1
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Parrilla-Doblas J, Morales-Ruiz T, Ariza R, Martínez-Macías M, Roldán-Arjona T. The C-terminal domain of Arabidopsis ROS1 DNA demethylase interacts with histone H3 and is required for DNA binding and catalytic activity. DNA Repair (Amst) 2022; 115:103341. [DOI: 10.1016/j.dnarep.2022.103341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/13/2022] [Accepted: 05/03/2022] [Indexed: 11/03/2022]
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2
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Parrilla-Doblas JT, Roldán-Arjona T, Ariza RR, Córdoba-Cañero D. Active DNA Demethylation in Plants. Int J Mol Sci 2019; 20:E4683. [PMID: 31546611 PMCID: PMC6801703 DOI: 10.3390/ijms20194683] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/17/2019] [Accepted: 09/19/2019] [Indexed: 02/06/2023] Open
Abstract
Methylation of cytosine (5-meC) is a critical epigenetic modification in many eukaryotes, and genomic DNA methylation landscapes are dynamically regulated by opposed methylation and demethylation processes. Plants are unique in possessing a mechanism for active DNA demethylation involving DNA glycosylases that excise 5-meC and initiate its replacement with unmodified C through a base excision repair (BER) pathway. Plant BER-mediated DNA demethylation is a complex process involving numerous proteins, as well as additional regulatory factors that avoid accumulation of potentially harmful intermediates and coordinate demethylation and methylation to maintain balanced yet flexible DNA methylation patterns. Active DNA demethylation counteracts excessive methylation at transposable elements (TEs), mainly in euchromatic regions, and one of its major functions is to avoid methylation spreading to nearby genes. It is also involved in transcriptional activation of TEs and TE-derived sequences in companion cells of male and female gametophytes, which reinforces transposon silencing in gametes and also contributes to gene imprinting in the endosperm. Plant 5-meC DNA glycosylases are additionally involved in many other physiological processes, including seed development and germination, fruit ripening, and plant responses to a variety of biotic and abiotic environmental stimuli.
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Affiliation(s)
- Jara Teresa Parrilla-Doblas
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071 Córdoba, Spain.
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain.
- Reina Sofía University Hospital, 14071 Córdoba, Spain.
| | - Teresa Roldán-Arjona
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071 Córdoba, Spain.
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain.
- Reina Sofía University Hospital, 14071 Córdoba, Spain.
| | - Rafael R Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071 Córdoba, Spain.
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain.
- Reina Sofía University Hospital, 14071 Córdoba, Spain.
| | - Dolores Córdoba-Cañero
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071 Córdoba, Spain.
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain.
- Reina Sofía University Hospital, 14071 Córdoba, Spain.
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3
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Wiechmann T, Röh S, Sauer S, Czamara D, Arloth J, Ködel M, Beintner M, Knop L, Menke A, Binder EB, Provençal N. Identification of dynamic glucocorticoid-induced methylation changes at the FKBP5 locus. Clin Epigenetics 2019; 11:83. [PMID: 31122292 PMCID: PMC6533766 DOI: 10.1186/s13148-019-0682-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 05/09/2019] [Indexed: 01/30/2023] Open
Abstract
Background Epigenetic mechanisms may play a major role in the biological embedding of early-life stress (ELS). One proposed mechanism is that glucocorticoid (GC) release following ELS exposure induces long-lasting alterations in DNA methylation (DNAm) of important regulatory genes of the stress response. Here, we investigate the dynamics of GC-dependent methylation changes in key regulatory regions of the FKBP5 locus in which ELS-associated DNAm changes have been reported. Results We repeatedly measured DNAm in human peripheral blood samples from 2 independent cohorts exposed to the GC agonist dexamethasone (DEX) using a targeted bisulfite sequencing approach, complemented by data from Illumina 450K arrays. We detected differentially methylated CpGs in enhancers co-localizing with GC receptor binding sites after acute DEX treatment (1 h, 3 h, 6 h), which returned to baseline levels within 23 h. These changes withstood correction for immune cell count differences. While we observed main effects of sex, age, body mass index, smoking, and depression symptoms on FKBP5 methylation levels, only the functional FKBP5 SNP (rs1360780) moderated the dynamic changes following DEX. This genotype effect was observed in both cohorts and included sites previously shown to be associated with ELS. Conclusion Our study highlights that DNAm levels within regulatory regions of the FKBP5 locus show dynamic changes following a GC challenge and suggest that factors influencing the dynamics of this regulation may contribute to the previously reported alterations in DNAm associated with current and past ELS exposure. Electronic supplementary material The online version of this article (10.1186/s13148-019-0682-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tobias Wiechmann
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Simone Röh
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Susann Sauer
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Janine Arloth
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany.,Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Maik Ködel
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Madita Beintner
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Lisanne Knop
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany
| | - Andreas Menke
- Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Wuerzburg, Wuerzburg, Germany.,Comprehensive Heart Failure Center, University Hospital of Wuerzburg, Wuerzburg, Germany
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany. .,Department of Psychiatry and Behavioral Sciences, Emory University Medical School, Atlanta, GA, USA.
| | - Nadine Provençal
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Kraepelinstr. 2-10, 80804, Munich, Germany. .,Faculty of Health Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada. .,BC Children's Hospital Research Institute, Vancouver, BC, Canada.
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4
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Karumathil S, Raveendran NT, Ganesh D, Kumar Ns S, Nair RR, Dirisala VR. Evolution of Synonymous Codon Usage Bias in West African and Central African Strains of Monkeypox Virus. Evol Bioinform Online 2018; 14:1176934318761368. [PMID: 29551886 PMCID: PMC5846927 DOI: 10.1177/1176934318761368] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 02/01/2018] [Indexed: 12/17/2022] Open
Abstract
The evolution of bias in synonymous codon usage in chosen monkeypox viral genomes and the factors influencing its diversification have not been reported so far. In this study, various trends associated with synonymous codon usage in chosen monkeypox viral genomes were investigated, and the results are reported. Identification of factors that influence codon usage in chosen monkeypox viral genomes was done using various codon usage indices, such as the relative synonymous codon usage, the effective number of codons, and the codon adaptation index. The Spearman rank correlation analysis and a correspondence analysis were used for correlating various factors with codon usage. The results revealed that mutational pressure due to compositional constraints, gene expression level, and selection at the codon level for utilization of putative optimal codons are major factors influencing synonymous codon usage bias in monkeypox viral genomes. A cluster analysis of relative synonymous codon usage values revealed a grouping of more virulent strains as one major cluster (Central African strains) and a grouping of less virulent strains (West African strains) as another major cluster, indicating a relationship between virulence and synonymous codon usage bias. This study concluded that a balance between the mutational pressure acting at the base composition level and the selection pressure acting at the amino acid level frames synonymous codon usage bias in the chosen monkeypox viruses. The natural selection from the host does not seem to have influenced the synonymous codon usage bias in the analyzed monkeypox viral genomes.
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Affiliation(s)
- Sudeesh Karumathil
- Centre for Evolutionary Ecology, Aushmath Biosciences, Coimbatore, India
| | - Nimal T Raveendran
- Amrita Centre for Nanosciences, Amrita Vishwa Vidyapeetham, Kochi, India
| | - Doss Ganesh
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | | | - Rahul R Nair
- Centre for Evolutionary Ecology, Aushmath Biosciences, Coimbatore, India
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5
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Parrilla-Doblas JT, Ariza RR, Roldán-Arjona T. Targeted DNA demethylation in human cells by fusion of a plant 5-methylcytosine DNA glycosylase to a sequence-specific DNA binding domain. Epigenetics 2017; 12:296-303. [PMID: 28277978 DOI: 10.1080/15592294.2017.1294306] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA methylation is a crucial epigenetic mark associated to gene silencing, and its targeted removal is a major goal of epigenetic editing. In animal cells, DNA demethylation involves iterative 5mC oxidation by TET enzymes followed by replication-dependent dilution and/or replication-independent DNA repair of its oxidized derivatives. In contrast, plants use specific DNA glycosylases that directly excise 5mC and initiate its substitution for unmethylated C in a base excision repair process. In this work, we have fused the catalytic domain of Arabidopsis ROS1 5mC DNA glycosylase (ROS1_CD) to the DNA binding domain of yeast GAL4 (GBD). We show that the resultant GBD-ROS1_CD fusion protein binds specifically a GBD-targeted DNA sequence in vitro. We also found that transient in vivo expression of GBD-ROS1_CD in human cells specifically reactivates transcription of a methylation-silenced reporter gene, and that such reactivation requires both ROS1_CD catalytic activity and GBD binding capacity. Finally, we show that reactivation induced by GBD-ROS1_CD is accompanied by decreased methylation levels at several CpG sites of the targeted promoter. All together, these results show that plant 5mC DNA glycosylases can be used for targeted active DNA demethylation in human cells.
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Affiliation(s)
- Jara Teresa Parrilla-Doblas
- a Maimónides Biomedical Research Institute of Córdoba (IMIBIC) , Córdoba , Spain.,b University of Córdoba , Córdoba , Spain.,c Reina Sofia University Hospital , Córdoba , Spain
| | - Rafael R Ariza
- a Maimónides Biomedical Research Institute of Córdoba (IMIBIC) , Córdoba , Spain.,b University of Córdoba , Córdoba , Spain.,c Reina Sofia University Hospital , Córdoba , Spain
| | - Teresa Roldán-Arjona
- a Maimónides Biomedical Research Institute of Córdoba (IMIBIC) , Córdoba , Spain.,b University of Córdoba , Córdoba , Spain.,c Reina Sofia University Hospital , Córdoba , Spain
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6
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Binder EB. Dissecting the molecular mechanisms of gene x environment interactions: implications for diagnosis and treatment of stress-related psychiatric disorders. Eur J Psychotraumatol 2017; 8:1412745. [PMID: 29372006 PMCID: PMC5774411 DOI: 10.1080/20008198.2017.1412745] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/03/2017] [Indexed: 12/14/2022] Open
Abstract
Epidemiological studies indicate a combined contribution of genetic and environmental factors, mainly exposure to adverse life events, in the risk for psychiatric disease. Understanding how adverse life events interact with genetic predisposition on the molecular level to shape risk and resilience to psychiatric disorders may yield important insight into disease mechanism. Using the example of the molecular mechanisms of interaction of functional genetic variants within the stress-regulating gene FKBP5 and early adversity, it is delineated how this interaction could contribute to transdiagnostic disease risk via a combined genetic and epigenetic disinhibition of FKBP5 transcription. This knowledge may now allow to develop biomarkers for a transdiagnostic subset of psychiatric patients and to personalize treatment.
