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Erdmann A, Halby L, Fahy J, Arimondo PB. Targeting DNA Methylation with Small Molecules: What’s Next? J Med Chem 2014; 58:2569-83. [DOI: 10.1021/jm500843d] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Alexandre Erdmann
- Epigenetic Targeting of Cancer,
USR3388 ETaC, CNRS-Pierre Fabre, 3 Avenue H. Curien, 31035 Toulouse Cedex 01, France
| | - Ludovic Halby
- Epigenetic Targeting of Cancer,
USR3388 ETaC, CNRS-Pierre Fabre, 3 Avenue H. Curien, 31035 Toulouse Cedex 01, France
| | - Jacques Fahy
- Epigenetic Targeting of Cancer,
USR3388 ETaC, CNRS-Pierre Fabre, 3 Avenue H. Curien, 31035 Toulouse Cedex 01, France
| | - Paola B Arimondo
- Epigenetic Targeting of Cancer,
USR3388 ETaC, CNRS-Pierre Fabre, 3 Avenue H. Curien, 31035 Toulouse Cedex 01, France
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Abstract
Most human phenotypes are influenced by a combination of genomic and environmental factors. Engaging in regular physical exercise prevents many chronic diseases, decreases mortality risk and increases longevity. However, the mechanisms involved are poorly understood. The modulating effect of physical (aerobic and resistance) exercise on gene expression has been known for some time now and has provided us with an understanding of the biological responses to physical exercise. Emerging research data suggest that epigenetic modifications are extremely important for both development and disease in humans. In the current review, we summarise findings on the effect of exercise on epigenetic modifications and their effects on gene expression. Current research data suggest epigenetic modifications (DNA methylation and histone acetylation) and microRNAs (miRNAs) are responsive to acute aerobic and resistance exercise in brain, blood, skeletal and cardiac muscle, adipose tissue and even buccal cells. Six months of aerobic exercise alters whole-genome DNA methylation in skeletal muscle and adipose tissue and directly influences lipogenesis. Some miRNAs are related to maximal oxygen consumption (VO(2max)) and VO(2max) trainability, and are differentially expressed amongst individuals with high and low VO(2max). Remarkably, miRNA expression profiles discriminate between low and high responders to resistance exercise (miR-378, -26a, -29a and -451) and correlate to gains in lean body mass (miR-378). The emerging field of exercise epigenomics is expected to prosper and additional studies may elucidate the clinical relevance of miRNAs and epigenetic modifications, and delineate mechanisms by which exercise confers a healthier phenotype and improves performance.
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53
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Hyun BR, McElwee JL, Soloway PD. Single molecule and single cell epigenomics. Methods 2014; 72:41-50. [PMID: 25204781 DOI: 10.1016/j.ymeth.2014.08.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 08/19/2014] [Accepted: 08/27/2014] [Indexed: 01/24/2023] Open
Abstract
Dynamically regulated changes in chromatin states are vital for normal development and can produce disease when they go awry. Accordingly, much effort has been devoted to characterizing these states under normal and pathological conditions. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the most widely used method to characterize where in the genome transcription factors, modified histones, modified nucleotides and chromatin binding proteins are found; bisulfite sequencing (BS-seq) and its variants are commonly used to characterize the locations of DNA modifications. Though very powerful, these methods are not without limitations. Notably, they are best at characterizing one chromatin feature at a time, yet chromatin features arise and function in combination. Investigators commonly superimpose separate ChIP-seq or BS-seq datasets, and then infer where chromatin features are found together. While these inferences might be correct, they can be misleading when the chromatin source has distinct cell types, or when a given cell type exhibits any cell to cell variation in chromatin state. These ambiguities can be eliminated by robust methods that directly characterize the existence and genomic locations of combinations of chromatin features in very small inputs of cells or ideally, single cells. Here we review single molecule epigenomic methods under development to overcome these limitations, the technical challenges associated with single molecule methods and their potential application to single cells.
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Affiliation(s)
- Byung-Ryool Hyun
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - John L McElwee
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Paul D Soloway
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA.
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54
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Pacaud R, Sery Q, Oliver L, Vallette FM, Tost J, Cartron PF. DNMT3L interacts with transcription factors to target DNMT3L/DNMT3B to specific DNA sequences: role of the DNMT3L/DNMT3B/p65-NFκB complex in the (de-)methylation of TRAF1. Biochimie 2014; 104:36-49. [PMID: 24952347 DOI: 10.1016/j.biochi.2014.05.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 05/07/2014] [Indexed: 11/15/2022]
Abstract
DNMT3L i.e. DNA (cytosine-5)-methyltransferase 3-like protein, is devoid of cytosine methyltransferase activity, despite clear homology to DNMT3A and DNMT3B, due to the mutation of key catalytic residues. However, DNMT3L participates in de novo methylation reactions through its direct interaction with DNMT3A and DNMT3B. In the present study, we investigated if DNMT3L interacts also directly with transcription factors (TFs). Using TF arrays, we identified 73 TFs that interacted with DNMT3L, 13 of which (ASH2L, ATF1, ATF3, BLZF1, CDX2, CERM, E2F3, E2F4, GCNF, GTF2I, GTF3C5, NFkB-p65 and RXRα) interacted only with DNMT3L, but not with DNMT3A/B. By focusing on the interaction with NFkB-p65, we demonstrate that DNMT3L forms a complex with DNMT3B and NFkB-p65 and that this complex is required for the control of DNA methylation at the TRAF1 promoter in the T98G glioma cell line. In addition, our experiments describe the DNA methylation at TRAF1 as being dynamic with a demethylation phase involving TET3. Thus, our data suggests that DNMT3L can address DNMT3A/B to specific sites by directly interacting with TFs that do not directly interact with DNMT3A/B. In summary, our data provide a new avenue for the direction of site-specific de novo DNA methylation catalyzed by DNMT3A/B.
