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Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu C, He B, Gao YQ, Yi C. Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry. Angew Chem Int Ed Engl 2018; 58:130-133. [DOI: 10.1002/anie.201807845] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/25/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Hu Zeng
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Manas Mondal
- Institute of Theoretical and Computational Chemistry; College of Chemistry and Molecular Engineering and Biomedical Pioneering Innovation Center; Peking University; Beijing 100871 China
| | - Ruyi Song
- Institute of Theoretical and Computational Chemistry; College of Chemistry and Molecular Engineering and Biomedical Pioneering Innovation Center; Peking University; Beijing 100871 China
| | - Jun Zhang
- Institute of Theoretical and Computational Chemistry; College of Chemistry and Molecular Engineering and Biomedical Pioneering Innovation Center; Peking University; Beijing 100871 China
| | - Bo Xia
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Menghao Liu
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Chenxu Zhu
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Bo He
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
| | - Yi Qin Gao
- Institute of Theoretical and Computational Chemistry; College of Chemistry and Molecular Engineering and Biomedical Pioneering Innovation Center; Peking University; Beijing 100871 China
| | - Chengqi Yi
- School of Life Sciences; Department of Chemical Biology and Synthetic and Functional Biomolecules Center; College of Chemistry and Molecular Engineering and Peking-Tsinghua Center for Life Sciences; Peking University; Beijing 100871 China
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52
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Sardina JL, Collombet S, Tian TV, Gómez A, Di Stefano B, Berenguer C, Brumbaugh J, Stadhouders R, Segura-Morales C, Gut M, Gut IG, Heath S, Aranda S, Di Croce L, Hochedlinger K, Thieffry D, Graf T. Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate. Cell Stem Cell 2018; 23:727-741.e9. [DOI: 10.1016/j.stem.2018.08.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 07/07/2018] [Accepted: 08/23/2018] [Indexed: 10/28/2022]
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Tan D, Chung TH, Sun X, Jia XY. Mirror Bisulfite Sequencing: A Method for Single-Base Resolution of Hydroxymethylcytosine. Anal Chem 2018; 90:13200-13206. [DOI: 10.1021/acs.analchem.8b02832] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Darany Tan
- Zymo Research Corporation, 17062 Murphy Avenue, Irvine, California 92614, United States
| | - Tzu Hung Chung
- Zymo Research Corporation, 17062 Murphy Avenue, Irvine, California 92614, United States
| | - Xueguang Sun
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
- Division of Human genetics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, Ohio 45229, United States
| | - Xi-Yu Jia
- Zymo Research Corporation, 17062 Murphy Avenue, Irvine, California 92614, United States
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Schutsky EK, DeNizio JE, Hu P, Liu MY, Nabel CS, Fabyanic EB, Hwang Y, Bushman FD, Wu H, Kohli RM. Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase. Nat Biotechnol 2018; 36:nbt.4204. [PMID: 30295673 PMCID: PMC6453757 DOI: 10.1038/nbt.4204] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/03/2018] [Indexed: 12/17/2022]
Abstract
Here we present APOBEC-coupled epigenetic sequencing (ACE-seq), a bisulfite-free method for localizing 5-hydroxymethylcytosine (5hmC) at single-base resolution with low DNA input. The method builds on the observation that AID/APOBEC family DNA deaminase enzymes can potently discriminate between cytosine modification states and exploits the non-destructive nature of enzymatic, rather than chemical, deamination. ACE-seq yielded high-confidence 5hmC profiles with at least 1,000-fold less DNA input than conventional methods. Applying ACE-seq to generate a base-resolution map of 5hmC in tissue-derived cortical excitatory neurons, we found that 5hmC was almost entirely confined to CG dinucleotides. The whole-genome map permitted cytosine, 5-methylcytosine (5mC) and 5hmC to be parsed and revealed genomic features that diverged from global patterns, including enhancers and imprinting control regions with high and low 5hmC/5mC ratios, respectively. Enzymatic deamination overcomes many challenges posed by bisulfite-based methods, thus expanding the scope of epigenome profiling to include scarce samples and opening new lines of inquiry regarding the role of cytosine modifications in genome biology.
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Affiliation(s)
- Emily K. Schutsky
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jamie E. DeNizio
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peng Hu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Monica Yun Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Emily B. Fabyanic
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Young Hwang
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederic D. Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M. Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
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Stage-specific epigenetic regulation of CD4 expression by coordinated enhancer elements during T cell development. Nat Commun 2018; 9:3594. [PMID: 30185805 PMCID: PMC6125341 DOI: 10.1038/s41467-018-05834-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/27/2018] [Indexed: 11/30/2022] Open
Abstract
The inheritance of gene expression patterns is dependent on epigenetic regulation, but the establishment and maintenance of epigenetic landscapes during T cell differentiation are incompletely understood. Here we show that two stage-specific Cd4 cis-elements, the previously characterized enhancer E4p and a novel enhancer E4m, coordinately promote Cd4 transcription in mature thymic MHC-II-specific T cells, in part through the canonical Wnt pathway. Specifically, E4p licenses E4m to orchestrate DNA demethylation by TET1 and TET3, which in turn poises the Cd4 locus for transcription in peripheral T cells. Cd4 locus demethylation is important for subsequent Cd4 transcription in activated peripheral T cells wherein these cis-elements become dispensable. By contrast, in developing thymocytes the loss of TET1/3 does not affect Cd4 transcription, highlighting an uncoupled event between transcription and epigenetic modifications. Together our findings reveal an important function for thymic cis-elements in governing gene expression in the periphery via a heritable epigenetic mechanism. The expression of CD4, a critical co-receptor providing T cell help in adaptive immunity, is finely tuned during development. Here the authors show that two enhancer elements, E4p and the newly-defined E4m, coordinate the expression and heritable demethylation of Cd4 in thymocytes but are dispensable for its sustained expression in peripheral T cells.
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57
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Ren R, Horton JR, Zhang X, Blumenthal RM, Cheng X. Detecting and interpreting DNA methylation marks. Curr Opin Struct Biol 2018; 53:88-99. [PMID: 30031306 DOI: 10.1016/j.sbi.2018.06.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/19/2018] [Indexed: 12/22/2022]
Abstract
The generation, alteration, recognition, and erasure of epigenetic modifications of DNA are fundamental to controlling gene expression in mammals. These covalent DNA modifications include cytosine methylation by AdoMet-dependent methyltransferases and 5-methylcytosine oxidation by Fe(II)-dependent and α-ketoglutarate-dependent dioxygenases. Sequence-specific transcription factors are responsible for interpreting the modification status of specific regions of chromatin. This review focuses on recent developments in characterizing the functional and structural links between the modification status of two DNA bases: 5-methylcytosine and 5-methyluracil (thymine).
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Affiliation(s)
- Ren Ren
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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58
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Kweon SM, Zhu B, Chen Y, Aravind L, Xu SY, Feldman DE. Erasure of Tet-Oxidized 5-Methylcytosine by a SRAP Nuclease. Cell Rep 2018; 21:482-494. [PMID: 29020633 DOI: 10.1016/j.celrep.2017.09.055] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 08/15/2017] [Accepted: 09/18/2017] [Indexed: 12/15/2022] Open
Abstract
Enzymatic oxidation of 5-methylcytosine (5mC) in DNA by the Tet dioxygenases reprograms genome function in embryogenesis and postnatal development. Tet-oxidized derivatives of 5mC such as 5-hydroxymethylcytosine (5hmC) act as transient intermediates in DNA demethylation or persist as durable marks, yet how these alternative fates are specified at individual CpGs is not understood. Here, we report that the SOS response-associated peptidase (SRAP) domain protein Srap1, the mammalian ortholog of an ancient protein superfamily associated with DNA damage response operons in bacteria, binds to Tet-oxidized forms of 5mC in DNA and catalyzes turnover of these bases to unmodified cytosine by an autopeptidase-coupled nuclease. Biallelic inactivation of murine Srap1 causes embryonic sublethality associated with widespread accumulation of ectopic 5hmC. These findings establish a function for a class of DNA base modification-selective nucleases and position Srap1 as a determinant of 5mC demethylation trajectories during mammalian embryonic development.
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Affiliation(s)
- Soo-Mi Kweon
- Department of Pathology, University of Southern California, Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Bing Zhu
- Department of Pathology, University of Southern California, Keck School of Medicine, Los Angeles, CA 90033, USA
| | - Yibu Chen
- Bioinformatics Service, Department of Health Sciences Libraries, University of Southern California, Keck School of Medicine, Los Angeles, CA 90033, USA
| | | | - Shuang-Yong Xu
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Douglas E Feldman
- Department of Pathology, University of Southern California, Keck School of Medicine, Los Angeles, CA 90033, USA.
