451
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PRDM14: a unique regulator for pluripotency and epigenetic reprogramming. Trends Biochem Sci 2014; 39:289-98. [PMID: 24811060 DOI: 10.1016/j.tibs.2014.04.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/03/2014] [Accepted: 04/08/2014] [Indexed: 11/20/2022]
Abstract
PRDM14 belongs to the PR domain-containing (PRDM) transcriptional regulators. Among the PRDM family members, PRDM14 shows specific expression in preimplantation embryos, primordial germ cells (PGCs), and embryonic stem cells (ESCs) in vitro, and accordingly plays a key role in the regulation of their pluripotency and epigenetic reprogramming, most notably, genome-wide DNA demethylation. The function of PRDM14 appears to be conserved between mice and humans, but it shows several characteristic differences between the two species. A precise understanding of the function of PRDM14 in mice and humans would shed new light on the regulation of pluripotency and the epigenome in these two species, providing a foundation for better control of stem cell fates in a broader context.
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452
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Abstract
Genes that are subject to genomic imprinting in mammals are preferentially expressed from a single parental allele. This imprinted expression of a small number of genes is crucial for normal development, as these genes often directly regulate fetal growth. Recent work has also demonstrated intricate roles for imprinted genes in the brain, with important consequences on behavior and neuronal function. Finally, new studies have revealed the importance of proper expression of specific imprinted genes in induced pluripotent stem cells and in adult stem cells. As we review here, these findings highlight the complex nature and developmental importance of imprinted genes.
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453
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Crichton JH, Dunican DS, MacLennan M, Meehan RR, Adams IR. Defending the genome from the enemy within: mechanisms of retrotransposon suppression in the mouse germline. Cell Mol Life Sci 2014; 71:1581-605. [PMID: 24045705 PMCID: PMC3983883 DOI: 10.1007/s00018-013-1468-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 08/27/2013] [Accepted: 08/29/2013] [Indexed: 12/15/2022]
Abstract
The viability of any species requires that the genome is kept stable as it is transmitted from generation to generation by the germ cells. One of the challenges to transgenerational genome stability is the potential mutagenic activity of transposable genetic elements, particularly retrotransposons. There are many different types of retrotransposon in mammalian genomes, and these target different points in germline development to amplify and integrate into new genomic locations. Germ cells, and their pluripotent developmental precursors, have evolved a variety of genome defence mechanisms that suppress retrotransposon activity and maintain genome stability across the generations. Here, we review recent advances in understanding how retrotransposon activity is suppressed in the mammalian germline, how genes involved in germline genome defence mechanisms are regulated, and the consequences of mutating these genome defence genes for the developing germline.
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Affiliation(s)
- James H. Crichton
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Donncha S. Dunican
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Marie MacLennan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Richard R. Meehan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Ian R. Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
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454
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Abstract
Epigenetic mechanisms play a crucial role in regulating gene expression. The main mechanisms involve methylation of DNA and covalent modifications of histones by methylation, acetylation, phosphorylation, or ubiquitination. The complex interplay of different epigenetic mechanisms is mediated by enzymes acting in the nucleus. Modifications in DNA methylation are performed mainly by DNA methyltransferases (DNMTs) and ten-eleven translocation (TET) proteins, while a plethora of enzymes, such as histone acetyltransferases (HATs), histone deacetylases (HDACs), histone methyltransferases (HMTs), and histone demethylases (HDMs) regulate covalent histone modifications. In many diseases, such as cancer, the epigenetic regulatory system is often disturbed. Vitamin D interacts with the epigenome on multiple levels. Firstly, critical genes in the vitamin D signaling system, such as those coding for vitamin D receptor (VDR) and the enzymes 25-hydroxylase (CYP2R1), 1α-hydroxylase (CYP27B1), and 24-hydroxylase (CYP24A1) have large CpG islands in their promoter regions and therefore can be silenced by DNA methylation. Secondly, VDR protein physically interacts with coactivator and corepressor proteins, which in turn are in contact with chromatin modifiers, such as HATs, HDACs, HMTs, and with chromatin remodelers. Thirdly, a number of genes encoding for chromatin modifiers and remodelers, such as HDMs of the Jumonji C (JmjC)-domain containing proteins and lysine-specific demethylase (LSD) families are primary targets of VDR and its ligands. Finally, there is evidence that certain VDR ligands have DNA demethylating effects. In this review we will discuss regulation of the vitamin D system by epigenetic modifications and how vitamin D contributes to the maintenance of the epigenome, and evaluate its impact in health and disease.
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Affiliation(s)
- Irfete S Fetahu
- Department of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Comprehensive Cancer Center, Medical University of Vienna Vienna, Austria
| | - Julia Höbaus
- Department of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Comprehensive Cancer Center, Medical University of Vienna Vienna, Austria
| | - Enikő Kállay
- Department of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Comprehensive Cancer Center, Medical University of Vienna Vienna, Austria
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455
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456
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Bagci H, Fisher AG. DNA demethylation in pluripotency and reprogramming: the role of tet proteins and cell division. Cell Stem Cell 2014; 13:265-9. [PMID: 24012367 DOI: 10.1016/j.stem.2013.08.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cytosine methylation is found in the genomes of many plants and animals and has been associated with transcriptional silencing in mammals. At critical stages in embryo development, when cellular potential is reset, DNA methylation is lost in a series of "sequential waves." The mechanism underlying this is controversial and complex. Several new reports now suggest that TET enzymes and cell division are important for these in vivo transitions as well as for experimentally induced reprogramming.
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Affiliation(s)
- Hakan Bagci
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College London, Du Cane Road, London W12 0NN, UK
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457
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Wu H, Zhang Y. Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell 2014; 156:45-68. [PMID: 24439369 DOI: 10.1016/j.cell.2013.12.019] [Citation(s) in RCA: 755] [Impact Index Per Article: 75.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Indexed: 12/28/2022]
Abstract
Methylation of cytosines in the mammalian genome represents a key epigenetic modification and is dynamically regulated during development. Compelling evidence now suggests that dynamic regulation of DNA methylation is mainly achieved through a cyclic enzymatic cascade comprised of cytosine methylation, iterative oxidation of methyl group by TET dioxygenases, and restoration of unmodified cytosines by either replication-dependent dilution or DNA glycosylase-initiated base excision repair. In this review, we discuss the mechanism and function of DNA demethylation in mammalian genomes, focusing particularly on how developmental modulation of the cytosine-modifying pathway is coupled to active reversal of DNA methylation in diverse biological processes.
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Affiliation(s)
- Hao Wu
- Howard Hughes Medical Institute, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA.
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458
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Zhang G, Pradhan S. Mammalian epigenetic mechanisms. IUBMB Life 2014; 66:240-56. [PMID: 24706538 DOI: 10.1002/iub.1264] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 03/19/2014] [Indexed: 12/31/2022]
Abstract
The mammalian genome is packaged into chromatin that is further compacted into three-dimensional structures consisting of distinct functional domains. The higher order structure of chromatin is in part dictated by enzymatic DNA methylation and histone modifications to establish epigenetic layers controlling gene expression and cellular functions, without altering the underlying DNA sequences. Apart from DNA and histone modifications, non-coding RNAs can also regulate the dynamics of the mammalian gene expression and various physiological functions including cell division, differentiation, and apoptosis. Aberrant epigenetic signatures are associated with abnormal developmental processes and diseases such as cancer. In this review, we will discuss the different layers of epigenetic regulation, including writer enzymes for DNA methylation, histone modifications, non-coding RNA, and chromatin conformation. We will highlight the combinatorial role of these structural and chemical modifications along with their partners in various cellular processes in mammalian cells. We will also address the cis and trans interacting "reader" proteins that recognize these modifications and "eraser" enzymes that remove these marks. Furthermore, an attempt will be made to discuss the interplay between various epigenetic writers, readers, and erasures in the establishment of mammalian epigenetic mechanisms.