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Affiliation(s)
- Romain Pacaud
- Centre de Recherche en Cancérologie Nantes-Angers, INSERM, U892, Equipe Apoptose et Progression Tumorale, 8 Quai Moncousu, BP7021, 44007 Nantes, France; Université de Nantes, Faculté de Médecine, Département de Recherche en Cancérologie, IFR26, F-44000 Nantes, France
| | - Quentin Sery
- Centre de Recherche en Cancérologie Nantes-Angers, INSERM, U892, Equipe Apoptose et Progression Tumorale, 8 Quai Moncousu, BP7021, 44007 Nantes, France; Université de Nantes, Faculté de Médecine, Département de Recherche en Cancérologie, IFR26, F-44000 Nantes, France
| | - Lisa Oliver
- Centre de Recherche en Cancérologie Nantes-Angers, INSERM, U892, Equipe Apoptose et Progression Tumorale, 8 Quai Moncousu, BP7021, 44007 Nantes, France; Université de Nantes, Faculté de Médecine, Département de Recherche en Cancérologie, IFR26, F-44000 Nantes, France
| | - François M Vallette
- Centre de Recherche en Cancérologie Nantes-Angers, INSERM, U892, Equipe Apoptose et Progression Tumorale, 8 Quai Moncousu, BP7021, 44007 Nantes, France; Université de Nantes, Faculté de Médecine, Département de Recherche en Cancérologie, IFR26, F-44000 Nantes, France; Institut de Cancérologie de l'Ouest - LaBCT, René Gauducheau, Boulevard J. Monod, F-44805 St Herblain, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environnement, Centre National de Génotypage, CEA - Institut de Génomique, F-91000 Evry, France
| | - Pierre-François Cartron
- Centre de Recherche en Cancérologie Nantes-Angers, INSERM, U892, Equipe Apoptose et Progression Tumorale, 8 Quai Moncousu, BP7021, 44007 Nantes, France; Université de Nantes, Faculté de Médecine, Département de Recherche en Cancérologie, IFR26, F-44000 Nantes, France; Institut de Cancérologie de l'Ouest - LaBCT, René Gauducheau, Boulevard J. Monod, F-44805 St Herblain, France; Membre du réseau Epigénétique du Cancéropole Grand Ouest, France.
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55
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Franchini DM, Petersen-Mahrt SK. AID and APOBEC deaminases: balancing DNA damage in epigenetics and immunity. Epigenomics 2014; 6:427-43. [DOI: 10.2217/epi.14.35] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
DNA mutations and genomic recombinations are the origin of oncogenesis, yet parts of developmental programs as well as immunity are intimately linked to, or even depend on, such DNA damages. Therefore, the balance between deleterious DNA damages and organismal survival utilizing DNA editing (modification and repair) is in continuous flux. The cytosine deaminases AID/APOBEC are a DNA editing family and actively participate in various biological processes. In conjunction with altered DNA repair, the mutagenic potential of the family allows for APOBEC3 proteins to restrict viral infection and transposons propagation, while AID can induce somatic hypermutation and class switch recombination in antibody genes. On the other hand, the synergy between effective DNA repair and the nonmutagenic potential of the DNA deaminases can induce local DNA demethylation to support epigenetic cellular identity. Here, we review the current state of knowledge on the mechanisms of action of the AID/APOBEC family in immunity and epigenetics.
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Affiliation(s)
- Don-Marc Franchini
- DNA Editing in Immunity and Epigenetics, IFOM-Fondazione Instituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milano, Italy
| | - Svend K Petersen-Mahrt
- DNA Editing in Immunity and Epigenetics, IFOM-Fondazione Instituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milano, Italy
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56
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Ratnu VS, Wei W, Bredy TW. Activation-induced cytidine deaminase regulates activity-dependent BDNF expression in post-mitotic cortical neurons. Eur J Neurosci 2014; 40:3032-9. [PMID: 25041363 DOI: 10.1111/ejn.12678] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 06/11/2014] [Accepted: 06/16/2014] [Indexed: 01/22/2023]
Abstract
Activity-dependent gene expression depends, in part, on transcriptional regulation that is coordinated by rapid changes in the chromatin landscape as well as the covalent modification of DNA. Here we demonstrate that the expression of brain-derived neurotrophic factor (BDNF), a gene that is critically involved in neural plasticity and subject to epigenetic regulation, is regulated by the RNA/DNA editing enzyme, activation-induced cytidine deaminase (AID). Similar to previous reports, we observed an activity-dependent induction of BDNF exon IV mRNA expression, which correlated with a reduction in DNA methylation within the BDNF P4 promoter. Lentiviral-mediated knockdown of AID disrupted these effects and inhibited BDNF exon IV mRNA expression, an effect that was associated with decreased cAMP response element-binding protein occupancy within the BDNF P4 promoter. Thus, together with other epigenetic mechanisms, AID plays a key role in regulating activity-dependent BDNF expression in post-mitotic cortical neurons.
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Affiliation(s)
- Vikram S Ratnu
- Psychiatric Epigenomics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane, Qld, 4072, Australia
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57
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Processive DNA demethylation via DNA deaminase-induced lesion resolution. PLoS One 2014; 9:e97754. [PMID: 25025377 PMCID: PMC4098905 DOI: 10.1371/journal.pone.0097754] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/23/2014] [Indexed: 12/13/2022] Open
Abstract
Base modifications of cytosine are an important aspect of chromatin biology, as they can directly regulate gene expression, while DNA repair ensures that those modifications retain genome integrity. Here we characterize how cytosine DNA deaminase AID can initiate DNA demethylation. In vitro, AID initiated targeted DNA demethylation of methyl CpGs when in combination with DNA repair competent extracts. Mechanistically, this is achieved by inducing base alterations at or near methyl-cytosine, with the lesion being resolved either via single base substitution or a more efficient processive polymerase dependent repair. The biochemical findings are recapitulated in an in vivo transgenic targeting assay, and provide the genetic support of the molecular insight into DNA demethylation. This targeting approach supports the hypothesis that mCpG DNA demethylation can proceed via various pathways and mCpGs do not have to be targeted to be demethylated.
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58
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Vidal BDC, Ghiraldini FG, Mello MLS. Changes in liver cell DNA methylation status in diabetic mice affect its FT-IR characteristics. PLoS One 2014; 9:e102295. [PMID: 25019512 PMCID: PMC4096918 DOI: 10.1371/journal.pone.0102295] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 06/16/2014] [Indexed: 12/21/2022] Open
Abstract
Background Lower levels of cytosine methylation have been found in the liver cell DNA from non-obese diabetic (NOD) mice under hyperglycemic conditions. Because the Fourier transform-infrared (FT-IR) profiles of dry DNA samples are differently affected by DNA base composition, single-stranded form and histone binding, it is expected that the methylation status in the DNA could also affect its FT-IR profile. Methodology/Principal Findings The DNA FT-IR signatures obtained from the liver cell nuclei of hyperglycemic and normoglycemic NOD mice of the same age were compared. Dried DNA samples were examined in an IR microspectroscope equipped with an all-reflecting objective (ARO) and adequate software. Conclusions/Significance Changes in DNA cytosine methylation levels induced by hyperglycemia in mouse liver cells produced changes in the respective DNA FT-IR profiles, revealing modifications to the vibrational intensities and frequencies of several chemical markers, including νas –CH3 stretching vibrations in the 5-methylcytosine methyl group. A smaller band area reflecting lower energy absorbed in the DNA was found in the hyperglycemic mice and assumed to be related to the lower levels of –CH3 groups. Other spectral differences were found at 1700–1500 cm−1 and in the fingerprint region, and a slight change in the DNA conformation at the lower DNA methylation levels was suggested for the hyperglycemic mice. The changes that affect cytosine methylation levels certainly affect the DNA-protein interactions and, consequently, gene expression in liver cells from the hyperglycemic NOD mice.