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Affiliation(s)
- Elisabeth B Binder
- Department of Translational Research in PsychiatryMax-Planck Institute of Psychiatry, Munich, Germany.,Department of Psychiatry and Behavioral SciencesEmory University School of Medicine, Atlanta, GA, USA
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7
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DNA methylation-based variation between human populations. Mol Genet Genomics 2016; 292:5-35. [PMID: 27815639 DOI: 10.1007/s00438-016-1264-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 10/25/2016] [Indexed: 12/16/2022]
Abstract
Several studies have proved that DNA methylation affects regulation of gene expression and development. Epigenome-wide studies have reported variation in methylation patterns between populations, including Caucasians, non-Caucasians (Blacks), Hispanics, Arabs, and numerous populations of the African continent. Not only has DNA methylation differences shown to impact externally visible characteristics, but is also a potential biomarker for underlying racial health disparities between human populations. Ethnicity-related methylation differences set their mark during early embryonic development. Genetic variations, such as single-nucleotide polymorphisms and environmental factors, such as age, dietary folate, socioeconomic status, and smoking, impacts DNA methylation levels, which reciprocally impacts expression of phenotypes. Studies show that it is necessary to address these external influences when attempting to differentiate between populations since the relative impacts of these factors on the human methylome remain uncertain. The present review summarises several reported attempts to establish the contribution of differential DNA methylation to natural human variation, and shows that DNA methylation could represent new opportunities for risk stratification and prevention of several diseases amongst populations world-wide. Variation of methylation patterns between human populations is an exciting prospect which inspires further valuable research to apply the concept in routine medical and forensic casework. However, trans-generational inheritance needs to be quantified to decipher the proportion of variation contributed by DNA methylation. The future holds thorough evaluation of the epigenome to understand quantification, heritability, and the effect of DNA methylation on phenotypes. In addition, methylation profiling of the same ethnic groups across geographical locations will shed light on conserved methylation differences in populations.
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8
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Panikar CS, Rajpathak SN, Abhyankar V, Deshmukh S, Deobagkar DD. Presence of DNA methyltransferase activity and CpC methylation in Drosophila melanogaster. Mol Biol Rep 2015; 42:1615-21. [PMID: 26547851 DOI: 10.1007/s11033-015-3931-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/03/2015] [Indexed: 12/30/2022]
Abstract
Drosophila melanogaster lacks DNMT1/DNMT3 based methylation machinery. Despite recent reports confirming the presence of low DNA methylation in Drosophila; little is known about the methyltransferase. Therefore, in this study, we have aimed to investigate the possible functioning of DNA methyltransferase in Drosophila. The 14 K oligo microarray slide was incubated with native cell extract from adult Drosophila to check the presence of the methyltransferase activity. After incubation under appropriate conditions, the methylated oligo sequences were identified by the binding of anti 5-methylcytosine monoclonal antibody. The antibody bound to the methylated oligos was detected using Cy3 labeled secondary antibody. Methylation sensitive restriction enzyme mediated PCR was used to assess the methylation at a few selected loci identified on the array. It could be seen that a few of the total oligos got methylated under the assay conditions. Analysis of methylated oligo sequences provides evidence for the presence of de novo methyltransferase activity and allows identification of its sequence specificity in adult Drosophila. With the help of methylation sensitive enzymes we could detect presence of CpC methylation in the selected genomic regions. This study reports presence of an active DNA methyltransferase in adult Drosophila, which exhibits sequence specificity confirmed by presence of asymmetric methylation at corresponding sites in the genomic DNA. It also provides an innovative approach to investigate methylation specificity of a native methyltransferase.
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Affiliation(s)
- Chitra S Panikar
- Molecular Biology Research Laboratory, Department of Zoology, Centre for Advanced Studies, University of Pune, Pune, 411007, India
| | - Shriram N Rajpathak
- Molecular Biology Research Laboratory, Department of Zoology, Centre for Advanced Studies, University of Pune, Pune, 411007, India
| | - Varada Abhyankar
- Molecular Biology Research Laboratory, Department of Zoology, Centre for Advanced Studies, University of Pune, Pune, 411007, India
| | - Saniya Deshmukh
- Molecular Biology Research Laboratory, Department of Zoology, Centre for Advanced Studies, University of Pune, Pune, 411007, India
| | - Deepti D Deobagkar
- Molecular Biology Research Laboratory, Department of Zoology, Centre for Advanced Studies, University of Pune, Pune, 411007, India. .,Bioinformatics Center, University of Pune, Pune, 411007, India.
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9
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Klengel T, Binder EB. Epigenetics of Stress-Related Psychiatric Disorders and Gene × Environment Interactions. Neuron 2015; 86:1343-57. [PMID: 26087162 DOI: 10.1016/j.neuron.2015.05.036] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A deeper understanding of the pathomechanisms leading to stress-related psychiatric disorders is important for the development of more efficient preventive and therapeutic strategies. Epidemiological studies indicate a combined contribution of genetic and environmental factors in the risk for disease. The environment, particularly early life severe stress or trauma, can lead to lifelong molecular changes in the form of epigenetic modifications that can set the organism off on trajectories to health or disease. Epigenetic modifications are capable of shaping and storing the molecular response of a cell to its environment as a function of genetic predisposition. This provides a potential mechanism for gene-environment interactions. Here, we review epigenetic mechanisms associated with the response to stress and trauma exposure and the development of stress-related psychiatric disorders. We also look at how they may contribute to our understanding of the combined effects of genetic and environmental factors in shaping disease risk.
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Affiliation(s)
- Torsten Klengel
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322, USA.
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10
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Gavin DP, Floreani C. Epigenetics of schizophrenia: an open and shut case. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2014; 115:155-201. [PMID: 25131545 DOI: 10.1016/b978-0-12-801311-3.00005-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
During the last decade and a half, there has been an explosion of data regarding epigenetic changes in schizophrenia. Most initial studies have suggested that schizophrenia is characterized by an overly restrictive chromatin state based on increases in transcription silencing histone modifications and DNA methylation at schizophrenia candidate gene promoters and increases in the expression of enzymes that catalyze their formation. However, recent studies indicate that the pathology is more complex. This complexity may greatly impact pharmacological approaches directed at targeting epigenetic abnormalities in schizophrenia. The current review explores epigenetic studies of schizophrenia and what this can tell us about the underlying pathophysiology. We hypothesize based on recent studies that it is also plausible that drugs that further restrict chromatin may be efficacious.
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Affiliation(s)
- David P Gavin
- Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA; Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA.
| | - Christina Floreani
- Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA; Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
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11
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Burd CJ, Archer TK. Chromatin architecture defines the glucocorticoid response. Mol Cell Endocrinol 2013; 380:25-31. [PMID: 23545159 PMCID: PMC3762934 DOI: 10.1016/j.mce.2013.03.020] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 03/19/2013] [Accepted: 03/21/2013] [Indexed: 01/10/2023]
Abstract
The glucocorticoid receptor (GR) functions to regulate a wide group of physiological processes through hormone inducible interaction with genomic loci and subsequent manipulation of the transcriptional output of target genes. Despite expression in a wide variety of tissues, the GR has diverse roles that are regulated tightly in a cell type specific manner. With the advent of whole genome approaches, the details of that diversity and the mechanisms regulating them are beginning to be elucidated. This review aims describe the recent advances detailing the role chromatin structure plays in dictating GR specificity.
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Affiliation(s)
- Craig J Burd
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, United States.
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12
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Gavin DP, Chase KA, Sharma RP. Active DNA demethylation in post-mitotic neurons: a reason for optimism. Neuropharmacology 2013; 75:233-45. [PMID: 23958448 DOI: 10.1016/j.neuropharm.2013.07.036] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 07/22/2013] [Accepted: 07/30/2013] [Indexed: 12/13/2022]
Abstract
Over the last several years proteins involved in base excision repair (BER) have been implicated in active DNA demethylation. We review the literature supporting BER as a means of active DNA demethylation, and explain how the various components function and cooperate to remove the potentially most enduring means of epigenetic gene regulation. Recent evidence indicates that the same pathways implicated during periods of widespread DNA demethylation, such as the erasure of methyl marks in the paternal pronucleus soon after fertilization, are operational in post-mitotic neurons. Neuronal functional identities, defined here as the result of a combination of neuronal subtype, location, and synaptic connections are largely maintained through DNA methylation. Chronic mental illnesses, such as schizophrenia, may be the result of both altered neurotransmitter levels and neurons that have assumed dysfunctional neuronal identities. A limitation of most current psychopharmacological agents is their focus on the former, while not addressing the more profound latter pathophysiological process. Previously, it was believed that active DNA demethylation in post-mitotic neurons was rare if not impossible. If this were the case, then reversing the factors that maintain neuronal identity, would be highly unlikely. The emergence of an active DNA demethylation pathway in the brain is a reason for great optimism in psychiatry as it provides a means by which previously pathological neurons may be reprogrammed to serve a more favorable role. Agents targeting epigenetic processes have shown much promise in this regard, and may lead to substantial gains over traditional pharmacological approaches.