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459
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Devakumar D, Birch M, Osrin D, Sondorp E, Wells JCK. The intergenerational effects of war on the health of children. BMC Med 2014; 12:57. [PMID: 24694212 PMCID: PMC3997818 DOI: 10.1186/1741-7015-12-57] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Accepted: 02/26/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The short- and medium-term effects of conflict on population health are reasonably well documented. Less considered are its consequences across generations and potential harms to the health of children yet to be born. DISCUSSION Looking first at the nature and effects of exposures during conflict, and then at the potential routes through which harm may propagate within families, we consider the intergenerational effects of four features of conflict: violence, challenges to mental health, infection and malnutrition. Conflict-driven harms are transmitted through a complex permissive environment that includes biological, cultural and economic factors, and feedback loops between sources of harm and weaknesses in individual and societal resilience to them. We discuss the multiplicative effects of ongoing conflict when hostilities are prolonged. SUMMARY We summarize many instances in which the effects of war can propagate across generations. We hope that the evidence laid out in the article will stimulate research and--more importantly--contribute to the discussion of the costs of war; particularly in the longer-term in post-conflict situations in which interventions need to be sustained and adapted over many years.
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Affiliation(s)
- Delan Devakumar
- Institute for Global Health, University College London, London, UK
| | | | - David Osrin
- Institute for Global Health, University College London, London, UK
| | | | - Jonathan CK Wells
- Childhood Nutrition Research Centre, Institute of Child Health, University College London, London, UK
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460
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Zhao C, Wang H, Zhao B, Li C, Yin R, Song M, Liu B, Liu Z, Jiang G. Boronic acid-mediated polymerase chain reaction for gene- and fragment-specific detection of 5-hydroxymethylcytosine. Nucleic Acids Res 2014; 42:e81. [PMID: 24682822 PMCID: PMC4027215 DOI: 10.1093/nar/gku216] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The gene- or fragment-specific detection of newly recognized deoxyribonucleic acid (DNA) base 5-hydroxymethylcytosine (5hmC) will provide insights into its critical functions in development and diseases, and is also important for screening 5hmC-rich genes as an indicator of epigenetic states, pathogenic processes and pharmacological responses. Current analytical technologies for gene-specific detection of 5hmC are heavily dependent on glucosylated 5hmC-resistant restriction endonuclease cleavage. Here, we find that boronic acid (BA) can inhibit the amplification activity of Taq DNA polymerase for replicating glucosylated 5hmC bases in template DNA by interacting with their glucose moiety. On the basis of this finding, we propose for the first time a BA-mediated polymerase chain reaction (PCR) assay for rapid and sensitive detection of gene- or fragment-specific 5hmC without restriction-assay-like sequence limitations. To optimize the BA-mediated PCR assay, we further tested BA derivatives and show that one BA derivative, 2-(2′-chlorobenzyloxy) phenylboronic acid, displays the highest inhibitory efficiency. Using the optimized assay, we demonstrate the enrichment of 5hmC in an intron region of Pax5 gene (a member of the paired box family of transcription factors) in mouse embryonic stem cells. Our work potentially opens a new way for the screening and identification of 5hmC-rich genes and for high throughput analysis of 5hmC in mammalian cells.
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Affiliation(s)
- Chao Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Bailin Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Cuiping Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ruichuan Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Maoyong Song
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Baodong Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhen Liu
- Department of Chemistry, Nanjing University, Nanjing 210093, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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461
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Staszewski O, Prinz M. Glial epigenetics in neuroinflammation and neurodegeneration. Cell Tissue Res 2014; 356:609-16. [PMID: 24652504 DOI: 10.1007/s00441-014-1815-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/14/2014] [Indexed: 01/01/2023]
Abstract
Epigenetic regulation shapes the differentiation and response to stimuli of all tissues and cells beyond what genetics would dictate. Epigenetic regulation acts through covalent modifications of DNA and histones while leaving the nucleotide code intact. However, these chromatin modifications are known to be vital components of the regulation of cell fate and response. With regards to the central nervous system (CNS), little is known about how epigenetic regulation shapes the function of neural cell types. The focus of research so far has been on epigenetic regulation of neuronal function and the role of epigenetics in tumorigenesis. However, the glial cell compartment, which makes up 90 % of all CNS cells, has so far received scant attention as to how epigenetics shape their differentiation and function. Here, we highlight current knowledge about epigenetic changes in glial cells occurring during CNS injury, neuroinflammatory conditions and neurodegenerative disease. This review offers an overview of the current understanding of epigenetic regulation in glial cells in CNS disease.
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Affiliation(s)
- Ori Staszewski
- Institute of Neuropathology, University of Freiburg, Breisacher Str. 64, D-79106, Freiburg, Germany
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462
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Crichton JH, Playfoot CJ, Adams IR. The role of chromatin modifications in progression through mouse meiotic prophase. J Genet Genomics 2014; 41:97-106. [PMID: 24656230 DOI: 10.1016/j.jgg.2014.01.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/10/2013] [Accepted: 01/06/2014] [Indexed: 12/15/2022]
Abstract
Meiosis is a key event in gametogenesis that generates new combinations of genetic information and is required to reduce the chromosome content of the gametes. Meiotic chromosomes undergo a number of specialised events during prophase to allow meiotic recombination, homologous chromosome synapsis and reductional chromosome segregation to occur. In mammalian cells, DNA physically associates with histones to form chromatin, which can be modified by methylation, phosphorylation, ubiquitination and acetylation to help regulate higher order chromatin structure, gene expression, and chromosome organisation. Recent studies have identified some of the enzymes responsible for generating chromatin modifications in meiotic mammalian cells, and shown that these chromatin modifying enzymes are required for key meiosis-specific events that occur during meiotic prophase. This review will discuss the role of chromatin modifications in meiotic recombination, homologous chromosome synapsis and regulation of meiotic gene expression in mammals.
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Affiliation(s)
- James H Crichton
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Christopher J Playfoot
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Ian R Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
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463
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Tsagaratou A, Rao A. TET proteins and 5-methylcytosine oxidation in the immune system. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2014; 78:1-10. [PMID: 24619230 DOI: 10.1101/sqb.2013.78.020248] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA methylation in the form of 5-methylcytosine (5mC) is essential for normal development in mammals and influences a variety of biological processes, including transcriptional regulation, imprinting, and the maintenance of genomic stability. The recent discovery of TET proteins, which oxidize 5mC to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine, has changed our understanding of the process of DNA demethylation. Here, we summarize our current knowledge of the roles of DNA methylation and TET proteins in cell differentiation and function. The intensive research on this subject has so far focused primarily on embryonic stem (ES) cells and neurons. In addition, we summarize what is known about DNA methylation in T-cell function.
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Affiliation(s)
- Ageliki Tsagaratou
- La Jolla Institute for Allergy and Immunology, La Jolla, California 92037
| | - Anjana Rao
- La Jolla Institute for Allergy and Immunology, La Jolla, California 92037 Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0636 Sanford Consortium for Regenerative Medicine, La Jolla, California 92037
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464
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Chromatin modifiers and the promise of epigenetic therapy in acute leukemia. Leukemia 2014; 28:1396-406. [PMID: 24609046 DOI: 10.1038/leu.2014.94] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 02/04/2014] [Accepted: 02/14/2014] [Indexed: 12/31/2022]
Abstract
Hematopoiesis is a tightly regulated process involving the control of gene expression that directs the transition from hematopoietic stem and progenitor cells to terminally differentiated blood cells. In leukemia, the processes directing self-renewal, differentiation and progenitor cell expansion are disrupted, leading to the accumulation of immature, non-functioning malignant cells. Insights into these processes have come in stages, based on technological advances in genetic analyses, bioinformatics and biological sciences. The first cytogenetic studies of leukemic cells identified chromosomal translocations that generate oncogenic fusion proteins and most commonly affect regulators of transcription. This was followed by the discovery of recurrent somatic mutations in genes encoding regulators of the signal transduction pathways that control cell proliferation and survival. Recently, studies of global changes in methylation and gene expression have led to the understanding that the output of transcriptional regulators and the proliferative signaling pathways are ultimately influenced by chromatin structure. Candidate gene, whole-genome and whole-exome sequencing studies have identified recurrent somatic mutations in genes encoding epigenetic modifiers in both acute myeloid leukemia (AML) and acute lymphoid leukemia (ALL). In contrast to the two-hit model of leukemogenesis, emerging evidence suggests that these epigenetic modifiers represent a class of mutations that are critical to the development of leukemia and affect the regulation of various other oncogenic pathways. In this review, we discuss the range of recurrent, somatic mutations in epigenetic modifiers found in leukemia and how these modifiers relate to the classical leukemogenic pathways that lead to impaired cell differentiation and aberrant self-renewal and proliferation.
