht CB, Zeiger MA. Human telomerase reverse transcriptase regulation by DNA methylation, transcription factor binding and alternative splicing (Review). Int J Oncol 2016; 49:2199-2205. [PMID: 27779655 DOI: 10.3892/ijo.2016.3743] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 10/17/2016] [Indexed: 12/31/2022] Open
Abstract
The catalytic subunit of telomerase, human telomerase reverse transcriptase (hTERT), plays an essential role in telomere maintenance to oppose cellular senescence and, is highly regulated in normal and cancerous cells. Regulation of hTERT occurs through multiple avenues, including a unique pattern of CpG promoter methylation and alternative splicing. Promoter methylation affects the binding of transcription factors, resulting in changes in expression of the gene. In addition to expression level changes, changes in promoter binding can affect alternative splicing in a cotranscriptional manner. The alternative splicing of hTERT results in either the full length transcript which can form the active telomerase complex with hTR, or numerous inactive isoforms. Both regulation strategies are exploited in cancer to activate telomerase, however, the exact mechanism is unknown. Therefore, unraveling the link between promoter methylation status and alternative splicing for hTERT could expose yet another level of hTERT regulation. In an attempt to provide insight into the cellular control of active telomerase in cancer, this review will discuss our current perspective on CpG methylation of the hTERT promoter region, summarize the different forms of alternatively spliced variants, and examine examples of transcription factor binding that affects splicing.
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Affiliation(s)
- Brittany A Avin
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christopher B Umbricht
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Martha A Zeiger
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Yu CE, Foraker J. Epigenetic considerations of the APOE gene. [corrected]. Biomol Concepts 2016; 6:77-84. [PMID: 25741792 DOI: 10.1515/bmc-2014-0039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 02/03/2015] [Indexed: 11/15/2022] Open
Abstract
The apolipoprotein E (APOE) gene is robustly linked with numerous physiological conditions, including healthy aging, altered cardiovascular fitness, and cognitive function. These connections have been established primarily by phenotype-genotype association studies using APOE's three common genetic variants (ε2, ε3, and ε4). These variants encode for the three apoE protein isoforms (E2, E3, and E4), which have slightly different structures and, consequently, distinct functions in lipid metabolism. However, the differential lipid binding and transferring properties of these isoforms cannot fully explain the association of APOE with such a wide range of physiological phenotypes. One potential explanation for APOE's pleiotropic roles may lie in its unique epigenetic properties. In this article, we present a brief review of the APOE gene and protein, its disease associations, and epigenetic components, with a focus on DNA methylation. We close with a discussion of the prospective epigenetic implications of APOE in disease.
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Li C, Guo S, Zhang M, Gao J, Guo Y. DNA methylation and histone modification patterns during the late embryonic and early postnatal development of chickens. Poult Sci 2015; 94:706-21. [PMID: 25691759 DOI: 10.3382/ps/pev016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Early mammalian embryonic cells have been proven to be essential for embryonic development and the health of neonates. A series of epigenetic reprogramming events, including DNA methylation and histone modifications, occur during early embryonic development. However, epigenetic marks in late embryos and neonates are not well understood, especially in avian species. To investigate the epigenetic patterns of developing embryos and posthatched chicks, embryos at embryonic day 5 (E5), E8, E11, E14, E17, and E20 and newly hatched chicks on day of life 1 (D1), D7, D14, D21 were collected. The levels of global DNA methylation and histone H3 at lysine 9 residue (H3K9) modifications were measured in samples of liver, jejunum, and breast skeletal muscles by Western blotting and immunofluorescence staining. According to our data, decreased levels of proliferating cell nuclear antigen expression were found in the liver and a V-shaped pattern of proliferating cell nuclear antigen expression was found in the jejunum. The level of proliferating cell nuclear antigen in muscle was relatively stable. Caspase 3 expression gradually decreased over time in liver, was stable in the jejunum, and increased in muscle. Levels of DNA methylation and H3K9 acetylation decreased in liver over time, while the pattern was N-shaped in jejunal tissue and W-shaped in pectoral muscles, and these changes were accompanied by dynamic changes of DNA methyltransferases, histone acetyltransferases 1, and histone deacetylase 2. Moreover, dimethylation, trimethylation, and acetylation of H3K9 were expressed in a time- and tissue-dependent manner. After birth, epigenetic marks were relatively stable and found at lower levels. These results indicate that spatiotemporal specific epigenetic alterations could be critical for the late development of chick embryos and neonates.
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Affiliation(s)
- Changwu Li
- State Key Laboratory of Animal Nutrition, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, P. R. China
| | - Shuangshuang Guo
- State Key Laboratory of Animal Nutrition, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, P. R. China
| | - Ming Zhang
- State Key Laboratory of Animal Nutrition, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, P. R. China
| | - Jing Gao
- State Key Laboratory of Animal Nutrition, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, P. R. China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, Hubei Collaborative Innovation Center for Animal Nutrition and Feed Science, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, P. R. China
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Szyf M. The genome- and system-wide response of DNA methylation to early life adversity and its implication on mental health. CANADIAN JOURNAL OF PSYCHIATRY. REVUE CANADIENNE DE PSYCHIATRIE 2013; 58:697-704. [PMID: 24331290 DOI: 10.1177/070674371305801208] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Early life adversity is associated with long-tem impacts on behaviour and physical and mental health. The mechanisms mediating the impact of early life environment on the phenotype are proposed to involve a change in the state of deoxyribonucleic acid (DNA) methylation and, as a consequence, in the stable programming of gene expression. Recent studies suggest that the changes in DNA methylation affect broad genomic regions, as well as peripheral tissues in addition to brain regions. Although the data are still scarce, it points to the possibility that DNA methylation is a mechanism of genome adaptation to signals from early life social environment. This modulation of the DNA methylation pattern is proposed to result in long-term impact on the phenotype that could become maladaptive under certain contexts later in life. This model has implications on our understanding of behavioural and mental health pathologies, as well as their diagnosis and therapeutics.
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Affiliation(s)
- Moshe Szyf
- Professor, Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec
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Abstract
Although epidemiological data provide evidence that early life experience plays a critical role in human development, the mechanism of how this works remains in question. Recent data from human and animal literature suggest that epigenetic changes, such as DNA methylation, are involved not only in cellular differentiation but also in the modulation of genome function in response to early life experience affecting gene function and the phenotype. Such modulations may serve as a mechanism for life-long genome adaptation. These changes seem to be widely distributed across the genome and to involve central and peripheral systems. Examining the environmental circumstances associated with the onset and reversal of DNA methylation will be critical for understanding risk and resiliency.
