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Pang APS, Sugai C, Maunakea AK. High-throughput sequencing offers new insights into 5-hydroxymethylcytosine. Biomol Concepts 2017; 7:169-78. [PMID: 27356236 DOI: 10.1515/bmc-2016-0011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/01/2016] [Indexed: 01/15/2023] Open
Abstract
Chemical modifications of DNA comprise epigenetic mechanisms that contribute to the maintenance of cellular activities and memory. Although the function of 5-methylcytosine (5-mC) has been extensively studied, little is known about the function(s) of relatively rarer and underappreciated cytosine modifications including 5-hydroxymethylcytosine (5-hmC). The discovery that ten-eleven translocation (Tet) proteins mediate conversion of 5-mC to 5-hmC, and other oxidation derivatives, sparked renewed interest to understand the biological role of 5-hmC. Studies examining total 5-hmC levels revealed the highly dynamic yet tissue-specific nature of this modification, implicating a role in epigenetic regulation and development. Intriguingly, 5-hmC levels are highest during early development and in the brain where abnormal patterns of 5-hmC have been observed in disease conditions. Thus, 5-hmC adds to the growing list of epigenetic modifications with potential utility in clinical applications and warrants further investigation. This review discusses the emerging functional roles of 5-hmC in normal and disease states, focusing primarily on insights provided by recent studies exploring the genome-wide distribution of this modification in mammals.
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52
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Jeong M, Guzman AG, Goodell MA. Genome-Wide Analysis of DNA Methylation in Hematopoietic Cells: DNA Methylation Analysis by WGBS. Methods Mol Biol 2017; 1633:137-149. [PMID: 28735485 DOI: 10.1007/978-1-4939-7142-8_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
DNA methylation is a major epigenetic modification that regulates gene expression, genome imprinting, and development and has a role in diseases including cancer. There are various methods for whole-genome methylation profiling that differ in cost and resolution. Recent advances in high-throughput sequencing technologies coupled with bisulfite treatment enable absolute DNA methylation quantification and genome-wide single-nucleotide resolution analysis. In this chapter, we provide detailed protocols for whole-genome bisulfite sequencing (WGBS), which captures the complete methylome. Using WGBS, we are able to generate a reference DNA methylome for normal or malignant hematopoietic cells.
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Affiliation(s)
- Mira Jeong
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA.,Dan L. Duncan Cancer Center, Department of Molecular and Human Genetics, Stem Cells and Regenerative Medicine Center, and Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Anna G Guzman
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA.,Dan L. Duncan Cancer Center, Department of Molecular and Human Genetics, Stem Cells and Regenerative Medicine Center, and Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Margaret A Goodell
- Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA. .,Dan L. Duncan Cancer Center, Department of Molecular and Human Genetics, Stem Cells and Regenerative Medicine Center, and Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.
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53
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Zhou FC, Resendiz M, Lo CL, Chen Y. Cell-Wide DNA De-Methylation and Re-Methylation of Purkinje Neurons in the Developing Cerebellum. PLoS One 2016; 11:e0162063. [PMID: 27583369 PMCID: PMC5008790 DOI: 10.1371/journal.pone.0162063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/16/2016] [Indexed: 01/15/2023] Open
Abstract
Global DNA de-methylation is thought to occur only during pre-implantation and gametogenesis in mammals. Scalable, cell-wide de-methylation has not been demonstrated beyond totipotent stages. Here, we observed a large scale de-methylation and subsequent re-methylation (CDR) (including 5-methylcytosine (5mC) and 5-hydroxylmethylcytosine (5hmC)) in post-mitotic cerebellar Purkinje cells (PC) through the course of normal development. Through single cell immuno-identification and cell-specific quantitative methylation assays, we demonstrate that the CDR event is an intrinsically scheduled program, occurring in nearly every PC. Meanwhile, cerebellar granule cells and basket interneurons adopt their own DNA methylation program, independent of PCs. DNA de-methylation was further demonstrated at the gene level, on genes pertinent to PC development. The PC, being one of the largest neurons in the brain, may showcase an amplified epigenetic cycle which may mediate stage transformation including cell cycle arrest, vast axonal-dendritic growth, and synaptogenesis at the onset of neuronal specificity. This discovery is a key step toward better understanding the breadth and role of DNA methylation and de-methylation during neural ontology.
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Affiliation(s)
- Feng C. Zhou
- Department of Anatomy & Cell Biology, Indiana University School of Medicine, Indianapolis, Indiana, 46202, United States of America
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, 46202, United States of America
- * E-mail:
| | - Marisol Resendiz
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, 46202, United States of America
| | - Chiao-Ling Lo
- Department of Anatomy & Cell Biology, Indiana University School of Medicine, Indianapolis, Indiana, 46202, United States of America
| | - Yuanyuan Chen
- Department of Anatomy & Cell Biology, Indiana University School of Medicine, Indianapolis, Indiana, 46202, United States of America
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Madrid A, Papale LA, Alisch RS. New hope: the emerging role of 5-hydroxymethylcytosine in mental health and disease. Epigenomics 2016; 8:981-91. [DOI: 10.2217/epi-2016-0020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Historically biomedical research has examined genetic influences on mental health but these approaches have been limited, likely due to the broad heritability of brain-related disorders (e.g., 30–90%). Epigenetic modifications, such as DNA methylation, are environmentally sensitive mechanisms that may play a role in the origins and progression of mental illness. Recently, genome-wide disruptions of 5-hydroxymethylcytosine (5hmC) were associated with the development of early and late onset mental illnesses such as autism and Alzheimer’s disease, bringing new hope to the field of psychiatry. Here, we review the recent links of 5hmC to mental illness and discuss several putative functions of 5hmC in the context of its promising clinical relevance.