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59
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Abstract
Single-cell multiomics technologies typically measure multiple types of molecule from the same individual cell, enabling more profound biological insight than can be inferred by analyzing each molecular layer from separate cells. These single-cell multiomics technologies can reveal cellular heterogeneity at multiple molecular layers within a population of cells and reveal how this variation is coupled or uncoupled between the captured omic layers. The data sets generated by these techniques have the potential to enable a deeper understanding of the key biological processes and mechanisms driving cellular heterogeneity and how they are linked with normal development and aging as well as disease etiology. This review details both established and novel single-cell mono- and multiomics technologies and considers their limitations, applications, and likely future developments.
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Affiliation(s)
- Lia Chappell
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom; , ,
| | | | - Thierry Voet
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom; , , .,Department of Human Genetics, KU Leuven, B-3000 Leuven, Belgium;
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60
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Galactic Cosmic Radiation Induces Persistent Epigenome Alterations Relevant to Human Lung Cancer. Sci Rep 2018; 8:6709. [PMID: 29712937 PMCID: PMC5928241 DOI: 10.1038/s41598-018-24755-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 03/27/2018] [Indexed: 12/14/2022] Open
Abstract
Human deep space and planetary travel is limited by uncertainties regarding the health risks associated with exposure to galactic cosmic radiation (GCR), and in particular the high linear energy transfer (LET), heavy ion component. Here we assessed the impact of two high-LET ions 56Fe and 28Si, and low-LET X rays on genome-wide methylation patterns in human bronchial epithelial cells. We found that all three radiation types induced rapid and stable changes in DNA methylation but at distinct subsets of CpG sites affecting different chromatin compartments. The 56Fe ions induced mostly hypermethylation, and primarily affected sites in open chromatin regions including enhancers, promoters and the edges ("shores") of CpG islands. The 28Si ion-exposure had mixed effects, inducing both hyper and hypomethylation and affecting sites in more repressed heterochromatic environments, whereas X rays induced mostly hypomethylation, primarily at sites in gene bodies and intergenic regions. Significantly, the methylation status of 56Fe ion sensitive sites, but not those affected by X ray or 28Si ions, discriminated tumor from normal tissue for human lung adenocarcinomas and squamous cell carcinomas. Thus, high-LET radiation exposure leaves a lasting imprint on the epigenome, and affects sites relevant to human lung cancer. These methylation signatures may prove useful in monitoring the cumulative biological impact and associated cancer risks encountered by astronauts in deep space.
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61
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Chen Y, Hong T, Wang S, Mo J, Tian T, Zhou X. Epigenetic modification of nucleic acids: from basic studies to medical applications. Chem Soc Rev 2018; 46:2844-2872. [PMID: 28352906 DOI: 10.1039/c6cs00599c] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The epigenetic modification of nucleic acids represents one of the most significant areas of study in the field of nucleic acids because it makes gene regulation more complex and heredity more complicated, thus indicating its profound impact on aspects of heredity, growth, and diseases. The recent characterization of epigenetic modifications of DNA and RNA using chemical labelling strategies has promoted the discovery of these modifications, and the newly developed single-base or single-cell resolution mapping strategies have enabled large-scale epigenetic studies in eukaryotes. Due to these technological breakthroughs, several new epigenetic marks have been discovered that have greatly extended the scope and impact of epigenetic modifications in nucleic acids over the past few years. Because epigenetics is reversible and susceptible to environmental factors, it could potentially be a promising direction for clinical medicine research. In this review, we have comprehensively discussed how these epigenetic marks are involved in disease, including the pathogenesis, prevention, diagnosis and treatment of disease. These findings have revealed that the epigenetic modification of nucleic acids has considerable significance in various areas from methodology to clinical medicine and even in biomedical applications.
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Affiliation(s)
- Yuqi Chen
- College of Chemistry and Molecular Sciences, Institute of Advanced Studies, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Hubei, Wuhan 430072, P. R. China.
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62
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Zhu Q, Stöger R, Alberio R. A Lexicon of DNA Modifications: Their Roles in Embryo Development and the Germline. Front Cell Dev Biol 2018; 6:24. [PMID: 29637072 PMCID: PMC5880922 DOI: 10.3389/fcell.2018.00024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 02/27/2018] [Indexed: 12/12/2022] Open
Abstract
5-methylcytosine (5mC) on CpG dinucleotides has been viewed as the major epigenetic modification in eukaryotes for a long time. Apart from 5mC, additional DNA modifications have been discovered in eukaryotic genomes. Many of these modifications are thought to be solely associated with DNA damage. However, growing evidence indicates that some base modifications, namely 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), 5-carboxylcytosine (5caC), and N6-methadenine (6mA), may be of biological relevance, particularly during early stages of embryo development. Although abundance of these DNA modifications in eukaryotic genomes can be low, there are suggestions that they cooperate with other epigenetic markers to affect DNA-protein interactions, gene expression, defense of genome stability and epigenetic inheritance. Little is still known about their distribution in different tissues and their functions during key stages of the animal lifecycle. This review discusses current knowledge and future perspectives of these novel DNA modifications in the mammalian genome with a focus on their dynamic distribution during early embryonic development and their potential function in epigenetic inheritance through the germ line.
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Affiliation(s)
- Qifan Zhu
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Reinhard Stöger
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Ramiro Alberio
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
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63
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64
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Carell T, Kurz MQ, Müller M, Rossa M, Spada F. Non-canonical Bases in the Genome: The Regulatory Information Layer in DNA. Angew Chem Int Ed Engl 2018; 57:4296-4312. [DOI: 10.1002/anie.201708228] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Thomas Carell
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Matthias Q. Kurz
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Markus Müller
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Martin Rossa
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Fabio Spada
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
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65
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Hassan HM, Kolendowski B, Isovic M, Bose K, Dranse HJ, Sampaio AV, Underhill TM, Torchia J. Regulation of Active DNA Demethylation through RAR-Mediated Recruitment of a TET/TDG Complex. Cell Rep 2018; 19:1685-1697. [PMID: 28538185 DOI: 10.1016/j.celrep.2017.05.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 03/28/2017] [Accepted: 05/01/2017] [Indexed: 02/07/2023] Open
Abstract
Retinoic acid (RA) plays important roles in development, growth, and homeostasis through regulation of the nuclear receptors for RA (RARs). Herein, we identify Hypermethylated in Cancer 1 (Hic1) as an RA-inducible gene. HIC1 encodes a tumor suppressor, which is often silenced by promoter hypermethylation in cancer. Treatment of cells with an RAR agonist causes a rapid recruitment of an RAR/RXR complex consisting of TDG, the lysine acetyltransferase CBP, and TET 1/2 to the Hic1 promoter. Complex binding coincides with a transient accumulation of 5fC/5caC and concomitant upregulation of Hic1 expression, both of which are TDG dependent. Furthermore, conditional deletion of Tdg in vivo is associated with Hic1 silencing and DNA hypermethylation of the Hic1 promoter. These findings suggest that the catalytic and scaffolding activities of TDG are essential for RA-dependent gene expression and provide important insights into the mechanisms underlying targeting of TET-TDG complexes.
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Affiliation(s)
- Haider M Hassan
- Department of Biochemistry, Western University, London, ON N6A 5C1, Canada; Department of Oncology, The London Regional Cancer Program and the Lawson Health Research Institute, London, ON N6A 4L6, Canada
| | - Bart Kolendowski
- Department of Biochemistry, Western University, London, ON N6A 5C1, Canada; Department of Oncology, The London Regional Cancer Program and the Lawson Health Research Institute, London, ON N6A 4L6, Canada
| | - Majdina Isovic
- Department of Oncology, The London Regional Cancer Program and the Lawson Health Research Institute, London, ON N6A 4L6, Canada
| | - Kerstin Bose
- Department of Cellular and Physiological Sciences and the Biomedical Research Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Helen J Dranse
- Department of Cellular and Physiological Sciences and the Biomedical Research Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Arthur V Sampaio
- Department of Cellular and Physiological Sciences and the Biomedical Research Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - T Michael Underhill
- Department of Cellular and Physiological Sciences and the Biomedical Research Centre, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| | - Joseph Torchia
- Department of Biochemistry, Western University, London, ON N6A 5C1, Canada; Department of Oncology, The London Regional Cancer Program and the Lawson Health Research Institute, London, ON N6A 4L6, Canada.