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Herrera LA, Prada D, Andonegui MA, Dueñas-González A. The epigenetic origin of aneuploidy. Curr Genomics 2011; 9:43-50. [PMID: 19424483 PMCID: PMC2674307 DOI: 10.2174/138920208783884883] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Revised: 02/26/2008] [Accepted: 02/26/2008] [Indexed: 02/06/2023] Open
Abstract
Theodore Boveri, eminent German pathologist, observed aneuploidy in cancer cells more than a century ago and suggested that cancer cells derived from a single progenitor cell that acquires the potential for uncontrolled continuous proliferation. Currently, it is well known that aneuploidy is observed in virtually all cancers. Gain and loss of chromosomal material in neoplastic cells is considered to be a process of diversification that leads to survival of the fittest clones. According to Darwin’s theory of evolution, the environment determines the grounds upon which selection takes place and the genetic characteristics necessary for better adaptation. This concept can be applied to the carcinogenesis process, connecting the ability of cancer cells to adapt to different environments and to resist chemotherapy, genomic instability being the driving force of tumor development and progression. What causes this genome instability? Mutations have been recognized for a long time as the major source of genome instability in cancer cells. Nevertheless, an alternative hypothesis suggests that aneuploidy is a primary cause of genome instability rather than solely a simple consequence of the malignant transformation process. Whether genome instability results from mutations or from aneuploidy is not a matter of discussion in this review. It is most likely both phenomena are intimately related; however, we will focus on the mechanisms involved in aneuploidy formation and more specifically on the epigenetic origin of aneuploid cells. Epigenetic inheritance is defined as cellular information—other than the DNA sequence itself—that is heritable during cell division. DNA methylation and histone modifications comprise two of the main epigenetic modifications that are important for many physiological and pathological conditions, including cancer. Aberrant DNA methylation is the most common molecular cancer-cell lesion, even more frequent than gene mutations; tumor suppressor gene silencing by CpG island promoter hypermethylation is perhaps the most frequent epigenetic modification in cancer cells. Epigenetic characteristics of cells may be modified by several factors including environmental exposure, certain nutrient deficiencies, radiation, etc. Some of these alterations have been correlated with the formation of aneuploid cells in vivo. A growing body of evidence suggests that aneuploidy is produced and caused by chromosomal instability. We propose and support in this manuscript that not only genetics but also epigenetics, contribute in a major fashion to aneuploid cell formation.
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Affiliation(s)
- Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer (UIBC)-Instituto Nacional de Cancerología (INCan)-Instituto de Investigaciones Biomédicas (IIBM)-Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
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12
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Abstract
DNA methyltransferases catalyze the transfer of a methyl group from S-adenosyl-L-methionine to cytosine or adenine bases in DNA. These enzymes challenge the Watson/Crick dogma in two instances: 1) They attach inheritable information to the DNA that is not encoded in the nucleotide sequence. This so-called epigenetic information has many important biological functions. In prokaryotes, DNA methylation is used to coordinate DNA replication and the cell cycle, to direct postreplicative mismatch repair, and to distinguish self and nonself DNA. In eukaryotes, DNA methylation contributes to the control of gene expression, the protection of the genome against selfish DNA, maintenance of genome integrity, parental imprinting, X-chromosome inactivation in mammals, and regulation of development. 2) The enzymatic mechanism of DNA methyltransferases is unusual, because these enzymes flip their target base out of the DNA helix and, thereby, locally disrupt the B-DNA helix. This review describes the biological functions of DNA methylation in bacteria, fungi, plants, and mammals. In addition, the structures and mechanisms of the DNA methyltransferases, which enable them to specifically recognize their DNA targets and to induce such large conformational changes of the DNA, are discussed.
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Affiliation(s)
- Albert Jeltsch
- Institut für Biochemie, FB 8, Justus-Liebig-Universität, Heinrich-Buff-Ring 58, 35392 Giessen, Germany.
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Zardo G, Reale A, Passananti C, Pradhan S, Buontempo S, De Matteis G, Adams RLP, Caiafa P. Inhibition of poly(ADP-ribosyl)ation induces DNA hypermethylation: a possible molecular mechanism. FASEB J 2002; 16:1319-21. [PMID: 12154007 DOI: 10.1096/fj.01-0827fje] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The pattern of DNA methylation established during embryonic development is necessary for the control of gene expression and is preserved during the replicative process. DNA regions of about 1-2 kb in size, termed CpG islands and located mostly in the promoter regions of housekeeping genes, are protected from methylation, despite being about 6-10 times richer in the dinucleotide CpG than the rest of DNA. Their unmethylated state guarantees the expression of the corresponding housekeeping genes. At present, the mechanism by which CpG islands remain protected from methylation is not clear. However, some results suggest that poly(ADP-ribosyl)ation, an enzymatic process that introduces a postsynthetic modification onto chromatin proteins, might be involved. Here we show in L929 mouse fibroblast cells that inhibition of poly(ADP-ribose) polymerase(s) at different cell-cycle phases increases the mRNA and protein levels of the major maintenance DNA methyltransferase (DNMT1) in G1/S border. Increase of DNMT1 results in a premature PCNA-DNMT1 complex formation, which facilitates robust maintenance, as well as de novo DNA methylation processes during the G1/S border, which leads to abnormal hypermethylation.
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Affiliation(s)
- Giuseppe Zardo
- Department of Cellular Biotechnologies and Haematology, University of Rome La Sapienza, Rome, Italy
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Bhattacharya SK, Dubey AK. The N-terminus of m5C-DNA methyltransferase MspI is involved in its topoisomerase activity. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:2491-7. [PMID: 12027887 DOI: 10.1046/j.1432-1033.2002.02913.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
DNA cytosine methyltransferase MspI (M.MspI) must require a different type of interaction of protein with DNA from other bacterial DNA cytosine methyltransferases (m5C-MTases) to evoke the topoisomerase activity that it possesses in addition to DNA-methylation ability. This may require a different structural organization in the solution phase from the reported consensus structural arrangement for m5C-MTases. Limited proteolysis of M.MspI, however, generates two peptide fragments, a large one (p26) and a small one (p18), consistent with reported m5C-MTase structures. Examination of the amino-acid sequence of M.MspI revealed similarity to human topoisomerase I at the N-terminus. Alignment of the amino-acid sequence of M.MspI also uncovered similarity (residues 245-287) to the active site of human DNA ligase I. To evaluate the role of the N-terminus of M.MspI, 2-hydroxy-5-nitrobenzyl bromide (HNBB) was used to truncate M.MspI between residues 34 and 35. The purified HNBB-truncated protein has a molecular mass of approximately equal 45 kDa, retains DNA binding and methyltransferase activity, but does not possess topoisomerase activity. These findings were substantiated using a purified recombinant MspI protein with the N-terminal 34 amino acids deleted. Changing the N-terminal residues Trp34 and Tyr74 to alanine results in abolition of the topoisomerase I activity while the methyltransferase activity remains intact.