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Affiliation(s)
- Andy Madrid
- Department of Psychiatry, University of Wisconsin, Madison, WI 53719, USA
- Neuroscience training program, University of Wisconsin, Madison, WI 53719, USA
| | - Ligia A Papale
- Department of Psychiatry, University of Wisconsin, Madison, WI 53719, USA
| | - Reid S Alisch
- Department of Psychiatry, University of Wisconsin, Madison, WI 53719, USA
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55
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The key culprit in the pathogenesis of systemic lupus erythematosus: Aberrant DNA methylation. Autoimmun Rev 2016; 15:684-9. [DOI: 10.1016/j.autrev.2016.03.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 02/28/2016] [Indexed: 01/21/2023]
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56
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Kong L, Tan L, Lv R, Shi Z, Xiong L, Wu F, Rabidou K, Smith M, He C, Zhang L, Qian Y, Ma D, Lan F, Shi Y, Shi YG. A primary role of TET proteins in establishment and maintenance of De Novo bivalency at CpG islands. Nucleic Acids Res 2016; 44:8682-8692. [PMID: 27288448 PMCID: PMC5062965 DOI: 10.1093/nar/gkw529] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 06/01/2016] [Indexed: 12/15/2022] Open
Abstract
Ten Eleven Translocation (TET) protein-catalyzed 5mC oxidation not only creates novel DNA modifications, such as 5hmC, but also initiates active or passive DNA demethylation. TETs’ role in the crosstalk with specific histone modifications, however, is largely elusive. Here, we show that TET2-mediated DNA demethylation plays a primary role in the de novo establishment and maintenance of H3K4me3/H3K27me3 bivalent domains underlying methylated DNA CpG islands (CGIs). Overexpression of wild type (WT), but not catalytic inactive mutant (Mut), TET2 in low-TET-expressing cells results in an increase in the level of 5hmC with accompanying DNA demethylation at a subset of CGIs. Most importantly, this alteration is sufficient in making de novo bivalent domains at these loci. Genome-wide analysis reveals that these de novo synthesized bivalent domains are largely associated with a subset of essential developmental gene promoters, which are located within CGIs and are previously silenced due to DNA methylation. On the other hand, deletion of Tet1 and Tet2 in mouse embryonic stem (ES) cells results in an apparent loss of H3K27me3 at bivalent domains, which are associated with a particular set of key developmental gene promoters. Collectively, this study demonstrates the critical role of TET proteins in regulating the crosstalk between two key epigenetic mechanisms, DNA methylation and histone methylation (H3K4me3 and H3K27me3), particularly at CGIs associated with developmental genes.
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Affiliation(s)
- Lingchun Kong
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Li Tan
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Ruitu Lv
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Zhennan Shi
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Lijun Xiong
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Feizhen Wu
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Kimberlie Rabidou
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Smith
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Celestine He
- Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Lei Zhang
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanyan Qian
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Duan Ma
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Fei Lan
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yang Shi
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China Division of Newborn Medicine, Children's Hospital Boston and Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Yujiang Geno Shi
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China Division of Endocrinology, Diabetes and Hypertension, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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57
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Ye C, Tao R, Cao Q, Zhu D, Wang Y, Wang J, Lu J, Chen E, Li L. Whole-genome DNA methylation and hydroxymethylation profiling for HBV-related hepatocellular carcinoma. Int J Oncol 2016; 49:589-602. [DOI: 10.3892/ijo.2016.3535] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/13/2016] [Indexed: 11/06/2022] Open
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58
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Wang H, Huang N, Liu Y, Cang J, Xue Z. Genomic distribution of 5-Hydroxymethylcytosine in mouse kidney and its relationship with gene expression. Ren Fail 2016; 38:982-8. [DOI: 10.3109/0886022x.2016.1172973] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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59
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Abstract
Neurogenesis is not limited to the embryonic stage, but continually proceeds in the adult brain throughout life. Epigenetic mechanisms, including DNA methylation, histone modification and noncoding RNA, play important roles in neurogenesis. For decades, DNA methylation was thought to be a stable modification, except for demethylation in the early embryo. In recent years, DNA methylation has proved to be dynamic during development. In this review, we summarize the latest understanding about DNA methylation dynamics in neurogenesis, including the roles of different methylation forms (5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine), as well as their 'writers', 'readers' and interactions with histone modifications.
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Affiliation(s)
- Zhiqin Wang
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, PR China
| | - Yuquan He
- Department of Cardiology, The Third Affiliated Hospital of Jilin University, Jilin University, Changchun, Jilin, PR China
| | - Peng Jin
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
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60
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Devall M, Roubroeks J, Mill J, Weedon M, Lunnon K. Epigenetic regulation of mitochondrial function in neurodegenerative disease: New insights from advances in genomic technologies. Neurosci Lett 2016; 625:47-55. [PMID: 26876477 DOI: 10.1016/j.neulet.2016.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 10/22/2022]
Abstract
The field of mitochondrial epigenetics has received increased attention in recent years and changes in mitochondrial DNA (mtDNA) methylation has been implicated in a number of diseases, including neurodegenerative diseases such as amyotrophic lateral sclerosis. However, current publications have been limited by the use of global or targeted methods of measuring DNA methylation. In this review, we discuss current findings in mitochondrial epigenetics as well as its potential role as a regulator of mitochondria within the brain. Finally, we summarize the current technologies best suited to capturing mtDNA methylation, and how a move towards whole epigenome sequencing of mtDNA may help to advance our current understanding of the field.