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66
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Xing J, Ai Y, Liu Y, Du J, Chen W, Lu Z, Wang X. Theoretical Studies on the Photophysics and Photochemistry of 5-Formylcytosine and 5-Carboxylcytosine: The Oxidative Products of Epigenetic Modification of Cytosine in DNA. J Phys Chem B 2018; 122:2704-2714. [DOI: 10.1021/acs.jpcb.7b10218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jinlu Xing
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P. R. China
- School of Mathematics and Physical Science, North China Electric Power University, Beijing 102206, P. R. China
| | - Yuejie Ai
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P. R. China
| | - Yang Liu
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P. R. China
| | - Jia Du
- School of Mathematics and Physical Science, North China Electric Power University, Beijing 102206, P. R. China
| | - Weiqiang Chen
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P. R. China
- School of Mathematics and Physical Science, North China Electric Power University, Beijing 102206, P. R. China
| | - Zhanhui Lu
- School of Mathematics and Physical Science, North China Electric Power University, Beijing 102206, P. R. China
| | - Xiangke Wang
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, P. R. China
- NAAM Research Group, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, School for Radiological and Interdisciplinary Sciences, Soochow University, Suzhou 215123, P. R. China
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67
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Kolendowski B, Hassan H, Krstic M, Isovic M, Thillainadesan G, Chambers AF, Tuck AB, Torchia J. Genome-wide analysis reveals a role for TDG in estrogen receptor-mediated enhancer RNA transcription and 3-dimensional reorganization. Epigenetics Chromatin 2018; 11:5. [PMID: 29378668 PMCID: PMC5787930 DOI: 10.1186/s13072-018-0176-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 01/15/2018] [Indexed: 01/25/2023] Open
Abstract
Background The estrogen receptor (ER) is a ligand-dependant transcription factor expressed in many breast cancers and is the target of many endocrine-based cancer therapies. Genome-wide studies have shown that the ER binds to gene-specific enhancer regions in response to β-estradiol (E2) which undergo transcription producing noncoding enhancer RNA (eRNA). While eRNAs are important for transcriptional activation of neighboring genes, the mechanism remains poorly understood. Results Using ChIP-Seq we generate a global profile of thymine DNA glycosylase (TDG), an ER coactivator that plays an essential role in DNA demethylation, in response to E2 in the MCF7 breast cancer cell line. Remarkably, we found that in response to E2 TDG localized to enhancers which also recruit ERα, RNA Pol II and other coregulators and which are marked by histone modifications indicative of active enhancers. Importantly, depletion of TDG inhibits E2-mediated transcription of eRNAs and transcription of ER-target genes. Functionally, we find that TDG both sensitizes MCF7 cells to tamoxifen-mediated cytostasis and increases migration and invasion of MCF7 cells. Conclusions Taken together we find that TDG plays a central role in mediating transcription at a subset of enhancers and governs how MCF7 cells respond to both estrogenic and anti-estrogenic compounds and may be an effective therapeutic target. Electronic supplementary material The online version of this article (10.1186/s13072-018-0176-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bart Kolendowski
- Department of Biochemistry, Western University, London, ON, Canada.,Department of Oncology, Western University, London, ON, Canada.,The London Regional Cancer Program and the Lawson Health Research Institute, Western University, London, ON, Canada
| | - Haider Hassan
- Department of Biochemistry, Western University, London, ON, Canada.,Department of Oncology, Western University, London, ON, Canada.,The London Regional Cancer Program and the Lawson Health Research Institute, Western University, London, ON, Canada
| | - Milica Krstic
- Department of Pathology, Western University, London, ON, Canada.,The London Regional Cancer Program and the Lawson Health Research Institute, Western University, London, ON, Canada
| | - Majdina Isovic
- Department of Oncology, Western University, London, ON, Canada
| | - Gobi Thillainadesan
- Department of Biochemistry, Western University, London, ON, Canada.,Department of Oncology, Western University, London, ON, Canada
| | - Ann F Chambers
- The London Regional Cancer Program and the Lawson Health Research Institute, Western University, London, ON, Canada
| | - Alan B Tuck
- Department of Oncology, Western University, London, ON, Canada.,Department of Pathology, Western University, London, ON, Canada
| | - Joseph Torchia
- Department of Biochemistry, Western University, London, ON, Canada. .,Department of Oncology, Western University, London, ON, Canada. .,The London Regional Cancer Program and the Lawson Health Research Institute, Western University, London, ON, Canada. .,Cancer Research Laboratories, London Regional Cancer Program, London, ON, N6A 4L6, Canada.
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68
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Abstract
There are multiple chemical modifications of cytosine that are important to the regulation and ultimately the functional expression of the genome. To date no single experiment can capture these separate modifications, and integrative experimental designs are needed to fully characterize cytosine methylation and chemical modification. This chapter describes a generative probabilistic model, Lux, for integrative analysis of cytosine methylation and its oxidized variants. Lux simultaneously analyzes partially orthogonal bisulfite sequencing data sets to estimate proportions of different cytosine methylation modifications and estimate multiple cytosine modifications for a single sample by integrating across experimental designs composed of multiple parallel destructive genomic measurements. Lux also considers the variation in measurements introduced by different imperfect experimental steps; the experimental variation can be quantified by using appropriate spike-in controls, allowing Lux to deconvolve the measurements and recover accurately the underlying signal.
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Affiliation(s)
- Tarmo Äijö
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, New York, NY, USA
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Courant Institute of Mathematical Sciences, New York University, New York, NY, USA
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University School of Science, Aalto, Finland.
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69
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Tierling S, Schmitt B, Walter J. Comprehensive Evaluation of Commercial Bisulfite-Based DNA Methylation Kits and Development of an Alternative Protocol With Improved Conversion Performance. GENETICS & EPIGENETICS 2018; 10:1179237X18766097. [PMID: 29636635 PMCID: PMC5888801 DOI: 10.1177/1179237x18766097] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/01/2018] [Indexed: 04/30/2023]
Abstract
DNA methylation is the most studied epigenetic modification with a wide range of regulatory functions in mammalian genomes. It almost exclusively resides on CpG dinucleotides and, among others, plays important roles in early embryo development, onset, and maintenance of cancer. During the past 3 decades, many approaches have been developed to discriminate methylated from unmethylated DNA including antibody-based enrichment of methylated DNA, restriction enzyme-based, or hybridization-based methods. The conversion of unmethylated cytosines to uracils by sodium or ammonium bisulfite is regarded as golden standard as this approach requires no enzymatic reaction and provides deep and reliable insight in methylation patterns at single-base resolution. Nowadays, there are many commercial kits for bisulfite conversion available but they perform differently and also vary in protocols and chemicals used. Here, we provide the first comprehensive and comparative evaluation of bisulfite conversion kits observing major differences in conversion efficiency and DNA degradation which greatly affect the performance of downstream applications, ie, polymerase chain reactions (PCRs). Moreover, deep sequencing of amplicons containing oxidized derivates of 5'-methylC shows that none of the tested kits efficiently converts 5'-formylC without substantial conversion of 5'-methylC or 5'-hydroxymethylC. Consequently, we developed a robust and easy-to-use protocol that allows maximal discrimination between 5'-formylC and 5'-methylC/5'-hydroxymethylC with low DNA degradation and high PCR efficiency on the bisulfite-treated DNA. We highly recommend to use our time- and cost-efficient protocol for any genome-wide or local high-resolution bisulfite sequencing application to minimize conversion-dependent error rates.
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Affiliation(s)
- Sascha Tierling
- Sascha Tierling, Faculty of Natural Sciences and Technology, Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany.
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70
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Ravichandran M, Jurkowska RZ, Jurkowski TP. Target specificity of mammalian DNA methylation and demethylation machinery. Org Biomol Chem 2018; 16:1419-1435. [DOI: 10.1039/c7ob02574b] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review here the molecular mechanisms employed by DNMTs and TET enzymes that are responsible for shaping the DNA methylation pattern of a mammalian cell.