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Affiliation(s)
- Sanjoy K Bhattacharya
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology-Delhi, New Delhi, India.
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15
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Abstract
DNA methyltransferases catalyze the transfer of a methyl group from S-adenosyl-L-methionine to cytosine or adenine bases in DNA. These enzymes challenge the Watson/Crick dogma in two instances: 1) They attach inheritable information to the DNA that is not encoded in the nucleotide sequence. This so-called epigenetic information has many important biological functions. In prokaryotes, DNA methylation is used to coordinate DNA replication and the cell cycle, to direct postreplicative mismatch repair, and to distinguish self and nonself DNA. In eukaryotes, DNA methylation contributes to the control of gene expression, the protection of the genome against selfish DNA, maintenance of genome integrity, parental imprinting, X-chromosome inactivation in mammals, and regulation of development. 2) The enzymatic mechanism of DNA methyltransferases is unusual, because these enzymes flip their target base out of the DNA helix and, thereby, locally disrupt the B-DNA helix. This review describes the biological functions of DNA methylation in bacteria, fungi, plants, and mammals. In addition, the structures and mechanisms of the DNA methyltransferases, which enable them to specifically recognize their DNA targets and to induce such large conformational changes of the DNA, are discussed.
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Affiliation(s)
- Albert Jeltsch
- Institut für Biochemie, FB 8, Justus-Liebig-Universität, Heinrich-Buff-Ring 58, 35392 Giessen, Germany.
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16
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Kiss A, Pósfai G, Zsurka G, Raskó T, Venetianer P. Role of DNA minor groove interactions in substrate recognition by the M.SinI and M.EcoRII DNA (cytosine-5) methyltransferases. Nucleic Acids Res 2001; 29:3188-94. [PMID: 11470876 PMCID: PMC55819 DOI: 10.1093/nar/29.15.3188] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The SinI and EcoRII DNA methyltransferases recognize sequences (GG(A)/(T)CC and CC(A)/(T)GG, respectively), which are characterized by an (A)/(T) ambiguity. Recognition of the A.T and T.A base pair was studied by in vitro methyltransferase assays using oligonucleotide substrates containing a hypoxanthine.C base pair in the central position of the recognition sequence. Both enzymes methylated the substituted oligonucleotide with an efficiency that was comparable to methylation of the canonical substrate. These observations indicate that M.SinI and M.EcoRII discriminate between their canonical recognition site and the site containing a G.C or a C.G base pair in the center of the recognition sequence (GG(G)/(C)CC and CC(G)/(C)GG, respectively) by interaction(s) in the DNA minor groove. M.SinI mutants displaying a decreased capacity to discriminate between the GG(A)/(T)CC and GG(G)/(C)CC sequences were isolated by random mutagenesis and selection for the relaxed specificity phenotype. These mutations led to amino acid substitutions outside the variable region, previously thought to be the sole determinant of sequence specificity. These observations indicate that (A)/(T) versus (G)/(C) discrimination is mediated by interactions between the large domain of the methyltransferase and the minor groove surface of the DNA.
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Affiliation(s)
- A Kiss
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, PO Box 521, Szeged 6701, Hungary.
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17
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Di Giaimo R, Locascio A, Aniello F, Branno M, del Gaudio R, Potenza N, Geraci G. DNA (cytosine-5) methyltransferase turnover and cellular localization in developing Paracentrotus lividus sea urchin embryo. Gene 2001; 272:199-208. [PMID: 11470526 DOI: 10.1016/s0378-1119(01)00539-x] [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: 10/17/2022]
Abstract
The turnover and localization of the enzyme DNA (cytosine-5) methyltransferase (Dnmt1) were studied during Paracentrotus lividus sea urchin embryo development using antibody preparations against the NH(2) and COOH-terminal regions of the molecule. The antibodies reveal, by Western blots and whole-mount analyses, that the enzyme is differently required during embryonic development. The changeover point is at blastula stage, where a proteolytic mechanism hydrolyses the enzyme present in all embryonic cells by removing a peptide of about 45 kDa from the amino terminal region of the 190 kDa enzyme initially synthesized on maternal transcripts. The resulting 145 kDa enzyme shows modified catalytic properties, different antibody reactivity and is rapidly destroyed in the few hours before gastrulation. At more advanced stages of development the enzyme is newly synthesized but only in particular cell types, among which neurons. The data show that Dnmt1 is removed from embryonic cells before gastrulation to be synthesized again at different levels in different cell types, indicating that the concentration of Dnmt1 is critical for the various differentiated cells of the developing sea urchin embryo.