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Affiliation(s)
- David P Gavin
- The Psychiatric Institute, Department of Psychiatry, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612, USA; Jesse Brown Veterans Affairs Medical Center, 820 South Damen Avenue (M/C 151), Chicago, IL 60612, USA.
| | - Kayla A Chase
- The Psychiatric Institute, Department of Psychiatry, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612, USA
| | - Rajiv P Sharma
- The Psychiatric Institute, Department of Psychiatry, University of Illinois at Chicago, 1601 W. Taylor St., Chicago, IL 60612, USA; Jesse Brown Veterans Affairs Medical Center, 820 South Damen Avenue (M/C 151), Chicago, IL 60612, USA
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13
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Yao B, Jin P. Cytosine modifications in neurodevelopment and diseases. Cell Mol Life Sci 2013; 71:405-18. [PMID: 23912899 DOI: 10.1007/s00018-013-1433-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/19/2013] [Accepted: 07/22/2013] [Indexed: 12/11/2022]
Abstract
DNA methylation has been studied comprehensively and linked to both normal neurodevelopment and neurological diseases. The recent identification of several new DNA modifications, including 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine, has given us a new perspective on the previously observed plasticity in 5mC-dependent regulatory processes. Here, we review the latest research into these cytosine modifications, focusing mainly on their roles in neurodevelopment and diseases.
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Affiliation(s)
- Bing Yao
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, GA, 30322, USA
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14
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Xu J, Cheng YQ, Chen B, Bai R, Li S, Xu XF, Xu L, Wen JF, Lu ZP, Zeng XF. Depression in systemic lupus erythematosus patients is associated with link-polymorphism but not methylation status of the 5HTT promoter region. Lupus 2013; 22:1001-10. [PMID: 23893825 DOI: 10.1177/0961203313498793] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A higher prevalence of depression in systemic lupus erythematosus (SLE) patients has been reported, though the mechanism underlying this phenomenon remains unclear. The present study was conducted to explore whether the polymorphism and methylation status of the serotonin transporter gene (5HTT) promoter region (PR-5HTT) contribute to depression in SLE patients from both genetic and epigenetic perspectives. In this study, 96 SLE patients and 96 healthy controls (HCs) were recruited. Depression levels of all subjects were evaluated using the Hamilton Depression Rating Scale (HDRS). The serotonin transporter-linked polymorphism (5HTTLPR) and the DNA methylation status of PR-5HTT were detected in peripheral lymphocytes of SLE patients and HCs. The differences in 5HTTLPR and DNA methylation of PR-5HTT between SLEs and HCs were compared. In SLE patients, the frequencies of short allele (S) and SS genotype of 5HTTLPR were higher in depressive SLE (SLE-D) patients than in non-depressive SLE (SLE-ND) patients. The mean HDRS score of SS homozygote patients was higher than that of patients with SL/LL genotypes. Conversely, PR-5HTT was hypomethylated in HCs as well as SLE patients. There was no difference in the methylation status between HCs and SLEs. Thus, the functional expression of PR-5HTT may be primarily regulated by gene polymorphism and not by DNA methylation. The risk allele of 5HTTLPR appears to be a major contributor to depression in SLE patients.
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Affiliation(s)
- J Xu
- Department of Rheumatology and Immunology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China
- Department of Rheumatology and Immunology, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, PR China
| | - YQ Cheng
- Department of Psychiatry, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, PR China
| | - B Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, PR China
| | - R Bai
- Department of Rheumatology and Immunology, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, PR China
| | - S Li
- Department of Rheumatology and Immunology, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, PR China
| | - XF Xu
- Department of Psychiatry, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, PR China
| | - L Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, PR China
| | - JF Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, PR China
| | - ZP Lu
- Department of Rheumatology and Immunology, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, PR China
| | - XF Zeng
- Department of Rheumatology and Immunology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China
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Abstract
DNA methylation has long been considered a very stable DNA modification in mammals that could only be removed by replication in the absence of remethylation - that is, by mere dilution of this epigenetic mark (so-called passive DNA demethylation). However, in recent years, a significant number of studies have revealed the existence of active processes of DNA demethylation in mammals, with important roles in development and transcriptional regulation, allowing the molecular mechanisms of active DNA demethylation to be unraveled. In this article, we review the recent literature highlighting the prominent role played in active DNA demethylation by base excision repair and especially by TDG.
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Affiliation(s)
- Shannon R Dalton
- Cancer Biology Program, Epigenetics & Progenitor Cells Program, Fox Chase Cancer Center, PA 19111, USA
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16
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DNA Hypomethylation and Hemimethylation in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 754:31-56. [DOI: 10.1007/978-1-4419-9967-2_2] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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17
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Zhang RP, Shao JZ, Xiang LX. GADD45A protein plays an essential role in active DNA demethylation during terminal osteogenic differentiation of adipose-derived mesenchymal stem cells. J Biol Chem 2011; 286:41083-94. [PMID: 21917922 PMCID: PMC3220515 DOI: 10.1074/jbc.m111.258715] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2011] [Revised: 09/14/2011] [Indexed: 12/13/2022] Open
Abstract
Methylation and demethylation of DNA are the complementary processes of epigenetic regulation. These two types of regulation influence a diverse array of cellular activities, including the maintenance of pluripotency and self-renewal in embryonic stem cells. It was generally believed that DNA demethylation occurs passively over several cycles of DNA replication and that active DNA demethylation is rare. Recently, evidence for active DNA demethylation has been obtained in several cancer, neuronal, and embryonic stem cell lines. Studies in embryonic stem cell models, however, suggested that active DNA demethylation might be restricted to the early development of progenitor cells. Whether active demethylation is involved in terminal differentiation of adult stem cells is poorly understood. We provide evidence that active DNA demethylation does occur during terminal specification of stem cells in an adipose-derived mesenchymal stem cell-derived osteogenic differentiation model. The medium CpG regions in promoters of the Dlx5, Runx2, Bglap, and Osterix osteogenic lineage-specific genes were demethylated during the increase in gene expression associated with osteogenic differentiation. The growth arrest and DNA damage-inducible protein GADD45A was up-regulated in these processes. Knockdown of GADD45A led to hypermethylation of Dlx5, Runx2, Bglap, and Osterix promoters, followed by suppression of the expression of these genes and interruption of osteogenic differentiation. These results reveal that GADD45A plays an essential role in gene-specific active DNA demethylation during adult stem cell differentiation. They enhance the current knowledge of osteogenic specification and may also lead to a better understanding of the common mechanisms underlying epigenetic regulation in adult stem cell differentiation.
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Affiliation(s)
- Rui-peng Zhang
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058 and
- the Key Laboratory for Cell and Gene Engineering, Hangzhou 310058, Zhejiang Province, China
| | - Jian-zhong Shao
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058 and
- the Key Laboratory for Cell and Gene Engineering, Hangzhou 310058, Zhejiang Province, China
| | - Li-xin Xiang
- From the College of Life Sciences, Zhejiang University, Hangzhou 310058 and
- the Key Laboratory for Cell and Gene Engineering, Hangzhou 310058, Zhejiang Province, China
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18
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Abstract
Steroid hormone receptors regulate gene transcription in a highly tissue-specific manner. The local chromatin structure underlying promoters and hormone response elements is a major component involved in controlling these highly restricted expression patterns. Chromatin remodeling complexes, as well as histone and DNA modifying enzymes, are directed to gene-specific regions and create permissive or repressive chromatin environments. These structures further enable proper communication between transcription factors, co-regulators and basic transcription machinery. The regulatory elements active at target genes can be either constitutively accessible to receptors or subject to rapid receptor-dependent modification. The chromatin states responsible for these processes are in turn determined during development and differentiation. Thus access of regulatory factors to elements in chromatin provides a major level of cell selective regulation.
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Affiliation(s)
- Malgorzata Wiench
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, Bethesda, MD 20892-5055, USA
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19
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5-Aza-2'-deoxycytidine stress response and apoptosis in prostate cancer. Clin Epigenetics 2011; 2:339-48. [PMID: 22704346 PMCID: PMC3365594 DOI: 10.1007/s13148-010-0019-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Accepted: 12/15/2010] [Indexed: 12/31/2022] Open
Abstract
While studying on epigenetic regulatory mechanisms (DNA methylation at C-5 of -CpG- cytosine and demethylation of methylated DNA) of certain genes (FAS, CLU, E-cadh, CD44, and Cav-1) associated with prostate cancer development and its better management, we noticed that the used in vivo dose of 5-aza-2'-deoxycytidine (5.0 to 10.0 nM, sufficient to inhibit DNA methyltransferase activity in vitro) helped in the transcription of various genes with known (steroid receptors, AR and ER; ER variants, CD44, CDH1, BRCA1, TGFβR1, MMP3, MMP9, and UPA) and unknown (DAZ and Y-chromosome specific) proteins and the respective cells remained healthy in culture. At a moderate dose (20 to 200 nM) of the inhibitor, cells remain growth arrested. Upon subsequent challenge with increased dose (0.5 to 5.0 μM) of the inhibitor, we observed that the cellular morphology was changing and led to death of the cells with progress of time. Analyses of DNA and anti-, pro-, and apoptotic factors of the affected cells revealed that the molecular events that went on are characteristics of programmed cell death (apoptosis).