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465
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Gapp K, von Ziegler L, Tweedie-Cullen RY, Mansuy IM. Early life epigenetic programming and transmission of stress-induced traits in mammals. Bioessays 2014; 36:491-502. [DOI: 10.1002/bies.201300116] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Katharina Gapp
- Brain Research Institute; Medical Faculty of the University Zürich and Department of Health Science and Technology of the ETH Zürich, Neuroscience Center Zürich; Switzerland
| | - Lukas von Ziegler
- Brain Research Institute; Medical Faculty of the University Zürich and Department of Health Science and Technology of the ETH Zürich, Neuroscience Center Zürich; Switzerland
| | - Ry Yves Tweedie-Cullen
- Brain Research Institute; Medical Faculty of the University Zürich and Department of Health Science and Technology of the ETH Zürich, Neuroscience Center Zürich; Switzerland
| | - Isabelle M. Mansuy
- Brain Research Institute; Medical Faculty of the University Zürich and Department of Health Science and Technology of the ETH Zürich, Neuroscience Center Zürich; Switzerland
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466
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Abstract
Primordial germ cells (PGCs) are the precursors of sperm and eggs, which generate a new organism that is capable of creating endless new generations through germ cells. PGCs are specified during early mammalian postimplantation development, and are uniquely programmed for transmission of genetic and epigenetic information to subsequent generations. In this Primer, we summarise the establishment of the fundamental principles of PGC specification during early development and discuss how it is now possible to make mouse PGCs from pluripotent embryonic stem cells, and indeed somatic cells if they are first rendered pluripotent in culture.
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Affiliation(s)
- Erna Magnúsdóttir
- Wellcome Trust, Cancer Research UK, Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
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467
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Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming. Cell Stem Cell 2014; 14:512-22. [PMID: 24529596 DOI: 10.1016/j.stem.2014.01.001] [Citation(s) in RCA: 243] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 11/25/2013] [Accepted: 12/26/2013] [Indexed: 11/24/2022]
Abstract
Tet-mediated DNA oxidation is a recently identified mammalian epigenetic modification, and its functional role in cell-fate transitions remains poorly understood. Here, we derive mouse embryonic fibroblasts (MEFs) deleted in all three Tet genes and examine their capacity for reprogramming into induced pluripotent stem cells (iPSCs). We show that Tet-deficient MEFs cannot be reprogrammed because of a block in the mesenchymal-to-epithelial transition (MET) step. Reprogramming of MEFs deficient in TDG is similarly impaired. The block in reprogramming is caused at least in part by defective activation of key miRNAs, which depends on oxidative demethylation promoted by Tet and TDG. Reintroduction of either the affected miRNAs or catalytically active Tet and TDG restores reprogramming in the knockout MEFs. Thus, oxidative demethylation to promote gene activation appears to be functionally required for reprogramming of fibroblasts to pluripotency. These findings provide mechanistic insight into the role of epigenetic barriers in cell-lineage conversion.
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468
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Kelliher T, Walbot V. Maize germinal cell initials accommodate hypoxia and precociously express meiotic genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:639-52. [PMID: 24387628 PMCID: PMC3928636 DOI: 10.1111/tpj.12414] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/24/2013] [Accepted: 12/09/2013] [Indexed: 05/20/2023]
Abstract
In flowering plants, anthers are the site of de novo germinal cell specification, male meiosis, and pollen development. Atypically, anthers lack a meristem. Instead, both germinal and somatic cell types differentiate from floral stem cells packed into anther lobes. To better understand anther cell fate specification and to provide a resource for the reproductive biology community, we isolated cohorts of germinal and somatic initials from maize anthers within 36 h of fate acquisition, identifying 815 specific and 1714 significantly enriched germinal transcripts, plus 2439 specific and 2112 significantly enriched somatic transcripts. To clarify transcripts involved in cell differentiation, we contrasted these profiles to anther primordia prior to fate specification and to msca1 anthers arrested in the first step of fate specification and hence lacking normal cell types. The refined cell-specific profiles demonstrated that both germinal and somatic cell populations differentiate quickly and express unique transcription factor sets; a subset of transcript localizations was validated by in situ hybridization. Surprisingly, germinal initials starting 5 days of mitotic divisions were enriched significantly in >100 transcripts classified in meiotic processes that included recombination and synapsis, along with gene sets involved in RNA metabolism, redox homeostasis, and cytoplasmic ATP generation. Enrichment of meiotic-specific genes in germinal initials challenges current dogma that the mitotic to meiotic transition occurs later in development during pre-meiotic S phase. Expression of cytoplasmic energy generation genes suggests that male germinal cells accommodate hypoxia by diverting carbon away from mitochondrial respiration into alternative pathways that avoid producing reactive oxygen species (ROS).
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Affiliation(s)
- Timothy Kelliher
- Department of Biology, Stanford University, Stanford, CA 94305-5020, U.S.A
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, CA 94305-5020, U.S.A
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469
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Durruthy Durruthy J, Ramathal C, Sukhwani M, Fang F, Cui J, Orwig KE, Reijo Pera RA. Fate of induced pluripotent stem cells following transplantation to murine seminiferous tubules. Hum Mol Genet 2014; 23:3071-84. [PMID: 24449759 PMCID: PMC4030765 DOI: 10.1093/hmg/ddu012] [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] [Indexed: 12/12/2022] Open
Abstract
Studies of human germ cell development are limited in large part by inaccessibility of germ cells during development. Moreover, although several studies have reported differentiation of mouse and human germ cells from pluripotent stem cells (PSCs) in vitro, differentiation of human germ cells from PSCs in vivo has not been reported. Here, we tested whether mRNA reprogramming in combination with xeno-transplantation may provide a viable system to probe the genetics of human germ cell development via use of induced pluripotent stem cells (iPSCs). For this purpose, we derived integration-free iPSCs via mRNA-based reprogramming with OCT3/4, SOX2, KLF4 and cMYC alone (OSKM) or in combination with the germ cell-specific mRNA, VASA (OSKMV). All iPSC lines met classic criteria of pluripotency. Moreover, global gene expression profiling did not distinguish large differences between undifferentiated OSKM and OSKMV iPSCs; however, some differences were observed in expression of pluripotency factors and germ cell-specific genes, and in epigenetic profiles and in vitro differentiation studies. In contrast, transplantation of undifferentiated iPSCs directly into the seminiferous tubules of germ cell-depleted immunodeficient mice revealed divergent fates of iPSCs produced with different factors. Transplantation resulted in morphologically and immunohistochemically recognizable germ cells in vivo, particularly in the case of OSKMV cells. Significantly, OSKMV cells also did not form tumors while OSKM cells that remained outside the seminiferous tubule proliferated extensively and formed tumors. Results indicate that mRNA reprogramming in combination with transplantation may contribute to tools for genetic analysis of human germ cell development.