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Affiliation(s)
- Benedicto de Campos Vidal
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Flávia Gerelli Ghiraldini
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Maria Luiza S. Mello
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
- * E-mail:
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59
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Salminen A, Kauppinen A, Hiltunen M, Kaarniranta K. Krebs cycle intermediates regulate DNA and histone methylation: epigenetic impact on the aging process. Ageing Res Rev 2014; 16:45-65. [PMID: 24910305 DOI: 10.1016/j.arr.2014.05.004] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 05/20/2014] [Accepted: 05/29/2014] [Indexed: 02/01/2023]
Abstract
Many aging theories have proposed that mitochondria and energy metabolism have a major role in the aging process. There are recent studies indicating that Krebs cycle intermediates can shape the epigenetic landscape of chromatin by regulating DNA and histone methylation. A growing evidence indicates that epigenetics plays an important role in the regulation of healthspan but also is involved in the aging process. 2-Oxoglutarate (α-ketoglutarate) is a key metabolite in the Krebs cycle but it is also an obligatory substrate for 2-oxoglutarate-dependent dioxygenases (2-OGDO). The 2-OGDO enzyme family includes the major enzymes of DNA and histone demethylation, i.e. Ten-Eleven Translocation (TETs) and Jumonji C domain containing (JmjC) demethylases. In addition, 2-OGDO members can regulate collagen synthesis and hypoxic responses in a non-epigenetical manner. Interestingly, succinate and fumarate, also Krebs cycle intermediates, are potent inhibitors of 2-OGDO enzymes, i.e. the balance of Krebs cycle reactions can affect the level of DNA and histone methylation and thus control gene expression. We will review the epigenetic mechanisms through which Krebs cycle intermediates control the DNA and histone methylation. We propose that age-related disturbances in the Krebs cycle function induce stochastic epigenetic changes in chromatin structures which in turn promote the aging process.
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Affiliation(s)
- Antero Salminen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Department of Neurology, Kuopio University Hospital, P.O. Box 1777, FIN-70211 Kuopio, Finland.
| | - Anu Kauppinen
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Department of Ophthalmology, Kuopio University Hospital, P.O. Box 1777, FIN-70211 Kuopio, Finland
| | - Mikko Hiltunen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Department of Neurology, Kuopio University Hospital, P.O. Box 1777, FIN-70211 Kuopio, Finland
| | - Kai Kaarniranta
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, P.O. Box 1627, FIN-70211 Kuopio, Finland; Department of Ophthalmology, Kuopio University Hospital, P.O. Box 1777, FIN-70211 Kuopio, Finland
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60
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Adusumalli S, Mohd Omar MF, Soong R, Benoukraf T. Methodological aspects of whole-genome bisulfite sequencing analysis. Brief Bioinform 2014; 16:369-79. [DOI: 10.1093/bib/bbu016] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 04/17/2014] [Indexed: 12/17/2022] Open
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61
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The mechanistic role of DNA methylation in myeloid leukemogenesis. Leukemia 2014; 28:1765-73. [PMID: 24913729 DOI: 10.1038/leu.2014.163] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 03/28/2014] [Accepted: 04/28/2014] [Indexed: 12/11/2022]
Abstract
The importance of epigenetic aberrations in the pathogenesis of leukemias has been revealed by recurrent gene mutations that highlight epigenetic pathways as well as by the clinical success of therapies like 5-azacytidine and decitabine that work through epigenetic mechanisms. However, precise mechanisms of how gene mutations lead to leukemias and how epigenetic therapies induce clinical remissions are elusive. Current scientific inquiries that take advantage of techniques that can distinguish among the various covalent cytosine modifications at single base resolution are likely to shed light on the ways epigenetic pathways drive leukemogenesis as well as how the hypomethylating drugs induce clinical remissions. The hope is that these studies will also reveal which patients are likely to respond to epigenetic therapies. Thus, the future is likely to bring a new wave of diagnostic and prognostic tools that probe the epigenomics of leukemia to help clinicians in their management of patients.
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62
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Pfaffeneder T, Spada F, Wagner M, Brandmayr C, Laube SK, Eisen D, Truss M, Steinbacher J, Hackner B, Kotljarova O, Schuermann D, Michalakis S, Kosmatchev O, Schiesser S, Steigenberger B, Raddaoui N, Kashiwazaki G, Müller U, Spruijt CG, Vermeulen M, Leonhardt H, Schär P, Müller M, Carell T. Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA. Nat Chem Biol 2014; 10:574-81. [PMID: 24838012 DOI: 10.1038/nchembio.1532] [Citation(s) in RCA: 219] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 04/17/2014] [Indexed: 12/25/2022]
Abstract
Ten eleven translocation (Tet) enzymes oxidize the epigenetically important DNA base 5-methylcytosine (mC) stepwise to 5-hydroxymethylcytosine (hmC), 5-formylcytosine and 5-carboxycytosine. It is currently unknown whether Tet-induced oxidation is limited to cytosine-derived nucleobases or whether other nucleobases are oxidized as well. We synthesized isotopologs of all major oxidized pyrimidine and purine bases and performed quantitative MS to show that Tet-induced oxidation is not limited to mC but that thymine is also a substrate that gives 5-hydroxymethyluracil (hmU) in mouse embryonic stem cells (mESCs). Using MS-based isotope tracing, we show that deamination of hmC does not contribute to the steady-state levels of hmU in mESCs. Protein pull-down experiments in combination with peptide tracing identifies hmU as a base that influences binding of chromatin remodeling proteins and transcription factors, suggesting that hmU has a specific function in stem cells besides triggering DNA repair.