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20
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Morandi L, Franceschi E, de Biase D, Marucci G, Tosoni A, Ermani M, Pession A, Tallini G, Brandes A. Promoter methylation analysis of O6-methylguanine-DNA methyltransferase in glioblastoma: detection by locked nucleic acid based quantitative PCR using an imprinted gene (SNURF) as a reference. BMC Cancer 2010; 10:48. [PMID: 20167086 PMCID: PMC2843669 DOI: 10.1186/1471-2407-10-48] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Accepted: 02/18/2010] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Epigenetic silencing of the MGMT gene by promoter methylation is associated with loss of MGMT expression, diminished DNA-repair activity and longer overall survival in patients with glioblastoma who, in addition to radiotherapy, received alkylating chemotherapy with carmustine or temozolomide. We describe and validate a rapid methylation sensitive quantitative PCR assay (MS-qLNAPCR) using Locked Nucleic Acid (LNA) modified primers and an imprinted gene as a reference. METHODS An analysis was made of a database of 159 GBM patients followed between April 2004 and October 2008. After bisulfite treatment, methylated and unmethylated CpGs were recognized by LNA primers and molecular beacon probes. The SNURF promoter of an imprinted gene mapped on 15q12, was used as a reference. This approach was used because imprinted genes have a balanced copy number of methylated and unmethylated alleles, and this feature allows an easy and a precise normalization. RESULTS Concordance between already described nested MS-PCR and MS-qLNAPCR was found in 158 of 159 samples (99.4%). The MS-qLNAPCR assay showed a PCR efficiency of 102% and a sensitivity of 0.01% for LNA modified primers, while unmodified primers revealed lower efficiency (69%) and lower sensitivity (0.1%). MGMT promoter was found to be methylated using MS-qLNAPCR in 70 patients (44.02%), and completely unmethylated in 89 samples (55.97%). Median overall survival was of 24 months, being 20 months and 36 months, in patients with MGMT unmethylated and methylated, respectively. Considering MGMT methylation data provided by MS-qLNAPCR as a binary variable, overall survival was different between patients with GBM samples harboring MGMT promoter unmethylated and other patients with any percentage of MGMT methylation (p = 0.003). This difference was retained using other cut off values for MGMT methylation rate (i.e. 10% and 20% of methylated allele), while the difference was lost when 50% of MGMT methylated allele was used as cut-off. CONCLUSIONS We report and clinically validate an accurate, robust, and cost effective MS-qLNAPCR protocol for the detection and quantification of methylated MGMT alleles in GBM samples. Using MS-qLNAPCR we demonstrate that even low levels of MGMT promoter methylation have to be taken into account to predict response to temozolomide-chemotherapy.
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Affiliation(s)
- Luca Morandi
- Department of Haemathology and Oncological Sciences Section of Pathology, Bellaria Hospital, University of Bologna, Italy
| | - Enrico Franceschi
- Medical Oncology and Radiotherapy Departments, Bellaria-Maggiore Hospital, Azienda Unità Sanitaria Locale of Bologna, Italy
| | - Dario de Biase
- Department of Haemathology and Oncological Sciences Section of Pathology, Bellaria Hospital, University of Bologna, Italy
| | - Gianluca Marucci
- Department of Haemathology and Oncological Sciences Section of Pathology, Bellaria Hospital, University of Bologna, Italy
| | - Alicia Tosoni
- Medical Oncology and Radiotherapy Departments, Bellaria-Maggiore Hospital, Azienda Unità Sanitaria Locale of Bologna, Italy
| | - Mario Ermani
- Neurosciences Department, Statistic and Informatic Unit, Azienda Ospedale-Universita' of Padova, Italy
| | - Annalisa Pession
- Department of Experimental Pathology, University of Bologna, Italy
| | - Giovanni Tallini
- Department of Haemathology and Oncological Sciences Section of Pathology, Bellaria Hospital, University of Bologna, Italy
| | - Alba Brandes
- Medical Oncology and Radiotherapy Departments, Bellaria-Maggiore Hospital, Azienda Unità Sanitaria Locale of Bologna, Italy
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Patra SK, Bettuzzi S. Epigenetic DNA-(cytosine-5-carbon) modifications: 5-aza-2'-deoxycytidine and DNA-demethylation. BIOCHEMISTRY (MOSCOW) 2009; 74:613-9. [PMID: 19645665 DOI: 10.1134/s0006297909060042] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
DNA (cytosine-5-carbon) methylation is one of the hallmarks of mammalian chromatin modifications. Distinct methylation pattern can generate synergistic or antagonistic interaction affinities for CpG-islands associated with methylated or unmethylated cytosine binding proteins, which also may dictate histone modifications and dynamic transition between transcriptionally silent or transcriptionally active chromatin states. The enzymes and cofactors associated with DNA-methylation reactions are convincing in terms of chemistry and chemical thermodynamics. The mechanism of demethylation, the candidate enzyme(s) exhibiting direct demethylase activity, and associated cofactors are not firmly established. Use of azanucleosides, such as 5-azacytidine and 5-aza-2'-deoxycytidine (AzadC), in cell culture produces re-expression of certain genes, which otherwise were repressed in association with hypermethylated CpG-rich promoters. Hence the notion developed that AzadC is a demethylating agent. Here we discuss the broad global pictures with the following points: first, chemical definition and recent advances regarding the mechanism of DNA (cytosine-5-carbon) methylation ((Me)CpG-DNA or (Me)CpNpG-DNA formation) and (Me)CpG/(Me)CpNpG-DNA-demethylation, and then with the mechanistic basis of inactivation of DNA-methyltransferase 1 by AzadC. This will clarify that: (i) AzadC has nothing to do with DNA-demethylation; (ii) it cannot prevent even de novo methylation in non-replicating cells; (iii) it can only prevent replication coupled maintenance as well as de novo methylations. Finally, we would like to suggest that terming/designating AzadC as DNA-demethylating agent is a serious misuse of chemistry and chemical terminology.
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Affiliation(s)
- S K Patra
- Division of Biochemistry, Department of Experimental Medicine, University of Parma, Parma, Italy.
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22
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Mazin AL. Suicidal function of DNA methylation in age-related genome disintegration. Ageing Res Rev 2009; 8:314-27. [PMID: 19464391 DOI: 10.1016/j.arr.2009.04.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 04/17/2009] [Accepted: 04/20/2009] [Indexed: 10/20/2022]
Abstract
This article is dedicated to the 60th anniversary of 5-methylcytosine discovery in DNA. Cytosine methylation can affect genetic and epigenetic processes, works as a part of the genome-defense system and has mutagenic activity; however, the biological functions of this enzymatic modification are not well understood. This review will put forward the hypothesis that the host-defense role of DNA methylation in silencing and mutational destroying of retroviruses and other intragenomic parasites was extended during evolution to most host genes that have to be inactivated in differentiated somatic cells, where it acquired a new function in age-related self-destruction of the genome. The proposed model considers DNA methylation as the generator of 5mC>T transitions that induce 40-70% of all spontaneous somatic mutations of the multiple classes at CpG and CpNpG sites and flanking nucleotides in the p53, FIX, hprt, gpt human genes and some transgenes. The accumulation of 5mC-dependent mutations explains: global changes in the structure of the vertebrate genome throughout evolution; the loss of most 5mC from the DNA of various species over their lifespan and the Hayflick limit of normal cells; the polymorphism of methylation sites, including asymmetric mCpNpN sites; cyclical changes of methylation and demethylation in genes. The suicidal function of methylation may be a special genetic mechanism for increasing DNA damage and the programmed genome disintegration responsible for cell apoptosis and organism aging and death.
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Seguín-Estévez Q, De Palma R, Krawczyk M, Leimgruber E, Villard J, Picard C, Tagliamacco A, Abbate G, Gorski J, Nocera A, Reith W. The transcription factor RFX protects MHC class II genes against epigenetic silencing by DNA methylation. THE JOURNAL OF IMMUNOLOGY 2009; 183:2545-53. [PMID: 19620312 DOI: 10.4049/jimmunol.0900376] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Classical and nonclassical MHC class II (MHCII) genes are coregulated by the transcription factor RFX (regulatory factor X) and the transcriptional coactivator CIITA. RFX coordinates the assembly of a multiprotein "enhanceosome" complex on MHCII promoters. This enhanceosome serves as a docking site for the binding of CIITA. Whereas the role of the enhanceosome in recruiting CIITA is well established, little is known about its CIITA-independent functions. A novel role of the enhanceosome was revealed by the analysis of HLA-DOA expression in human MHCII-negative B cell lines lacking RFX or CIITA. HLA-DOA was found to be reactivated by complementation of CIITA-deficient but not RFX-deficient B cells. Silencing of HLA-DOA was associated with DNA methylation at its promoter, and was relieved by the demethylating agent 5-azacytidine. Surprisingly, DNA methylation was also established at the HLA-DRA and HLA-DQB loci in RFX-deficient cells. This was a direct consequence of the absence of RFX, as it could be reversed by restoring RFX function. DNA methylation at the HLA-DOA, HLA-DRA, and HLA-DQB promoters was observed in RFX-deficient B cells and fibroblasts, but not in CIITA-deficient B cells and fibroblasts, or in wild-type fibroblasts, which lack CIITA expression. These results indicate that RFX and/or enhanceosome assembly plays a key CIITA-independent role in protecting MHCII promoters against DNA methylation. This function is likely to be crucial for retaining MHCII genes in an open chromatin configuration permissive for activation in MHCII-negative cells, such as the precursors of APC and nonprofessional APC before induction with IFN-gamma.
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Lee HY, Kang RH, Han SW, Paik JW, Chang HS, Jeong YJ, Lee MS. Association of glucocorticoid receptor polymorphisms with the susceptibility to major depressive disorder and treatment responses in Korean depressive patients. Acta Neuropsychiatr 2009; 21:11-7. [PMID: 25384524 DOI: 10.1111/j.1601-5215.2008.00342.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Major depressive disorder (MDD) is closely related to stress reactions and serotonin probably underpins the pathophysiology of MDD. Alterations of the hypothalamic-pituitary-adrenal axis at the gene level have reciprocal consequences on serotonin neurotransmission. Glucocorticoid receptor (GR) polymorphisms affect glucocorticoid sensitivity, which is associated with cortisol feedback effects. Therefore, we hypothesised that GR polymorphisms are associated with the susceptibility to MDD and predict the treatment response. METHOD Ninety-six subjects with a minimum score of 17 on the 21-item Hamilton Depression Scale (HAMD) at baseline were enrolled into the present study. The genotypes of GR (N363S, ER22/23EK, Bcl1, and TthIII1 polymorphisms) were analysed. The HAMD score was again measured after 1, 2, 4 and 8 weeks of antidepressant treatment to detect whether the therapeutic effects differed with the GR genotype. RESULTS Our subjects carried no N363S or ER22/23EK genetic polymorphisms and three types of Bcl1 and TthIII1 genetic polymorphisms. The C/C genotype and C allele at Bcl1 polymorphism were more frequent in MDD patients than in normal controls (p < 0.01 and p = 0.01, respectively). The genotype distributions did not differ significantly between responders and non-responders. CONCLUSION These results suggest that GR polymorphism cannot predict the therapeutic response after antidepressant administration. However, GR polymorphism (Bcl1) might play a role in the pathophysiology of MDD. Future studies should check this finding in larger populations with different characteristics.