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Affiliation(s)
- R Di Giaimo
- Department of Genetics, General and Molecular Biology, University of Naples Federico II, Via Mezzocannone 8, 80134 Naples, Italy
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18
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Fatemi M, Hermann A, Pradhan S, Jeltsch A. The activity of the murine DNA methyltransferase Dnmt1 is controlled by interaction of the catalytic domain with the N-terminal part of the enzyme leading to an allosteric activation of the enzyme after binding to methylated DNA. J Mol Biol 2001; 309:1189-99. [PMID: 11399088 DOI: 10.1006/jmbi.2001.4709] [Citation(s) in RCA: 179] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mammalian DNA methyltransferase Dnmt1 is responsible for the maintenance of the pattern of DNA methylation in vivo. It is a large multidomain enzyme comprising 1620 amino acid residues. We have purified and characterized individual domains of Dnmt1 (NLS-containing domain, NlsD, amino acid residues: 1-343; replication foci-directing domain, 350-609; Zn-binding domain (ZnD), 613-748; polybromo domain, 746-1110; and the catalytic domain (CatD), 1124-1620). CatD, ZnD and NlsD bind to DNA, demonstrating the existence of three independent DNA-binding sites in Dnmt1. CatD shows a preference for binding to hemimethylated CpG-sites; ZnD prefers methylated CpGs; and NlsD specifically binds to CpG-sites, but does not discriminate between unmethylated and methylated DNA. These results are not compatible with the suggestion that the target recognition domain of Dnmt1 resides in the N terminus of the enzyme. We show by protein-protein interaction assays that ZnD and CatD interact with each other. The isolated catalytic domain does not methylate DNA, neither alone nor in combination with other domains. Full-length Dnmt1 was purified from baculovirus-infected insect cells. Under the experimental conditions, Dnmt1 has a strong (50-fold) preference for hemimethylated DNA. Dnmt1 is stimulated to methylate unmodified CpG sites by the addition of fully methylated DNA. This effect is dependent on Zn, suggesting that binding of methylated DNA to ZnD triggers the allosteric activation of the catalytic center of Dnmt1. The allosteric activation model can explain kinetic data obtained by others. It suggests that Dnmt1 might be responsible for spreading of methylation, a process that is observed during aging and carcenogenesis but may be important for de novo methylation of DNA.
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Affiliation(s)
- M Fatemi
- Institut für Biochemie Fachbereich 8, Justus-Liebig-Universität, Heinrich-Buff-Ring 58, Giessen, 35392, Germany
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19
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Gowher H, Jeltsch A. Enzymatic properties of recombinant Dnmt3a DNA methyltransferase from mouse: the enzyme modifies DNA in a non-processive manner and also methylates non-CpG [correction of non-CpA] sites. J Mol Biol 2001; 309:1201-8. [PMID: 11399089 DOI: 10.1006/jmbi.2001.4710] [Citation(s) in RCA: 181] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We present the first in vitro study investigating the catalytic properties of a mammalian de novo DNA methyltransferase. Dnmt3a from mouse was cloned and expressed in Escherichia coli. It was shown to be catalytically active in E. coli cells in vivo. The methylation activity of the purified protein was highest at pH 7.0 and 30 mM KCl. Our data show that recombinant Dnmt3a protein is indeed a de novo methyltransferase, as it catalyzes the transfer of methyl groups to unmethylated substrates with similar efficiency as to hemimethylated substrates. With oligonucleotide substrates, the catalytic activity of Dnmt3a is similar to that of Dnmt1: the K(m) values for the unmethylated and hemimethylated oligonucleotide substrates are 2.5 microM, and the k(cat) values are 0.05 h(-1) and 0.07 h(-1), respectively. The enzyme catalyzes the methylation of DNA in a distributive manner, suggesting that Dnmt3a and Dnmt1 may cooperate during de novo methylation of DNA. Further, we investigated the methylation activity of Dnmt3a at non-canonical sites. Even though the enzyme shows maximum activity at CpG sites, with oligonucleotide substrates, a high methylation activity was also found at CpA sites, which are modified only twofold slower than CpG sites. Therefore, the specificity of Dnmt3a is completely different from that of the maintenance methyltransferase Dnmt1, which shows a 40 to 50-fold preference for hemimethylated over unmethylated CpG sites and has almost no methylation activity at non-CpG sites.
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Affiliation(s)
- H Gowher
- Institut für Biochemie Fachbereich 8, Justus-Liebig-Universität, Heinrich-Buff-Ring 58, Giessen, 35392, Germany
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20
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Abstract
The first half of the 20th century has seen an enormous growth in our knowledge of DNA repair, in no small part due to the work of Dirk Bootsma, Philip Hanawalt and Bryn Bridges; those honored by this issue. For the new millennium, we have asked three general questions: (A) Do we know all possible strategies of nucleotide excision repair (NER) in all organisms? (B) How is NER integrated and regulated in cells and tissues? (C) Does DNA replication represent a new frontier in the roles of DNA repair? We make some suggestions for the kinds of answers the next generation may provide. The kingdom of archea represents an untapped field for investigation of DNA repair in organisms with extreme lifestyles. NER appears to involve a similar strategy to the other kingdoms of prokaryotes and eukaryotes, but subtle differences suggest that individual components of the system may differ. NER appears to be regulated by several major factors, especially p53 and Rb which interact with transcription coupled repair and global genomic repair, respectively. Examples can be found of major regulatory changes in repair in testicular tissue and melanoma cells. Our understanding of replication of damaged DNA has undergone a revolution in recent years, with the discovery of multiple low-fidelity DNA polymerases that facilitate replicative bypass. A secondary mechanism of replication in the absence of NER or of one or more of these polymerases involves sister chromatid exchange and recombination (hMre11/hRad50/Nbs1). The relative importance of bypass and recombination is determined by the action of p53. We hypothesise that these polymerases may be involved in resolution of complex DNA structures during completion of replication and sister chromatid resolution. With these fascinating problems to investigate, the field of DNA repair will surely not disappoint the next generation.
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Affiliation(s)
- J E Cleaver
- Department of Dermatology and UCSF Cancer Center, University of California, San Francisco, CA 94143-0808, USA.
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21
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Wahnon DC, Shier VK, Benkovic SJ. Mechanism-based inhibition of an essential bacterial adenine DNA methyltransferase: rationally designed antibiotics. J Am Chem Soc 2001; 123:976-7. [PMID: 11456633 DOI: 10.1021/ja003285o] [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: 11/28/2022]
Affiliation(s)
- D C Wahnon
- The Pennsylvania State University Department of Chemistry, 414 Wartik Laboratory University Park, Pennsylvania 16802, USA
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22
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Zlatanova J, Caiafa P, Van Holde K. Linker histone binding and displacement: versatile mechanism for transcriptional regulation. FASEB J 2000; 14:1697-704. [PMID: 10973918 DOI: 10.1096/fj.99-0869rev] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In recent years, the connection between chromatin structure and its transcriptional activity has attracted considerable experimental effort. The post-translational modifications to both the core histones and the linker histones are finely tuned through interactions with transcriptional regulators and change chromatin structure in a way to allow transcription to occur. Here we review evidence for the involvement of linker histones in transcriptional regulation and suggest a scenario in which the reversible and controllable binding/displacement of proteins of this class to the nucleosome entry/exit point determine the accessibility of the nucleosomal DNA to the transcriptional machinery.