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Affiliation(s)
- Matthew Devall
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, University of Exeter, Devon, UK
| | - Janou Roubroeks
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, University of Exeter, Devon, UK; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHENS), Maastricht University, Maastricht, The Netherlands
| | - Jonathan Mill
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, University of Exeter, Devon, UK; Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, De Crespigny Park, London, UK
| | - Michael Weedon
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, University of Exeter, Devon, UK
| | - Katie Lunnon
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, University of Exeter, Devon, UK.
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61
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Peng L, Li Y, Xi Y, Li W, Li J, Lv R, Zhang L, Zou Q, Dong S, Luo H, Wu F, Yu W. MBD3L2 promotes Tet2 enzymatic activity for mediating 5-methylcytosine oxidation. J Cell Sci 2016; 129:1059-71. [PMID: 26769901 DOI: 10.1242/jcs.179044] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/10/2016] [Indexed: 12/25/2022] Open
Abstract
Ten-eleven translocation (Tet) proteins are key players involved in the dynamic regulation of cytosine methylation and demethylation. Inactivating mutations of Tet2 are frequently found in human malignancies, highlighting the essential role of Tet2 in cellular transformation. However, the factors that control Tet enzymatic activity remain largely unknown. Here, we found that methyl-CpG-binding domain protein 3 (MBD3) and its homolog MBD3-like 2 (MBD3L2) can specifically modulate the enzymatic activity of Tet2 protein, but not Tet1 and Tet3 proteins, in converting 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC). Moreover, MBD3L2 is more effective than MBD3 in promoting Tet2 enzymatic activity through strengthening the binding affinity between Tet2 and the methylated DNA target. Further analysis revealed pronounced decreases in 5mC levels at MBD3L2 and Tet2 co-occupied genomic regions, most of which are promoter elements associated with either cancer-related genes or genes involved in the regulation of cellular metabolic processes. Our data add new insights into the regulation of Tet2 activity by MBD3 and MBD3L2, and into how that affects Tet2-mediated modulation of its target genes in cancer development. Thus, they have important applications in understanding how dysregulation of Tet2 might contribute to human malignancy.
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Affiliation(s)
- Lina Peng
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Yan Li
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Yanping Xi
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Wei Li
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Jin Li
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Ruitu Lv
- Laboratory of Epigenetics, School of Basic Medicine and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Lei Zhang
- Biomedical Core Facility, School of Basic Medicine and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Qingping Zou
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Shihua Dong
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Huaibing Luo
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Feizhen Wu
- Laboratory of Epigenetics, School of Basic Medicine and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Wenqiang Yu
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200032, China
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62
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Wu Q, Wong JR, Qing Yeo PL, Zhang D, Shao F. Methylation on CpG repeats modulates hydroxymethylcytosine induced duplex destabilization. RSC Adv 2016. [DOI: 10.1039/c6ra08647k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The destabilization effect of 5-hydroxymethylcytosine on CpG repeats can be reversed in heavily methylated duplex.
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Affiliation(s)
- Qiong Wu
- Division of Chemistry and Biological Chemistry
- Nanyang Technological University
- Singapore 637371
- Singapore
| | - Jiun Ru Wong
- Division of Chemistry and Biological Chemistry
- Nanyang Technological University
- Singapore 637371
- Singapore
| | - Penny Liu Qing Yeo
- Division of Chemistry and Biological Chemistry
- Nanyang Technological University
- Singapore 637371
- Singapore
| | - Dawei Zhang
- Division of Chemistry and Biological Chemistry
- Nanyang Technological University
- Singapore 637371
- Singapore
| | - Fangwei Shao
- Division of Chemistry and Biological Chemistry
- Nanyang Technological University
- Singapore 637371
- Singapore
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Veazey KJ, Parnell SE, Miranda RC, Golding MC. Dose-dependent alcohol-induced alterations in chromatin structure persist beyond the window of exposure and correlate with fetal alcohol syndrome birth defects. Epigenetics Chromatin 2015; 8:39. [PMID: 26421061 PMCID: PMC4587584 DOI: 10.1186/s13072-015-0031-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/15/2015] [Indexed: 01/16/2023] Open
Abstract
Background In recent years, we have come to recognize that a multitude of in utero exposures have the capacity to induce the development of congenital and metabolic defects. As most of these encounters manifest their effects beyond the window of exposure, deciphering the mechanisms of teratogenesis is incredibly difficult. For many agents, altered epigenetic programming has become suspect in transmitting the lasting signature of exposure leading to dysgenesis. However, while several chemicals can perturb chromatin structure acutely, for many agents (particularly alcohol) it remains unclear if these modifications represent transient responses to exposure or heritable lesions leading to pathology. Results Here, we report that mice encountering an acute exposure to alcohol on gestational Day-7 exhibit significant alterations in chromatin structure (histone 3 lysine 9 dimethylation, lysine 9 acetylation, and lysine 27 trimethylation) at Day-17, and that these changes strongly correlate with the development of craniofacial and central nervous system defects. Using a neural cortical stem cell model, we find that the epigenetic changes arising as a consequence of alcohol exposure are heavily dependent on the gene under investigation, the dose of alcohol encountered, and that the signatures arising acutely differ significantly from those observed after a 4-day recovery period. Importantly, the changes observed post-recovery are consistent with those modeled in vivo, and associate with alterations in transcripts encoding multiple homeobox genes directing neurogenesis. Unexpectedly, we do not observe a correlation between alcohol-induced changes in chromatin structure and alterations in transcription. Interestingly, the majority of epigenetic changes observed occur in marks associated with repressive chromatin structure, and we identify correlative disruptions in transcripts encoding Dnmt1, Eed, Ehmt2 (G9a), EzH2, Kdm1a, Kdm4c, Setdb1, Sod3, Tet1 and Uhrf1. Conclusions These observations suggest that the immediate and long-term impacts of alcohol exposure on chromatin structure are distinct, and hint at the existence of a possible coordinated