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Affiliation(s)
- Jens Durruthy Durruthy
- Department of Genetics and Department of Obstetrics and Gynecology, Institute for Stem Cell Biology and Regenerative Medicine, Center for Reproductive and Stem Cell Biology, Stanford University, Stanford, CA 94305, USA and
| | - Cyril Ramathal
- Department of Genetics and Department of Obstetrics and Gynecology, Institute for Stem Cell Biology and Regenerative Medicine, Center for Reproductive and Stem Cell Biology, Stanford University, Stanford, CA 94305, USA and
| | - Meena Sukhwani
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Magee-Womens Research Institute, Pittsburgh, PA 15213, USA
| | - Fang Fang
- Department of Genetics and Department of Obstetrics and Gynecology, Institute for Stem Cell Biology and Regenerative Medicine, Center for Reproductive and Stem Cell Biology, Stanford University, Stanford, CA 94305, USA and
| | - Jun Cui
- Department of Genetics and Department of Obstetrics and Gynecology, Institute for Stem Cell Biology and Regenerative Medicine, Center for Reproductive and Stem Cell Biology, Stanford University, Stanford, CA 94305, USA and
| | - Kyle E Orwig
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Magee-Womens Research Institute, Pittsburgh, PA 15213, USA
| | - Renee A Reijo Pera
- Department of Genetics and Department of Obstetrics and Gynecology, Institute for Stem Cell Biology and Regenerative Medicine, Center for Reproductive and Stem Cell Biology, Stanford University, Stanford, CA 94305, USA and
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470
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Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells. Proc Natl Acad Sci U S A 2014; 111:1361-6. [PMID: 24474761 DOI: 10.1073/pnas.1322921111] [Citation(s) in RCA: 194] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Dioxygenases of the Ten-Eleven Translocation (TET) family are 5-methylcytosine oxidases that convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidation products in DNA. We show that Tet1 and Tet2 have distinct roles in regulating 5hmC in mouse embryonic stem cells (mESC). Tet1 depletion diminishes 5hmC levels at transcription start sites (TSS), whereas Tet2 depletion is predominantly associated with decreased 5hmC in gene bodies. Enrichment of 5hmC is observed at the boundaries of exons that are highly expressed, and Tet2 depletion results in substantial loss of 5hmC at these boundaries. In contrast, at promoter/TSS regions, Tet2 depletion results in increased 5hmC, potentially because of the redundant activity of Tet1. Together, the data point to a complex interplay between Tet1 and Tet2 in mESC, and to distinct roles for these two proteins in regulating promoter, exon, and polyadenylation site usage in cells.
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471
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Kawasaki Y, Lee J, Matsuzawa A, Kohda T, Kaneko-Ishino T, Ishino F. Active DNA demethylation is required for complete imprint erasure in primordial germ cells. Sci Rep 2014; 4:3658. [PMID: 24413819 PMCID: PMC3888974 DOI: 10.1038/srep03658] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 12/16/2013] [Indexed: 01/23/2023] Open
Abstract
In mammalian primordial germ cells (PGCs), DNA demethylation is indispensible for parental imprint erasure, which is a reprogramming process essential for normal developmental potential. Thus, it is important to elucidate how DNA demethylation occurs in each imprinted region in PGCs and to determine which DNA demethylation pathway, passive or active, essentially contributes to the erasure of the imprint. Here, we report that active DNA demethylation via a putative Poly(ADP-ribose) polymerase (PARP) pathway is involved in H19-DMR imprint erasure in PGCs, as shown by an in vivo small molecule inhibitor assay. To the best of our knowledge, this is the first direct demonstration of a DNA replication-independent active DNA demethylation pathway in the erasure process of genomic imprinting in PGCs in vivo. The data also suggest that active DNA demethylation plays a significant role in the complete erasure of paternal imprinting in the female germ line.
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Affiliation(s)
- Yuki Kawasaki
- Department of Epigenetics, Medical Research Institute, Japan
- Global Center of Excellence Program for International Research Center for Molecular Science in Tooth and Bone Diseases, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
- These authors contributed equally to this work
| | - Jiyoung Lee
- Department of Epigenetics, Medical Research Institute, Japan
- Global Center of Excellence Program for International Research Center for Molecular Science in Tooth and Bone Diseases, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
- Japan Science and Technology Agency, PRESTO, Japan
- These authors contributed equally to this work
| | - Ayumi Matsuzawa
- Department of Epigenetics, Medical Research Institute, Japan
| | - Takashi Kohda
- Department of Epigenetics, Medical Research Institute, Japan
| | - Tomoko Kaneko-Ishino
- School of Health Sciences, Tokai University, Bohseidai, Isehara, Kanagawa 259-1193, Japan
| | - Fumitoshi Ishino
- Department of Epigenetics, Medical Research Institute, Japan
- Global Center of Excellence Program for International Research Center for Molecular Science in Tooth and Bone Diseases, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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472
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Stem Cell Epigenetics: Insights from Studies on Embryonic, Induced Pluripotent, and Germline Stem Cells. CURRENT PATHOBIOLOGY REPORTS 2014. [DOI: 10.1007/s40139-013-0038-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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473
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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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474
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Morris M, Rogers SM. Integrating phenotypic plasticity within an Ecological Genomics framework: recent insights from the genomics, evolution, ecology, and fitness of plasticity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 781:73-105. [PMID: 24277296 DOI: 10.1007/978-94-007-7347-9_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
E.B. Ford's 1964 book Ecological Genetics was a call for biologists to engage in multidisciplinary work in order to elucidate the link between genotype, phenotype, and fitness for ecologically relevant traits. In this review, we argue that the integration of an ecological genomics framework in studies of phenotypic plasticity is a promising approach to elucidate the causal links between genes and the environment, particularly during colonization of novel environments, environmental change, and speciation. This review highlights some of the questions and hypotheses generated from a mechanistic, evolutionary, and ecological perspective, in order to direct the continued and future use of genomic tools in the study of phenotypic plasticity.
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Affiliation(s)
- Matthew Morris
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada,
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475
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Wang CJR, Tseng CC. Recent advances in understanding of meiosis initiation and the apomictic pathway in plants. FRONTIERS IN PLANT SCIENCE 2014; 5:497. [PMID: 25295051 PMCID: PMC4171991 DOI: 10.3389/fpls.2014.00497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/08/2014] [Indexed: 05/21/2023]
Abstract
Meiosis, a specialized cell division to produce haploid cells, marks the transition from a sporophytic to a gametophytic generation in the life cycle of plants. In angiosperms, meiosis takes place in sporogenous cells that develop de novo from somatic cells in anthers or ovules. A successful transition from the mitotic cycle to the meiotic program in sporogenous cells is crucial for sexual reproduction. By contrast, when meiosis is bypassed or a mitosis-like division occurs to produce unreduced cells, followed by the development of an embryo sac, clonal seeds can be produced by apomixis, an asexual reproduction pathway found in 400 species of flowering plants. An understanding of the regulation of entry into meiosis and molecular mechanisms of apomictic pathway will provide vital insight into reproduction for plant breeding. Recent findings suggest that AM1/SWI1 may be the key gene for entry into meiosis, and increasing evidence has shown that the apomictic pathway is epigenetically controlled. However, the mechanism for the initiation of meiosis during sexual reproduction or for its omission in the apomictic pathway still remains largely unknown. Here we review the current understanding of meiosis initiation and the apomictic pathway and raised several questions that are awaiting further investigation.