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Affiliation(s)
- J Zlatanova
- Biochip Technology Center, Argonne National Laboratory, Argonne, Illinois 60439-4833, USA.
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23
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Raskó T, Finta C, Kiss A. DNA bending induced by DNA (cytosine-5) methyltransferases. Nucleic Acids Res 2000; 28:3083-91. [PMID: 10931923 PMCID: PMC108446 DOI: 10.1093/nar/28.16.3083] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA bending induced by six DNA (cytosine-5) methyltransferases was studied using circular permutation gel mobility shift assay. The following bend angles were obtained: M.BSP:RI (GG(m5)CC), 46-50 degrees; M.HAE:III (GG(m5)CC), 40-43 degrees; M.SIN:I (GGW(m5)CC), 34-37 degrees; M.SAU:96I (GGN(m5)CC), 52-57 degrees; M.HPA:II (C(m5)CGG), 30 degrees; and M.HHA:I (G(m5)CGC), 13 degrees. M. HAE:III was also tested with fragments carrying a methylated binding site, and it was found to induce a 32 degrees bend. A phase-sensitive gel mobility shift assay, using a set of DNA fragments with a sequence-directed bend and a single methyltransferase binding site, indicated that M.HAE:III and M. BSP:RI bend DNA toward the minor groove. The DNA curvature induced by M.HAE:III contrasts with the lack of DNA bend observed for a covalent M.HAE:III-DNA complex in an earlier X-ray study. Our results and data from other laboratories show a correlation between the bending properties and the recognition specificities of (cytosine-5) methyltransferases: enzymes recognizing a cytosine 3' to the target cytosine tend to induce greater bends than enzymes with guanine in this position. We suggest that the observed differences indicate different mechanisms employed by (cytosine-5) methyltransferases to stabilize the helix after the target base has flipped out.
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Affiliation(s)
- T Raskó
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, PO Box 521, Szeged 6701, Hungary
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24
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Limoli CL, Giedzinski E, Morgan WF, Cleaver JE. Polymerase eta deficiency in the xeroderma pigmentosum variant uncovers an overlap between the S phase checkpoint and double-strand break repair. Proc Natl Acad Sci U S A 2000; 97:7939-46. [PMID: 10859352 PMCID: PMC16649 DOI: 10.1073/pnas.130182897] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2000] [Indexed: 11/18/2022] Open
Abstract
The xeroderma pigmentosum variant (XPV) is a genetic disease involving high levels of solar-induced cancer that has normal excision repair but shows defective DNA replication after UV irradiation because of mutations in the damage-specific polymerase hRAD30. We previously found that the induction of sister chromatid exchanges by UV irradiation was greatly enhanced in transformed XPV cells, indicating the activation of a recombination pathway. We now have identified that XPV cells make use of a homologous recombination pathway involving the hMre11/hRad50/Nbs1 protein complex, but not the Rad51 recombination pathway. The hMre11 complexes form at arrested replication forks, in association with proliferating cell nuclear antigen. In x-ray-damaged cells, in contrast, there is no association between hMre11 and proliferating cell nuclear antigen. This recombination pathway assumes greater importance in transformed XPV cells that lack a functional p53 pathway and can be detected at lower frequencies in excision-defective XPA fibroblasts and normal cells. DNA replication arrest after UV damage, and the associated S phase checkpoint, is therefore a complex process that can recruit a recombination pathway that has a primary role in repair of double-strand breaks from x-rays. The symptoms of elevated solar carcinogenesis in XPV patients therefore may be associated with increased genomic rearrangements that result from double-strand breakage and rejoining in cells of the skin in which p53 is inactivated by UV-induced mutations.
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Affiliation(s)
- C L Limoli
- Departments of Radiology and Radiation Oncology, University of California, San Francisco, CA 94103-0806, USA
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25
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Roth M, Jeltsch A. Biotin-avidin microplate assay for the quantitative analysis of enzymatic methylation of DNA by DNA methyltransferases. Biol Chem 2000; 381:269-72. [PMID: 10782999 DOI: 10.1515/bc.2000.035] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
An assay is described to measure methylation of biotinylated oligonucleotide substrates by DNA methyltransferases using [methyl-3H]-AdoMet. After the methylation reaction the oligonucleotides are immobilized on an avidin-coated microplate. The incorporation of [3H] into the DNA is quenched by addition of unlabeled AdoMet to the binding buffer. Unreacted AdoMet and enzyme are removed by washing. To release the radioactivity incorporated into the DNA, the wells are incubated with a non-specific endonuclease and the radioactivity determined by liquid scintillation counting. As an example, we have studied methylation of DNA by the EcoRV DNA methyltransferase. The reaction progress curves measured with this assay are linear with respect to time. Methylation rates linearly increase with enzyme concentration. The rates are comparable to results obtained with the same enzyme using a different assay. The biotin-avidin assay is inexpensive, convenient, quantitative, fast and well suited to process many samples in parallel. The accuracy of the assay is high, allowing to reproduce results within +/- 10%. The assay is very sensitive as demonstrated by the detection of incorporation of 0.8 fmol methyl groups into the DNA. Under the experimental conditions, this corresponds to methylation of only 0.03% of all target sites of the substrate. Using this assay, the DNA methylation activity of some M.EcoRV variants could be detected that was not visible by other in vitro methylation assays.
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Affiliation(s)
- M Roth
- Institut für Biochemie, Justus-Liebig-Universität, Giessen, Germany
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26
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del Gaudio R, Di Giaimo R, Potenza N, Branno M, Aniello F, Geraci G. Characterization of a new variant DNA (cytosine-5)-methyltransferase unable to methylate double stranded DNA isolated from the marine annelid worm Chaetopterus variopedatus. FEBS Lett 1999; 460:380-4. [PMID: 10544268 DOI: 10.1016/s0014-5793(99)01379-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The enzyme S-adenosylmethionine-DNA (cytosine-5)-methyltransferase has been identified, first time for invertebrates, in embryos of the marine polychaete annelid worm Chaetopterus variopedatus. The molecule has been isolated from embryos at 15 h of development. It is a single peptide of about 200 kDa molecular weight, cross-reacting with antibodies against sea urchin DNA methyltransferase. The enzymatic properties of the molecule are similar to those of Dnmt1 methyltransferases isolated from other organisms, but with the peculiarity to be unable to make 'de novo' methylation on double stranded DNA.
