101
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Lee CW, Huang WC, Huang HD, Huang YH, Ho JH, Yang MH, Yang VW, Lee OK. DNA Methyltransferases Modulate Hepatogenic Lineage Plasticity of Mesenchymal Stromal Cells. Stem Cell Reports 2017; 9:247-263. [PMID: 28602611 PMCID: PMC5511371 DOI: 10.1016/j.stemcr.2017.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 12/20/2022] Open
Abstract
The irreversibility of developmental processes in mammalian cells has been challenged by rising evidence that de-differentiation of hepatocytes occurs in adult liver. However, whether reversibility exists in mesenchymal stromal cell (MSC)-derived hepatocytes (dHeps) remains elusive. In this study, we find that hepatogenic differentiation (HD) of MSCs is a reversible process and is modulated by DNA methyltransferases (DNMTs). DNMTs are regulated by transforming growth factor β1 (TGFβ1), which in turn controls hepatogenic differentiation and de-differentiation. In addition, a stepwise reduction in TGFβ1 concentrations in culture media increases DNMT1 and decreases DNMT3 in primary hepatocytes (Heps) and confers Heps with multi-differentiation potentials similarly to MSCs. Hepatic lineage reversibility of MSCs and lineage conversion of Heps are regulated by DNMTs in response to TGFβ1. This previously unrecognized TGFβ1-DNMTs-MSC-HD axis may further increase the understanding the normal and pathological processes in the liver, as well as functions of MSCs after transplantation to treat liver diseases.
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Affiliation(s)
- Chien-Wei Lee
- Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei 11221, Taiwan; Institute of Clinical Medicine, National Yang-Ming University, Taipei 11221, Taiwan
| | - Wei-Chih Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu 30010, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu 30010, Taiwan; Department of Biological Science and Technology, National Chiao Tung University, HsinChu 30010, Taiwan; Center for Bioinformatics Research, National Chiao Tung University, HsinChu 30010, Taiwan; Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yi-Hsiang Huang
- Division of Gastroenterology, Department of Medicine, Taipei Veterans General Hospital, Taipei 11221, Taiwan
| | - Jennifer H Ho
- Center for Stem Cell Research, Taipei Medical University-Wan Fang Hospital, Taipei 11031, Taiwan
| | - Muh-Hwa Yang
- Institute of Biotechnology in Medicine, National Yang-Ming University, Taipei 11221, Taiwan; Genome Research Center, National Yang-Ming University, Taipei 11221, Taiwan; Immunity and Inflammation Research Center, National Yang-Ming University, Taipei 11221, Taiwan; Division of Hematology and Oncology, Department of Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan; Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Vincent W Yang
- Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Oscar K Lee
- Taipei City Hospital, Taipei 10341, Taiwan; Institute of Clinical Medicine, National Yang-Ming University, Taipei 11221, Taiwan; Stem Cell Research Center, National Yang-Ming University, Taipei 11221, Taiwan; Department of Medical Research, Taipei Veterans General Hospital, Taipei 11221, Taiwan.
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102
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Teissandier A, Bourc'his D. Gene body DNA methylation conspires with H3K36me3 to preclude aberrant transcription. EMBO J 2017; 36:1471-1473. [PMID: 28442531 DOI: 10.15252/embj.201796812] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Aurélie Teissandier
- "Epigenetic Decisions and Reproduction" Group, Institut Curie, PSL University, CNRS, INSERM, Paris, France
| | - Déborah Bourc'his
- "Epigenetic Decisions and Reproduction" Group, Institut Curie, PSL University, CNRS, INSERM, Paris, France
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103
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Rinaldi L, Avgustinova A, Martín M, Datta D, Solanas G, Prats N, Benitah SA. Loss of Dnmt3a and Dnmt3b does not affect epidermal homeostasis but promotes squamous transformation through PPAR-γ. eLife 2017; 6:e21697. [PMID: 28425913 PMCID: PMC5429093 DOI: 10.7554/elife.21697] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 04/13/2017] [Indexed: 12/12/2022] Open
Abstract
The DNA methyltransferase Dnmt3a suppresses tumorigenesis in models of leukemia and lung cancer. Conversely, deregulation of Dnmt3b is thought to generally promote tumorigenesis. However, the role of Dnmt3a and Dnmt3b in many types of cancer remains undefined. Here, we show that Dnmt3a and Dnmt3b are dispensable for homeostasis of the murine epidermis. However, loss of Dnmt3a-but not Dnmt3b-increases the number of carcinogen-induced squamous tumors, without affecting tumor progression. Only upon combined deletion of Dnmt3a and Dnmt3b, squamous carcinomas become more aggressive and metastatic. Mechanistically, Dnmt3a promotes the expression of epidermal differentiation genes by interacting with their enhancers and inhibits the expression of lipid metabolism genes, including PPAR-γ, by directly methylating their promoters. Importantly, inhibition of PPAR-γ partially prevents the increase in tumorigenesis upon deletion of Dnmt3a. Altogether, we demonstrate that Dnmt3a and Dnmt3b protect the epidermis from tumorigenesis and that squamous carcinomas are sensitive to inhibition of PPAR-γ.