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Affiliation(s)
- Toni Pfaffeneder
- 1] Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany. [2]
| | - Fabio Spada
- 1] Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany. [2]
| | - Mirko Wagner
- 1] Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany. [2]
| | - Caterina Brandmayr
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Silvia K Laube
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - David Eisen
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Matthias Truss
- Charité Universitätsklinikum, Otto-Heubner-Centrum für Kinder und Jugendmedizin, Klinik für Allgemeine Pädiatrie, Labor für Pädiatrische Molekularbiologie, Berlin, Germany
| | - Jessica Steinbacher
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Benjamin Hackner
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Olga Kotljarova
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - David Schuermann
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Stylianos Michalakis
- Center for Integrated Protein Science at the Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, München, Germany
| | - Olesea Kosmatchev
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Stefan Schiesser
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Barbara Steigenberger
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Nada Raddaoui
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Gengo Kashiwazaki
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Udo Müller
- Center for Integrated Protein Science at the Department of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Cornelia G Spruijt
- Department of Molecular Cancer Research, Cancer Genomics Netherlands, Utrecht, The Netherlands
| | - Michiel Vermeulen
- 1] Department of Molecular Cancer Research, Cancer Genomics Netherlands, Utrecht, The Netherlands. [2]
| | - Heinrich Leonhardt
- Center for Integrated Protein Science at the Department of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Primo Schär
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Markus Müller
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
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63
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Yan B, Yao J, Tao ZF, Jiang Q. Epigenetics and ocular diseases: from basic biology to clinical study. J Cell Physiol 2014; 229:825-33. [PMID: 24318407 DOI: 10.1002/jcp.24522] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 12/02/2013] [Indexed: 12/23/2022]
Abstract
Epigenetics is an emerging field in ophthalmology and has opened a new avenue for understanding ocular development and ocular diseases related to aging and environment. Epigenetic mechanisms, including DNA methylation, histone modifications, chromatin remodeling, and deployment of non-coding RNAs, result in the heritable silencing of gene expression without any change in DNA sequence. Accumulating evidence suggests a potential link between gene expression, chromatin structure, non-coding RNAs, and cellular differentiation during ocular development. Disruption of the balance of epigenetic networks could become the etiology of several ocular diseases. Here, we summarized the current knowledge about epigenetic regulatory mechanisms in ocular development and diseases.
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Affiliation(s)
- Biao Yan
- Eye Hospital, Nanjing Medical University, Nanjing, China
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64
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Miao CG, Yang JT, Yang YY, Du CL, Huang C, Huang Y, Zhang L, Lv XW, Jin Y, Li J. Critical role of DNA methylation in the pathogenesis of systemic lupus erythematosus: new advances and future challenges. Lupus 2014; 23:730-42. [PMID: 24644011 DOI: 10.1177/0961203314527365] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 02/10/2014] [Indexed: 01/12/2023]
Abstract
Systemic lupus erythematosus (SLE) is a systemic multi-organ autoimmune disease with different immunological characteristics and clinical manifestations characterized by an autoantibody response to nuclear and cytoplasmic antigens; the etiology of this disease remains largely unknown. Most recent genome-wide association studies demonstrate that genetics significantly predispose to SLE onset, but the incomplete disease concordance rates between monozygotic twins indicates a role for other complementary factors in SLE pathogenesis. Recently, much evidence strongly supports other molecular mechanisms involved in the regulation of gene expression ultimately causing autoimmune disease, and several studies, both in clinical settings and experimental models, have demonstrated that epigenetic modifications may hold the key to a better understanding of SLE initiation and development. DNA methylation changes the structure of chromatin, being typically able to modulate the fine interactions between promoter-transcription factors and encoding genes within the transcription machinery. Alteration in DNA methylation has been confirmed as a major epigenetic mechanism that may potentially cause a breakdown of immune tolerance and perpetuation of SLE. Based on recent findings, DNA methylation treatments already being used in oncology may soon prove beneficial to patients with SLE. We herein discuss what we currently know, and what we expect in the future.
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Affiliation(s)
- C-G Miao
- School of Food and Drug, Anhui Science and Technology University, Bengbu, China School of Pharmacy, Institute for Liver Diseases of Anhui Medical University, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China
| | - J-T Yang
- School of Food and Drug, Anhui Science and Technology University, Bengbu, China
| | - Y-Y Yang
- School of Pharmacy, Institute for Liver Diseases of Anhui Medical University, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China
| | - C-L Du
- School of Food and Drug, Anhui Science and Technology University, Bengbu, China
| | - C Huang
- School of Pharmacy, Institute for Liver Diseases of Anhui Medical University, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China
| | - Y Huang
- School of Pharmacy, Institute for Liver Diseases of Anhui Medical University, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China
| | - L Zhang
- School of Pharmacy, Institute for Liver Diseases of Anhui Medical University, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China
| | - X-W Lv
- School of Pharmacy, Institute for Liver Diseases of Anhui Medical University, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China
| | - Y Jin
- School of Pharmacy, Institute for Liver Diseases of Anhui Medical University, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China
| | - J Li
- School of Pharmacy, Institute for Liver Diseases of Anhui Medical University, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China
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65
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Robinson CM, Ohh M. The multifaceted von Hippel-Lindau tumour suppressor protein. FEBS Lett 2014; 588:2704-11. [PMID: 24583008 DOI: 10.1016/j.febslet.2014.02.026] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/14/2014] [Accepted: 02/17/2014] [Indexed: 11/26/2022]
Abstract
Loss of von Hippel-Lindau protein (pVHL) is known to contribute to the initiation and progression of tumours associated with VHL disease as well as certain sporadic tumours including clear cell renal cell carcinoma (ccRCC). The VHL gene was first identified and cloned over 20 years ago and our understanding of its functions and effects has significantly increased since then. The best-known function of pVHL is its role in promoting the degradation of hypoxia-inducible factor α subunit (HIFα) as part of an E3 ubiquitin ligase complex. HIF stabilisation and transcriptional activation are also associated with various epigenetic alterations, indicating a potential role for VHL loss with changes in the epigenome. This review will highlight current knowledge regarding pVHL as well as discuss potentially novel roles of pVHL and how these may impact on cancer progression.
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Affiliation(s)
- Claire M Robinson
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Michael Ohh
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
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66
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Azzi A, Dallmann R, Casserly A, Rehrauer H, Patrignani A, Maier B, Kramer A, Brown SA. Circadian behavior is light-reprogrammed by plastic DNA methylation. Nat Neurosci 2014; 17:377-82. [PMID: 24531307 DOI: 10.1038/nn.3651] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 01/17/2014] [Indexed: 12/12/2022]
Abstract
The timing of daily circadian behavior can be highly variable among different individuals, and twin studies have suggested that about half of this variability is environmentally controlled. Similar plasticity can be seen in mice exposed to an altered lighting environment, for example, 22-h instead of 24-h, which stably alters the genetically determined period of circadian behavior for months. The mechanisms mediating these environmental influences are unknown. We found that transient exposure of mice to such lighting stably altered global transcription in the suprachiasmatic nucleus (SCN) of the hypothalamus (the master clock tissue regulating circadian behavior in mammals). In parallel, genome-wide methylation profiling revealed global alterations in promoter DNA methylation in the SCN that correlated with these changes. Behavioral, transcriptional and DNA methylation changes were reversible after prolonged re-entrainment to 24-h d. Notably, infusion of a methyltransferase inhibitor to the SCN suppressed period changes. We conclude that the SCN utilizes DNA methylation as a mechanism to drive circadian clock plasticity.