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Affiliation(s)
- Hwa-Young Lee
- 1Clinical Research Center for Depression, Korea University, Seoul, Korea
| | - Rhee-Hun Kang
- 1Clinical Research Center for Depression, Korea University, Seoul, Korea
| | - Sang-Woo Han
- 4Department of Psychiatry, College of Medicine, Soonchunhyang University, Seoul, Korea
| | - Jong-Woo Paik
- 5Department of Psychiatry, College of Medicine, Kyunghee University, Seoul, Korea
| | - Hun Soo Chang
- 1Clinical Research Center for Depression, Korea University, Seoul, Korea
| | - Yoo Jung Jeong
- 1Clinical Research Center for Depression, Korea University, Seoul, Korea
| | - Min-Soo Lee
- 1Clinical Research Center for Depression, Korea University, Seoul, Korea
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Meister GE, Chandrasegaran S, Ostermeier M. An engineered split M.HhaI-zinc finger fusion lacks the intended methyltransferase specificity. Biochem Biophys Res Commun 2008; 377:226-30. [PMID: 18835252 PMCID: PMC2586766 DOI: 10.1016/j.bbrc.2008.09.099] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Accepted: 09/24/2008] [Indexed: 11/20/2022]
Abstract
The ability to site-specifically methylate DNA in vivo would have wide applicability to the study of basic biomedical problems as well as enable studies on the potential of site-specific DNA methylation as a therapeutic strategy for the treatment of diseases. Natural DNA methyltransferases lack the specificity required for these applications. Nomura and Barbas [W. Nomura, C.F. Barbas 3rd, In vivo site-specific DNA methylation with a designed sequence-enabled DNA methylase, J. Am. Chem. Soc. 129 (2007) 8676-8677] have reported that an engineered DNA methyltransferase comprised of fragments of M.HhaI methyltransferase and zinc finger proteins has very high specificity for the chosen target site. Our analysis of this engineered enzyme shows that the fusion protein methylates target and non-target sites with similar efficiency.
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Affiliation(s)
- Glenna E. Meister
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
| | - Srinivasan Chandrasegaran
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
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26
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Active DNA demethylation and DNA repair. Differentiation 2008; 77:1-11. [PMID: 19281759 DOI: 10.1016/j.diff.2008.09.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2008] [Revised: 06/19/2008] [Accepted: 07/07/2008] [Indexed: 12/17/2022]
Abstract
DNA methylation on cytosine is an epigenetic modification and is essential for gene regulation and genome stability in vertebrates. Traditionally DNA methylation was considered as the most stable of all heritable epigenetic marks. However, it has become clear that DNA methylation is reversible by enzymatic "active" DNA demethylation, with examples in plant cells, animal development and immune cells. It emerges that "pruning" of methylated cytosines by active DNA demethylation is an important determinant for the DNA methylation signature of a cell. Work in plants and animals shows that demethylation occurs by base excision and nucleotide excision repair. Far from merely protecting genomic integrity from environmental insult, DNA repair is therefore at the heart of an epigenetic activation process.
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Ikeda Y, Kinoshita T. DNA demethylation: a lesson from the garden. Chromosoma 2008; 118:37-41. [PMID: 18839198 DOI: 10.1007/s00412-008-0183-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Accepted: 09/11/2008] [Indexed: 11/30/2022]
Abstract
Gene silencing by DNA methylation is well documented and known to be essential for various biological phenomena in many organisms. In contrast, the processes that convert the silent state of a gene whose DNA is methylated and predicted to form facultative heterochromatin to the actively transcribed state remain elusive. In Arabidopsis, recent studies have shown that the DNA glycosylases DEMETER (DME) and REPRESSOR OF SILENCING1 (ROS1) participate in DNA demethylation. DME is necessary for genomic imprinting in the endosperm, while ROS1 is involved in pruning DNA methylation patterns in transposons and genic regions of vegetative tissues. These findings provide us with molecular clues for understanding the underlying mechanisms of DNA demethylation and gene activation. In this review, we will consider and discuss the processes of controlling gene activation through DNA demethylation, which are predicted to include the recognition of target sequences, DNA demethylation, the transformation of the chromatin to the active state, and transcription. Many of these processes remain poorly understood at this stage.
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Affiliation(s)
- Yoko Ikeda
- Plant Reproductive Genetics, GCOE Research Group, Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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28
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Patra SK, Szyf M. DNA methylation-mediated nucleosome dynamics and oncogenic Ras signaling: insights from FAS, FAS ligand and RASSF1A. FEBS J 2008; 275:5217-35. [PMID: 18803665 DOI: 10.1111/j.1742-4658.2008.06658.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cytosine methylation at the 5-carbon position is the only known stable base modification found in the mammalian genome. The organization and modification of chromatin is a key factor in programming gene expression patterns. Recent findings suggest that DNA methylation at the junction of transcription initiation and elongation plays a critical role in suppression of transcription. This effect is mechanistically mediated by the state of chromatin modification. DNA methylation attracts binding of methyl-CpG-binding domain proteins that trigger repression of transcription, whereas DNA demethylation facilitates transcription activation. Understanding the rules that guide differential gene expression, as well as transcription dynamics and transcript abundance, has proven to be a taxing problem for molecular biologists and oncologists alike. The use of novel molecular modeling methods is providing exciting insights into the challenging problem of how methylation mediates chromatin dynamics. New data implicate lipid rafts as the coordinators of signals emanating from the cell membrane and are converging on the mechanisms linking DNA methylation and chromatin dynamics. This review focuses on some of these recent advances and uses lipid-raft-facilitated Ras signaling as a paradigm for understanding DNA methylation, chromatin dynamics and apoptosis.
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Kuriyama M, Udagawa A, Yoshimoto S, Ichinose M, Sato K, Yamazaki K, Matsuno Y, Shiota K, Mori C. DNA Methylation Changes during Cleft Palate Formation Induced by Retinoic Acid in Mice. Cleft Palate Craniofac J 2008; 45:545-51. [DOI: 10.1597/07-134.1] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Objectives:The aim of this study was to analyze epigenetic (specifically, DNA methylation) participation in the mechanisms of cleft palate only induced by maternal exposure to all-trans retinoic acid in mice.Design:Cleft palate only was induced in fetuses by maternal exposure to all-trans retinoic acid. Their secondary palates were excised for analysis. Cytosine extension assay and restriction landmark genomic scanning were performed to analyze DNA methylation status. The expression levels of the DNA methyltransferases were examined by real-time reverse transcriptase–polymerase chain reaction.Results:Using cytosine extension assay, on gestation day 14.5, the status of DNA methylation within CpG islands and in global DNA was decreased significantly in all-trans retinoic acid–treated groups compared with the controls (p < .01 and p < .05). In the controls, the status within CpG islands on gestation day 14.5 was significantly increased compared with gestation days 13.5 and 18.5 (p < .01). Using real-time reverse transcriptase–polymerase chain reaction, there was no significant change in the expression of DNA methyltransferases, except on gestation day 18.5. Using restriction landmark genomic scanning on gestation day 18.5, five spots (0.49%) in the controls and one spot (0.1%) in all-trans retinoic acid–treated groups were specifically detected.Conclusions:These results indicate that changes in DNA methylation may play an important role in the manifestation of cleft palate only caused by environmental factors such as maternal exposure to all-trans retinoic acid.
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Affiliation(s)
- Motone Kuriyama
- Department of Plastic and Reconstructive Surgery, Graduate School of Medicine, Chiba University, Japan
| | - Akikazu Udagawa
- Department of Plastic, Reconstructive and Aesthetic Surgery, Chiba University Hospital, Japan
| | - Shinya Yoshimoto
- Department of Plastic and Reconstructive Surgery, Graduate School of Medicine, Chiba University, Japan
| | - Masaharu Ichinose
- Department of Plastic and Reconstructive Surgery, Graduate School of Medicine, Chiba University, Japan
| | - Koji Sato
- Department of Bioenvironmental Medicine, Graduate School of Medicine, Chiba University, Japan
| | - Koji Yamazaki
- Department of Bioenvironmental Medicine, Graduate School of Medicine, Chiba University, Japan
| | - Yoshiharu Matsuno
- Department of Bioenvironmental Medicine, Graduate School of Medicine, Chiba University, Japan
| | - Kunio Shiota
- Graduate School of Agriculture and Life Science, the University of Tokyo, Japan
| | - Chisato Mori
- Department of Bioenvironmental Medicine, Graduate School of Medicine, Chiba University, Japan
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Ortega-Galisteo AP, Morales-Ruiz T, Ariza RR, Roldán-Arjona T. Arabidopsis DEMETER-LIKE proteins DML2 and DML3 are required for appropriate distribution of DNA methylation marks. PLANT MOLECULAR BIOLOGY 2008; 67:671-81. [PMID: 18493721 DOI: 10.1007/s11103-008-9346-0] [Citation(s) in RCA: 187] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Accepted: 05/07/2008] [Indexed: 05/19/2023]
Abstract
Cytosine DNA methylation is a stable epigenetic mark for maintenance of gene silencing across cellular divisions, but it is a reversible modification. Genetic and biochemical studies have revealed that the Arabidopsis DNA glycosylase domain-containing proteins ROS1 (REPRESSOR OF SILENCING 1) and DME (DEMETER) initiate erasure of 5-methylcytosine through a base excision repair process. The Arabidopsis genome encodes two paralogs of ROS1 and DME, referred to as DEMETER-LIKE proteins DML2 and DML3. We have found that DML2 and DML3 are 5-methylcytosine DNA glycosylases that are expressed in a wide range of plant organs. We analyzed the distribution of methylation marks at two methylated loci in wild-type and dml mutant plants. Mutations in DML2 and/or DML3 lead to hypermethylation of cytosine residues that are unmethylated or weakly methylated in wild-type plants. In contrast, sites that are heavily methylated in wild-type plants are hypomethylated in mutants. These results suggest that DML2 and DML3 are required not only for removing DNA methylation marks from improperly-methylated cytosines, but also for maintenance of high methylation levels in properly targeted sites.