epigenetic response to ethanol during development. Collectively, our results indicate that alcohol-induced modifications to chromatin structure persist beyond the window of exposure, and likely contribute to the development of fetal alcohol syndrome-associated congenital abnormalities. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0031-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kylee J Veazey
- Room 338 VMA, 4466 TAMU, Department of Veterinary Physiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4466 USA
| | - Scott E Parnell
- Bowles Center for Alcohol Studies and Department of Cell Biology and Physiology, School of Medicine, CB# 7178, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Rajesh C Miranda
- Texas A&M Health Sciences Center, Texas A&M University, 8441 State Highway 47, Clinical Building 1, Suite 3100, Bryan, TX 77807 USA
| | - Michael C Golding
- Room 338 VMA, 4466 TAMU, Department of Veterinary Physiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4466 USA
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Zhu L, Lv R, Kong L, Cheng H, Lan F, Li X. Genome-Wide Mapping of 5mC and 5hmC Identified Differentially Modified Genomic Regions in Late-Onset Severe Preeclampsia: A Pilot Study. PLoS One 2015. [PMID: 26214307 PMCID: PMC4516306 DOI: 10.1371/journal.pone.0134119] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Preeclampsia (PE) is a leading cause of perinatal morbidity and mortality. However, as a common form of PE, the etiology of late-onset PE is elusive. We analyzed 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) levels in the placentas of late-onset severe PE patients (n = 4) and normal controls (n = 4) using a (hydroxy)methylated DNA immunoprecipitation approach combined with deep sequencing ([h]MeDIP-seq), and the results were verified by (h)MeDIP-qPCR. The most significant differentially methylated regions (DMRs) were verified by MassARRAY EppiTYPER in an enlarged sample size (n = 20). Bioinformatics analysis identified 714 peaks of 5mC that were associated with 403 genes and 119 peaks of 5hmC that were associated with 61 genes, thus showing significant differences between the PE patients and the controls (>2-fold, p<0.05). Further, only one gene, PTPRN2, had both 5mC and 5hmC changes in patients. The ErbB signaling pathway was enriched in those 403 genes that had significantly different5mC level between the groups. This genome-wide mapping of 5mC and 5hmC in late-onset severe PE and normal controls demonstrates that both 5mC and 5hmC play epigenetic roles in the regulation of the disease, but work independently. We reveal the genome-wide mapping of DNA methylation and DNA hydroxymethylation in late-onset PE placentas for the first time, and the identified ErbB signaling pathway and the gene PTPRN2 may be relevant to the epigenetic pathogenesis of late-onset PE.
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Affiliation(s)
- Lisha Zhu
- Obstetrics Department, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China, 200011
| | - Ruitu Lv
- Key Laboratory of Epigenetics of Shanghai Ministry of Education, School of Basic Medicine and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Lingchun Kong
- Key Laboratory of Epigenetics of Shanghai Ministry of Education, School of Basic Medicine and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Haidong Cheng
- Obstetrics Department, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China, 200011
- * E-mail: (XTL); (FL); (HDC)
| | - Fei Lan
- Key Laboratory of Epigenetics of Shanghai Ministry of Education, School of Basic Medicine and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
- Key Laboratory of Birth Defect, Children’s Hospital of Fudan University, Shanghai 201102, China
- * E-mail: (XTL); (FL); (HDC)
| | - Xiaotian Li
- Obstetrics Department, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China, 200011
- * E-mail: (XTL); (FL); (HDC)
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Uribe-Lewis S, Stark R, Carroll T, Dunning MJ, Bachman M, Ito Y, Stojic L, Halim S, Vowler SL, Lynch AG, Delatte B, de Bony EJ, Colin L, Defrance M, Krueger F, Silva AL, ten Hoopen R, Ibrahim AEK, Fuks F, Murrell A. 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer. Genome Biol 2015; 16:69. [PMID: 25853800 PMCID: PMC4380107 DOI: 10.1186/s13059-015-0605-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 02/04/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is globally reduced in proliferating cells such as colon tumours and the gut crypt progenitors, from which tumours can arise. RESULTS Here, we show that colorectal tumours and cancer cells express Ten-Eleven-Translocation (TET) transcripts at levels similar to normal tissues. Genome-wide analyses show that promoters marked by 5hmC in normal tissue, and those identified as TET2 targets in colorectal cancer cells, are resistant to methylation gain in cancer. In vitro studies of TET2 in cancer cells confirm that these promoters are resistant to methylation gain independently of sustained TET2 expression. We also find that a considerable number of the methylation gain-resistant promoters marked by 5hmC in normal colon overlap with those that are marked with poised bivalent histone modifications in embryonic stem cells. CONCLUSIONS Together our results indicate that promoters that acquire 5hmC upon normal colon differentiation are innately resistant to neoplastic hypermethylation by mechanisms that do not require high levels of 5hmC in tumours. Our study highlights the potential of cytosine modifications as biomarkers of cancerous cell proliferation.