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Affiliation(s)
- Lorenzo Rinaldi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Alexandra Avgustinova
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Mercè Martín
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Debayan Datta
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Guiomar Solanas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Neus Prats
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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104
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Rwigemera A, Joao F, Delbes G. Fetal testis organ culture reproduces the dynamics of epigenetic reprogramming in rat gonocytes. Epigenetics Chromatin 2017; 10:19. [PMID: 28413450 PMCID: PMC5387332 DOI: 10.1186/s13072-017-0127-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/05/2017] [Indexed: 12/16/2022] Open
Abstract
Background Epigenetic reprogramming is a critical step in male germ cell development that occurs during perinatal life. It is characterized by the remodeling of different epigenetic marks such as DNA methylation (5mC) and methylation of histone H3. It has been suggested that endocrine disruptors can affect the male germline epigenome by altering epigenetic reprogramming, but the mechanisms involved are still unknown. We have previously used an organ culture system that maintains the development of the different fetal testis cell types, to evaluate the effects of various endocrine disruptors on gametogenesis and steroidogenesis in the rat. We hypothesize that this culture model can reproduce the epigenetic reprogramming in gonocytes. Our aim was to establish the kinetics of three epigenetic marks throughout perinatal development in rats in vivo and compare them after different culture times. Results Using immunofluorescence, we showed that H3K4me2 transiently increased in gonocytes at 18.5 days post-coitum (dpc), while H3K4me3 displayed a stable increase in gonocytes from 18.5 dpc until after birth. 5mC progressively increased from 20.5 dpc until after birth. Using GFP-positive gonocytes purified from GCS-EGFP rats, we established the chronology of re-methylation of H19 and Snrpn in rat gonocytes. Most importantly, using testis explanted at 16.5 or 18.5 dpc and cultured for 2–4 days, we demonstrated that the kinetics of changes in H3K4me2, H3K4me3, global DNA methylation and on parental imprints can generally be reproduced ex vivo with the model of organ culture without the addition of serum. Conclusions This study reveals the chronology of three epigenetic marks (H3K4me2, H3K4me3 and 5mC) and the patterns of methylation of H19 and Snrpn differentially methylated regions in rat gonocytes during perinatal development. Most importantly, our results suggest that the organ culture can reproduce the process of epigenetic reprogramming and can be used to study the impact of environmental chemicals on the establishment of the male germ cell epigenome. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0127-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Arlette Rwigemera
- Institut National de la Recherche Scientifique, Centre INRS - Institut Armand-Frappier, 531, boulevard des Prairies, Laval, QC H7V 1B7 Canada
| | - Fabien Joao
- Institut National de la Recherche Scientifique, Centre INRS - Institut Armand-Frappier, 531, boulevard des Prairies, Laval, QC H7V 1B7 Canada
| | - Geraldine Delbes
- Institut National de la Recherche Scientifique, Centre INRS - Institut Armand-Frappier, 531, boulevard des Prairies, Laval, QC H7V 1B7 Canada
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105
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Shaping the cellular landscape with Set2/SETD2 methylation. Cell Mol Life Sci 2017; 74:3317-3334. [PMID: 28386724 DOI: 10.1007/s00018-017-2517-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/24/2017] [Accepted: 03/28/2017] [Indexed: 12/15/2022]
Abstract
Chromatin structure is a major barrier to gene transcription that must be disrupted and re-set during each round of transcription. Central to this process is the Set2/SETD2 methyltransferase that mediates co-transcriptional methylation to histone H3 at lysine 36 (H3K36me). Studies reveal that H3K36me not only prevents inappropriate transcriptional initiation from arising within gene bodies, but that it has other conserved functions that include the repair of damaged DNA and regulation of pre-mRNA splicing. Consistent with the importance of Set2/SETD2 in chromatin biology, mutations of SETD2, or mutations at or near H3K36 in H3.3, have recently been found to underlie cancer development. This review will summarize the latest insights into the functions of Set2/SETD2 in genome regulation and cancer development.