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Affiliation(s)
- Chung-Ju R. Wang
- Institute of Plant and Microbial Biology, Academia Sinica, TaipeiTaiwan
- *Correspondence: Chung-Ju R. Wang, Institute of Plant and Microbial Biology, Academia Sinica, Room 120, Section 2, Academia Road, Taipei 11529, Taiwan e-mail:
| | - Ching-Chih Tseng
- Institute of Plant and Microbial Biology, Academia Sinica, TaipeiTaiwan
- Institute of Plant Biology, National Taiwan University, TaipeiTaiwan
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476
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Abstract
Epigenetic reprogramming of germ cells involves the genome-wide erasure and subsequent re-establishment of DNA methylation, along with reprogramming of histone modification profiles and the eventual incorporation of histone variants. These linked processes appear to be key for the establishment of the correct epigenetic regulation of this cell lineage. Mouse studies indicate that DNA demethylation may be initiated at E (embryonic day) 8 with rapid and substantial erasure occurring between E11.5 and E12.5. This is accompanied by a reduction in H3K9 dimethylation and an increase in H3K27 trimethylation. DNA remethylation subsequently occurs in late gestation in male germ cells and postnatally in female germ cells. This reprogramming occurs throughout the genome, with the exception of specific sequences. The conservation of this process across species remains largely undetermined, and, with recent discoveries of new DNA modifications, there is still much to be explored.
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477
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Lehle S, Hildebrand DG, Merz B, Malak PN, Becker MS, Schmezer P, Essmann F, Schulze-Osthoff K, Rothfuss O. LORD-Q: a long-run real-time PCR-based DNA-damage quantification method for nuclear and mitochondrial genome analysis. Nucleic Acids Res 2013; 42:e41. [PMID: 24371283 PMCID: PMC3973301 DOI: 10.1093/nar/gkt1349] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
DNA damage is tightly associated with various biological and pathological processes, such as aging and tumorigenesis. Although detection of DNA damage is attracting increasing attention, only a limited number of methods are available to quantify DNA lesions, and these techniques are tedious or only detect global DNA damage. In this study, we present a high-sensitivity long-run real-time PCR technique for DNA-damage quantification (LORD-Q) in both the mitochondrial and nuclear genome. While most conventional methods are of low-sensitivity or restricted to abundant mitochondrial DNA samples, we established a protocol that enables the accurate sequence-specific quantification of DNA damage in >3-kb probes for any mitochondrial or nuclear DNA sequence. In order to validate the sensitivity of this method, we compared LORD-Q with a previously published qPCR-based method and the standard single-cell gel electrophoresis assay, demonstrating a superior performance of LORD-Q. Exemplarily, we monitored induction of DNA damage and repair processes in human induced pluripotent stem cells and isogenic fibroblasts. Our results suggest that LORD-Q provides a sequence-specific and precise method to quantify DNA damage, thereby allowing the high-throughput assessment of DNA repair, genotoxicity screening and various other processes for a wide range of life science applications.
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Affiliation(s)
- Simon Lehle
- Interfaculty Institute for Biochemistry, Department of Molecular Medicine, University of Tübingen, 72076 Tübingen, Germany, Division of Immunogenetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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478
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Hackett JA, Dietmann S, Murakami K, Down TA, Leitch HG, Surani MA. Synergistic mechanisms of DNA demethylation during transition to ground-state pluripotency. Stem Cell Reports 2013; 1:518-31. [PMID: 24371807 PMCID: PMC3871394 DOI: 10.1016/j.stemcr.2013.11.010] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 11/25/2013] [Accepted: 11/25/2013] [Indexed: 11/16/2022] Open
Abstract
Pluripotent stem cells (PSCs) occupy a spectrum of reversible molecular states ranging from a naive ground-state in 2i, to metastable embryonic stem cells (ESCs) in serum, to lineage-primed epiblast stem cells (EpiSCs). To investigate the role of DNA methylation (5mC) across distinct pluripotent states, we mapped genome-wide 5mC and 5-hydroxymethycytosine (5hmC) in multiple PSCs. Ground-state ESCs exhibit an altered distribution of 5mC and 5hmC at regulatory elements and dramatically lower absolute levels relative to ESCs in serum. By contrast, EpiSCs exhibit increased promoter 5mC coupled with reduced 5hmC, which contributes to their developmental restriction. Switch to 2i triggers rapid onset of both the ground-state gene expression program and global DNA demethylation. Mechanistically, repression of de novo methylases by PRDM14 drives DNA demethylation at slow kinetics, whereas TET1/TET2-mediated 5hmC conversion enhances both the rate and extent of hypomethylation. These processes thus act synergistically during transition to ground-state pluripotency to promote a robust hypomethylated state.
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Affiliation(s)
- Jamie A Hackett
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK ; Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK ; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Sabine Dietmann
- Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - Kazuhiro Murakami
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK ; Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK ; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Thomas A Down
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Harry G Leitch
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK ; Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK
| | - M Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK ; Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK ; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
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479
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Okashita N, Kumaki Y, Ebi K, Nishi M, Okamoto Y, Nakayama M, Hashimoto S, Nakamura T, Sugasawa K, Kojima N, Takada T, Okano M, Seki Y. PRDM14 promotes active DNA demethylation through the ten-eleven translocation (TET)-mediated base excision repair pathway in embryonic stem cells. Development 2013; 141:269-80. [PMID: 24335252 DOI: 10.1242/dev.099622] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ten-eleven translocation (TET) proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). 5fC and 5caC can be excised and repaired by the base excision repair (BER) pathway, implicating 5mC oxidation in active DNA demethylation. Genome-wide DNA methylation is erased in the transition from metastable states to the ground state of embryonic stem cells (ESCs) and in migrating primordial germ cells (PGCs), although some resistant regions become demethylated only in gonadal PGCs. Understanding the mechanisms underlying global hypomethylation in naive ESCs and developing PGCs will be useful for realizing cellular pluripotency and totipotency. In this study, we found that PRDM14, the PR domain-containing transcriptional regulator, accelerates the TET-BER cycle, resulting in the promotion of active DNA demethylation in ESCs. Induction of Prdm14 expression transiently elevated 5hmC, followed by the reduction of 5mC at pluripotency-associated genes, germline-specific genes and imprinted loci, but not across the entire genome, which resembles the second wave of DNA demethylation observed in gonadal PGCs. PRDM14 physically interacts with TET1 and TET2 and enhances the recruitment of TET1 and TET2 at target loci. Knockdown of TET1 and TET2 impaired transcriptional regulation and DNA demethylation by PRDM14. The repression of the BER pathway by administration of pharmacological inhibitors of APE1 and PARP1 and the knockdown of thymine DNA glycosylase (TDG) also impaired DNA demethylation by PRDM14. Furthermore, DNA demethylation induced by PRDM14 takes place normally in the presence of aphidicolin, which is an inhibitor of G1/S progression. Together, our analysis provides mechanistic insight into DNA demethylation in naive pluripotent stem cells and developing PGCs.
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Affiliation(s)
- Naoki Okashita
- Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669-1337, Japan
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480
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Otani J, Kimura H, Sharif J, Endo TA, Mishima Y, Kawakami T, Koseki H, Shirakawa M, Suetake I, Tajima S. Cell cycle-dependent turnover of 5-hydroxymethyl cytosine in mouse embryonic stem cells. PLoS One 2013; 8:e82961. [PMID: 24340069 PMCID: PMC3858372 DOI: 10.1371/journal.pone.0082961] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 10/30/2013] [Indexed: 11/29/2022] Open
Abstract
Hydroxymethylcytosine in the genome is reported to be an intermediate of demethylation. In the present study, we demonstrated that maintenance methyltransferase Dnmt1 scarcely catalyzed hemi-hydroxymethylated DNA and that the hemi-hydroxymethylated DNA was not selectively recognized by the SRA domain of Uhrf1, indicating that hydroxymethylcytosine is diluted in a replication-dependent manner. A high level of 5-hydroxymethylcytosine in mouse embryonic stem cells was produced from the methylcytosine supplied mainly by de novo-type DNA methyltransferases Dnmt3a and Dnmt3b. The promoter regions of the HoxA gene cluster showed a high hydroxymethylation level whilst the methylcytosine level was quite low, suggesting that methylated CpG is actively hydroxylated during proliferation. All the results indicate that removal and production of hydroxymethylcytosine are regulated in replication-dependent manners in mouse embryonic stem cells.