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Affiliation(s)
- R del Gaudio
- Department of Genetics, General and Molecular Biology, University of Naples Federico II, Via Mezzocannone, 8, 80134, Napoli, Italy
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27
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DNA Methylation. Development 1999. [DOI: 10.1007/978-3-642-59828-9_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Jones AL, Thomas CL, Maule AJ. De novo methylation and co-suppression induced by a cytoplasmically replicating plant RNA virus. EMBO J 1998; 17:6385-93. [PMID: 9799246 PMCID: PMC1170963 DOI: 10.1093/emboj/17.21.6385] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The relationship between co-suppression and DNA methylation was explored in transgenic plants showing inducible co-suppression following infection with a cytoplasmically replicating RNA virus. Induction resulted in a loss of transgene mRNA and resistance to further infection, factors typical of post-transcriptional gene silencing. In infected plants, de novo methylation of the transgene appeared to precede the onset of resistance and only occurred in plants where the outcome was co-suppression. The methylation was limited to sequences homologous to the viral RNA and occurred at both symmetric and non-symmetric sites on the DNA. Although methylation is predicted to occur in mitotic cells, the virus was found not to access the meristem. A diffusible sequence-specific signal may account for the epigenetic changes in those tissues.
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Affiliation(s)
- A L Jones
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
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29
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Roth M, Helm-Kruse S, Friedrich T, Jeltsch A. Functional roles of conserved amino acid residues in DNA methyltransferases investigated by site-directed mutagenesis of the EcoRV adenine-N6-methyltransferase. J Biol Chem 1998; 273:17333-42. [PMID: 9651316 DOI: 10.1074/jbc.273.28.17333] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
All DNA methyltransferases (MTases) have similar catalytic domains containing nine blocks of conserved amino acid residues. We have investigated by site-directed mutagenesis the function of 17 conserved residues in the EcoRV alpha-adenine-N6-DNA methyltransferase. The structure of this class of MTases has been predicted recently. The variants were characterized with respect to their catalytic activities and their abilities to bind to DNA and the S-adenosylmethionine (AdoMet) cofactor. Amino acids located in motifs X, I, and II are shown to be involved in AdoMet binding (Lys16, Glu37, Phe39, and Asp58). Some of the mutants defective in AdoMet binding are also impaired in DNA binding, suggesting allosteric interactions between the AdoMet and DNA binding site. Asp78 (motif III), which was supposed to form a hydrogen bond to the AdoMet on the basis of the structure predictions, turned out not to be important for AdoMet binding, suggesting that motif III has not been identified correctly. R128A and N130A, having mutations in the putative DNA binding domain, are unable to bind to DNA. Residues located in motifs IV, V, VI, and VIII are involved in catalysis (Asp193, Tyr196, Asp211, Ser229, Trp231, and Tyr258), some of them presumably in binding the flipped target base, because mutations at these residues fail to significantly interfere with DNA and AdoMet binding but strongly reduce catalysis. Our results are in substantial agreement with the structure prediction for EcoRV alpha-adenine-N6-methyltransferase and x-ray structures of other MTases.
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Affiliation(s)
- M Roth
- Institut für Biochemie, Fachbereich Biologie, Justus-Liebig-Universität, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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30
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Goto T, Monk M. Regulation of X-chromosome inactivation in development in mice and humans. Microbiol Mol Biol Rev 1998; 62:362-78. [PMID: 9618446 PMCID: PMC98919 DOI: 10.1128/mmbr.62.2.362-378.1998] [Citation(s) in RCA: 202] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Dosage compensation for X-linked genes in mammals is accomplished by inactivating one of the two X chromosomes in females. X-chromosome inactivation (XCI) occurs during development, coupled with cell differentiation. In somatic cells, XCI is random, whereas in extraembryonic tissues, XCI is imprinted in that the paternally inherited X chromosome is preferentially inactivated. Inactivation is initiated from an X-linked locus, the X-inactivation center (Xic), and inactivity spreads along the chromosome toward both ends. XCI is established by complex mechanisms, including DNA methylation, heterochromatinization, and late replication. Once established, inactivity is stably maintained in subsequent cell generations. The function of an X-linked regulatory gene, Xist, is critically involved in XCI. The Xist gene maps to the Xic, it is transcribed only from the inactive X chromosome, and the Xist RNA associates with the inactive X chromosome in the nucleus. Investigations with Xist-containing transgenes and with deletions of the Xist gene have shown that the Xist gene is required in cis for XCI. Regulation of XCI is therefore accomplished through regulation of Xist. Transcription of the Xist gene is itself regulated by DNA methylation. Hence, the differential methylation of the Xist gene observed in sperm and eggs and its recognition by protein binding constitute the most likely mechanism regulating imprinted preferential expression of the paternal allele in preimplantation embryos and imprinted paternal XCI in extraembryonic tissues. This article reviews the mechanisms underlying XCI and recent advances elucidating the functions of the Xist gene in mice and humans.
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Affiliation(s)
- T Goto
- Molecular Embryology Unit, Institute of Child Health, London WC1N 1EH, United Kingdom.
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31
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Bensaada M, Kiefer H, Tachdjian G, Lapierre JM, Cacheux V, Niveleau A, Métézeau P. Altered patterns of DNA methylation on chromosomes from leukemia cell lines: identification of 5-methylcytosines by indirect immunodetection. CANCER GENETICS AND CYTOGENETICS 1998; 103:101-9. [PMID: 9614907 DOI: 10.1016/s0165-4608(97)00409-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An immunodetection technique has been developed to map with high resolution the methylated sites of human chromosomes. We have used this method to define the methylated areas of chromosomes from normal donors and from leukemia cell lines. The chromosomes were exposed for a short time to UV light to induce mild denaturation. The methylated sites were detected in situ by using monoclonal antibodies against 5-methylcytosine (prepared in mouse), and fluorescein-conjugated antimouse immunoglobulins. The chromosomes from normal cells exhibited a fluorescent pattern with RCT banding, although some differences from previously reported patterns could be detected. With this method we have been able to show the presence of two types of R-bands: High fluorescence R-band (HFR) and low fluorescence R-band (LFR). Chromosomes from leukemia cell lines exhibited low global staining with disrupted RCT banding of the chromosomes. The decreased level of the methylation status of the chromosomes from leukemia cells was confirmed by detection of 5-methylcytosines on total immobilized DNA. Thus, we have shown that this method can be used to determine the methylated status of chromosomes and, in turn, to map not only the structural (banding) but also the functional (methylation status) properties of the different chromosome domains in normal and pathologic human cells.