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106
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Neri F, Rapelli S, Krepelova A, Incarnato D, Parlato C, Basile G, Maldotti M, Anselmi F, Oliviero S. Intragenic DNA methylation prevents spurious transcription initiation. Nature 2017; 543:72-77. [PMID: 28225755 DOI: 10.1038/nature21373] [Citation(s) in RCA: 463] [Impact Index Per Article: 66.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/05/2017] [Indexed: 12/12/2022]
Abstract
In mammals, DNA methylation occurs mainly at CpG dinucleotides. Methylation of the promoter suppresses gene expression, but the functional role of gene-body DNA methylation in highly expressed genes has yet to be clarified. Here we show that, in mouse embryonic stem cells, Dnmt3b-dependent intragenic DNA methylation protects the gene body from spurious RNA polymerase II entry and cryptic transcription initiation. Using different genome-wide approaches, we demonstrate that this Dnmt3b function is dependent on its enzymatic activity and recruitment to the gene body by H3K36me3. Furthermore, the spurious transcripts can either be degraded by the RNA exosome complex or capped, polyadenylated, and delivered to the ribosome to produce aberrant proteins. Elongating RNA polymerase II therefore triggers an epigenetic crosstalk mechanism that involves SetD2, H3K36me3, Dnmt3b and DNA methylation to ensure the fidelity of gene transcription initiation, with implications for intragenic hypomethylation in cancer.
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Affiliation(s)
- Francesco Neri
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Stefania Rapelli
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Anna Krepelova
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Danny Incarnato
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Caterina Parlato
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Giulia Basile
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Mara Maldotti
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Francesca Anselmi
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
| | - Salvatore Oliviero
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, via Accademia Albertina 13, 10123 Torino, Italy
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107
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Rinaldi L, Datta D, Serrat J, Morey L, Solanas G, Avgustinova A, Blanco E, Pons JI, Matallanas D, Von Kriegsheim A, Di Croce L, Benitah SA. Dnmt3a and Dnmt3b Associate with Enhancers to Regulate Human Epidermal Stem Cell Homeostasis. Cell Stem Cell 2016; 19:491-501. [PMID: 27476967 DOI: 10.1016/j.stem.2016.06.020] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/25/2016] [Accepted: 06/29/2016] [Indexed: 12/22/2022]
Abstract
The genome-wide localization and function of endogenous Dnmt3a and Dnmt3b in adult stem cells are unknown. Here, we show that in human epidermal stem cells, the two proteins bind in a histone H3K36me3-dependent manner to the most active enhancers and are required to produce their associated enhancer RNAs. Both proteins prefer super-enhancers associated to genes that either define the ectodermal lineage or establish the stem cell and differentiated states. However, Dnmt3a and Dnmt3b differ in their mechanisms of enhancer regulation: Dnmt3a associates with p63 to maintain high levels of DNA hydroxymethylation at the center of enhancers in a Tet2-dependent manner, whereas Dnmt3b promotes DNA methylation along the body of the enhancer. Depletion of either protein inactivates their target enhancers and profoundly affects epidermal stem cell function. Altogether, we reveal novel functions for Dnmt3a and Dnmt3b at enhancers that could contribute to their roles in disease and tumorigenesis.