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Affiliation(s)
| | | | - T. P. Jurkowski
- Universität Stuttgart
- Abteilung Biochemie
- Institute für Biochemie und Technische Biochemie
- Stuttgart D-70569
- Germany
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71
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Laqqan M, Hammadeh ME. Alterations in DNA methylation patterns and gene expression in spermatozoa of subfertile males. Andrologia 2017; 50. [DOI: 10.1111/and.12934] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2017] [Indexed: 02/06/2023] Open
Affiliation(s)
- M. Laqqan
- Department of Obstetrics & Gynecology; Assisted Reproduction Laboratory; Saarland University; Homburg Germany
| | - M. E. Hammadeh
- Department of Obstetrics & Gynecology; Assisted Reproduction Laboratory; Saarland University; Homburg Germany
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72
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Wen L, Tang F. Single cell epigenome sequencing technologies. Mol Aspects Med 2017; 59:62-69. [PMID: 28923782 DOI: 10.1016/j.mam.2017.09.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/05/2017] [Accepted: 09/13/2017] [Indexed: 10/18/2022]
Abstract
Epigenetic regulation plays crucial roles in the development and disease processes. Since different cell types with distinct epigenetic characteristics are always intermingled together in the tissues or organs, the single cell analysis provides a universal resolution for dissecting their intrinsic complexities. In this review, we discuss recent advances of developing single cell epigenome sequencing techniques for profiling DNA modifications (5mC, 5hmC, 5fC and 5caC), chromatin accessibility, histone modifications, protein-DNA interactions and three-dimensional genome architecture (Hi-C) in an individual mammalian cell. Recent progresses of single cell multi-omics sequencing techniques are also reviewed. These techniques are emerging as powerful tools for unravelling the unique epigenomic features of rare cell types and epigenetic heterogeneity within a seemingly homogenous cell population. We also discussed the current limitations and future development trend of single cell epigenome sequencing techniques.
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73
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Raiber EA, Hardisty R, van Delft P, Balasubramanian S. Mapping and elucidating the function of modified bases in DNA. Nat Rev Chem 2017. [DOI: 10.1038/s41570-017-0069] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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74
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Wang D, Hashimoto H, Zhang X, Barwick BG, Lonial S, Boise LH, Vertino PM, Cheng X. MAX is an epigenetic sensor of 5-carboxylcytosine and is altered in multiple myeloma. Nucleic Acids Res 2017; 45:2396-2407. [PMID: 27903915 PMCID: PMC5389568 DOI: 10.1093/nar/gkw1184] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 11/15/2016] [Indexed: 12/31/2022] Open
Abstract
The oncogenic transcription factor MYC and its binding partner MAX regulate gene expression by binding to DNA at enhancer-box (E-box) elements 5΄-CACGTG-3΄. In mammalian genomes, the central E-box CpG has the potential to be methylated at the 5-position of cytosine (5mC), or to undergo further oxidation to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), or 5-carboxyl (5caC) forms. We find that MAX exhibits the greatest affinity for a 5caC or unmodified C-containing E-box, and much reduced affinities for the corresponding 5mC, 5hmC or 5fC forms. Crystallization of MAX with a 5caC modified E-box oligonucleotide revealed that MAX Arg36 recognizes 5caC using a 5caC–Arg–Guanine triad, with the next nearest residue to the carboxylate group being Arg60. In an analysis of >800 primary multiple myelomas, MAX alterations occurred at a frequency of ∼3%, more than half of which were single nucleotide substitutions affecting a basic clamp-like interface important for DNA interaction. Among these, arginines 35, 36 and 60 were the most frequently altered. In vitro binding studies showed that whereas mutation of Arg36 (R36W) or Arg35 (R35H/L) completely abolished DNA binding, mutation of Arg60 (R60Q) significantly reduced DNA binding, but retained a preference for the 5caC modified E-box. Interestingly, MAX alterations define a subset of myeloma patients with lower MYC expression and a better overall prognosis. Together these data indicate that MAX can act as a direct epigenetic sensor of E-box cytosine modification states and that local CpG modification and MAX variants converge to modulate the MAX-MYC transcriptional network.
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Affiliation(s)
- Dongxue Wang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hideharu Hashimoto
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Benjamin G Barwick
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA.,The Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Lawrence H Boise
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA.,The Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Paula M Vertino
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA.,The Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,The Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
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75
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Gillingham D, Geigle S, Anatole von Lilienfeld O. Properties and reactivity of nucleic acids relevant to epigenomics, transcriptomics, and therapeutics. Chem Soc Rev 2017; 45:2637-55. [PMID: 26992131 DOI: 10.1039/c5cs00271k] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Developments in epigenomics, toxicology, and therapeutic nucleic acids all rely on a precise understanding of nucleic acid properties and chemical reactivity. In this review we discuss the properties and chemical reactivity of each nucleobase and attempt to provide some general principles for nucleic acid targeting or engineering. For adenine-thymine and guanine-cytosine base pairs, we review recent quantum chemical estimates of their Watson-Crick interaction energy, π-π stacking energies, as well as the nuclear quantum effects on tautomerism. Reactions that target nucleobases have been crucial in the development of new sequencing technologies and we believe further developments in nucleic acid chemistry will be required to deconstruct the enormously complex transcriptome.
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Affiliation(s)
- Dennis Gillingham
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel, CH-4056, Switzerland.
| | - Stefanie Geigle
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, Basel, CH-4056, Switzerland.
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76
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Abstract
In mammals, DNA methylation in the form of 5-methylcytosine (5mC) can be actively reversed to unmodified cytosine (C) through TET dioxygenase-mediated oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), followed by replication-dependent dilution or thymine DNA glycosylase (TDG)-dependent base excision repair. In the past few years, biochemical and structural studies have revealed mechanistic insights into how TET and TDG mediate active DNA demethylation. Additionally, many regulatory mechanisms of this process have been identified. Technological advances in mapping and tracing the oxidized forms of 5mC allow further dissection of their functions. Furthermore, the biological functions of active DNA demethylation in various biological contexts have also been revealed. In this Review, we summarize the recent advances and highlight key unanswered questions.
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77
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Abstract
Recent technological advances have made it possible to decode DNA methylomes at single-base-pair resolution under various physiological conditions. Many aberrant or differentially methylated sites have been discovered, but the mechanisms by which changes in DNA methylation lead to observed phenotypes, such as cancer, remain elusive. The classical view of methylation-mediated protein-DNA interactions is that only proteins with a methyl-CpG binding domain (MBD) can interact with methylated DNA. However, evidence is emerging to suggest that transcription factors lacking a MBD can also interact with methylated DNA. The identification of these proteins and the elucidation of their characteristics and the biological consequences of methylation-dependent transcription factor-DNA interactions are important stepping stones towards a mechanistic understanding of methylation-mediated biological processes, which have crucial implications for human development and disease.
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78
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An J, Rao A, Ko M. TET family dioxygenases and DNA demethylation in stem cells and cancers. Exp Mol Med 2017; 49:e323. [PMID: 28450733 PMCID: PMC6130217 DOI: 10.1038/emm.2017.5] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 12/15/2022] Open
Abstract
The methylation of cytosine and subsequent oxidation constitutes a fundamental epigenetic modification in mammalian genomes, and its abnormalities are intimately coupled to various pathogenic processes including cancer development. Enzymes of the Ten–eleven translocation (TET) family catalyze the stepwise oxidation of 5-methylcytosine in DNA to 5-hydroxymethylcytosine and further oxidation products. These oxidized 5-methylcytosine derivatives represent intermediates in the reversal of cytosine methylation, and also serve as stable epigenetic modifications that exert distinctive regulatory roles. It is becoming increasingly obvious that TET proteins and their catalytic products are key regulators of embryonic development, stem cell functions and lineage specification. Over the past several years, the function of TET proteins as a barrier between normal and malignant states has been extensively investigated. Dysregulation of TET protein expression or function is commonly observed in a wide range of cancers. Notably, TET loss-of-function is causally related to the onset and progression of hematologic malignancy in vivo. In this review, we focus on recent advances in the mechanistic understanding of DNA methylation–demethylation dynamics, and their potential regulatory functions in cellular differentiation and oncogenic transformation.