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32
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Van den Wyngaert I, Sprengel J, Kass SU, Luyten WH. Cloning and analysis of a novel human putative DNA methyltransferase. FEBS Lett 1998; 426:283-9. [PMID: 9599025 DOI: 10.1016/s0014-5793(98)00362-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA methylation is intricately involved in a variety of cellular processes, such as differentiation, cell cycle progression, X-chromosome inactivation and genomic imprinting. However, little is known about how specific DNA methylation patterns are established and maintained. Previously one mammalian DNA methyltransferase has been described, but there has been considerable speculation about the presence of a second activity capable of methylation. Here we report the identification and characterization of a novel human putative DNA methyltransferase. Using a bioinformatics screen we have identified several expressed sequence tags which show high sequence similarity to the Schizosaccharomyces pombe gene pmt1+. The cDNA for PuMet (for putative DNA methyltransferase) was cloned and the predicted amino acid sequence deduced. The gene is ubiquitously expressed, albeit at low levels. Like several other DNA methyltransferases, the bacterially overexpressed protein is not active in methylation assays.
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Affiliation(s)
- I Van den Wyngaert
- Department of Experimental Molecular Biology, Janssen Research Foundation, Beerse, Belgium
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33
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Abstract
Proliferating cell nuclear antigen (PCNA) has recently been identified as a target for the binding of several proteins. The cell cycle regulatory protein, p21, and the replication endonuclease, Fen1, have already been described as competing for PCNA binding. Two recent reports have identified DNA (cytosine-5)methyltransferase (MCMT) and the DNA repair endonuclease XPG as binding to PCNA. The remarkable thing about these interactions is that they all seem to occur through a conserved motif that is likely to contact the same site on PCNA. This has fascinating implications for a regulatory network linking these diverse protein functions.
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Affiliation(s)
- E Warbrick
- Department of Biochemistry, University of Dundee, Scotland.
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Liu Y, Oakeley EJ, Sun L, Jost JP. Multiple domains are involved in the targeting of the mouse DNA methyltransferase to the DNA replication foci. Nucleic Acids Res 1998; 26:1038-45. [PMID: 9461465 PMCID: PMC147368 DOI: 10.1093/nar/26.4.1038] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
It has been shown that, during the S-phase of the cell cycle, the mouse DNA methyltransferase (DNA MTase) is targeted to sites of DNA replication by an amino acid sequence (aa 207-455) lying in the N-terminal domain of the enzyme [Leonhardt, H., Page, A. W., Weier, H. U. and Bestor, T. H. (1992) Cell , 71, 865-873]. In this paper it is shown, by using enhanced green fluorescent protein (EGFP) fusions, that other peptide sequences of DNA MTase are also involved in this targeting. The work focuses on a sequence, downstream of the reported targeting sequence (TS), which is homologous to the Polybromo-1 protein. This motif (designated as PBHD) is separated from the reported targeting sequence by a zinc-binding motif [Bestor , T. H. (1992) EMBO J , 11, 2611-2617]. Primed in situ extension using centromeric-specific primers was used to show that both the host DNA MTase and EGFP fusion proteins containing the targeting sequences were localized to centromeric, but not telomeric, regions during late S-phase and mitosis. Also found was that, in approximately 10% of the S-phase cells, the EGFP fusions did not co-localize with the centromeric regions. Mutants containing either, or both, of these targeting sequences could act as dominant negative mutants against the host DNA MTase. EGFP fusion proteins, containing the reported TS (aa 207-455), were targeted to centromeric regions throughout the mitotic stage which lead to the discovery of a similar behavior of the endogenous DNA MTase although the host MTase showed much less intense staining than in S-phase cells. The biological role of the centromeric localization of DNA MTase during mitosis is currently unknown.
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Affiliation(s)
- Y Liu
- Friedrich Miescher-Institut, P.O. Box 2543, Basel, Switzerland
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Bernacchia G, Primo A, Giorgetti L, Pitto L, Cella R. Carrot DNA-methyltransferase is encoded by two classes of genes with differing patterns of expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 1998; 13:317-329. [PMID: 9680985 DOI: 10.1046/j.1365-313x.1998.00034.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In the present study, the isolation and characterization of two distinct cDNAs that code for carrot DNA (cytosine-5)-methyltransferase (DNA-METase) are reported. The screening of a cDNA library with a carrot genomic DNA fragment, previously obtained by PCR using degenerate primers, has led to the isolation of clones that belong to two distinct classes of genes (Met1 and Met2) which differ in sequence and size. Met1-5 and Met2-21 derived amino acid sequences are more than 85% identical for most of the polypeptide and completely diverge at the N-terminus. The larger size of the Met2-21 cDNA is due to the presence of nearly perfect fivefold repeat of a 171 bp sequence present only once in the Met1-5 cDNA. Northern and in situ hybridization analyses with young carrot plants and somatic embryos indicate that both genes are maximally expressed in proliferating cells (suspension cells, meristems and leaf primordia), but differ quantitatively and spatially in their mode of expression. Polyclonal antibodies were raised in rabbit using fusion proteins corresponding to the regulatory and catalytic regions of the most highly expressed gene (Met1-5). In nuclear carrot extracts, both antibodies were found to recognize a band of about 200 kDa along with some additional bands of lower size. These results provide the first direct demonstration that DNA-METases of a higher eukaryote are encoded by a gene family.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies
- Base Sequence
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/immunology
- DNA Primers/genetics
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- DNA, Plant/genetics
- DNA, Plant/isolation & purification
- Daucus carota/enzymology
- Daucus carota/genetics
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Plant
- Genes, Plant
- In Situ Hybridization
- Molecular Sequence Data
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Rabbits
- Repetitive Sequences, Nucleic Acid
- Sequence Homology, Amino Acid
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Affiliation(s)
- G Bernacchia
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Italy
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Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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37
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Mostoslavsky R, Bergman Y. DNA methylation: regulation of gene expression and role in the immune system. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1333:F29-50. [PMID: 9294017 DOI: 10.1016/s0304-419x(97)00010-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- R Mostoslavsky
- The Hubert H. Humphrey Center for Experimental Medicine and Cancer Research, The Hebrew University Hadassah Medical School, Jerusalem, Israel
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38
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Abstract
Epigenetic mechanisms can serve as genome defense systems. In haploid nuclei of special sexual cells of fungi, such as Neurospora and Ascobolus, duplicated genes are silenced by hypermutation, DNA methylation, or both. In some cases, DNA introduced into the genome of Neurospora cells by transformation can also inhibit homologous genes by a silencing mechanism that does not involve DNA pairing or methylation and appears to be post-transcriptional. Transforming DNA can also trigger de novo methylation in vegetative cells, which then causes transcriptional silencing. The rules governing silencing in vegetative cells of fungi are undefined, but repeated sequences seem particularly susceptible to these processes. Thus, fungi exhibit both repeat-induced and repeat-associated silencing mechanisms. Additionally, some native genes depend on homologous pairing in the diplophase for proper regulation. Together, these processes should limit the proliferation of transposable elements and serve to preserve the overall structure of the genome.