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Affiliation(s)
- Lorenzo Rinaldi
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain.
| | - Debayan Datta
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Judit Serrat
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Lluis Morey
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Guiomar Solanas
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Alexandra Avgustinova
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain
| | - José Ignacio Pons
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - David Matallanas
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Alex Von Kriegsheim
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
| | - Luciano Di Croce
- ICREA, Passeig de Lluís Companys 23, 08010 Barcelona, Spain; Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Doctor Aiguader 88, 08003 Barcelona, Spain.
| | - Salvador Aznar Benitah
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; ICREA, Passeig de Lluís Companys 23, 08010 Barcelona, Spain.
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108
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Abstract
Epigenetic modifications established during gametogenesis regulate transcription and other nuclear processes in gametes, but also have influences in the zygote, embryo and postnatal life. This is best understood for DNA methylation which, established at discrete regions of the oocyte and sperm genomes, governs genomic imprinting. In this review, we describe how imprinting has informed our understanding of de novo DNA methylation mechanisms, highlight how recent genome-wide profiling studies have provided unprecedented insights into establishment of the sperm and oocyte methylomes and consider the fate and function of gametic methylation and other epigenetic modifications after fertilization.
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Affiliation(s)
- Kathleen R Stewart
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.,Biotech Research & Innovation Centre (BRIC), University of Copenhagen, DK2200 Copenhagen, Denmark
| | - Lenka Veselovska
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.,Laboratory of Developmental Biology & Genetics, Department of Molecular Biology, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
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109
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Long HK, King HW, Patient RK, Odom DT, Klose RJ. Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved. Nucleic Acids Res 2016; 44:6693-706. [PMID: 27084945 PMCID: PMC5001583 DOI: 10.1093/nar/gkw258] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/09/2016] [Accepted: 04/01/2016] [Indexed: 12/19/2022] Open
Abstract
DNA methylation is a repressive epigenetic modification that covers vertebrate genomes. Regions known as CpG islands (CGIs), which are refractory to DNA methylation, are often associated with gene promoters and play central roles in gene regulation. Yet how CGIs in their normal genomic context evade the DNA methylation machinery and whether these mechanisms are evolutionarily conserved remains enigmatic. To address these fundamental questions we exploited a transchromosomic animal model and genomic approaches to understand how the hypomethylated state is formed in vivo and to discover whether mechanisms governing CGI formation are evolutionarily conserved. Strikingly, insertion of a human chromosome into mouse revealed that promoter-associated CGIs are refractory to DNA methylation regardless of host species, demonstrating that DNA sequence plays a central role in specifying the hypomethylated state through evolutionarily conserved mechanisms. In contrast, elements distal to gene promoters exhibited more variable methylation between host species, uncovering a widespread dependence on nucleotide frequency and occupancy of DNA-binding transcription factors in shaping the DNA methylation landscape away from gene promoters. This was exemplified by young CpG rich lineage-restricted repeat sequences that evaded DNA methylation in the absence of co-evolved mechanisms targeting methylation to these sequences, and species specific DNA binding events that protected against DNA methylation in CpG poor regions. Finally, transplantation of mouse chromosomal fragments into the evolutionarily distant zebrafish uncovered the existence of a mechanistically conserved and DNA-encoded logic which shapes CGI formation across vertebrate species.
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Affiliation(s)
- Hannah K Long
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Hamish W King
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Roger K Patient
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
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110
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Jeltsch A, Jurkowska RZ. Allosteric control of mammalian DNA methyltransferases - a new regulatory paradigm. Nucleic Acids Res 2016; 44:8556-8575. [PMID: 27521372 PMCID: PMC5062992 DOI: 10.1093/nar/gkw723] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 08/08/2016] [Indexed: 12/23/2022] Open
Abstract
In mammals, DNA methylation is introduced by the DNMT1, DNMT3A and DNMT3B methyltransferases, which are all large multi-domain proteins containing a catalytic C-terminal domain and an N-terminal part with regulatory functions. Recently, two novel regulatory principles of DNMTs were uncovered. It was shown that their catalytic activity is under allosteric control of N-terminal domains with autoinhibitory function, the RFT and CXXC domains in DNMT1 and the ADD domain in DNMT3. Moreover, targeting and activity of DNMTs were found to be regulated in a concerted manner by interactors and posttranslational modifications (PTMs). In this review, we describe the structures and domain composition of the DNMT1 and DNMT3 enzymes, their DNA binding, catalytic mechanism, multimerization and the processes controlling their stability in cells with a focus on their regulation and chromatin targeting by PTMs, interactors and chromatin modifications. We propose that the allosteric regulation of DNMTs by autoinhibitory domains acts as a general switch for the modulation of the function of DNMTs, providing numerous possibilities for interacting proteins, nucleic acids or PTMs to regulate DNMT activity and targeting. The combined regulation of DNMT targeting and catalytic activity contributes to the precise spatiotemporal control of DNMT function and genome methylation in cells.