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Affiliation(s)
- Junji Otani
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan
| | - Hironobu Kimura
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Jafar Sharif
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Takaho A. Endo
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Yuichi Mishima
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Toru Kawakami
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Masahiro Shirakawa
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Isao Suetake
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Shoji Tajima
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
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481
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Abstract
Genomic imprinting is an allele-specific gene expression system important for mammalian development and function 1. The molecular basis of genomic imprinting is allele-specific DNA methylation 1,2. While it is well known that the de novo DNA methyltransferases Dnmt3a/b are responsible for the establishment of genomic imprinting 3, how the methylation mark is erased during primordial germ cell (PGC) reprogramming remains a mystery. Tet1 is one of the ten-eleven translocation family proteins, which have the capacity to oxidize 5-methylcytosine (5mC) 4-6, specifically expressed in reprogramming PGCs 7. Here we report that Tet1 plays a critical role in the erasure of genomic imprinting. We show that despite their identical genotype, progenies derived from mating between Tet1-KO males and wild-type females exhibit a number of variable phenotypes including placental, fetal and postnatal growth defects, and early embryonic lethality. These defects are, at least in part, caused by the dysregulation of imprinted genes, such as Peg10 and Peg3, which exhibit aberrant hypermethylation in the paternal allele of differential methylated regions (DMRs). RNA-seq reveals extensive dysregulation of imprinted genes in the next generation due to paternal loss function of Tet1. Genome-wide DNA methylation analysis of E13.5 PGCs and sperms of Tet1-KO mice revealed hypermethylation of DMRs of imprinted genes in sperm, which can be traced back to PGCs. Analysis of the DNA methylation dynamics in reprogramming PGCs suggests that Tet1 functions to wipe out remaining methylation, including imprinted genes, at the late reprogramming stage. We further provide evidence supporting Tet1's role in the erasure of paternal imprints in female germline. Thus, our study establishes a critical function of Tet1 in genomic imprinting erasure.
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482
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Lercher L, McDonough MA, El-Sagheer AH, Thalhammer A, Kriaucionis S, Brown T, Schofield CJ. Structural insights into how 5-hydroxymethylation influences transcription factor binding. Chem Commun (Camb) 2013; 50:1794-6. [PMID: 24287551 DOI: 10.1039/c3cc48151d] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Transcription factor binding and high resolution crystallographic studies (1.3 Å) of Dickerson-Drew duplexes with cytosine, methylcytosine and hydroxymethylcytosine bases provide evidence that C-5 cytosine modifications could regulate transcription by context dependent effects on DNA transcription factor interactions.
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Affiliation(s)
- Lukas Lercher
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, Chemistry Research Laboratory, Oxford, UK.
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483
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Kristensen DG, Nielsen JE, Jørgensen A, Skakkebæk NE, Rajpert-De Meyts E, Almstrup K. Evidence that active demethylation mechanisms maintain the genome of carcinoma in situ cells hypomethylated in the adult testis. Br J Cancer 2013; 110:668-78. [PMID: 24292451 PMCID: PMC3915112 DOI: 10.1038/bjc.2013.727] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 10/18/2013] [Accepted: 10/23/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Developmental arrest of fetal germ cells may lead to neoplastic transformation and formation of germ cell tumours via carcinoma in situ (CIS) cells. Normal fetal germ cell development requires complete erasure and re-establishment of DNA methylation. In contrast to normal spermatogonia, the genome of CIS cells remains unmethylated in the adult testis. We here investigated the possible active and passive pathways that can sustain the CIS genome hypomethylated in the adult testis. METHODS The levels of 5-methyl-cytosine (5mC) and 5-hydroxy-methyl-cytosine (5hmC) in DNA from micro-dissected CIS cells were assessed by quantitative measurements. The expression of TET1, TET2, APOBEC1, MBD4, APEX1, PARP1, DNMT1, DNMT3A, DNMT3B and DNMT3L in adult testis specimens with CIS and in human fetal testis was investigated by immunohistochemistry and immunofluorescence. RESULTS DNA from micro-dissected CIS cells contained very low levels of 5hmC produced by ten eleven translocation (TET) enzymes. CIS cells and fetal germ cells expressed the suggested initiator of active demethylation, APOBEC1, and the base excision repair proteins MBD4, APEX1 and PARP1, whereas TETs - the alternative initiators were absent. Both maintenance and de novo methyltransferases were detected in CIS cells. CONCLUSION The data are consistent with the presence of an active DNA de-methylation pathway in CIS cells. The hypomethylated genome of CIS cells may contribute to phenotypic plasticity and invasive capabilities of this testicular cancer precursor.
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Affiliation(s)
- D G Kristensen
- University Department of Growth and Reproduction GR-5064, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - J E Nielsen
- University Department of Growth and Reproduction GR-5064, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - A Jørgensen
- University Department of Growth and Reproduction GR-5064, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - N E Skakkebæk
- University Department of Growth and Reproduction GR-5064, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - E Rajpert-De Meyts
- University Department of Growth and Reproduction GR-5064, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - K Almstrup
- University Department of Growth and Reproduction GR-5064, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
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484
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TET enzymes, TDG and the dynamics of DNA demethylation. Nature 2013; 502:472-9. [PMID: 24153300 DOI: 10.1038/nature12750] [Citation(s) in RCA: 1112] [Impact Index Per Article: 101.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 08/06/2013] [Indexed: 01/17/2023]
Abstract
DNA methylation has a profound impact on genome stability, transcription and development. Although enzymes that catalyse DNA methylation have been well characterized, those that are involved in methyl group removal have remained elusive, until recently. The transformative discovery that ten-eleven translocation (TET) family enzymes can oxidize 5-methylcytosine has greatly advanced our understanding of DNA demethylation. 5-Hydroxymethylcytosine is a key nexus in demethylation that can either be passively depleted through DNA replication or actively reverted to cytosine through iterative oxidation and thymine DNA glycosylase (TDG)-mediated base excision repair. Methylation, oxidation and repair now offer a model for a complete cycle of dynamic cytosine modification, with mounting evidence for its significance in the biological processes known to involve active demethylation.
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485
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Abstract
The mouse is the first species in which genomic imprinting was studied. Imprinting research in farm species has lagged behind owing to a lack of sequencing and genetic background information, as well as long generation intervals and high costs in tissue collection. Since the creation of Dolly, the first cloned mammal from an adult sheep, studies on genomic imprinting in domestic species have accelerated because animals from cloning and other assisted reproductive technologies exhibit phenotypes of imprinting disruptions. Although this review focuses on new developments in farm animals, most of the imprinting mechanism information was derived from the mouse.
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Affiliation(s)
- Xiuchun Cindy Tian
- Department of Animal Science, Center for Regenerative Biology, University of Connecticut, Storrs, Connecticut 06269-4163;
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486
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Abstract
The momentum of genomic science will carry it far into the future and into the heart of research on typical and atypical behavioral development. The purpose of this paper is to focus on a few implications and applications of these advances for understanding behavioral development. Quantitative genetics is genomic and will chart the course for molecular genomic research now that these two worlds of genetics are merging in the search for many genes of small effect. Although current attempts to identify specific genes have had limited success, known as the missing heritability problem, whole-genome sequencing will improve this situation by identifying all DNA sequence variations, including rare variants. Because the heritability of complex traits is caused by many DNA variants of small effect in the population, polygenic scores that are composites of hundreds or thousands of DNA variants will be used by developmentalists to predict children's genetic risk and resilience. The most far-reaching advance will be the widespread availability of whole-genome sequence for children, which means that developmentalists would no longer need to obtain DNA or to genotype children in order to use genomic information in research or in the clinic.