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Affiliation(s)
- Abdelhalim Azzi
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Robert Dallmann
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Alison Casserly
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Centre, University of Zurich, Zurich, Switzerland
| | - Andrea Patrignani
- Functional Genomics Centre, University of Zurich, Zurich, Switzerland
| | - Bert Maier
- Laboratory of Chronobiology, Institute of Medical Immunology, Charité Universitätsmedizin, Berlin, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Institute of Medical Immunology, Charité Universitätsmedizin, Berlin, Germany
| | - Steven A Brown
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
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67
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Bucher DB, Pilles BM, Pfaffeneder T, Carell T, Zinth W. Fingerprinting DNA oxidation processes: IR characterization of the 5-methyl-2'-deoxycytidine radical cation. Chemphyschem 2014; 15:420-3. [PMID: 24382745 DOI: 10.1002/cphc.201300954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Indexed: 11/08/2022]
Abstract
Methylated cytidine plays an important role as an epigenetic signal in gene regulation. Its oxidation products are assumed to be involved in active demethylation processes but also in damaging DNA. Here, we report the photochemical production of the 5-methyl-2'-deoxycytidine radical cation via a two-photon ionization process. The radical cation is detected by time-resolved IR spectroscopy and identified by band assignment using density functional theory calculations. Two final oxidation products are characterized with liquid chromatography coupled to mass spectrometry.
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Affiliation(s)
- Dominik B Bucher
- BioMolecular Optics and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München (Germany), Fax: (+49) 89-2180-9202; Center for Integrated Protein Science, Department für Chemie, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377 München (Germany)
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68
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Kato T, Iwamoto K. Comprehensive DNA methylation and hydroxymethylation analysis in the human brain and its implication in mental disorders. Neuropharmacology 2014; 80:133-9. [PMID: 24389572 DOI: 10.1016/j.neuropharm.2013.12.019] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 12/14/2013] [Accepted: 12/18/2013] [Indexed: 01/02/2023]
Abstract
Covalent modifications of nucleotides, such as methylation or hydroxymethylation of cytosine, regulate gene expression. Early environmental risk factors play a role in mental disorders in adulthood. This may be in part mediated by epigenetic DNA modifications. Methods for comprehensive analysis of DNA methylation and hydroxymethylation include DNA modification methods such as bisulfite sequencing, or collection of methylated, hydroxymethylated, or unmethylated DNA by specific binding proteins, antibodies, or restriction enzymes, followed by sequencing or microarray analysis. Results from these experiments should be interpreted with caution because each method gives different result. Cytosine hydroxymethylation has different effects on gene expression than cytosine methylation; methylation of CpG islands is associated with lower gene expression, whereas hydroxymethylation in intragenic regions is associated with higher gene expression. The role of hydroxymethylcytosine is of particular interest in mental disorders because the modification is enriched in the brain and synapse related genes, and it exhibits dynamic regulation during development. Many DNA methylation patterns are conserved across species, but there are also human specific signatures. Comprehensive analysis of DNA methylation shows characteristic changes associated with tissues, brain regions, cell types, and developmental states. Thus, differences in DNA methylation status between tissues, brain regions, cell types, and developmental stages should be considered when the role of DNA methylation in mental disorders is studied. Several disease-associated changes in methylation have been reported: hypermethylation of SOX10 in schizophrenia, hypomethylation of HCG9 (HLA complex group 9) in bipolar disorder, hypermethylation of PRIMA1, hypermethylation of SLC6A4 (serotonin transporter) in bipolar disorder, and hypomethylation of ST6GALNAC1 in bipolar disorder. These findings need to be replicated in different patient populations to be generalized. Further studies including animal experiments are necessary to understand the roles of DNA methylation in mental disorders.
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Affiliation(s)
- Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Kazuya Iwamoto
- Department of Molecular Psychiatry, Graduate School of Medicine, University of Tokyo, Tokyo 113-8655, Japan
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69
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Ohnishi T, Sekine D, Kinoshita T. Genomic Imprinting in Plants. EPIGENETIC SHAPING OF SOCIOSEXUAL INTERACTIONS - FROM PLANTS TO HUMANS 2014; 86:1-25. [DOI: 10.1016/b978-0-12-800222-3.00001-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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70
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Abstract
In this review, I discuss the currently available experimental evidence concerning the molecular interactions of the activation-induced cytidine deaminase (AID) with transcription of its target genes. The basic question that underlies the transcription relationship is how the process of somatic hypermutation of Ig genes can be restricted to their variable (V) regions. This hallmark of SHM assures that high affinity antibodies can be created while the biological functions of their constant (C) region are undisturbed. I present a revised model of AID function in somatic hypermutation (SHM): In a B cell that produces AID protein and undergoes mutation of the V regions of the expressed Ig heavy and light chain genes, only some of the transcription complexes initiating at the active V-region promoters are associated with AID. When AID travels with the elongating RNA polymerase (pol), it attracts proteins that cause the pausing/stalling of pol and termination of transcription, followed by termination of SHM. This differential AID loading model would allow the mutating B cell to continue producing full-length Ig proteins that are required to avoid apoptosis by permitting the cell to assemble functional B cell receptors.
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Affiliation(s)
- Ursula Storb
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, USA.
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71
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Wang S, Long Y, Wang J, Ge Y, Guo P, Liu Y, Tian T, Zhou X. Systematic investigations of different cytosine modifications on CpG dinucleotide sequences: the effects on the B-Z transition. J Am Chem Soc 2013; 136:56-9. [PMID: 24364741 DOI: 10.1021/ja4107012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have first demonstrated the distinctive effects of three newly reported epigenetic modifications, including 5hmC, 5fC, and 5caC, on B-Z transition of CpG dinucleotide DNAs. We have performed detailed assays and compared their effects. We further studied the regulation of B-Z transition of CpG dinucleotide dodecamers by alternating oxidation and alternating reduction.