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Affiliation(s)
- Albert Jeltsch
- Institute of Biochemistry, Pfaffenwaldring 55, Faculty of Chemistry, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Renata Z Jurkowska
- BioMed X Innovation Center, Im Neuenheimer Feld 583, D-69120 Heidelberg, Germany
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111
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Rondelet G, Dal Maso T, Willems L, Wouters J. Structural basis for recognition of histone H3K36me3 nucleosome by human de novo DNA methyltransferases 3A and 3B. J Struct Biol 2016; 194:357-67. [PMID: 26993463 DOI: 10.1016/j.jsb.2016.03.013] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/14/2016] [Accepted: 03/15/2016] [Indexed: 01/01/2023]
Abstract
DNA methylation is an important epigenetic modification involved in chromatin organization and gene expression. The function of DNA methylation depends on cell context and is correlated with histone modification patterns. In particular, trimethylation of Lys36 on histone H3 tail (H3K36me3) is associated with DNA methylation and elongation phase of transcription. PWWP domains of the de novo DNA methyltransferases DNMT3A and DNMT3B read this epigenetic mark to guide DNA methylation. Here we report the first crystal structure of the DNMT3B PWWP domain-H3K36me3 complex. Based on this structure, we propose a model of the DNMT3A PWWP domain-H3K36me3 complex and build a model of DNMT3A (PWWP-ADD-CD) in a nucleosomal context. The trimethylated side chain of Lys36 (H3K36me3) is inserted into an aromatic cage similar to the "Royal" superfamily domains known to bind methylated histones. A key interaction between trimethylated Lys36 and a conserved water molecule stabilized by Ser270 explains the lack of affinity of mutated DNMT3B (S270P) for the H3K36me3 epigenetic mark in the ICF (Immunodeficiency, Centromeric instability and Facial abnormalities) syndrome. The model of the DNMT3A-DNMT3L heterotetramer in complex with a dinucleosome highlights the mechanism for recognition of nucleosome by DNMT3s and explains the periodicity of de novo DNA methylation.
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Affiliation(s)
- Grégoire Rondelet
- Department of Chemistry, University of Namur, 61 rue de Bruxelles, B-5000 Namur, Belgium.
| | - Thomas Dal Maso
- Department of Chemistry, University of Namur, 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Luc Willems
- Molecular and Cellular Epigenetics (GIGA) and Molecular Biology (Gembloux Agro-Bio Tech), University of Liège (ULg), 4000 Liège, Belgium
| | - Johan Wouters
- Department of Chemistry, University of Namur, 61 rue de Bruxelles, B-5000 Namur, Belgium
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112
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Voon HPJ, Gibbons RJ. Maintaining memory of silencing at imprinted differentially methylated regions. Cell Mol Life Sci 2016; 73:1871-9. [PMID: 26883803 PMCID: PMC4819931 DOI: 10.1007/s00018-016-2157-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 02/04/2016] [Indexed: 01/09/2023]
Abstract
Imprinted genes are an exceptional cluster of genes which are expressed in a parent-of-origin dependent fashion. This allele-specific expression is dependent on differential DNA methylation which is established in the parental germlines in a sex-specific manner. The DNA methylation imprint is accompanied by heterochromatin modifications which must be continuously maintained through development. This review summarises the factors which are important for protecting the epigenetic modifications at imprinted differentially methylated regions (DMRs), including PGC7, ZFP57 and the ATRX/Daxx/H3.3 complex. We discuss how these factors maintain heterochromatin silencing, not only at imprinted DMRs, but also other heterochromatic regions in the genome.