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Affiliation(s)
- Santiago Uribe-Lewis
- />Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| | - Rory Stark
- />Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| | - Thomas Carroll
- />Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| | - Mark J Dunning
- />Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| | - Martin Bachman
- />Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| | - Yoko Ito
- />Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| | - Lovorka Stojic
- />Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| | - Silvia Halim
- />Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| | - Sarah L Vowler
- />Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| | - Andy G Lynch
- />Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
| | - Benjamin Delatte
- />Laboratory of Cancer Epigenetics, Université Libre de Bruxelles, Faculty of Medicine, Route de Lennik 808, 1070 Brussels, Belgium
| | - Eric J de Bony
- />Laboratory of Cancer Epigenetics, Université Libre de Bruxelles, Faculty of Medicine, Route de Lennik 808, 1070 Brussels, Belgium
| | - Laurence Colin
- />Laboratory of Cancer Epigenetics, Université Libre de Bruxelles, Faculty of Medicine, Route de Lennik 808, 1070 Brussels, Belgium
| | - Matthieu Defrance
- />Laboratory of Cancer Epigenetics, Université Libre de Bruxelles, Faculty of Medicine, Route de Lennik 808, 1070 Brussels, Belgium
| | - Felix Krueger
- />Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT UK
| | - Ana-Luisa Silva
- />Department of Pathology, Addenbrooke’s Hospital, Box 231, Level 3, Hills Road, Cambridge, CB2 0QQ UK
| | - Rogier ten Hoopen
- />Department of Pathology, Addenbrooke’s Hospital, Box 231, Level 3, Hills Road, Cambridge, CB2 0QQ UK
| | - Ashraf EK Ibrahim
- />Department of Pathology, Addenbrooke’s Hospital, Box 231, Level 3, Hills Road, Cambridge, CB2 0QQ UK
| | - François Fuks
- />Laboratory of Cancer Epigenetics, Université Libre de Bruxelles, Faculty of Medicine, Route de Lennik 808, 1070 Brussels, Belgium
| | - Adele Murrell
- />Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE UK
- />Department of Biology and Biochemistry, Centre for Regenerative Medicine, University of Bath, Claverton Down, Bath, BA2 7AY UK
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66
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Santiago M, Antunes C, Guedes M, Sousa N, Marques CJ. TET enzymes and DNA hydroxymethylation in neural development and function - how critical are they? Genomics 2014; 104:334-40. [PMID: 25200796 DOI: 10.1016/j.ygeno.2014.08.018] [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: 06/14/2014] [Revised: 08/25/2014] [Accepted: 08/26/2014] [Indexed: 11/30/2022]
Abstract
Epigenetic modifications of the genome play important roles in controlling gene transcription thus regulating several molecular and cellular processes. A novel epigenetic modification - 5-hydroxymethylcytosine (5hmC) - has been recently described and attracted a lot of attention due to its possible involvement in the active DNA demethylation mechanism. TET enzymes are dioxygenases capable of oxidizing the methyl group of 5-methylcytosines (5mC) and thus converting 5mC into 5hmC. Although most of the work on TET enzymes and 5hmC has been carried out in embryonic stem (ES) cells, the highest levels of 5hmC occur in the brain and in neurons, pointing to a role for this epigenetic modification in the control of neuronal differentiation, neural plasticity and brain functions. Here we review the most recent advances on the role of TET enzymes and DNA hydroxymethylation in neuronal differentiation and function.
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Affiliation(s)
- Mafalda Santiago
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Claudia Antunes
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Marta Guedes
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Nuno Sousa
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - C Joana Marques
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal.
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67
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Resendiz M, Mason S, Lo CL, Zhou FC. Epigenetic regulation of the neural transcriptome and alcohol interference during development. Front Genet 2014; 5:285. [PMID: 25206361 PMCID: PMC4144008 DOI: 10.3389/fgene.2014.00285] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/02/2014] [Indexed: 01/07/2023] Open
Abstract
Alcohol intoxicated cells broadly alter their metabolites – among them methyl and acetic acid can alter the DNA and histone epigenetic codes. Together with the promiscuous effect of alcohol on enzyme activities (including DNA methyltransferases) and the downstream effect on microRNA and transposable elements, alcohol is well placed to affect intrinsic transcriptional programs of developing cells. Considering that the developmental consequences of early alcohol exposure so profoundly affect neural systems, it is not unfounded to reason that alcohol exploits transcriptional regulators to challenge canonical gene expression and in effect, intrinsic developmental pathways to achieve widespread damage in the developing nervous system. To fully evaluate the role of epigenetic regulation in alcohol-related developmental disease, it is important to first gather the targets of epigenetic players in neurodevelopmental models. Here, we attempt to review the cellular and genomic windows of opportunity for alcohol to act on intrinsic neurodevelopmental programs. We also discuss some established targets of fetal alcohol exposure and propose pathways for future study. Overall, this review hopes to illustrate the known epigenetic program and its alterations in normal neural stem cell development and further, aims to depict how alcohol, through neuroepigenetics, may lead to neurodevelopmental deficits observed in fetal alcohol spectrum disorders.