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Affiliation(s)
- Shaoru Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University , Wuhan, Hubei 430072, P. R. China
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72
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Dean W. DNA methylation and demethylation: a pathway to gametogenesis and development. Mol Reprod Dev 2013; 81:113-25. [PMID: 24214338 DOI: 10.1002/mrd.22280] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 11/03/2013] [Indexed: 12/21/2022]
Abstract
The generation of gametes falls between two reprogramming phases. These phases are characterised by profound periods of transcriptional activity, which define and reinforce lineage decisions. The control of these transcriptional programs and the interpretation of the underlying genetic instruction is the task of the epigenome. As such, dynamic processes during reprogramming are critical for the development of the germ line and its resetting, which propels that developmental process forward and provides the transfer of genetic and epigenetic information between generations. Central in this reprogramming is the addition and subtraction of DNA methylation and its oxidative products, coupled to the mechanisms at play to achieve this goal. The activities competent to add DNA methylation, and identification of those enzymes able to modify it, have heralded a new chapter in our understanding of the complexities that dictate and direct cellular fates. How the early embryos makes use of these marks and how they are modulated will give us insight into cellular differentiation and reprogramming critical for health and into the process of aging. This review details some of these processes and the activities essential to achieve the immortality of the mammalian germ line.
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Affiliation(s)
- Wendy Dean
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
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73
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Santos F, Peat J, Burgess H, Rada C, Reik W, Dean W. Active demethylation in mouse zygotes involves cytosine deamination and base excision repair. Epigenetics Chromatin 2013; 6:39. [PMID: 24279473 PMCID: PMC4037648 DOI: 10.1186/1756-8935-6-39] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/30/2013] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND DNA methylation in mammals is an epigenetic mark necessary for normal embryogenesis. During development active loss of methylation occurs in the male pronucleus during the first cell cycle after fertilisation. This is accompanied by major chromatin remodelling and generates a marked asymmetry between the paternal and maternal genomes. The mechanism(s) by which this is achieved implicate, among others, base excision repair (BER) components and more recently a major role for TET3 hydroxylase. To investigate these methylation dynamics further we have analysed DNA methylation and hydroxymethylation in fertilised mouse oocytes by indirect immunofluorescence (IF) and evaluated the relative contribution of different candidate factors for active demethylation in knock-out zygotes by three-dimensional imaging and IF semi-quantification. RESULTS We find two distinct phases of loss of paternal methylation in the zygote, one prior to and another coincident with, but not dependent on, DNA replication. TET3-mediated hydroxymethylation is limited to the replication associated second phase of demethylation. Analysis of cytosine deaminase (AID) null fertilised oocytes revealed a role for this enzyme in the second phase of loss of paternal methylation, which is independent from hydroxymethylation. Investigation into the possible repair pathways involved supports a role for AID-mediated cytosine deamination with subsequent U-G mismatch long-patch BER by UNG2 while no evidence could be found for an involvement of TDG. CONCLUSIONS There are two observable phases of DNA demethylation in the mouse zygote, before and coincident with DNA replication. TET3 is only involved in the second phase of loss of methylation. Cytosine deamination and long-patch BER mediated by UNG2 appear to independently contribute to this second phase of active demethylation. Further work will be necessary to elucidate the mechanism(s) involved in the first phase of active demethylation that will potentially involve activities required for early sperm chromatin remodelling.
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74
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Abstract
Transcription is apparently risky business. Its intrinsic mutagenic potential must be kept in check by networks of DNA repair factors that monitor the transcription process to repair DNA lesions that could otherwise compromise transcriptional fidelity and genome integrity. Intriguingly, recent studies point to an even more direct function of DNA repair complexes as coactivators of transcription and the unexpected role of "scheduled" DNA damage/repair at gene promoters. Paradoxically, spontaneous DNA double-strand breaks also induce ectopic transcription that is essential for repair. Thus, transcription, DNA damage, and repair may be more physically and functionally intertwined than previously appreciated.
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Affiliation(s)
- Yick W. Fong
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Claudia Cattoglio
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Robert Tjian
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, CA 94720, USA
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75
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Blattler A, Farnham PJ. Cross-talk between site-specific transcription factors and DNA methylation states. J Biol Chem 2013; 288:34287-94. [PMID: 24151070 DOI: 10.1074/jbc.r113.512517] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA methylation, which occurs predominantly at CpG dinucleotides, is a potent epigenetic repressor of transcription. Because DNA methylation is reversible, there is much interest in understanding the mechanisms by which it can be regulated by DNA-binding transcription factors. We discuss several models that, by incorporating sequence motifs, CpG density, and methylation levels, attempt to link the binding of a transcription factor with the acquisition or loss of DNA methylation at promoters and distal regulatory elements. Additional in vivo genome-wide characterization of transcription factor binding patterns and high-resolution DNA methylation analyses are clearly required for stronger support of each model.
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Affiliation(s)
- Adam Blattler
- From the Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California 90089 and
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76
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Abstract
Epigenetic mechanisms are proposed to underlie aberrant gene expression in systemic lupus erythematosus (SLE) that results in dysregulation of the immune system and loss of tolerance. Modifications of DNA and histones require substrates derived from diet and intermediary metabolism. DNA and histone methyltransferases depend on S-adenosylmethionine (SAM) as a methyl donor. SAM is generated from adenosine triphosphate (ATP) and methionine by methionine adenosyltransferase (MAT), a redox-sensitive enzyme in the SAM cycle. The availability of B vitamins and methionine regulate SAM generation. The DNA of SLE patients is hypomethylated, indicating dysfunction in the SAM cycle and methyltransferase activity. Acetyl-CoA, which is necessary for histone acetylation, is generated from citrate produced in mitochondria. Mitochondria are also responsible for de novo synthesis of flavin adenine dinucleotide (FAD) for histone demethylation. Mitochondrial oxidative phosphorylation is the dominant source of ATP. The depletion of ATP in lupus T cells may affect MAT activity as well as adenosine monophosphate (AMP) activated protein kinase (AMPK), which phosphorylates histones and inhibits mechanistic target of rapamycin (mTOR). In turn, mTOR can modify epigenetic pathways including methylation, demethylation, and histone phosphorylation and mediates enhanced T-cell activation in SLE. Beyond their role in metabolism, mitochondria are the main source of reactive oxygen intermediates (ROI), which activate mTOR and regulate the activity of histone and DNA modifying enzymes. In this review we will focus on the sources of metabolites required for epigenetic regulation and how the flux of the underlying metabolic pathways affects gene expression.
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Affiliation(s)
- Zachary Oaks
- Division of Rheumatology, Departments of Medicine, Microbiology and Immunology, and Biochemistry and Molecular Biology, State University of New York, Upstate Medical University, College of Medicine , Syracuse, NY , USA
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77
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Lötsch J, Schneider G, Reker D, Parnham MJ, Schneider P, Geisslinger G, Doehring A. Common non-epigenetic drugs as epigenetic modulators. Trends Mol Med 2013; 19:742-53. [PMID: 24054876 DOI: 10.1016/j.molmed.2013.08.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 12/15/2022]
Abstract
Epigenetic effects are exerted by a variety of factors and evidence increases that common drugs such as opioids, cannabinoids, valproic acid, or cytostatics may induce alterations in DNA methylation patterns or histone conformations. These effects occur via chemical structural interactions with epigenetic enzymes, through interactions with DNA repair mechanisms. Computational predictions indicate that one-twentieth of all drugs might potentially interact with human histone deacetylase, which was prospectively experimentally verified for the compound with the highest predicted interaction probability. These epigenetic effects add to wanted and unwanted drug effects, contributing to mechanisms of drug resistance or disease-related and unrelated phenotypes. Because epigenetic changes might be transmitted to offspring, the need for reliable and cost-effective epigenetic screening tools becomes acute.