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Affiliation(s)
- E U Selker
- Institute of Molecular Biology, University of Oregon, Eugene 97403, USA.
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39
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Abstract
Overexpression of chimeric transgenes in plants can trigger post-transcriptional gene silencing that is dependent on epigenetic information and physiological conditions. The current view is that unproductive RNA serves as a crucial signal for gene silencing, although direct evidence is lacking for this theory. A signalling cascade then leads to strongly enhanced turnover of all RNAs that share a critical degree of sequence similarity. The molecular details of the mechanism are, however, insufficiently understood to explain the phenomenon completely and to comprehend its biological significance.
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Affiliation(s)
- A Depicker
- Laboratorium voor Genetica, Department of Genetics, Flanders Interuniversity Institute for Biotechnology (VIB), Universiteit Gent, KL Ledeganckstraat 35, B-9000, Gent, Belgium
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40
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Jost JP, Bruhat A. The formation of DNA methylation patterns and the silencing of genes. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1997; 57:217-48. [PMID: 9175435 DOI: 10.1016/s0079-6603(08)60282-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- J P Jost
- Friedrich Miescher Institute, Basel, Switzerland
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41
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Abstract
Mouse DNA methyltransferase is able to catalyse the transfer of a methyl group to certain CG-containing single-stranded oligonucleotides. The presence of a methylcytosine is required for efficient transfer. This methylcytosine may or may not be on the same oligonucleotide as that containing the accepting CG dinucleotide. When the accepting CG dinucleotide forms part of an unmethylated CG dinucleotide pair, its accepting activity is dramatically reduced. This provides the potential for methylation to spread along the DNA when it is rendered single-stranded at replication. It could also help to maintain fully methylated CG islands and asymmetrically methylated sites.
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Affiliation(s)
- H Lindsay
- Institute of Biomedical and Life Sciences, University of Glasgow, U.K
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42
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Abstract
The modification of DNA by cytosine methylation is crucial for normal development. DNA methylation patterns are distinctive between tissues and are maintained with high fidelity during cell division. DNA methylation probably exerts its effects through alterations in chromatin structure, with a resultant effect on genetic transcription. 5-methylcytosine is also prone to spontaneous hydrolytic deamination to thymine. Whilst most G:T mismatches so produced are repaired, failure of mismatch repair leads to established mutation. Indeed, mutations that are the result of 5-methylcytosine transitions account for a disproportionate number of genetic mutations described in malignant and non-malignant disease. There is also evidence for substantial deregulation of DNA methylation in malignancy. Whether this deregulation is crucial for the transformation process, or simply an epiphenomenon associated with it, is still not established.
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Affiliation(s)
- B H Ramsahoye
- Department of Haematology, University of Wales College of Medicine, Health Park, Cardiff, UK
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Hohn T, Corsten S, Rieke S, Müller M, Rothnie H. Methylation of coding region alone inhibits gene expression in plant protoplasts. Proc Natl Acad Sci U S A 1996; 93:8334-9. [PMID: 8710871 PMCID: PMC38671 DOI: 10.1073/pnas.93.16.8334] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Derivatives of the cauliflower mosaic virus 35S promoter lacking CG and CNG methylation targets were constructed and used to direct transcription of reporter gene constructs in transiently transformed protoplasts. Such methylation-target-free (MTF) promoters, although weaker than the 35S promoter, retain significant activity despite mutation of the as-1 element. The effect of methylation on gene expression in MTF- and 35S-promoter driven constructs was examined. Even when the promoter region was free of methylation targets, reporter gene expression was markedly reduced when cytosine residues in CG dinucleotides were methylated in vitro prior to transformation. Mosaic methylation experiments, in which only specific parts of the plasmids were methylated, revealed that methylation of the coding region alone has a negative effect on reporter gene expression. Methylation nearer the 5' end of the coding region was more inhibitory, consistent with inhibition of transcription elongation.
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Affiliation(s)
- T Hohn
- Friedrich Miescher Institute, Basel, Switzerland
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44
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Liu Y, Sun L, Jost JP. In differentiating mouse myoblasts DNA methyltransferase is posttranscriptionally and posttranslationally regulated. Nucleic Acids Res 1996; 24:2718-22. [PMID: 8759002 PMCID: PMC145988 DOI: 10.1093/nar/24.14.2718] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Upon the onset of mouse myoblast differentiation there is a rapid drop in DNA methyltransferase activity followed by a genome wide demethylation [Jost and Jost (1994) J. Biol. Chem. 269, 10040-10043]. Here we show by using specific antibodies directed against DNA methyltransferase that upon differentiation there was a rapid drop in nuclear DNA methyltransferase whilst the internal control histone H1 remained constant. The loss of nuclear methyltransferase was not due to a translocation of the enzyme from the nucleus to the cytoplasm where there was an increase in creatine phosphokinase protein. In vitro run on experiments carried out with growing and differentiating myoblast nuclei showed no difference in the rate of DNA methyltransferase mRNA synthesis. As measured by Northern blot hybridization the relative half life of DNA methyltransferase mRNA in growing and differentiating cells in the presence of Actinomycin D was 5 h and 1 h 30 min respectively, whereas in the same cells the half life of histone H4 mRNA was in both cases 80 min. As measured by a combination of pulse chase experiments with labeled leucine and immunoprecipitation, the relative half-life of DNA methyltransferase in growing and differentiating cells was approximately 18 h and 4 h 30 min respectively.
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Affiliation(s)
- Y Liu
- Friedrich Miescher Institut, Basel, Switzerland
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