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Affiliation(s)
- Jungeun An
- Department of Biological Sciences, Chonbuk National University, Jeonju, Korea
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA.,Department of Pharmacology and Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Myunggon Ko
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, Korea.,School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Korea
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79
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Wu X, Inoue A, Suzuki T, Zhang Y. Simultaneous mapping of active DNA demethylation and sister chromatid exchange in single cells. Genes Dev 2017; 31:511-523. [PMID: 28360182 PMCID: PMC5393065 DOI: 10.1101/gad.294843.116] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/01/2017] [Indexed: 12/21/2022]
Abstract
To understand mammalian active DNA demethylation, various methods have been developed to map the genomic distribution of the demethylation intermediates 5-formylcysotine (5fC) and 5-carboxylcytosine (5caC). However, the majority of these methods requires a large number of cells to begin with. In this study, we describe low-input methylase-assisted bisulfite sequencing (liMAB-seq ) and single-cell MAB-seq (scMAB-seq), capable of profiling 5fC and 5caC at genome scale using ∼100 cells and single cells, respectively. liMAB-seq analysis of preimplantation embryos reveals the oxidation of 5mC to 5fC/5caC and the positive correlation between chromatin accessibility and processivity of ten-eleven translocation (TET) enzymes. scMAB-seq captures the cell-to-cell heterogeneity of 5fC and 5caC and reveals the strand-biased distribution of 5fC and 5caC. scMAB-seq also allows the simultaneous high-resolution mapping of sister chromatid exchange (SCE), facilitating the study of this type of genomic rearrangement. Therefore, our study not only establishes new methods for the genomic mapping of active DNA demethylation using limited numbers of cells or single cells but also demonstrates the utilities of the methods in different biological contexts.
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Affiliation(s)
- Xiaoji Wu
- Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,PhD Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Azusa Inoue
- Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Tsukasa Suzuki
- Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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80
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Zhu C, Gao Y, Guo H, Xia B, Song J, Wu X, Zeng H, Kee K, Tang F, Yi C. Single-Cell 5-Formylcytosine Landscapes of Mammalian Early Embryos and ESCs at Single-Base Resolution. Cell Stem Cell 2017; 20:720-731.e5. [PMID: 28343982 DOI: 10.1016/j.stem.2017.02.013] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 12/14/2016] [Accepted: 02/23/2017] [Indexed: 12/21/2022]
Abstract
Active DNA demethylation in mammals involves ten-eleven translocation (TET) family protein-mediated oxidation of 5-methylcytosine (5mC). However, base-resolution landscapes of 5-formylcytosine (5fC) (an oxidized derivative of 5mC) at the single-cell level remain unexplored. Here, we present "CLEVER-seq" (chemical-labeling-enabled C-to-T conversion sequencing), which is a single-cell, single-base resolution 5fC-sequencing technology, based on biocompatible, selective chemical labeling of 5fC and subsequent C-to-T conversion during amplification and sequencing. CLEVER-seq shows intrinsic 5fC heterogeneity in mouse early embryos, Epi stem cells (EpiSCs), and embryonic stem cells (ESCs). CLEVER-seq of mouse early embryos also reveals the highly patterned genomic distribution and parental-specific dynamics of 5fC during mouse early pre-implantation development. Integrated analysis demonstrates that promoter 5fC production precedes the expression upregulation of a clear set of developmentally and metabolically critical genes. Collectively, our work reveals the dynamics of active DNA demethylation during mouse pre-implantation development and provides an important resource for further functional studies of epigenetic reprogramming in single cells.
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Affiliation(s)
- Chenxu Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, PRC
| | - Yun Gao
- Biodynamic Optical Imaging Center and Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, PRC
| | - Hongshan Guo
- Biodynamic Optical Imaging Center and Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, PRC
| | - Bo Xia
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, PRC
| | - Jinghui Song
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, PRC
| | - Xinglong Wu
- Biodynamic Optical Imaging Center and Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, PRC; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, PRC
| | - Hu Zeng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, PRC
| | - Kehkooi Kee
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Fuchou Tang
- Biodynamic Optical Imaging Center and Beijing Advanced Innovation Center for Genomics, School of Life Sciences, Peking University, Beijing 100871, PRC; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, PRC; Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Peking University, Beijing 100871, PRC.
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, PRC; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, PRC; Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, PRC.
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81
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Xiong J, Zhang Z, Chen J, Huang H, Xu Y, Ding X, Zheng Y, Nishinakamura R, Xu GL, Wang H, Chen S, Gao S, Zhu B. Cooperative Action between SALL4A and TET Proteins in Stepwise Oxidation of 5-Methylcytosine. Mol Cell 2016; 64:913-925. [PMID: 27840027 DOI: 10.1016/j.molcel.2016.10.013] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 07/28/2016] [Accepted: 10/06/2016] [Indexed: 11/30/2022]
Abstract
TET family enzymes successively oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine, leading to eventual demethylation. 5hmC and TET enzymes occupy distinct chromatin regions, suggesting unknown mechanisms controlling the fate of 5hmC within diverse chromatin environments. Here, we report that SALL4A preferentially associates with 5hmC in vitro and occupies enhancers in mouse embryonic stem cells in a largely TET1-dependent manner. Although most 5hmC at SALL4A peaks undergoes further oxidation, this process is abrogated upon deletion of Sall4 gene, with a concomitant reduction of TET2 at these regions. Thus, SALL4A facilitates further oxidation of 5hmC at its binding sites, which requires its 5hmC-binding activity and TET2, supporting a collaborative action between SALL4A and TET proteins in regulating stepwise oxidation of 5mC at enhancers. Our study identifies SALL4A as a 5hmC binder, which facilitates 5hmC oxidation by stabilizing TET2 association, thereby fine-tuning expression profiles of developmental genes in mouse embryonic stem cells.
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Affiliation(s)
- Jun Xiong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhuqiang Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Hua Huang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yali Xu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xiaojun Ding
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yong Zheng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Guo-Liang Xu
- The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hailin Wang
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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82
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Chen K, Zhao BS, He C. Nucleic Acid Modifications in Regulation of Gene Expression. Cell Chem Biol 2016; 23:74-85. [PMID: 26933737 DOI: 10.1016/j.chembiol.2015.11.007] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/13/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
Abstract
Nucleic acids carry a wide range of different chemical modifications. In contrast to previous views that these modifications are static and only play fine-tuning functions, recent research advances paint a much more dynamic picture. Nucleic acids carry diverse modifications and employ these chemical marks to exert essential or critical influences in a variety of cellular processes in eukaryotic organisms. This review covers several nucleic acid modifications that play important regulatory roles in biological systems, especially in regulation of gene expression: 5-methylcytosine (5mC) and its oxidative derivatives, and N(6)-methyladenine (6mA) in DNA; N(6)-methyladenosine (m(6)A), pseudouridine (Ψ), and 5-methylcytidine (m(5)C) in mRNA and long non-coding RNA. Modifications in other non-coding RNAs, such as tRNA, miRNA, and snRNA, are also briefly summarized. We provide brief historical perspective of the field, and highlight recent progress in identifying diverse nucleic acid modifications and exploring their functions in different organisms. Overall, we believe that work in this field will yield additional layers of both chemical and biological complexity as we continue to uncover functional consequences of known nucleic acid modifications and discover new ones.
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Affiliation(s)
- Kai Chen
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Boxuan Simen Zhao
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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83
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Gross JA, Nagy C, Lin L, Bonneil É, Maheu M, Thibault P, Mechawar N, Jin P, Turecki G. WITHDRAWN: Global and site-specific changes in 5-methylcytosine and 5-hydroxymethylcytosine after extended post-mortem interval. Exp Mol Pathol 2016:S0014-4800(16)30042-9. [PMID: 27746278 DOI: 10.1016/j.yexmp.2016.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 08/16/2016] [Accepted: 10/11/2016] [Indexed: 11/28/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Jeffrey A Gross
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Corina Nagy
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Li Lin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Éric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Marissa Maheu
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal, Quebec, Canada
| | - Naguib Mechawar
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada.
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84
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Hashimoto H, Zhang X, Zheng Y, Wilson GG, Cheng X. Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications. Nucleic Acids Res 2016; 44:10165-10176. [PMID: 27596598 PMCID: PMC5137435 DOI: 10.1093/nar/gkw766] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 01/10/2023] Open
Abstract
Mutations in human zinc-finger transcription factor WT1 result in abnormal development of the kidneys and genitalia and an array of pediatric problems including nephropathy, blastoma, gonadal dysgenesis and genital discordance. Several overlapping phenotypes are associated with WT1 mutations, including Wilms tumors, Denys-Drash syndrome (DDS), Frasier syndrome (FS) and WAGR syndrome (Wilms tumor, aniridia, genitourinary malformations, and mental retardation). These conditions vary in severity from individual to individual; they can be fatal in early childhood, or relatively benign into adulthood. DDS mutations cluster predominantly in zinc fingers (ZF) 2 and 3 at the C-terminus of WT1, which together with ZF4 determine the sequence-specificity of DNA binding. We examined three DDS associated mutations in ZF2 of human WT1 where the normal glutamine at position 369 is replaced by arginine (Q369R), lysine (Q369K) or histidine (Q369H). These mutations alter the sequence-specificity of ZF2, we find, changing its affinity for certain bases and certain epigenetic forms of cytosine. X-ray crystallography of the DNA binding domains of normal WT1, Q369R and Q369H in complex with preferred sequences revealed the molecular interactions responsible for these affinity changes. DDS is inherited in an autosomal dominant fashion, implying a gain of function by mutant WT1 proteins. This gain, we speculate, might derive from the ability of the mutant proteins to sequester WT1 into unproductive oligomers, or to erroneously bind to variant target sequences.