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Affiliation(s)
- Jörn Lötsch
- Institute of Clinical Pharmacology, Goethe University, Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany; Fraunhofer Institute of Molecular Biology and Applied Ecology - Project Group Translational Medicine and Pharmacology (IME-TMP), Theodor-Stern-Kai 7, D-60590 Frankfurt am Main, Germany.
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78
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Rots MG, Petersen-Mahrt SK. The 2012 IMB Conference: DNA demethylation, repair and beyond. Institute of Molecular Biology, Mainz, Germany, 18-21 October 2012. Epigenomics 2013; 5:25-8. [PMID: 23414316 DOI: 10.2217/epi.12.73] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Headline-grabbing attention has been given to DNA demethylation pathways as new epigenetic mechanisms, with reviews and hypotheses outnumbering research papers. As candidate proteins for DNA demethylation include well-known DNA repair enzymes, it was timely to join epigenetics and DNA repair experts at the first international meeting on DNA Demethylation, Repair and Beyond. New mechanistic insights were presented for known players orchestrating the symphony on cytosine - 'the symphony on C' (TET1, 2, 3; GADD45; AID; and TDG), while new instruments and classical themes were pulled into the amalgamation. What may appear as just an unintentional cacophony of random oxidative lesions and abasic sites in a bed of chromatin noise may turn out to be a gene-expressing regulatory melody.
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Affiliation(s)
- Marianne G Rots
- Epigenetic Editing, Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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79
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Keil KP, Altmann HM, Mehta V, Abler LL, Elton EA, Vezina CM. Catalog of mRNA expression patterns for DNA methylating and demethylating genes in developing mouse lower urinary tract. Gene Expr Patterns 2013; 13:413-24. [PMID: 23920106 DOI: 10.1016/j.gep.2013.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 06/07/2013] [Accepted: 07/25/2013] [Indexed: 10/26/2022]
Abstract
The mouse prostate develops from a component of the lower urinary tract (LUT) known as the urogenital sinus (UGS). This process requires androgens and signaling between mesenchyme and epithelium. Little is known about DNA methylation during prostate development, including which factors are expressed, whether their expression changes over time, and if DNA methylation contributes to androgen signaling or influences signaling between mesenchyme and epithelium. We used in situ hybridization to evaluate the spatial and temporal expression pattern of mRNAs which encode proteins responsible for establishing, maintaining or remodeling DNA methylation. These include DNA methyltransferases, DNA deaminases, DNA glycosylases, base excision repair and mismatch repair pathway members. The mRNA expression patterns were compared between male and female LUT prior to prostatic bud formation (14.5 days post coitus (dpc)), during prostatic bud formation (17.5 dpc) and during prostatic branching morphogenesis (postnatal day (P) 5). We found dramatic changes in the patterns of these mRNAs over the course of prostate development and identified examples of sexually dimorphic mRNA expression. Future investigation into how DNA methylation patterns are established, maintained and remodeled during the course of embryonic prostatic bud formation may provide insight into prostate morphogenesis and disease.
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Affiliation(s)
- Kimberly P Keil
- Department of Comparative Biosciences, University of Wisconsin-Madison, 1656 Linden Dr., Madison, WI 53706, USA
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80
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Zaina S, del Pilar Valencia-Morales M, Tristán-Flores FE, Lund G. Nuclear reprogramming and its role in vascular smooth muscle cells. Curr Atheroscler Rep 2013; 15:352. [PMID: 23881547 DOI: 10.1007/s11883-013-0352-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
In general terms, "nuclear reprogramming" refers to a change in gene expression profile that results in a significant switch in cellular phenotype. Nuclear reprogramming was first addressed by pioneering studies of cell differentiation during embryonic development. In recent years, nuclear reprogramming has been studied in great detail in the context of experimentally controlled dedifferentiation and transdifferentiation of mammalian cells for therapeutic purposes. In this review, we present a perspective on nuclear reprogramming in the context of spontaneous, pathophysiological phenotypic switch of vascular cells occurring in the atherosclerotic lesion. In particular, we focus on the current knowledge of epigenetic mechanisms participating in the extraordinary flexibility of the gene expression profile of vascular smooth muscle cells and other cell types participating in atherogenesis. Understanding how epigenetic changes participate in vascular cell plasticity may lead to effective therapies based on the remodelling of the vascular architecture.
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Affiliation(s)
- Silvio Zaina
- Department of Medical Sciences, Division of Health Sciences, León Campus, University of Guanajuato, 20 de Enero no. 929, 37320, León, Gto., Mexico.
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81
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Activation-induced cytidine deaminase (AID) is necessary for the epithelial-mesenchymal transition in mammary epithelial cells. Proc Natl Acad Sci U S A 2013; 110:E2977-86. [PMID: 23882083 DOI: 10.1073/pnas.1301021110] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Activation-induced cytidine deaminase (AID), which functions in antibody diversification, is also expressed in a variety of germ and somatic cells. Evidence that AID promotes DNA demethylation in epigenetic reprogramming phenomena, and that it is induced by inflammatory signals, led us to investigate its role in the epithelial-mesenchymal transition (EMT), a critical process in normal morphogenesis and tumor metastasis. We find that expression of AID is induced by inflammatory signals that induce the EMT in nontransformed mammary epithelial cells and in ZR75.1 breast cancer cells. shRNA-mediated knockdown of AID blocks induction of the EMT and prevents cells from acquiring invasive properties. Knockdown of AID suppresses expression of several key EMT transcriptional regulators and is associated with increased methylation of CpG islands proximal to the promoters of these genes; furthermore, the DNA demethylating agent 5 aza-2'deoxycytidine (5-Aza-dC) antagonizes the effects of AID knockdown on the expression of EMT factors. We conclude that AID is necessary for the EMT in this breast cancer cell model and in nontransformed mammary epithelial cells. Our results suggest that AID may act near the apex of a hierarchy of regulatory steps that drive the EMT, and are consistent with this effect being mediated by cytosine demethylation. This evidence links our findings to other reports of a role for AID in epigenetic reprogramming and control of gene expression.