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Affiliation(s)
- Hsiao P J Voon
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Richard J Gibbons
- University of Oxford, Oxford, UK.
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK.
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113
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Duymich CE, Charlet J, Yang X, Jones PA, Liang G. DNMT3B isoforms without catalytic activity stimulate gene body methylation as accessory proteins in somatic cells. Nat Commun 2016; 7:11453. [PMID: 27121154 PMCID: PMC4853477 DOI: 10.1038/ncomms11453] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 03/30/2016] [Indexed: 01/08/2023] Open
Abstract
Promoter DNA methylation is a key epigenetic mechanism for stable gene silencing, but is correlated with expression when located in gene bodies. Maintenance and de novo DNA methylation by catalytically active DNA methyltransferases (DNMT1 and DNMT3A/B) require accessory proteins such as UHRF1 and DNMT3L. DNMT3B isoforms are widely expressed, although some do not have active catalytic domains and their expression can be altered during cell development and tumourigenesis, questioning their biological roles. Here, we show that DNMT3B isoforms stimulate gene body methylation and re-methylation after methylation-inhibitor treatment. This occurs independently of the isoforms' catalytic activity, demonstrating a similar functional role to the accessory protein DNMT3L, which is only expressed in undifferentiated cells and recruits DNMT3A to initiate DNA methylation. This unexpected role for DNMT3B suggests that it might substitute for the absent accessory protein DNMT3L to recruit DNMT3A in somatic cells.
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Affiliation(s)
- Christopher E. Duymich
- Department of Urology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Jessica Charlet
- Department of Urology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Xiaojing Yang
- Department of Urology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Peter A. Jones
- Department of Urology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
| | - Gangning Liang
- Department of Urology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089, USA
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114
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Tompkins JD, Jung M, Chen CY, Lin Z, Ye J, Godatha S, Lizhar E, Wu X, Hsu D, Couture LA, Riggs AD. Mapping Human Pluripotent-to-Cardiomyocyte Differentiation: Methylomes, Transcriptomes, and Exon DNA Methylation "Memories". EBioMedicine 2016; 4:74-85. [PMID: 26981572 PMCID: PMC4776252 DOI: 10.1016/j.ebiom.2016.01.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 01/05/2016] [Accepted: 01/15/2016] [Indexed: 11/17/2022] Open
Abstract
The directed differentiation of human cardiomyocytes (CMs) from pluripotent cells provides an invaluable model for understanding mechanisms of cell fate determination and offers considerable promise in cardiac regenerative medicine. Here, we utilize a human embryonic stem cell suspension bank, produced according to a good manufacturing practice, to generate CMs using a fully defined and small molecule-based differentiation strategy. Primitive and cardiac mesoderm purification was used to remove non-committing and multi-lineage populations and this significantly aided the identification of key transcription factors, lncRNAs, and essential signaling pathways that define cardiomyogenesis. Global methylation profiles reflect CM development and we report on CM exon DNA methylation "memories" persisting beyond transcription repression and marking the expression history of numerous developmentally regulated genes, especially transcription factors.