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Affiliation(s)
- Hideharu Hashimoto
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yu Zheng
- RGENE, Inc., 953 Indiana Street, San Francisco, CA 94107, USA
| | | | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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85
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Äijö T, Yue X, Rao A, Lähdesmäki H. LuxGLM: a probabilistic covariate model for quantification of DNA methylation modifications with complex experimental designs. Bioinformatics 2016; 32:i511-i519. [PMID: 27587669 PMCID: PMC5013920 DOI: 10.1093/bioinformatics/btw468] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
MOTIVATION 5-methylcytosine (5mC) is a widely studied epigenetic modification of DNA. The ten-eleven translocation (TET) dioxygenases oxidize 5mC into oxidized methylcytosines (oxi-mCs): 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). DNA methylation modifications have multiple functions. For example, 5mC is shown to be associated with diseases and oxi-mC species are reported to have a role in active DNA demethylation through 5mC oxidation and DNA repair, among others, but the detailed mechanisms are poorly understood. Bisulphite sequencing and its various derivatives can be used to gain information about all methylation modifications at single nucleotide resolution. Analysis of bisulphite based sequencing data is complicated due to the convoluted read-outs and experiment-specific variation in biochemistry. Moreover, statistical analysis is often complicated by various confounding effects. How to analyse 5mC and oxi-mC data sets with arbitrary and complex experimental designs is an open and important problem. RESULTS We propose the first method to quantify oxi-mC species with arbitrary covariate structures from bisulphite based sequencing data. Our probabilistic modeling framework combines a previously proposed hierarchical generative model for oxi-mC-seq data and a general linear model component to account for confounding effects. We show that our method provides accurate methylation level estimates and accurate detection of differential methylation when compared with existing methods. Analysis of novel and published data gave insights into to the demethylation of the forkhead box P3 (Foxp3) locus during the induced T regulatory cell differentiation. We also demonstrate how our covariate model accurately predicts methylation levels of the Foxp3 locus. Collectively, LuxGLM method improves the analysis of DNA methylation modifications, particularly for oxi-mC species. AVAILABILITY AND IMPLEMENTATION An implementation of the proposed method is available under MIT license at https://github.org/tare/LuxGLM/ CONTACT: taijo@simonsfoundation.org or harri.lahdesmaki@aalto.fi SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Tarmo Äijö
- Center for Computational Biology, Simons Foundation, New York, NY 10010, USA Department of Computer Science, Aalto University School of Science, Aalto FI-00076, Finland
| | - Xiaojing Yue
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Anjana Rao
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA Department of Pharmacology and Moores Cancer Center, University of California, La Jolla, CA 92037, USA Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University School of Science, Aalto FI-00076, Finland
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86
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Abstract
Ten eleven translocation (TET) genes, and especially TET2, are frequently mutated in various cancers, but how the TET proteins contribute to the onset and maintenance of these malignancies is largely unknown. In this review, Rasmussen and Helin highlight recent advances in understanding the physiological function of the TET proteins and their role in regulating DNA methylation and transcription. The pattern of DNA methylation at cytosine bases in the genome is tightly linked to gene expression, and DNA methylation abnormalities are often observed in diseases. The ten eleven translocation (TET) enzymes oxidize 5-methylcytosines (5mCs) and promote locus-specific reversal of DNA methylation. TET genes, and especially TET2, are frequently mutated in various cancers, but how the TET proteins contribute to prevent the onset and maintenance of these malignancies is largely unknown. Here, we highlight recent advances in understanding the physiological function of the TET proteins and their role in regulating DNA methylation and transcription. In addition, we discuss some of the key outstanding questions in the field.
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Affiliation(s)
- Kasper Dindler Rasmussen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark; The Danish Stem Cell Center (Danstem), University of Copenhagen, 2200 Copenhagen, Denmark; Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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87
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Tamanaha E, Guan S, Marks K, Saleh L. Distributive Processing by the Iron(II)/α-Ketoglutarate-Dependent Catalytic Domains of the TET Enzymes Is Consistent with Epigenetic Roles for Oxidized 5-Methylcytosine Bases. J Am Chem Soc 2016; 138:9345-8. [PMID: 27362828 DOI: 10.1021/jacs.6b03243] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The ten-eleven translocation (TET) proteins catalyze oxidation of 5-methylcytosine ((5m)C) residues in nucleic acids to 5-hydroxymethylcytosine ((5hm)C), 5-formylcytosine ((5f)C), and 5-carboxycytosine ((5ca)C). These nucleotide bases have been implicated as intermediates on the path to active demethylation, but recent reports have suggested that they might have specific regulatory roles in their own right. In this study, we present kinetic evidence showing that the catalytic domains (CDs) of TET2 and TET1 from mouse and their homologue from Naegleria gruberi, the full-length protein NgTET1, are distributive in both chemical and physical senses, as they carry out successive oxidations of a single (5m)C and multiple (5m)C residues along a polymethylated DNA substrate. We present data showing that the enzyme neither retains (5hm)C/(5f)C intermediates of preceding oxidations nor slides along a DNA substrate (without releasing it) to process an adjacent (5m)C residue. These findings contradict a recent report by Crawford et al. ( J. Am. Chem. Soc. 2016 , 138 , 730 ) claiming that oxidation of (5m)C by CD of mouse TET2 is chemically processive (iterative). We further elaborate that this distributive mechanism is maintained for TETs in two evolutionarily distant homologues and posit that this mode of function allows the introduction of (5m)C forms as epigenetic markers along the DNA.
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Affiliation(s)
- Esta Tamanaha
- New England Biolabs, Inc. , 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Shengxi Guan
- New England Biolabs, Inc. , 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Katherine Marks
- New England Biolabs, Inc. , 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Lana Saleh
- New England Biolabs, Inc. , 240 County Road, Ipswich, Massachusetts 01938, United States
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88
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Iurlaro M, McInroy GR, Burgess HE, Dean W, Raiber EA, Bachman M, Beraldi D, Balasubramanian S, Reik W. In vivo genome-wide profiling reveals a tissue-specific role for 5-formylcytosine. Genome Biol 2016; 17:141. [PMID: 27356509 PMCID: PMC4928330 DOI: 10.1186/s13059-016-1001-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/06/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Genome-wide methylation of cytosine can be modulated in the presence of TET and thymine DNA glycosylase (TDG) enzymes. TET is able to oxidise 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). TDG can excise the oxidative products 5fC and 5caC, initiating base excision repair. These modified bases are stable and detectable in the genome, suggesting that they could have epigenetic functions in their own right. However, functional investigation of the genome-wide distribution of 5fC has been restricted to cell culture-based systems, while its in vivo profile remains unknown. RESULTS Here, we describe the first analysis of the in vivo genome-wide profile of 5fC across a range of tissues from both wild-type and Tdg-deficient E11.5 mouse embryos. Changes in the formylation profile of cytosine upon depletion of TDG suggest TET/TDG-mediated active demethylation occurs preferentially at intron-exon boundaries and reveals a major role for TDG in shaping 5fC distribution at CpG islands. Moreover, we find that active enhancer regions specifically exhibit high levels of 5fC, resulting in characteristic tissue-diagnostic patterns, which suggest a role in embryonic development. CONCLUSIONS The tissue-specific distribution of 5fC can be regulated by the collective contribution of TET-mediated oxidation and excision by TDG. The in vivo profile of 5fC during embryonic development resembles that of embryonic stem cells, sharing key features including enrichment of 5fC in enhancer and intragenic regions. Additionally, by investigating mouse embryo 5fC profiles in a tissue-specific manner, we identify targeted enrichment at active enhancers involved in tissue development.