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Affiliation(s)
- Marisol Resendiz
- Stark Neuroscience Research Institute Indianapolis, IN, USA ; Indiana Alcohol Research Center, Indiana University School of Medicine Indianapolis, IN, USA
| | - Stephen Mason
- Department of Anatomy and Cell Biology, Indiana University School of Medicine Indianapolis, IN, USA
| | - Chiao-Ling Lo
- Indiana Alcohol Research Center, Indiana University School of Medicine Indianapolis, IN, USA ; Department of Anatomy and Cell Biology, Indiana University School of Medicine Indianapolis, IN, USA
| | - Feng C Zhou
- Stark Neuroscience Research Institute Indianapolis, IN, USA ; Indiana Alcohol Research Center, Indiana University School of Medicine Indianapolis, IN, USA ; Department of Anatomy and Cell Biology, Indiana University School of Medicine Indianapolis, IN, USA
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68
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Choi I, Kim R, Lim HW, Kaestner KH, Won KJ. 5-hydroxymethylcytosine represses the activity of enhancers in embryonic stem cells: a new epigenetic signature for gene regulation. BMC Genomics 2014; 15:670. [PMID: 25106691 PMCID: PMC4133056 DOI: 10.1186/1471-2164-15-670] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/31/2014] [Indexed: 02/08/2023] Open
Abstract
Background Recent mapping of 5-hydroxymethylcytosine (5hmC) provides a genome-wide view of the distribution of this important chromatin mark. However, the role of 5hmC in specific regulatory regions is not clear, especially at enhancers. Results We found a group of distal transcription factor binding sites highly enriched for 5-hdroxymethylcytosine (5hmC), but lacking any known activating histone marks and being depleted for nascent transcripts, suggesting a repressive role for 5hmC in mouse embryonic stem cells (mESCs). 5-formylcytosine (5fC), which is known to mark poised enhancers where H3K4me1 is enriched, is also observed at these sites. Furthermore, the 5hmC levels were inversely correlated with RNA polymerase II (PolII) occupancy in mESCs as well as in fully differentiated adipocytes. Interestingly, activating H3K4me1/2 histone marks were enriched at these sites when the associated genes become activated following lineage specification. These putative enhancers were shown to be functional in embryonic stem cells when unmethylated. Together, these data suggest that 5hmC suppresses the activity of this group of enhancers, which we termed “silenced enhancers”. Conclusions Our findings indicate that 5hmC has a repressive role at specific proximal and distal regulatory regions in mESCs, and suggest that 5hmC is a new epigenetic mark for silenced enhancers. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-670) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Klaus H Kaestner
- Department of Genetics, Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, 3400 Civic Center Blvd, 19104 Philadelphia, PA, USA.
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69
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Jeong M, Goodell MA. New answers to old questions from genome-wide maps of DNA methylation in hematopoietic cells. Exp Hematol 2014; 42:609-17. [PMID: 24993071 PMCID: PMC4137036 DOI: 10.1016/j.exphem.2014.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 04/17/2014] [Accepted: 04/22/2014] [Indexed: 01/10/2023]
Abstract
DNA methylation is a well-studied epigenetic modification essential for efficient cellular differentiation. Aberrant DNA methylation patterns are a characteristic feature of cancer, including myeloid malignancies such as acute myeloid leukemia. Recurrent mutations in DNA-modifying enzymes were identified in acute myeloid leukemia and linked to distinct DNA methylation signatures. In addition, discovery of Tet enzymes provided new mechanisms for the reversal of DNA methylation. Advances in base-resolution profiling of DNA methylation have enabled a more comprehensive understanding of the methylome landscape in the genome. This review will summarize and discuss the key questions in the function of DNA methylation in the hematopoietic system, including where and how DNA methylation regulates diverse biological processes in the genome as elucidated by recent studies.
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Affiliation(s)
- Mira Jeong
- Stem Cells and Regenerative Medicine Center, Department of Pediatrics and Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Margaret A. Goodell
- Stem Cells and Regenerative Medicine Center, Department of Pediatrics and Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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70
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Recent advances in the bioanalysis of modified nucleotides in epigenetic studies. Bioanalysis 2014; 5:2947-56. [PMID: 24295120 DOI: 10.4155/bio.13.270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Epigenetic alterations, such as DNA methylation, are involved in the pathogenesis of various diseases, the toxicity of diverse agents, the process of aging, the development of stem cells and numerous other mechanisms. DNA methylation is one of the most well-studied epigenetic alterations in mammals. Nevertheless, the scientific interest is now focusing on novel modified nucleotides with potential regulatory roles, such as 5-hydroxymethylcytosine. We currently present and discuss novel bioanalytical strategies developed for the determination of various modified nucleotides in epigenetic studies.
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71
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Fitzsimons CP, van Bodegraven E, Schouten M, Lardenoije R, Kompotis K, Kenis G, van den Hurk M, Boks MP, Biojone C, Joca S, Steinbusch HWM, Lunnon K, Mastroeni DF, Mill J, Lucassen PJ, Coleman PD, van den Hove DLA, Rutten BPF. Epigenetic regulation of adult neural stem cells: implications for Alzheimer's disease. Mol Neurodegener 2014; 9:25. [PMID: 24964731 PMCID: PMC4080757 DOI: 10.1186/1750-1326-9-25] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 06/06/2014] [Indexed: 01/27/2023] Open
Abstract
Experimental evidence has demonstrated that several aspects of adult neural stem cells (NSCs), including their quiescence, proliferation, fate specification and differentiation, are regulated by epigenetic mechanisms. These control the expression of specific sets of genes, often including those encoding for small non-coding RNAs, indicating a complex interplay between various epigenetic factors and cellular functions.Previous studies had indicated that in addition to the neuropathology in Alzheimer's disease (AD), plasticity-related changes are observed in brain areas with ongoing neurogenesis, like the hippocampus and subventricular zone. Given the role of stem cells e.g. in hippocampal functions like cognition, and given their potential for brain repair, we here review the epigenetic mechanisms relevant for NSCs and AD etiology. Understanding the molecular mechanisms involved in the epigenetic regulation of adult NSCs will advance our knowledge on the role of adult neurogenesis in degeneration and possibly regeneration in the AD brain.