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Affiliation(s)
- Robert Plomin
- King’s College London, MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, De Crespigny Park, London, SE5 8AF, United Kingdom
| | - Michael A. Simpson
- King’s College London, Department of Medical and Molecular Genetics, London, SE1 9RT, United Kingdom
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487
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Guo H, Zhu P, Wu X, Li X, Wen L, Tang F. Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing. Genome Res 2013; 23:2126-35. [PMID: 24179143 PMCID: PMC3847781 DOI: 10.1101/gr.161679.113] [Citation(s) in RCA: 366] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
DNA methylation is crucial for a wide variety of biological processes, yet no technique suitable for the methylome analysis of DNA methylation at single-cell resolution is available. Here, we describe a methylome analysis technique that enables single-cell and single-base resolution DNA methylation analysis based on reduced representation bisulfite sequencing (scRRBS). The technique is highly sensitive and can detect the methylation status of up to 1.5 million CpG sites within the genome of an individual mouse embryonic stem cell (mESC). Moreover, we show that the technique can detect the methylation status of individual CpG sites in a haploid sperm cell in a digitized manner as either unmethylated or fully methylated. Furthermore, we show that the demethylation dynamics of maternal and paternal genomes after fertilization can be traced within the individual pronuclei of mouse zygotes. The demethylation process of the genic regions is faster than that of the intergenic regions in both male and female pronuclei. Our method paves the way for the exploration of the dynamic methylome landscapes of individual cells at single-base resolution during physiological processes such as embryonic development, or during pathological processes such as tumorigenesis.
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Affiliation(s)
- Hongshan Guo
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing 100871, China
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488
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Dias RP, Maher ER. Genes, assisted reproductive technology and trans-illumination. Epigenomics 2013; 5:331-40. [PMID: 23750647 DOI: 10.2217/epi.13.28] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Genomic imprinting is a parent-of-origin allele-specific epigenetic process that is critical for normal development and health. The establishment and maintenance of normal imprinting is dependent on both cis-acting imprinting control centers, which are marked by differentially (parental allele specific) methylated marks, and trans mechanisms, which regulate the establishment and/or maintenance of the correct methylation epigenotype at the imprinting control centers. Studies of rare human imprinting disorders such as familial hydatidiform mole, Beckwith-Wiedemann syndrome and familial transient neonatal diabetes mellitus have enabled the identification of genetic (e.g., mutations in KHDC3L [C6ORF221], NLRP2 [NALP2], NLRP7 [NALP7] and ZFP57) and environmental (assisted reproductive technologies) factors that can disturb the normal trans mechanisms for imprinting establishment and/or maintenance. Here we review the clinical and molecular aspects of these imprinting disorders in order to demonstrate how the study of rare inherited disorders can illuminate the molecular characteristics of fundamental epigenetic processes, such as genomic imprinting.
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Affiliation(s)
- Renuka P Dias
- Centre for Rare Diseases & Personalised Medicine, School of Clinical & Experimental Medicine, College of Medical & Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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489
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Apostolou E, Hochedlinger K. Chromatin dynamics during cellular reprogramming. Nature 2013; 502:462-71. [PMID: 24153299 PMCID: PMC4216318 DOI: 10.1038/nature12749] [Citation(s) in RCA: 290] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 08/05/2013] [Indexed: 12/13/2022]
Abstract
Induced pluripotency is a powerful tool to derive patient-specific stem cells. In addition, it provides a unique assay to study the interplay between transcription factors and chromatin structure. Here, we review the latest insights into chromatin dynamics that are inherent to induced pluripotency. Moreover, we compare and contrast these events with other physiological and pathological processes that involve changes in chromatin and cell state, including germ cell maturation and tumorigenesis. We propose that an integrated view of these seemingly diverse processes could provide mechanistic insights into cell fate transitions in general and might lead to new approaches in regenerative medicine and cancer treatment.
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Affiliation(s)
- Effie Apostolou
- Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine; Harvard Stem Cell Institute, 185 Cambridge Street, Boston, MA 02114, USA
- Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Medical School, 7 Divinity Avenue, Cambridge, MA 02138, USA
| | - Konrad Hochedlinger
- Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine; Harvard Stem Cell Institute, 185 Cambridge Street, Boston, MA 02114, USA
- Howard Hughes Medical Institute and Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Medical School, 7 Divinity Avenue, Cambridge, MA 02138, USA
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490
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Benyshek DC. The “early life” origins of obesity-related health disorders: New discoveries regarding the intergenerational transmission of developmentally programmed traits in the global cardiometabolic health crisis. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2013; 152 Suppl 57:79-93. [DOI: 10.1002/ajpa.22393] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 09/17/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Daniel C. Benyshek
- Department of Anthropology, University of Nevada; Las Vegas Las Vegas, NV 89154-5003
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491
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Fan A, Ma K, An X, Ding Y, An P, Song G, Tang L, Zhang S, Zhang P, Tan W, Tang B, Zhang X, Li Z. Effects of TET1 knockdown on gene expression and DNA methylation in porcine induced pluripotent stem cells. Reproduction 2013; 146:569-79. [PMID: 24051058 DOI: 10.1530/rep-13-0212] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
TET1 is implicated in maintaining the pluripotency of embryonic stem cells. However, its precise effects on induced pluripotent stem cells (iPSCs), and particularly on porcine iPSCs (piPSCs), are not well defined. To investigate the role of TET1 in the pluripotency and differentiation of piPSCs, piPSCs were induced from porcine embryonic fibroblasts by overexpression of POU5F1 (OCT4), SOX2, KLF4, and MYC (C-MYC). siRNAs targeting to TET1 were used to transiently knockdown the expression of TET1 in piPSCs. Morphological abnormalities and loss of the undifferentiated state of piPSCs were observed in the piPSCs after the downregulation of TET1. The effects of TET1 knockdown on the expression of key stem cell factors and differentiation markers were analyzed to gain insights into the molecular mechanisms underlying the phenomenon. The results revealed that knockdown of TET1 resulted in the downregulated expression of pluripotency-related genes, such as LEFTY2, KLF2, and SOX2, and the upregulated expression of differentiation-related genes including PITX2, HAND1, GATA6, and LEF1. However, POU5F1, MYC, KLF4, and NANOG were actually not downregulated. Further analysis showed that the methylation levels of the promoters for POU5F1 and MYC increased significantly after TET1 downregulation, whereas there were no obvious changes in the promoters of SOX2, KLF4, and NANOG. The methylation of the whole genome increased, while hydroxymethylation slightly declined. Taken together, these results suggest that TET1 may play important roles in the self-renewal of piPSCs and the maintenance of their characteristics by regulating the expression of genes and the DNA methylation.
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Affiliation(s)
- Anran Fan
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, The Center for Animal Embryo Engineering of Jilin Province, College of Veterinary Medicine
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492
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MicroRNA-26a targets ten eleven translocation enzymes and is regulated during pancreatic cell differentiation. Proc Natl Acad Sci U S A 2013; 110:17892-7. [PMID: 24114270 DOI: 10.1073/pnas.1317397110] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Ten eleven translocation (TET) enzymes (TET1/TET2/TET3) and thymine DNA glycosylase (TDG) play crucial roles in early embryonic and germ cell development by mediating DNA demethylation. However, the molecular mechanisms that regulate TETs/TDG expression and their role in cellular differentiation, including that of the pancreas, are not known. Here, we report that (i) TET1/2/3 and TDG can be direct targets of the microRNA miR-26a, (ii) murine TETs, especially TET2 and TDG, are down-regulated in islets during postnatal differentiation, whereas miR-26a is up-regulated, (iii) changes in 5-hydroxymethylcytosine accompany changes in TET mRNA levels, (iv) these changes in mRNA and 5-hydroxymethylcytosine are also seen in an in vitro differentiation system initiated with FACS-sorted adult ductal progenitor-like cells, and (v) overexpression of miR-26a in mice increases postnatal islet cell number in vivo and endocrine/acinar colonies in vitro. These results establish a previously unknown link between miRNAs and TET expression levels, and suggest a potential role for miR-26a and TET family proteins in pancreatic cell differentiation.