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Affiliation(s)
- Mario Iurlaro
- The Babraham Institute, Epigenetics Programme, Cambridge, CB22 3AT, UK
| | - Gordon R McInroy
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Heather E Burgess
- The Babraham Institute, Epigenetics Programme, Cambridge, CB22 3AT, UK
| | - Wendy Dean
- The Babraham Institute, Epigenetics Programme, Cambridge, CB22 3AT, UK
| | - Eun-Ang Raiber
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Martin Bachman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
- Present Address: Discovery Sciences, AstraZeneca, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Dario Beraldi
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK.
| | - Wolf Reik
- The Babraham Institute, Epigenetics Programme, 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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89
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Gross JA, Nagy C, Lin L, Bonneil É, Maheu M, Thibault P, Mechawar N, Jin P, Turecki G. Global and Site-Specific Changes in 5-Methylcytosine and 5-Hydroxymethylcytosine after Extended Post-mortem Interval. Front Genet 2016; 7:120. [PMID: 27446202 PMCID: PMC4917525 DOI: 10.3389/fgene.2016.00120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/11/2016] [Indexed: 02/04/2023] Open
Abstract
There has been a growing interest in the study of epigenetic mechanisms to elucidate the molecular bases of human brain-related diseases and disorders. Frequently, researchers utilize post-mortem tissue with the assumption that post-mortem tissue decay has little or no effect on epigenetic marks. Although previous studies show no effect of post-mortem interval on certain epigenetic marks, no such research has been performed on cytosine modifications. In this study, we use DNA from the brains of adult Sprague Dawley rats subjected to post-mortem intervals at room temperature, ranging from 0 to 96 h, to assess the stability of cytosine modifications, namely 5-methycytosine and 5-hydroxymethylcytosine. Our results indicate that neither global nor site-specific levels of 5-methycytosine and 5-hydroxymethylcytosine are affected by the post-mortem intervals we studied. As such, the use of post-mortem tissue to study cytosine modifications in the context of neurological or neuropsychiatric disorders is appropriate.
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Affiliation(s)
- Jeffrey A Gross
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal QC, Canada
| | - Corina Nagy
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal QC, Canada
| | - Li Lin
- Department of Human Genetics, Emory University School of Medicine, Atlanta GA, USA
| | - Éric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal QC, Canada
| | - Marissa Maheu
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal QC, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montreal QC, Canada
| | - Naguib Mechawar
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal QC, Canada
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta GA, USA
| | - Gustavo Turecki
- Department of Psychiatry, McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal QC, Canada
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90
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Abstract
A complete understanding of the function of the ten-eleven translocation (TET) family of dioxygenase-mediated DNA demethylation requires new methods to quantitatively map oxidized 5-methylcytosine (5mC) bases at high resolution. We have recently developed a methylase-assisted bisulfite sequencing (MAB-seq) method that allows base-resolution mapping of 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), two oxidized 5mC bases indicative of active DNA demethylation events. In standard bisulfite sequencing (BS-seq), unmodified C, 5fC and 5caC are read as thymine; thus 5fC and 5caC cannot be distinguished from C. In MAB-seq, unmodified C is enzymatically converted to 5mC, allowing direct mapping of rare modifications such as 5fC and 5caC. By combining MAB-seq with chemical reduction of 5fC to 5hmC, we also developed caMAB-seq, a method for direct 5caC mapping. Compared with subtraction-based mapping methods, MAB-seq and caMAB-seq require less sequencing effort and enable robust statistical calling of 5fC and/or 5caC. MAB-seq and caMAB-seq can be adapted to map 5fC/5caC at the whole-genome scale (WG-MAB-seq), within specific genomic regions enriched for enhancer-marking histone modifications (chromatin immunoprecipitation (ChIP)-MAB-seq), or at CpG-rich sequences (reduced-representation (RR)-MAB-seq) such as gene promoters. The full protocol, including DNA preparation, enzymatic treatment, library preparation and sequencing, can be completed within 6-8 d.
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91
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Wu H, Zhang Y. Charting oxidized methylcytosines at base resolution. Nat Struct Mol Biol 2016; 22:656-61. [PMID: 26333715 DOI: 10.1038/nsmb.3071] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 07/16/2015] [Indexed: 02/07/2023]
Abstract
DNA cytosine methylation is a key epigenetic mark that is required for normal mammalian development. Iterative oxidation of 5-methylcytosine (5mC) by the TET family of DNA dioxygenases generates three oxidized nucleotides: 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Recent advances in genomic mapping techniques have suggested that these oxidized cytosines not only function in the process of active reversal of 5mC but also may possess unique regulatory functions in the mammalian genome.
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Affiliation(s)
- Hao Wu
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston, Massachusetts, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, USA
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92
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Liao Y, Gu J, Wu Y, Long X, Ge DI, Xu J, Ding J. Low level of 5-Hydroxymethylcytosine predicts poor prognosis in non-small cell lung cancer. Oncol Lett 2016; 11:3753-3760. [PMID: 27313688 DOI: 10.3892/ol.2016.4474] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/18/2016] [Indexed: 02/02/2023] Open
Abstract
The loss of 5-hydroxymethylcytosine (5-hmC) has previously been demonstrated to be implicated in the initiation and progression of various tumors. However, its role in non-small cell lung cancer (NSCLC) remains unknown. The present study aimed to determine the level of 5-hmC in NSCLC and their adjacent normal lung tissues by immunohistochemistry and dot-blot analysis; then the relationship between 5-hmC level and the clinicopathological features of NSCLC and the prognostic significance of 5-hmC level in NSCLC patients were analyzed. By employing the dot-blot analysis, a significant reduction of 5-hmC level in NSCLC tissues compared with the adjacent normal tissues was detected, which were further verified by the immunohistochemistry results on tissue microarrays. Further analyses demonstrated that 65.38% (136/208) presented with low 5-hmC level, and low 5-hmC level was significantly associated with lymph node metastasis (P<0.001), histological type (P<0.001) and large tumor size (P=0.031). Notably, the 5-year overall survival rate of patients with low 5-hmC levels were significantly lower than patients with high 5-hmC levels (P<0.001). In addition, it was demonstrated that 5-hmC level was identified as independent prognostic factor in patients' overall survival. In conclusion, downregulation of 5-hmC may serve as a useful biomarker for NSCLC prognosis evaluation.
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Affiliation(s)
- Yunfei Liao
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China; Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Jie Gu
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Yongbing Wu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Xiang Long
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - D I Ge
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Jianjun Xu
- Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, P.R. China
| | - Jianyong Ding
- Department of Thoracic Surgery, The Affiliated Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
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93
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Abstract
Hundreds of distinct chemical modifications to DNA and histone amino acids have been described. Regulation exerted by these so-called epigenetic marks is vital to normal development, stability of cell identity through mitosis, and nongenetic transmission of traits between generations through meiosis. Loss of this regulation contributes to many diseases. Evidence indicates epigenetic marks function in combinations, whereby a given modification has distinct effects on local genome control, depending on which additional modifications are locally present. This review summarizes emerging methods for assessing combinatorial epigenomic states, as well as challenges and opportunities for their refinement.
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Affiliation(s)
- Paul D. Soloway
- Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, United States
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94
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Äijö T, Huang Y, Mannerström H, Chavez L, Tsagaratou A, Rao A, Lähdesmäki H. A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways. Genome Biol 2016; 17:49. [PMID: 26975309 PMCID: PMC4792102 DOI: 10.1186/s13059-016-0911-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/24/2016] [Indexed: 01/07/2023] Open
Abstract
We present a generative model, Lux, to quantify DNA methylation modifications from any combination of bisulfite sequencing approaches, including reduced, oxidative, TET-assisted, chemical-modification assisted, and methylase-assisted bisulfite sequencing data. Lux models all cytosine modifications (C, 5mC, 5hmC, 5fC, and 5caC) simultaneously together with experimental parameters, including bisulfite conversion and oxidation efficiencies, as well as various chemical labeling and protection steps. We show that Lux improves the quantification and comparison of cytosine modification levels and that Lux can process any oxidized methylcytosine sequencing data sets to quantify all cytosine modifications. Analysis of targeted data from Tet2-knockdown embryonic stem cells and T cells during development demonstrates DNA modification quantification at unprecedented detail, quantifies active demethylation pathways and reveals 5hmC localization in putative regulatory regions.