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Affiliation(s)
- Ana Pilar Ortega-Galisteo
- Departamento de Genética, Universidad de Córdoba, Edificio Gregor Mendel, Campus de Rabanales s/n, 14071, Córdoba, Spain
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Genomic imprinting: a balance between antagonistic roles of parental chromosomes. Semin Cell Dev Biol 2008; 19:574-9. [PMID: 18718545 DOI: 10.1016/j.semcdb.2008.07.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 07/21/2008] [Accepted: 07/24/2008] [Indexed: 11/21/2022]
Abstract
Maternally and paternally derived chromosomes might be expected to contribute equally to the various cellular and developmental processes in placental mammals and flowering plants. However, this is not true even in the case of the self-pollinated plant, Arabidopsis, which has identical DNA sequences in both parental genomes. The reason for this is that some genes, called "imprinted genes", are expressed exclusively from paternally or maternally inherited chromosomes. As a result, parental chromosomes express a distinct set of genes and play different roles in biological processes. Here, we review and compare roles of genomic imprinting in flowering plants and placental mammals.
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Epigenetic analysis reveals a euchromatic configuration in the FMR1 unmethylated full mutations. Eur J Hum Genet 2008; 16:1487-98. [PMID: 18628788 DOI: 10.1038/ejhg.2008.130] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Fragile X syndrome (FXS) is caused by the expansion of a CGG repeat in the 5'UTR of the FMR1 gene and the subsequent methylation of all CpG sites in the promoter region. We recently identified, in unrelated FXS families, two rare males with an unmethylated full mutation, that is, with an expanded CGG repeat (>200 triplets) lacking the typical CpG methylation in the FMR1 promoter. These individuals are not mentally retarded and do not appear to be mosaic for premutation or methylated full mutation alleles. We established lymphoblastoid and fibroblast cell lines that showed essentially normal levels of the FMR1-mRNA but reduced translational efficiency of the corresponding mRNA. Epigenetic analysis of the FMR1 gene demonstrated the lack of DNA methylation and a methylation pattern of lysines 4 and 27 on histone H3 similar to that of normal controls, in accordance with normal transcription levels and consistent with a euchromatic configuration. On the other hand, histone H3/H4 acetylation and lysine 9 methylation on histone H3 were similar to those of typical FXS cell lines, suggesting that these epigenetic changes are not sufficient for FMR1 gene inactivation. These findings demonstrate remarkable consistency and suggest a common genetic mechanism causing this rare FMR1 epigenotype. The discovery of such a mechanism may be important in view of therapeutic attempts to convert methylated into unmethylated full mutations, restoring the expression of the FMR1 gene.
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Patra SK, Patra A, Rizzi F, Ghosh TC, Bettuzzi S. Demethylation of (Cytosine-5-C-methyl) DNA and regulation of transcription in the epigenetic pathways of cancer development. Cancer Metastasis Rev 2008; 27:315-34. [DOI: 10.1007/s10555-008-9118-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Masaki H, Ishikawa T, Takahashi S, Okumura M, Sakai N, Haga M, Kominami K, Migita H, McDonald F, Shimada F, Sakurada K. Heterogeneity of pluripotent marker gene expression in colonies generated in human iPS cell induction culture. Stem Cell Res 2008; 1:105-15. [PMID: 19383391 DOI: 10.1016/j.scr.2008.01.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 01/09/2008] [Accepted: 01/12/2008] [Indexed: 01/01/2023] Open
Abstract
Induction of pluripotent stem cells from human fibroblasts has been achieved by the ectopic expression of two different sets of four genes. However, the mechanism of the pluripotent stem cell induction has not been elucidated. Here we identified a marked heterogeneity in colonies generated by the four-gene (Oct3/4, Sox2, c-Myc, and Klf4) transduction method in human neonatal skin-derived cells. The four-gene transduction gave a higher probability of induction for archetypal pluripotent stem cell marker genes (Nanog, TDGF, and Dnmt3b) than for marker genes that are less specific for pluripotent stem cells (CYP26A1 and TERT) in primary induction culture. This tendency may reflect the molecular mechanism underlying the induction of human skin-derived cells into pluripotent stem cells. Among the colonies induced by the four-gene transduction, small cells with a high nucleus-to-cytoplasm ratio could be established by repeated cloning. Subsequently established cell lines were similar to human embryonic stem cells as well as human induced pluripotent stem (iPS) cells derived from adult tissue in morphology, gene expression, long-term self-renewal ability, and teratoma formation. Genome-wide single-nucleotide polymorphism array analysis of the human iPS cell line indicates that the induction process did not induce DNA mutation.
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Affiliation(s)
- Hideki Masaki
- Department of Stem-Cell-Based Drug Discovery, Research Center Kobe, Bayer Yakuhin Ltd., Kobe, Hyogo, Japan
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Patra SK. Ras regulation of DNA-methylation and cancer. Exp Cell Res 2008; 314:1193-201. [PMID: 18282569 DOI: 10.1016/j.yexcr.2008.01.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2007] [Revised: 01/13/2008] [Accepted: 01/16/2008] [Indexed: 01/14/2023]
Abstract
Genome wide hypomethylation and regional hypermethylation of cancer cells and tissues remain a paradox, though it has received a convincing confirmation that epigenetic switching systems, including DNA-methylation represent a fundamental regulatory mechanism that has an impact on genome maintenance and gene transcription. Methylated cytosine residues of vertebrate DNA are transmitted by clonal inheritance through the strong preference of DNA methyltransferase, DNMT1, for hemimethylated-DNA. Maintenance of methylation patterns is necessary for normal development of mice, and aberrant methylation patterns are associated with many human tumours. DNMT1 interacts with many proteins during cell cycle progression, including PCNA, p53, EZH2 and HP1. Ras family of GTPases promotes cell proliferation by its oncogenic nature, which transmits signals by multiple pathways in both lipid raft dependent and independent fashion. DNA-methylation-mediated repression of DNA-repair protein O6-methylguanine DNA methyltransferase (MGMT) gene and increased rate of K-Ras mutation at codon for amino acids 12 and 13 have been correlated with a secondary role for Ras-effector homologues (RASSFs) in tumourigenesis. Lines of evidence suggest that DNA-methylation associated repression of tumour suppressors and apoptotic genes and ceaseless proliferation of tumour cells are regulated in part by Ras-signaling. Control of Ras GTPase signaling might reduce the aberrant methylation and accordingly may reduce the risk of cancer development.
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Affiliation(s)
- Samir Kumar Patra
- Cancer Epigenetics Research, Kalyani (B-7/183), Nadia, West Bengal, India.
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Abstract
Chromatin-modifying proteins mold the genome into areas that are accessible for transcriptional activity and areas that are transcriptionally silent. This epigenetic gene regulation allows for different transcriptional programs to be conducted in different cell types at different timepoints-despite the fact that all cells in the organism contain the same genetic information. A large amount of data gathered over the last decades has demonstrated that deregulation of chromatin-modifying proteins is etiologically involved in the development and progression of cancer. Here we discuss how epigenetic alterations influence cancer development and review known cancer-associated alterations in chromatin-modifying proteins.
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Affiliation(s)
- Cathrine K Fog
- Biotech Research & Innovation Centre and Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, DK- 2200 Copenhagen Denmark
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37
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Métivier R, Huet G, Gallais R, Finot L, Petit F, Tiffoche C, Mérot Y, LePéron C, Reid G, Penot G, Demay F, Gannon F, Flouriot G, Salbert G. Dynamics of estrogen receptor-mediated transcriptional activation of responsive genes in vivo: apprehending transcription in four dimensions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 617:129-38. [PMID: 18497037 DOI: 10.1007/978-0-387-69080-3_12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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38
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Morales-Ramírez P, Vallarino-Kelly T, Cruz-Vallejo VL. Mechanisms of DNA breaks inductionin vivo by 5-azacytidine: paths of micronucleus induction by azaC. J Appl Toxicol 2008; 28:254-9. [PMID: 17685412 DOI: 10.1002/jat.1274] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The aim of the present study was to correlate the time-response curves of micronucleated polychromatic erythrocyte (MN-PCE) induction by 5-azacytidine (azaC) with the possible processes involved in DNA break production; this is based on the results previously published by other authors. The MN-PCE induction at two different doses of azaC was determined by sampling blood from the tails of mice before the acute treatment and over nine periods of 8 h each afterwards. Both doses caused two peaks of MN-PCE induction, one at 32 h and another at 48 h, approximately; a shoulder was detected that remained high from 56 h up to the end of the study (72 h). These results suggest that azaC induced DNA breaks and subsequently MN (micronucleus) by three different mechanisms, and in agreement with data in the literature, these could be successively the following: (i) during excision of the large adduct comprising the DNA methyl transferase covalently linked to DNA; (ii) failure of recombination repair or mismatch repair; and (iii) persistent chromosome fragility in G-C rich sites due to DNA demethylation and chromatin decondensation.
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Affiliation(s)
- P Morales-Ramírez
- Instituto Nacional de Investigaciones Nucleares, AP 18-1027 México, D.F., México.