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493
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Getting rid of DNA methylation. Trends Cell Biol 2013; 24:136-43. [PMID: 24119665 DOI: 10.1016/j.tcb.2013.09.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/03/2013] [Accepted: 09/04/2013] [Indexed: 11/22/2022]
Abstract
Methylation of cytosine within DNA is associated with transcriptional repression and genome surveillance. In plants and animals, conserved pathways exist to establish and maintain this epigenetic mark. Mechanisms underlining its removal are, however, diverse and controversial and can depend on DNA synthesis (passive) or be independent of it (active). Ten-eleven translocation (Tet)-mediated conversion of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has recently been evoked as a possible mechanism in the initiation of active and passive DNA demethylation. This review discuses the recent progress in this exciting area.
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494
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495
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Veerappan CS, Sleiman S, Coppola G. Epigenetics of Alzheimer's disease and frontotemporal dementia. Neurotherapeutics 2013; 10:709-21. [PMID: 24150812 PMCID: PMC3805876 DOI: 10.1007/s13311-013-0219-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This article will review the recent advances in the understanding of the role of epigenetic modifications and the promise of future epigenetic therapy in neurodegenerative dementias, including Alzheimer's disease and frontotemporal dementia.
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Affiliation(s)
- Chendhore S Veerappan
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA,
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496
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Bogdanovi O, Gomez-Skarmeta JL. Embryonic DNA methylation: insights from the genomics era. Brief Funct Genomics 2013; 13:121-30. [DOI: 10.1093/bfgp/elt039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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497
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Dunwell TL, McGuffin LJ, Dunwell JM, Pfeifer GP. The mysterious presence of a 5-methylcytosine oxidase in the Drosophila genome: possible explanations. Cell Cycle 2013; 12:3357-65. [PMID: 24091536 DOI: 10.4161/cc.26540] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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498
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A set of genes critical to development is epigenetically poised in mouse germ cells from fetal stages through completion of meiosis. Proc Natl Acad Sci U S A 2013; 110:16061-6. [PMID: 24043772 DOI: 10.1073/pnas.1315204110] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In multicellular organisms, germ cells carry the hereditary material from one generation to the next. Developing germ cells are unipotent gamete precursors, and mature gametes are highly differentiated, specialized cells. However, upon gamete union at fertilization, their genomes drive a totipotent program, giving rise to a complete embryo as well as extraembryonic tissues. The biochemical basis for the ability to transition from differentiated cell to totipotent zygote is unknown. Here we report that a set of developmentally critical genes is maintained in an epigenetically poised (bivalent) state from embryonic stages through the end of meiosis. We performed ChIP-seq and RNA-seq analysis on flow-sorted male and female germ cells during embryogenesis at three time points surrounding sexual differentiation and female meiotic initiation, and then extended our analysis to meiotic and postmeiotic male germ cells. We identified a set of genes that is highly enriched for regulators of differentiation and retains a poised state (high H3K4me3, high H3K27me3, and lack of expression) across sexes and across developmental stages, including in haploid postmeiotic cells. The existence of such a state in embryonic stem cells has been well described. We now demonstrate that a subset of genes is maintained in a poised state in the germ line from the initiation of sexual differentiation during fetal development and into postmeiotic stages. We propose that the epigenetically poised condition of these developmental genes is a fundamental property of the mammalian germ-line nucleus, allowing differentiated gametes to unleash a totipotent program following fertilization.
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499
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Cadet J, Wagner JR. TET enzymatic oxidation of 5-methylcytosine, 5-hydroxymethylcytosine and 5-formylcytosine. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2013; 764-765:18-35. [PMID: 24045206 DOI: 10.1016/j.mrgentox.2013.09.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 09/04/2013] [Indexed: 12/14/2022]
Abstract
5-Methylcytosine and methylated histones have been considered for a long time as stable epigenetic marks of chromatin involved in gene regulation. This concept has been recently revisited with the detection of large amounts of 5-hydroxymethylcytosine, now considered as the sixth DNA base, in mouse embryonic stem cells, Purkinje neurons and brain tissues. The dioxygenases that belong to the ten eleven translocation (TET) oxygenase family have been shown to initiate the formation of this methyl oxidation product of 5-methylcytosine that is also generated although far less efficiently by radical reactions involving hydroxyl radical and one-electron oxidants. It was found as additional striking data that iterative TET-mediated oxidation of 5-hydroxymethylcytosine gives rise to 5-formylcytosine and 5-carboxylcytosine. This survey focuses on chemical and biochemical aspects of the enzymatic oxidation reactions of 5-methylcytosine that are likely to be involved in active demethylation pathways through the implication of enzymatic deamination of 5-methylcytosine oxidation products and/or several base excision repair enzymes. The high biological relevance of the latter modified bases explains why major efforts have been devoted to the design of a broad range of assays aimed at measuring globally or at the single base resolution, 5-hydroxymethylcytosine and the two other oxidation products in the DNA of cells and tissues. Another critical issue that is addressed in this review article deals with the assessment of the possible role of 5-methylcytosine oxidation products, when present in elevated amounts in cellular DNA, in terms of mutagenesis and interference with key cellular enzymes including DNA and RNA polymerases.
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Affiliation(s)
- Jean Cadet
- Direction des Sciences de la Matière, Institut Nanosciences et Cryogénie, CEA/Grenoble, 38054 Grenoble, France; Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Québec JIH 5N4, Canada.
| | - J Richard Wagner
- Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Québec JIH 5N4, Canada.
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500
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Ficz G, Hore T, Santos F, Lee H, Dean W, Arand J, Krueger F, Oxley D, Paul YL, Walter J, Cook S, Andrews S, Branco M, Reik W. FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency. Cell Stem Cell 2013; 13:351-9. [PMID: 23850245 PMCID: PMC3765959 DOI: 10.1016/j.stem.2013.06.004] [Citation(s) in RCA: 314] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/05/2013] [Accepted: 06/07/2013] [Indexed: 01/30/2023]
Abstract
Genome-wide erasure of DNA methylation takes place in primordial germ cells (PGCs) and early embryos and is linked with pluripotency. Inhibition of Erk1/2 and Gsk3β signaling in mouse embryonic stem cells (ESCs) by small-molecule inhibitors (called 2i) has recently been shown to induce hypomethylation. We show by whole-genome bisulphite sequencing that 2i induces rapid and genome-wide demethylation on a scale and pattern similar to that in migratory PGCs and early embryos. Major satellites, intracisternal A particles (IAPs), and imprinted genes remain relatively resistant to erasure. Demethylation involves oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), impaired maintenance of 5mC and 5hmC, and repression of the de novo methyltransferases (Dnmt3a and Dnmt3b) and Dnmt3L. We identify a Prdm14- and Nanog-binding cis-acting regulatory region in Dnmt3b that is highly responsive to signaling. These insights provide a framework for understanding how signaling pathways regulate reprogramming to an epigenetic ground state of pluripotency.
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Affiliation(s)
- Gabriella Ficz
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Timothy A. Hore
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Fátima Santos
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Heather J. Lee
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Wendy Dean
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Julia Arand
- Department of Biological Sciences, Institute of Genetics/Epigenetics, University of Saarland, 66123 Saarbrücken, Germany
| | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - David Oxley
- Proteomics Research Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Yu-Lee Paul
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Jörn Walter
- Department of Biological Sciences, Institute of Genetics/Epigenetics, University of Saarland, 66123 Saarbrücken, Germany
| | - Simon J. Cook
- Signalling Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Miguel R. Branco
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
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