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Affiliation(s)
- Carlos P Fitzsimons
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, SciencePark 904, 1098XH Amsterdam, The Netherlands
| | - Emma van Bodegraven
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, SciencePark 904, 1098XH Amsterdam, The Netherlands
| | - Marijn Schouten
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, SciencePark 904, 1098XH Amsterdam, The Netherlands
| | - Roy Lardenoije
- Department of Translational Neuroscience, School of Mental Health and Neuroscience (MHENS), Maastricht University, Maastricht, the Netherlands
| | - Konstantinos Kompotis
- Department of Translational Neuroscience, School of Mental Health and Neuroscience (MHENS), Maastricht University, Maastricht, the Netherlands
| | - Gunter Kenis
- Department of Translational Neuroscience, School of Mental Health and Neuroscience (MHENS), Maastricht University, Maastricht, the Netherlands
| | - Mark van den Hurk
- Department of Translational Neuroscience, School of Mental Health and Neuroscience (MHENS), Maastricht University, Maastricht, the Netherlands
| | - Marco P Boks
- Department Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Caroline Biojone
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Samia Joca
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Harry WM Steinbusch
- Department of Translational Neuroscience, School of Mental Health and Neuroscience (MHENS), Maastricht University, Maastricht, the Netherlands
| | - Katie Lunnon
- University of Exeter Medical School, RILD Level 4, Barrack Road, University of Exeter, Devon, UK
| | - Diego F Mastroeni
- University of Exeter Medical School, RILD Level 4, Barrack Road, University of Exeter, Devon, UK
| | - Jonathan Mill
- University of Exeter Medical School, RILD Level 4, Barrack Road, University of Exeter, Devon, UK
| | - Paul J Lucassen
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, SciencePark 904, 1098XH Amsterdam, The Netherlands
| | - Paul D Coleman
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, SciencePark 904, 1098XH Amsterdam, The Netherlands
| | - Daniel LA van den Hove
- Department of Translational Neuroscience, School of Mental Health and Neuroscience (MHENS), Maastricht University, Maastricht, the Netherlands
| | - Bart PF Rutten
- Department of Translational Neuroscience, School of Mental Health and Neuroscience (MHENS), Maastricht University, Maastricht, the Netherlands
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Centre, P.O. Box 616, 6200 MD Maastricht, The Netherlands
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72
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Teif VB, Beshnova DA, Vainshtein Y, Marth C, Mallm JP, Höfer T, Rippe K. Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development. Genome Res 2014; 24:1285-95. [PMID: 24812327 PMCID: PMC4120082 DOI: 10.1101/gr.164418.113] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
During differentiation of embryonic stem cells, chromatin reorganizes to establish cell type-specific expression programs. Here, we have dissected the linkages between DNA methylation (5mC), hydroxymethylation (5hmC), nucleosome repositioning, and binding of the transcription factor CTCF during this process. By integrating MNase-seq and ChIP-seq experiments in mouse embryonic stem cells (ESC) and their differentiated counterparts with biophysical modeling, we found that the interplay between these factors depends on their genomic context. The mostly unmethylated CpG islands have reduced nucleosome occupancy and are enriched in cell type-independent binding sites for CTCF. The few remaining methylated CpG dinucleotides are preferentially associated with nucleosomes. In contrast, outside of CpG islands most CpGs are methylated, and the average methylation density oscillates so that it is highest in the linker region between nucleosomes. Outside CpG islands, binding of TET1, an enzyme that converts 5mC to 5hmC, is associated with labile, MNase-sensitive nucleosomes. Such nucleosomes are poised for eviction in ESCs and become stably bound in differentiated cells where the TET1 and 5hmC levels go down. This process regulates a class of CTCF binding sites outside CpG islands that are occupied by CTCF in ESCs but lose the protein during differentiation. We rationalize this cell type-dependent targeting of CTCF with a quantitative biophysical model of competitive binding with the histone octamer, depending on the TET1, 5hmC, and 5mC state.
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Affiliation(s)
- Vladimir B Teif
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany
| | - Daria A Beshnova
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany
| | - Yevhen Vainshtein
- Division Theoretical Systems Biology, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany
| | - Caroline Marth
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany
| | - Jan-Philipp Mallm
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany
| | - Thomas Höfer
- Division Theoretical Systems Biology, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany
| | - Karsten Rippe
- Research Group Genome Organization and Function, Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, 69120 Heidelberg, Germany
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73
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Dao T, Cheng RYS, Revelo MP, Mitzner W, Tang W. Hydroxymethylation as a Novel Environmental Biosensor. Curr Environ Health Rep 2014; 1:1-10. [PMID: 24860723 PMCID: PMC4029614 DOI: 10.1007/s40572-013-0005-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Beyond the genome, epigenetics has become a promising approach in understanding the interactions between the gene and the environment. Epigenetic regulation includes DNA methylation, histone modifications, and non-coding RNAs. Among these, DNA methylation, which is the addition of a methyl group to the fifth base of cytosine to produce 5-methylcytosine (5-mC), is most commonly studied. Epigenetic regulation has changed given the discovery of 5-hydroxymethylcytosine (5-hmC), considered the "sixth base", and the nature of TET proteins to catalyze 5-mC oxidation to 5-hmC. 5-hydroxymethylation has been proposed to be a stable intermediate between methylation and demethylation and has raised questions about the functions of 5-hmC in gene regulation in cells, tissues, and organs in response to environmental exposure. Herein, we have provided an introduction to the chemistry of 5-hydroxymethylation, and the techniques for detection of 5-hydroxymethylation. In addition, we have reviewed current reports describing how 5-hmC responds to environmental factors, leading to the development of disease. And finally, we have discussed the potential use of 5-hmC in the study of disease development. All in all, it is our goal to provide innovative and convincing epigenetic studies for understanding the etiology of environmentally-related human disease, and translate these epigenetic findings into lifestyle recommendations and clinical practices to prevent and cure disease.