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82
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Hirose K, Shimoda N, Kikuchi Y. Transient reduction of 5-methylcytosine and 5-hydroxymethylcytosine is associated with active DNA demethylation during regeneration of zebrafish fin. Epigenetics 2013; 8:899-906. [PMID: 23880758 DOI: 10.4161/epi.25653] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Although dedifferentiation, transformation of differentiated cells into progenitor cells, is a critical step in the regeneration of amphibians and fish, the molecular mechanisms underlying this process, including epigenetic changes, remain unclear. Dot blot assays and immunohistochemical analyses revealed that, during regeneration of zebrafish fin, the levels of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are transiently reduced in blastema cells and cells adjacent to the amputation plane at 30 h post-amputation (hpa), and the level of 5mC, but not 5hmC, is almost restored by 72 hpa. We observed that the dedifferentiated cells showed reduced levels of 5mC and 5hmC independent of cell proliferation by 24 hpa. Furthermore, expressions of the proposed demethylation- and DNA repair-related genes were detected during fin regeneration. Taken together, our findings illustrate that the transient reduction of 5mC and 5hmC in dedifferentiated cells is associated with active demethylation during regeneration of zebrafish fin.
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Affiliation(s)
- Kentaro Hirose
- Department of Biological Science; Graduate School of Science; Hiroshima University; Hiroshima, Japan
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83
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Jaeger S, Fernandez B, Ferrier P. Epigenetic aspects of lymphocyte antigen receptor gene rearrangement or 'when stochasticity completes randomness'. Immunology 2013; 139:141-50. [PMID: 23278765 DOI: 10.1111/imm.12057] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 12/17/2012] [Accepted: 12/19/2012] [Indexed: 01/05/2023] Open
Abstract
To perform their specific functional role, B and T lymphocytes, cells of the adaptive immune system of jawed vertebrates, need to express one (and, preferably, only one) form of antigen receptor, i.e. the immunoglobulin or T-cell receptor (TCR), respectively. This end goal depends initially on a series of DNA cis-rearrangement events between randomly chosen units from separate clusters of V, D (at some immunoglobulin and TCR loci) and J gene segments, a biomolecular process collectively referred to as V(D)J recombination. V(D)J recombination takes place in immature T and B cells and relies on the so-called RAG nuclease, a site-specific DNA cleavage apparatus that corresponds to the lymphoid-specific moiety of the VDJ recombinase. At the genome level, this recombinase's mission presents substantial biochemical challenges. These relate to the huge distance between (some of) the gene segments that it eventually rearranges and the need to achieve cell-lineage-restricted and developmentally ordered routines with at times, mono-allelic versus bi-allelic discrimination. The entire process must be completed without any recombination errors, instigators of chromosome instability, translocation and, potentially, tumorigenesis. As expected, such a precisely choreographed and yet potentially risky process demands sophisticated controls; epigenetics demonstrates what is possible when calling upon its many facets. In this vignette, we will recall the evidence that almost from the start appeared to link the two topics, V(D)J recombination and epigenetics, before reviewing the latest advances in our knowledge of this joint venture.
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Affiliation(s)
- Sébastien Jaeger
- Centre d'Immunologie de Marseille-Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (Inserm) U1104, Centre National de la Recherche Scientifique (CNRS)UMR7280, Aix-Marseille University UM2, Marseille, France
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84
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Abstract
Chemical modifications to the DNA and histone protein components of chromatin can modulate gene expression and genome stability. Understanding the physiological impact of changes in chromatin structure remains an important question in biology. As one example, in order to generate antibody diversity with somatic hypermutation and class switch recombination, chromatin must be made accessible for activation-induced cytidine deaminase (AID)-mediated deamination of cytosines in DNA. These lesions are recognized and removed by various DNA repair pathways but, if not handled properly, can lead to formation of oncogenic chromosomal translocations. In this review, we focus the discussion on how chromatin-modifying activities and -binding proteins contribute to the native chromatin environment in which AID-induced DNA damage is targeted and repaired. Outstanding questions remain regarding the direct roles of histone posttranslational modifications and the significance of AID function outside of antibody diversity.
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Affiliation(s)
- Jeremy A. Daniel
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen N, Denmark
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85
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Sproul D, Meehan RR. Genomic insights into cancer-associated aberrant CpG island hypermethylation. Brief Funct Genomics 2013; 12:174-90. [PMID: 23341493 PMCID: PMC3662888 DOI: 10.1093/bfgp/els063] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Carcinogenesis is thought to occur through a combination of mutational and epimutational events that disrupt key pathways regulating cellular growth and division. The DNA methylomes of cancer cells can exhibit two striking differences from normal cells; a global reduction of DNA methylation levels and the aberrant hypermethylation of some sequences, particularly CpG islands (CGIs). This aberrant hypermethylation is often invoked as a mechanism causing the transcriptional inactivation of tumour suppressor genes that directly drives the carcinogenic process. Here, we review our current understanding of this phenomenon, focusing on how global analysis of cancer methylomes indicates that most affected CGI genes are already silenced prior to aberrant hypermethylation during cancer development. We also discuss how genome-scale analyses of both normal and cancer cells have refined our understanding of the elusive mechanism(s) that may underpin aberrant CGI hypermethylation.
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86
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Incorvaia E, Sicouri L, Petersen-Mahrt SK, Schmitz KM. Hormones and AID: Balancing immunity and autoimmunity. Autoimmunity 2013. [DOI: 10.3109/08916934.2012.748752] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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87
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Abstract
Complex developmental processes such as hematopoiesis require a series of precise and coordinated changes in cellular identity to ensure blood homeostasis. Epigenetic mechanisms help drive changes in gene expression that accompany the transition from hematopoietic stem cells to terminally differentiated blood cells. Genome-wide profiling technologies now provide valuable glimpses of epigenetic changes that occur during normal hematopoiesis, and genetic mouse models developed to investigate the in vivo functions of chromatin-modifying enzymes clearly demonstrate significant roles for these enzymes during embryonic and adult hematopoiesis. Here, we will review the basic science aspects of chromatin modifications and the enzymes that add, remove, and interpret these epigenetic marks. This overview will provide a framework for understanding the roles that these molecules play during normal hematopoiesis. Moreover, many chromatin-modifying enzymes are involved in hematologic malignancies, underscoring the importance of establishing and maintaining appropriate chromatin modification patterns to normal hematology.
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88
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Tian T, Zhang X, Fu B, Long Y, Peng S, Wang S, Zhou X, Zhou X. Systematic investigation of DNAs with modified cytosines under hot alkali treatment. Chem Commun (Camb) 2013; 49:9968-70. [DOI: 10.1039/c3cc45423a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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