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Key Words
- Cardiomyocytes
- Cardiomyogenesis
- DNA methylation
- Differentiation
- Epigenetic
- Good manufacturing practice, GMP, epigenetic memory, WNT, hedgehog, transforming growth factor, ROR2, PDGFRα, demethylation, TET, TDG, HOX, TBOX
- Human embryonic stem cells
- Long non-coding RNA
- Mesoderm
- Methylome
- Pluripotent
- Transcriptome
- lncRNA
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Affiliation(s)
- Joshua D. Tompkins
- Department of Diabetes Complications and Metabolism, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Marc Jung
- Department of Diabetes Complications and Metabolism, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Chang-yi Chen
- Center for Biomedicine and Genetics, Duarte, CA 91010, USA
- Sylvia R. and Isador A. Deutch Center for Applied Technology Development, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Ziguang Lin
- Center for Biomedicine and Genetics, Duarte, CA 91010, USA
- Sylvia R. and Isador A. Deutch Center for Applied Technology Development, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Jingjing Ye
- Center for Biomedicine and Genetics, Duarte, CA 91010, USA
- Sylvia R. and Isador A. Deutch Center for Applied Technology Development, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Swetha Godatha
- Department of Diabetes Complications and Metabolism, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Elizabeth Lizhar
- Department of Diabetes Complications and Metabolism, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Xiwei Wu
- Biomedical Informatics Core, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - David Hsu
- Center for Biomedicine and Genetics, Duarte, CA 91010, USA
- Sylvia R. and Isador A. Deutch Center for Applied Technology Development, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Larry A. Couture
- Center for Biomedicine and Genetics, Duarte, CA 91010, USA
- Sylvia R. and Isador A. Deutch Center for Applied Technology Development, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Arthur D. Riggs
- Department of Diabetes Complications and Metabolism, Duarte, CA 91010, USA
- Beckman Research Institute at City of Hope National Medical Center, Duarte, CA 91010, USA
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115
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Jurkowska RZ, Jeltsch A. Enzymology of Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:87-122. [PMID: 27826836 DOI: 10.1007/978-3-319-43624-1_5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is currently one of the hottest topics in basic and biomedical research. Despite tremendous progress in understanding the structures and biochemical properties of the mammalian DNA nucleotide methyltransferases (DNMTs), principles of their regulation in cells have only begun to be uncovered. In mammals, DNA methylation is introduced by the DNMT1, DNMT3A, and DNMT3B enzymes, which are all large multi-domain proteins. These enzymes contain a catalytic C-terminal domain with a characteristic cytosine-C5 methyltransferase fold and an N-terminal part with different domains that interacts with other proteins and chromatin and is involved in targeting and regulation of the DNMTs. The subnuclear localization of the DNMT enzymes plays an important role in their biological function: DNMT1 is localized to replicating DNA via interaction with PCNA and UHRF1. DNMT3 enzymes bind to heterochromatin via protein multimerization and are targeted to chromatin by their ADD and PWWP domains. Recently, a novel regulatory mechanism has been discovered in DNMTs, as latest structural and functional data demonstrated that the catalytic activities of all three enzymes are under tight allosteric control of their N-terminal domains having autoinhibitory functions. This mechanism provides numerous possibilities for the precise regulation of the methyltransferases via controlling the binding and release of autoinhibitory domains by protein factors, noncoding RNAs, or by posttranslational modifications of the DNMTs. In this chapter, we summarize key enzymatic properties of DNMTs, including their specificity and processivity, and afterward we focus on the regulation of their activity and targeting via allosteric processes, protein interactors, and posttranslational modifications.
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Affiliation(s)
- Renata Z Jurkowska
- BioMed X Innovation Center, Im Neuenheimer Feld 583, Heidelberg, D-69120, Germany.
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University of Stuttgart, Pfaffenwaldring 55, Stuttgart, D-70569, Germany.
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116
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Stewart KR, Veselovska L, Kim J, Huang J, Saadeh H, Tomizawa SI, Smallwood SA, Chen T, Kelsey G. Dynamic changes in histone modifications precede de novo DNA methylation in oocytes. Genes Dev 2015; 29:2449-62. [PMID: 26584620 PMCID: PMC4691949 DOI: 10.1101/gad.271353.115] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/04/2015] [Indexed: 12/21/2022]
Abstract
In mouse oogenesis, DNA methylation establishment occurs on a largely unmethylated genome and in nondividing cells, making it a highly informative model for examining how histone modifications can shape the DNA methylome. Stewart et al. present the first systematic study performing ChIP-seq in oocytes and show that histone remodeling in the mammalian oocyte helps direct de novo DNA methylation events. Erasure and subsequent reinstatement of DNA methylation in the germline, especially at imprinted CpG islands (CGIs), is crucial to embryogenesis in mammals. The mechanisms underlying DNA methylation establishment remain poorly understood, but a number of post-translational modifications of histones are implicated in antagonizing or recruiting the de novo DNA methylation complex. In mouse oogenesis, DNA methylation establishment occurs on a largely unmethylated genome and in nondividing cells, making it a highly informative model for examining how histone modifications can shape the DNA methylome. Using a chromatin immunoprecipitation (ChIP) and genome-wide sequencing (ChIP-seq) protocol optimized for low cell numbers and novel techniques for isolating primary and growing oocytes, profiles were generated for histone modifications implicated in promoting or inhibiting DNA methylation. CGIs destined for DNA methylation show reduced protective H3K4 dimethylation (H3K4me2) and trimethylation (H3K4me3) in both primary and growing oocytes, while permissive H3K36me3 increases specifically at these CGIs in growing oocytes. Methylome profiling of oocytes deficient in H3K4 demethylase KDM1A or KDM1B indicated that removal of H3K4 methylation is necessary for proper methylation establishment at CGIs. This work represents the first systematic study performing ChIP-seq in oocytes and shows that histone remodeling in the mammalian oocyte helps direct de novo DNA methylation events.