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Affiliation(s)
- T Dao
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - R Y S Cheng
- Radiation Biology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - M P Revelo
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States
| | - W Mitzner
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - Wy Tang
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
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74
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Chen Y, Chen Q, McEachin RC, Cavalcoli JD, Yu X. H2A.B facilitates transcription elongation at methylated CpG loci. Genome Res 2014; 24:570-9. [PMID: 24402521 PMCID: PMC3975057 DOI: 10.1101/gr.156877.113] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
H2A.B is a unique histone H2A variant that only exists in mammals. Here we found that H2A.B is ubiquitously expressed in major organs. Genome-wide analysis of H2A.B in mouse ES cells shows that H2A.B is associated with methylated DNA in gene body regions. Moreover, H2A.B-enriched gene loci are actively transcribed. One typical example is that H2A.B is enriched in a set of differentially methylated regions at imprinted loci and facilitates transcription elongation. These results suggest that H2A.B positively regulates transcription elongation by overcoming DNA methylation in the transcribed region. It provides a novel mechanism by which transcription is regulated at DNA hypermethylated regions.
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Affiliation(s)
- Yibin Chen
- Division of Molecular Medicine and Genetics, Department of Internal Medicine
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75
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Feldmann A, Ivanek R, Murr R, Gaidatzis D, Burger L, Schübeler D. Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions. PLoS Genet 2013; 9:e1003994. [PMID: 24367273 PMCID: PMC3868540 DOI: 10.1371/journal.pgen.1003994] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 10/14/2013] [Indexed: 11/18/2022] Open
Abstract
Distal regulatory elements, including enhancers, play a critical role in regulating gene activity. Transcription factor binding to these elements correlates with Low Methylated Regions (LMRs) in a process that is poorly understood. Here we ask whether and how actual occupancy of DNA-binding factors is linked to DNA methylation at the level of individual molecules. Using CTCF as an example, we observe that frequency of binding correlates with the likelihood of a demethylated state and sites of low occupancy display heterogeneous DNA methylation within the CTCF motif. In line with a dynamic model of binding and DNA methylation turnover, we find that 5-hydroxymethylcytosine (5hmC), formed as an intermediate state of active demethylation, is enriched at LMRs in stem and somatic cells. Moreover, a significant fraction of changes in 5hmC during differentiation occurs at these regions, suggesting that transcription factor activity could be a key driver for active demethylation. Since deletion of CTCF is lethal for embryonic stem cells, we used genetic deletion of REST as another DNA-binding factor implicated in LMR formation to test this hypothesis. The absence of REST leads to a decrease of hydroxymethylation and a concomitant increase of DNA methylation at its binding sites. These data support a model where DNA-binding factors can mediate turnover of DNA methylation as an integral part of maintenance and reprogramming of regulatory regions. Cell identity is determined by differential gene expression, which in turn is controlled by the combined activity of proximal and distal regulatory elements such as enhancers. DNA within active enhancer elements is marked by a hypomethylated state as a result of transcription factor (TF) binding. Here, using CTCF as an example for a DNA-binding factor, we explore the relationship between binding and DNA methylation at the level of single molecules by enriching for CTCF occupied DNA. To our surprise, methylation at molecules which are bound by CTCF does not differ from the average methylation levels at the binding sites defined by whole-genome bisulfite sequencing. We find that binding strength inversely correlates with DNA methylation within the CTCF motif with heterogenic methylation levels at low occupancy sites, suggesting that CTCF can bind to molecules with different methylation states. Moreover, we observed enrichment of 5-hydroxymethylcytosines at constitutive and cell-type specific TF binding sites indicative of an active demethylation process. To test the requirement of TF binding for the observed hydroxymethylation, and as CTCF deletion is incompatible with the survival of embryonic stem cells, we made use of cells in which REST – a factor which was previously shown to be involved in LMR formation - was genetically deleted. This deletion leads to loss of hydroxymethylation at its binding sites, suggesting that binding is necessary for turnover. Our data support a model in which TF occupancy mediates a continuous turnover of DNA methylation during maintenance and formation of active regulatory regions.
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Affiliation(s)
- Angelika Feldmann
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Robert Ivanek
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Rabih Murr
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Dimos Gaidatzis
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
- * E-mail:
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76
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Thomson JP, Hunter JM, Nestor CE, Dunican DS, Terranova R, Moggs JG, Meehan RR. Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques. Nucleic Acids Res 2013; 41:e206. [PMID: 24214958 PMCID: PMC3905904 DOI: 10.1093/nar/gkt1080] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The epigenetic modification of 5-hydroxymethylcytosine (5hmC) is receiving great attention due to its potential role in DNA methylation reprogramming and as a cell state identifier. Given this interest, it is important to identify reliable and cost-effective methods for the enrichment of 5hmC marked DNA for downstream analysis. We tested three commonly used affinity-based enrichment techniques; (i) antibody, (ii) chemical capture and (iii) protein affinity enrichment and assessed their ability to accurately and reproducibly report 5hmC profiles in mouse tissues containing high (brain) and lower (liver) levels of 5hmC. The protein-affinity technique is a poor reporter of 5hmC profiles, delivering 5hmC patterns that are incompatible with other methods. Both antibody and chemical capture-based techniques generate highly similar genome-wide patterns for 5hmC, which are independently validated by standard quantitative PCR (qPCR) and glucosyl-sensitive restriction enzyme digestion (gRES-qPCR). Both antibody and chemical capture generated profiles reproducibly link to unique chromatin modification profiles associated with 5hmC. However, there appears to be a slight bias of the antibody to bind to regions of DNA rich in simple repeats. Ultimately, the increased specificity observed with chemical capture-based approaches makes this an attractive method for the analysis of locus-specific or genome-wide patterns of 5hmC.
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Affiliation(s)
- John P Thomson
- Chromosomes and Gene Expression, MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK, Member of MARCAR Consortium, The Centre for Individualized Medication, Linköping University Hospital, Linköping University, Linköping SE-58185, Sweden and Discovery and Investigative Safety, Preclinical Safety, Novartis Institutes for Biomedical Research, Klybeckstrasse, Basel CH-4002, Switzerland
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