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Abstract
Although there is evidence to link schizophrenia (SCZ) and bipolar disorder (BD) to genetic and environmental factors, specific individual or groups of genes/factors causative of the disease have been elusive to the research community. An understanding of the molecular aberrations that cause these mental illnesses requires comprehensive approaches that examine both genetic and epigenetic factors. Because of the overwhelming evidence for the role of environmental factors in the disease presentation, our initial approach involved deciphering how epigenetic changes resulting from promoter DNA methylation affect gene expression in SCZ and BD. Apparently, the central reversible but covalent epigenetic modification to DNA is derived from methylation of the cytosine residues that is potentially heritable and can affect gene expression and downstream activities. Environmental factors can influence DNA methylation patterns and hence alter gene expression. Such changes can be especially problematic in individuals with genetic susceptibilities to specific diseases. Recent reports from our laboratory provided compelling evidence that both hyper- and hypo-DNA methylation changes of the regulatory regions play critical roles in defining the altered functionality of genes in major psychiatric disorders such as SCZ and BD. In this chapter, we outline the technical details of the methods that could help to expand this line of research to assist with compiling the differential methylation-mediated epigenetic alterations that are responsible for the pathogenesis of SCZ, BD, and other mental diseases. We use the genes of the extended dopaminergic (DAergic) system such as membrane-bound catechol-O-methyltransferase (MB-COMT), monoamine oxidase A (MAOA), dopamine transporter 1 (DAT1), tyrosine hydroxylase (TH), dopamine (DA) receptors1 and 2 (DRD1/2), and related genes (e.g., reelin [RELN] and brain-derived neurotrophic factor [BDNF]) to illustrate the associations between differential promoter DNA methylations and disease phenotype. It is our hope that comprehensive analyses of the DAergic system as the prototype could provide the impetus and molecular basis to uncover early markers for diagnosis, help in the understanding of differences in disease severity in individuals with similar or identical genetic makeup, and assist with the identification of novel targets for therapeutic applications.
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Huettel B, Kanno T, Daxinger L, Bucher E, van der Winden J, Matzke AJM, Matzke M. RNA-directed DNA methylation mediated by DRD1 and Pol IVb: A versatile pathway for transcriptional gene silencing in plants. ACTA ACUST UNITED AC 2007; 1769:358-74. [PMID: 17449119 DOI: 10.1016/j.bbaexp.2007.03.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2006] [Revised: 02/28/2007] [Accepted: 03/01/2007] [Indexed: 12/22/2022]
Abstract
RNA-directed DNA methylation, which is one of several RNAi-mediated pathways in the nucleus, has been highly elaborated in the plant kingdom. RNA-directed DNA methylation requires for the most part conventional DNA methyltransferases, histone modifying enzymes and RNAi proteins; however, several novel, plant-specific proteins that are essential for this process have been identified recently. DRD1 (defective in RNA-directed DNA methylation) is a putative SWI2/SNF2-like chromatin remodelling protein; DRD2 and DRD3 (renamed NRPD2a and NRPD1b, respectively) are subunits of Pol IVb, a putative RNA polymerase found only in plants. Interestingly, DRD1 and Pol IVb appear to be required not only for RNA-directed de novo methylation, but also for full erasure of methylation when the RNA trigger is withdrawn. These proteins thus have the potential to facilitate dynamic regulation of DNA methylation. Prominent targets of RNA-directed DNA methylation in the Arabidopsis thaliana genome include retrotransposon long terminal repeats (LTRs), which have bidirectional promoter/enhancer activities, and other types of intergenic transposons and repeats. Intergenic solitary LTRs that are targeted for reversible methylation by the DRD1/Pol IVb pathway can potentially act as switches or rheostats for neighboring plant genes. The resulting alterations in gene expression patterns may promote physiological flexibility and adaptation to the environment.
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Affiliation(s)
- Bruno Huettel
- Gregor Mendel Institute for Molecular Plant Biology, Austrian Academy of Sciences, Dr. Bohr-Gasse 3, A-1030 Vienna, Austria
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Roach HI, Aigner T. DNA methylation in osteoarthritic chondrocytes: a new molecular target. Osteoarthritis Cartilage 2007; 15:128-37. [PMID: 16908204 DOI: 10.1016/j.joca.2006.07.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Accepted: 07/09/2006] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To review the current knowledge of the mechanism of DNA methylation, its association with transcriptional silencing, possible mechanisms of hyper- and hypomethylation and how epigenetic changes may relate to the pathogenesis of osteoarthritis (OA). METHODS Journal literature was searched using Pubmed. Since there are very few publications directly on epigenetic phenomena in OA, the search was extended to give an overview of epigenetic mechanisms as they relate to the molecular mechanisms of the disease. RESULTS While the epigenetics of cancer cells have been intensively investigated, little attention has so far been paid as to whether epigenetic changes contribute to the pathology of non-neoplastic diseases such as OA. This review explains the mechanisms of DNA methylation, its role in transcriptional regulation, and possible demethylation mechanisms that may be applicable to OA. Preliminary evidence suggests that changes in DNA methylation, together with cytokines, growth factors and changes in matrix composition, are likely to be important in determining the complex gene expression patterns that are observed in osteoarthritic chondrocytes. CONCLUSION Early evidence points to a role of epigenetics in the pathogenesis of OA. Since epigenetic changes, although heritable at the cellular level, are potentially reversible, epigenetics could be a new molecular target for therapeutic intervention, especially early in the disease.
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Affiliation(s)
- H I Roach
- Bone and Joint Research Group, Division of Developmental Origins of Health and Disease, University of Southampton, UK.
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Barreto G, Schäfer A, Marhold J, Stach D, Swaminathan SK, Handa V, Döderlein G, Maltry N, Wu W, Lyko F, Niehrs C. Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation. Nature 2007; 445:671-5. [PMID: 17268471 DOI: 10.1038/nature05515] [Citation(s) in RCA: 553] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 12/04/2006] [Indexed: 12/21/2022]
Abstract
DNA methylation is an epigenetic modification that is essential for gene silencing and genome stability in many organisms. Although methyltransferases that promote DNA methylation are well characterized, the molecular mechanism underlying active DNA demethylation is poorly understood and controversial. Here we show that Gadd45a (growth arrest and DNA-damage-inducible protein 45 alpha), a nuclear protein involved in maintenance of genomic stability, DNA repair and suppression of cell growth, has a key role in active DNA demethylation. Gadd45a overexpression activates methylation-silenced reporter plasmids and promotes global DNA demethylation. Gadd45a knockdown silences gene expression and leads to DNA hypermethylation. During active demethylation of oct4 in Xenopus laevis oocytes, Gadd45a is specifically recruited to the site of demethylation. Active demethylation occurs by DNA repair and Gadd45a interacts with and requires the DNA repair endonuclease XPG. We conclude that Gadd45a relieves epigenetic gene silencing by promoting DNA repair, which erases methylation marks.
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Affiliation(s)
- Guillermo Barreto
- Division of Molecular Embryology, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
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43
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Morales-Ramírez P, Rodríguez-Reyes R, Toribio-Escobedo E, Olvera-Nestor C, García-Firó B. Mechanism of in vivo sister-chromatid exchange induction by 5-azacytidine. Mutagenesis 2007; 22:177-81. [PMID: 17267817 DOI: 10.1093/mutage/gel069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The aim of the present study was to explore the in vivo mechanism of sister-chromatid exchange (SCE) induction by 5-azacytidine (5-azaC) in murine bone marrow cells. Experiments were performed to examine SCE induction in response to different doses of 5-azaC as well as several exposures. Additionally, we examined the persistence of SCE induction and the effect of bromodeoxiuridine (BrdU) incorporation. Sister-chromatid differentiation was obtained by injecting mice intraperitoneally with BrdU absorbed to activated charcoal. Before BrdU injection, different doses of 5-azaC were administered intraperitoneally either singly or in multiples. Colchicine in an aqueous solution was administered subcutaneously 22 h after BrdU injection. Two hours later, animals were sacrificed by cervical dislocation and both femurs were dissected. Bone marrow cells were processed to obtain chromosome preparations, which were stained by the fluorescence plus Giemsa method. Results indicate that 5-azaC caused SCE, albeit to a limited extent. In order to discern whether the limitation was due to cytotoxicity or to partial 5-azaC incorporation, we administered multiple sub-toxic doses of 5-azaC. This treatment increased 5-azaC incorporation and reduced cytotoxicity, but did not raise SCE frequency, indicating that the limitation was not due to either of the two factors mentioned above. SCE frequency induced by 5-azaC persisted for at least eight cell divisions, confirming that this agent had caused inhibition of DNA methyltransferase and subsequently the reduction of DNA re-methylation, which in turn induced the expression of a number of SCE-prone sites. Finally, SCE induction in response to 5-azaC was completely dependent on BrdU incorporation. The data allow us to conclude that 5-azaC causes SCE to a limited extent; limited SCE induction was not due to the direct effect of incorporation or cytotoxicity of 5-azaC, but rather the generation of a number of SCE-prone sites, the expression of which persists for at least eight cell divisions and is dependent on BrdU incorporation.
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Affiliation(s)
- P Morales-Ramírez
- Instituto Nacional de Investigaciones Nucleares, AP 18-1027 México, D.F., México.
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44
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Kress C, Thomassin H, Grange T. Active cytosine demethylation triggered by a nuclear receptor involves DNA strand breaks. Proc Natl Acad Sci U S A 2006; 103:11112-7. [PMID: 16840560 PMCID: PMC1544051 DOI: 10.1073/pnas.0601793103] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2006] [Indexed: 12/31/2022] Open
Abstract
Cytosine methylation at CpG dinucleotides contributes to the epigenetic maintenance of gene silencing. Dynamic reprogramming of DNA methylation patterns is believed to play a key role during development and differentiation in vertebrates. The mechanisms of DNA demethylation remain unclear and controversial. Here, we present a detailed characterization of the demethylation of an endogenous gene in cultured cells. This demethylation is triggered in a regulatory region by a transcriptional activator, the glucocorticoid receptor. We show that DNA demethylation is an active process, occurring independently of DNA replication, and in a distributive manner without concerted demethylation of cytosines on both strands. We demonstrate that the DNA backbone is cleaved 3' to the methyl cytidine during demethylation, and we suggest that a DNA repair pathway may therefore be involved in this demethylation.