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Affiliation(s)
- Kathleen R Stewart
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Lenka Veselovska
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Jeesun Kim
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 77030, USA
| | - Jiahao Huang
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Heba Saadeh
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | | | | | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 77030, USA
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom; Centre for Trophoblast Research, University of Cambridge CB2 3EG, Cambridge, United Kingdom
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117
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Switching between Epigenetic States at Pericentromeric Heterochromatin. Trends Genet 2015; 31:661-672. [PMID: 26431676 DOI: 10.1016/j.tig.2015.09.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/21/2015] [Accepted: 09/04/2015] [Indexed: 02/05/2023]
Abstract
Pericentromeric DNA represents a large fraction of the mammalian genome that is usually assembled into heterochromatin. Recent advances have revealed that the composition of pericentromeric heterochromatin is surprisingly dynamic. Indeed, high levels of histone H3 trimethylation on lysine 9 (H3K9me3) and DNA methylation normally characterize the repressive environment of this region. However, in specific tissues and in cancer cells, Polycomb proteins can occupy pericentromeric heterochromatin and act as a molecular sink for transcriptional regulators. Restoring heterochromatin methylation marks could, thus, be an important way to bring back normal gene expression programs in disease. Here, I discuss the potential mechanisms by which Polycomb complexes are recruited to pericentromeric DNA.
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118
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Abstract
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely, to provide a guide to the multitude of nucleosome positioning resources available online. These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info.
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119
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Du J, Johnson LM, Jacobsen SE, Patel DJ. DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Biol 2015; 16:519-32. [PMID: 26296162 PMCID: PMC4672940 DOI: 10.1038/nrm4043] [Citation(s) in RCA: 625] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Methylation of DNA and of histone 3 at Lys 9 (H3K9) are highly correlated with gene silencing in eukaryotes from fungi to humans. Both of these epigenetic marks need to be established at specific regions of the genome and then maintained at these sites through cell division. Protein structural domains that specifically recognize methylated DNA and methylated histones are key for targeting enzymes that catalyse these marks to appropriate genome sites. Genetic, genomic, structural and biochemical data reveal connections between these two epigenetic marks, and these domains mediate much of the crosstalk.
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Affiliation(s)
- Jiamu Du
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Lianna M Johnson
- Howard Hughes Medical Institute and Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Steven E Jacobsen
- Howard Hughes Medical Institute and Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
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120
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Developmental windows of susceptibility for epigenetic inheritance through the male germline. Semin Cell Dev Biol 2015; 43:96-105. [DOI: 10.1016/j.semcdb.2015.07.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/20/2015] [Indexed: 02/02/2023]
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121
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Abstract
Non-CG DNA methylation modulates gene expression in the adult brain
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Affiliation(s)
- Chongyuan Luo
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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122
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Abstract
Stem cell decline is an important cellular driver of aging-associated pathophysiology in multiple tissues. Epigenetic regulation is central to establishing and maintaining stem cell function, and emerging evidence indicates that epigenetic dysregulation contributes to the altered potential of stem cells during aging. Unlike terminally differentiated cells, the impact of epigenetic dysregulation in stem cells is propagated beyond self; alterations can be heritably transmitted to differentiated progeny, in addition to being perpetuated and amplified within the stem cell pool through self-renewal divisions. This Review focuses on recent studies examining epigenetic regulation of tissue-specific stem cells in homeostasis, aging, and aging-related disease.
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Affiliation(s)
- Isabel Beerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02116, USA.
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