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Affiliation(s)
- Clémence Kress
- Institut Jacques Monod du Centre National de la Recherche Scientifique, Universités Paris 6-7, Tour 43, 2, Place Jussieu, 75251 Paris Cedex 05, France
| | - Hélène Thomassin
- Institut Jacques Monod du Centre National de la Recherche Scientifique, Universités Paris 6-7, Tour 43, 2, Place Jussieu, 75251 Paris Cedex 05, France
| | - Thierry Grange
- Institut Jacques Monod du Centre National de la Recherche Scientifique, Universités Paris 6-7, Tour 43, 2, Place Jussieu, 75251 Paris Cedex 05, France
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Vakhitova YV, Sadovnikov SV, Yamidanov RS, Seredenin SB. Cytosine demethylation in the tyrosine hydroxylase gene promoter in hypothalamus cells of rat brain under the action of 2-aminoadamantane compound Ladasten. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406070155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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46
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Morales-Ruiz T, Ortega-Galisteo AP, Ponferrada-Marín MI, Martínez-Macías MI, Ariza RR, Roldán-Arjona T. DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases. Proc Natl Acad Sci U S A 2006; 103:6853-8. [PMID: 16624880 PMCID: PMC1458983 DOI: 10.1073/pnas.0601109103] [Citation(s) in RCA: 254] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Indexed: 11/18/2022] Open
Abstract
Cytosine methylation is an epigenetic mark that promotes gene silencing and plays important roles in development and genome defense against transposons. Methylation patterns are established and maintained by DNA methyltransferases that catalyze transfer of a methyl group from S-adenosyl-L-methionine to cytosine bases in DNA. Erasure of cytosine methylation occurs during development, but the enzymatic basis of active demethylation remains controversial. In Arabidopsis thaliana, DEMETER (DME) activates the maternal expression of two imprinted genes silenced by methylation, and REPRESSOR OF SILENCING 1 (ROS1) is required for release of transcriptional silencing of a hypermethylated transgene. DME and ROS1 encode two closely related DNA glycosylase domain proteins, but it is unknown whether they participate directly in a DNA demethylation process or counteract silencing through an indirect effect on chromatin structure. Here we show that DME and ROS1 catalyze the release of 5-methylcytosine (5-meC) from DNA by a glycosylase/lyase mechanism. Both enzymes also remove thymine, but not uracil, mismatched to guanine. DME and ROS1 show a preference for 5-meC over thymine in the symmetric dinucleotide CpG context, where most plant DNA methylation occurs. Nevertheless, they also have significant activity on both substrates at CpApG and asymmetric sequences, which are additional methylation targets in plant genomes. These findings suggest that a function of ROS1 and DME is to initiate erasure of 5-meC through a base excision repair process and provide strong biochemical evidence for the existence of an active DNA demethylation pathway in plants.
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Affiliation(s)
| | | | | | | | - Rafael R. Ariza
- Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain
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Feng YQ, Desprat R, Fu H, Olivier E, Lin CM, Lobell A, Gowda SN, Aladjem MI, Bouhassira EE. DNA methylation supports intrinsic epigenetic memory in mammalian cells. PLoS Genet 2006; 2:e65. [PMID: 16683039 PMCID: PMC1449906 DOI: 10.1371/journal.pgen.0020065] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Accepted: 03/17/2006] [Indexed: 12/31/2022] Open
Abstract
We have investigated the role of DNA methylation in the initiation and maintenance of silenced chromatin in somatic mammalian cells. We found that a mutated transgene, in which all the CpG dinucleotides have been eliminated, underwent transcriptional silencing to the same extent as the unmodified transgene. These observations demonstrate that DNA methylation is not required for silencing. The silenced CpG-free transgene exhibited all the features of heterochromatin, including silencing of transcriptional activity, delayed DNA replication, lack of histone H3 and H4 acetylation, lack of H3-K4 methylation, and enrichment in tri-methyl-H3-K9. In contrast, when we tested for transgene reactivation using a Cre recombinase-mediated inversion assay, we observed a marked difference between a CpG-free and an unmodified transgene: the CpG-free transgene resumed transcription and did not exhibit markers of heterochromatin whereas the unmodified transgene remained silenced. These data indicate that methylation of CpG residues conferred epigenetic memory in this system. These results also suggest that replication delay, lack of histone H3 and H4 acetylation, H3-K4 methylation, and enrichment in tri-methyl-H3-K9 are not sufficient to confer epigenetic memory. We propose that DNA methylation within transgenes serves as an intrinsic epigenetic memory to permanently silence transgenes and prevent their reactivation.
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Affiliation(s)
- Yong-Qing Feng
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
| | - Romain Desprat
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
| | - Haiqing Fu
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Emmanuel Olivier
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
| | - Chii Mei Lin
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Amanda Lobell
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
| | - Shilpa N Gowda
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Mirit I Aladjem
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Eric E Bouhassira
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
- * To whom correspondence should be addressed. E-mail:
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van Rossum EFC, Binder EB, Majer M, Koper JW, Ising M, Modell S, Salyakina D, Lamberts SWJ, Holsboer F. Polymorphisms of the glucocorticoid receptor gene and major depression. Biol Psychiatry 2006; 59:681-8. [PMID: 16580345 DOI: 10.1016/j.biopsych.2006.02.007] [Citation(s) in RCA: 253] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2005] [Revised: 12/23/2005] [Accepted: 02/15/2006] [Indexed: 10/24/2022]
Abstract
BACKGROUND The most consistent biological finding in patients with depression is a hyperactivity of the hypothalamic-pituitary-adrenal (HPA)-axis, which might be caused by impaired glucocorticoid signaling. Glucocorticoids act through the glucocorticoid receptor (GR) for which several polymorphisms have been described. The N363S and BclI polymorphisms have been associated with hypersensitivity to glucocorticoids, whereas the ER22/23EK polymorphism is related to glucocorticoid resistance. METHODS We studied whether the susceptibility to develop a depression is related to these polymorphisms by comparing depressive inpatients (n = 490) and healthy control subjects (n = 496). Among depressed patients, we also investigated the relation between GR variants and dysregulation of the HPA-axis, as measured by the combined dexamethasone suppression/corticotropin-releasing hormone (CRH)-stimulation test, clinical response to antidepressive treatment, and cognitive functioning. RESULTS Homozygous carriers of the BclI polymorphism and ER22/23EK-carriers had an increased risk of developing a major depressive episode. We found no genetic associations with functional HPA-axis measures in depressed patients. The ER22/23EK-carriers, however, showed a significantly faster clinical response to antidepressant therapy as well as a trend toward better cognitive functioning during depression. CONCLUSIONS The BclI and ER22/23EK polymorphisms were associated with susceptibility to develop major depression. In addition, the ER22/23EK polymorphism is associated with a faster clinical response to antidepressant treatment. These findings support the notion that variants of the GR gene might play a role in the pathophysiology of a major depression and can contribute to the variability of antidepressant response.
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Shackelton LA, Parrish CR, Holmes EC. Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses. J Mol Evol 2006; 62:551-63. [PMID: 16557338 DOI: 10.1007/s00239-005-0221-1] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2005] [Accepted: 12/20/2005] [Indexed: 11/25/2022]
Abstract
Understanding the extent and causes of biases in codon usage and nucleotide composition is essential to the study of viral evolution, particularly the interplay between viruses and host cells or immune responses. To understand the common features and differences among viruses we analyzed the genomic characteristics of a representative collection of all sequenced vertebrate-infecting DNA viruses. This revealed that patterns of codon usage bias are strongly correlated with overall genomic GC content, suggesting that genome-wide mutational pressure, rather than natural selection for specific coding triplets, is the main determinant of codon usage. Further, we observed a striking difference in CpG content between DNA viruses with large and small genomes. While the majority of large genome viruses show the expected frequency of CpG, most small genome viruses had CpG contents far below expected values. The exceptions to this generalization, the large gammaherpesviruses and iridoviruses and the small dependoviruses, have sufficiently different life-cycle characteristics that they may help reveal some of the factors shaping the evolution of CpG usage in viruses.
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Affiliation(s)
- Laura A Shackelton
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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Ke X, Lei Q, James SJ, Kelleher SL, Melnyk S, Jernigan S, Yu X, Wang L, Callaway CW, Gill G, Chan GM, Albertine KH, McKnight RA, Lane RH. Uteroplacental insufficiency affects epigenetic determinants of chromatin structure in brains of neonatal and juvenile IUGR rats. Physiol Genomics 2005; 25:16-28. [PMID: 16380407 DOI: 10.1152/physiolgenomics.00093.2005] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Intrauterine growth retardation (IUGR) increases the risk of neuroendocrine reprogramming. In the rat, IUGR leads to persistent changes in cerebral mRNA levels. This suggests lasting alterations in IUGR cerebral transcriptional regulation, which may result from changes in chromatin structure. Candidate nutritional triggers for these changes include altered cerebral zinc and one-carbon metabolite levels. We hypothesized that IUGR affects cerebral chromatin structure in neonatal and postnatal rat brains. Rats were rendered IUGR by bilateral uterine artery ligation; controls (Con) underwent sham surgery. At day of life 0 (d0), we measured cerebral DNA methylation, histone acetylation, expression of chromatin-affecting enzymes, and cerebral levels of one-carbon metabolites and zinc. At day of life 21 (d21), we measured cerebral DNA methylation and histone acetylation, as well as the caloric content of Con and IUGR rat breast milk. At d0, IUGR significantly decreased genome-wide and CpG island methylation, as well as increased histone 3 lysine 9 (H3/K9) and histone 3 lysine 14 (H3/K14) acetylation in the hippocampus and periventricular white matter, respectively. IUGR also decreased expression of the chromatin-affecting enzymes DNA methyltransferase 1 (DNMT1), methyl-CpG binding protein 2 (MeCP2), and histone deacetylase (HDAC)1 in association with increased cerebral levels of zinc. In d21 female IUGR rats, cerebral CpG DNA methylation remained lower, whereas H3/K9 and H3/K14 hyperacetylation persisted in hippocampus and white matter, respectively. In d21 male rats, IUGR decreased acetylation of H3/K9 and H3/K14 in these respective regions compared with controls. Despite these differences, caloric, fat, and protein content were similar in breast milk from Con and IUGR dams. We conclude that IUGR results in postnatal changes in cerebral chromatin structure and that these changes are sex specific.
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Affiliation(s)
- X Ke
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah 84158, USA
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