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Affiliation(s)
- Tarmo Äijö
- />Department of Computer Science, Aalto University School of Science, Aalto, FI-00076 Finland
- />Present address: Simons Center for Data Analysis, Simons Foundation, New York, NY 10010 USA
| | - Yun Huang
- />La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037 USA
- />Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037 USA
- />Present address: Institute of Biosciences & Technology, Texas A&M University Health Science Center, 2121 W. Holcombe Blvd, Houston, TX 77030 USA
| | - Henrik Mannerström
- />Department of Computer Science, Aalto University School of Science, Aalto, FI-00076 Finland
| | - Lukas Chavez
- />La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037 USA
- />Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037 USA
- />Present address: Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, 69120 Germany
| | | | - Anjana Rao
- />La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037 USA
- />Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037 USA
- />Department of Pharmacology and Moores Cancer Center, University of California, La Jolla, CA 92037 USA
- />Department of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, San Diego, CA 92037 USA
| | - Harri Lähdesmäki
- />Department of Computer Science, Aalto University School of Science, Aalto, FI-00076 Finland
- />Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, FI-20520 Finland
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95
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Hypoxia, Epithelial-Mesenchymal Transition, and TET-Mediated Epigenetic Changes. J Clin Med 2016; 5:jcm5020024. [PMID: 26861406 PMCID: PMC4773780 DOI: 10.3390/jcm5020024] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 01/15/2016] [Accepted: 01/26/2016] [Indexed: 12/14/2022] Open
Abstract
Tumor hypoxia is a pathophysiologic outcome of disrupted microcirculation with inadequate supply of oxygen, leading to enhanced proliferation, epithelial-mesenchymal transition (EMT), metastasis, and chemo-resistance. Epigenetic changes induced by hypoxia are well documented, and they lead to tumor progression. Recent advances show that DNA demethylation mediated by the Ten-eleven translocation (TET) proteins induces major epigenetic changes and controls key steps of cancer development. TET enzymes serve as 5mC (5-methylcytosine)-specific dioxygenases and cause DNA demethylation. Hypoxia activates the expression of TET1, which also serves as a co-activator of HIF-1α transcriptional regulation to modulate HIF-1α downstream target genes and promote epithelial-mesenchymal transition. As HIF is a negative prognostic factor for tumor progression, hypoxia-activated prodrugs (HAPs) may provide a favorable therapeutic approach to lessen hypoxia-induced malignancy.
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96
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Abstract
Aberrant DNA methylation is a characteristic feature of cancer including blood malignancies. Mutations in the DNA methylation regulators DNMT3A, TET1/2 and IDH1/2 are recurrent in leukemia and lymphoma. Specific and distinct DNA methylation patterns characterize subtypes of AML and lymphoma. Regulatory regions such as promoter CpG islands, CpG shores and enhancers show changes in methylation during transformation. However, the reported poor correlation between changes in methylation and gene expression in many mouse models and human studies reflects the complexity in the precise molecular mechanism for why aberrant DNA methylation promotes malignancies. This review will summarize current concepts regarding the mechanisms behind aberrant DNA methylation in hematopoietic malignancy and discuss its importance in cancer prognosis, tumor heterogeneity and relapse.
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Affiliation(s)
- Maria Guillamot
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, 10016, USA
| | - Luisa Cimmino
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, 10016, USA
| | - Iannis Aifantis
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY, 10016, USA
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97
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Peng J, Xia B, Yi C. Single-base resolution analysis of DNA epigenome via high-throughput sequencing. SCIENCE CHINA-LIFE SCIENCES 2016; 59:219-26. [PMID: 26825949 DOI: 10.1007/s11427-016-5013-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/27/2015] [Indexed: 12/21/2022]
Abstract
Epigenetic changes caused by DNA methylation and histone modifications play important roles in the regulation of various cellular processes and development. Recent discoveries of 5-methylcytosine (5mC) oxidation derivatives including 5-hydroxymethylcytosine (5hmC), 5-formylcytsine (5fC) and 5-carboxycytosine (5caC) in mammalian genome further expand our understanding of the epigenetic regulation. Analysis of DNA modification patterns relies increasingly on sequencing-based profiling methods. A number of different approaches have been established to map the DNA epigenomes with single-base resolution, as represented by the bisulfite-based methods, such as classical bisulfite sequencing (BS-seq), TAB-seq (TET-assisted bisulfite sequencing), oxBS-seq (oxidative bisulfite sequencing) and etc. These methods have been used to generate base-resolution maps of 5mC and its oxidation derivatives in genomic samples. The focus of this review will be to discuss the chemical methodologies that have been developed to detect the cytosine derivatives in the genomic DNA.
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Affiliation(s)
- Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Bo Xia
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. .,Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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98
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Peng L, Li Y, Xi Y, Li W, Li J, Lv R, Zhang L, Zou Q, Dong S, Luo H, Wu F, Yu W. MBD3L2 promotes Tet2 enzymatic activity for mediating 5-methylcytosine oxidation. J Cell Sci 2016; 129:1059-71. [PMID: 26769901 DOI: 10.1242/jcs.179044] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/10/2016] [Indexed: 12/25/2022] Open
Abstract
Ten-eleven translocation (Tet) proteins are key players involved in the dynamic regulation of cytosine methylation and demethylation. Inactivating mutations of Tet2 are frequently found in human malignancies, highlighting the essential role of Tet2 in cellular transformation. However, the factors that control Tet enzymatic activity remain largely unknown. Here, we found that methyl-CpG-binding domain protein 3 (MBD3) and its homolog MBD3-like 2 (MBD3L2) can specifically modulate the enzymatic activity of Tet2 protein, but not Tet1 and Tet3 proteins, in converting 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC). Moreover, MBD3L2 is more effective than MBD3 in promoting Tet2 enzymatic activity through strengthening the binding affinity between Tet2 and the methylated DNA target. Further analysis revealed pronounced decreases in 5mC levels at MBD3L2 and Tet2 co-occupied genomic regions, most of which are promoter elements associated with either cancer-related genes or genes involved in the regulation of cellular metabolic processes. Our data add new insights into the regulation of Tet2 activity by MBD3 and MBD3L2, and into how that affects Tet2-mediated modulation of its target genes in cancer development. Thus, they have important applications in understanding how dysregulation of Tet2 might contribute to human malignancy.
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Affiliation(s)
- Lina Peng
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Yan Li
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200032, China
| | - Yanping Xi
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Wei Li
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Jin Li
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Ruitu Lv
- Laboratory of Epigenetics, School of Basic Medicine and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Lei Zhang
- Biomedical Core Facility, School of Basic Medicine and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Qingping Zou
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Shihua Dong
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Huaibing Luo
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China
| | - Feizhen Wu
- Laboratory of Epigenetics, School of Basic Medicine and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Wenqiang Yu
- Laboratory of RNA Epigenetics, Institutes of Biomedical Sciences & Department of Biochemistry and Molecular Biology, Shanghai Medical College, Fudan University, 130 Dong-An Road, Shanghai 200032, China Key Laboratory of Ministry of Education, Department of Molecular Biology, Fudan University, 130 Dong-An Road, Shanghai 200032, China State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200032, China
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99
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Crawford DJ, Liu MY, Nabel CS, Cao XJ, Garcia BA, Kohli RM. Tet2 Catalyzes Stepwise 5-Methylcytosine Oxidation by an Iterative and de novo Mechanism. J Am Chem Soc 2016; 138:730-3. [PMID: 26734843 PMCID: PMC4762542 DOI: 10.1021/jacs.5b10554] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Modification of cytosine-guanine
dinucleotides (CpGs) is a key
part of mammalian epigenetic regulation and helps shape cellular identity.
Tet enzymes catalyze stepwise oxidation of 5-methylcytosine (mC) in
CpGs to 5-hydroxymethylcytosine (hmC), or onward to 5-formylcytosine
(fC) or 5-carboxylcytosine (caC). The multiple mC oxidation products,
while intricately linked, are postulated to play independent epigenetic
roles, making it critical to understand how the products of stepwise
oxidation are established and maintained. Using highly sensitive isotope-based
studies, we newly show that Tet2 can yield fC and caC by iteratively
acting in a single encounter with mC-containing DNA, without release
of the hmC intermediate, and that the modification state of the complementary
CpG has little impact on Tet2 activity. By revealing Tet2 as an iterative, de novo mC oxygenase, our study provides insight into how
features intrinsic to Tet2 shape the epigenetic landscape.
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Affiliation(s)
- Daniel J Crawford
- Department of Medicine, ‡Department of Biochemistry and Biophysics, and §Epigenetics Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Monica Yun Liu
- Department of Medicine, ‡Department of Biochemistry and Biophysics, and §Epigenetics Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Christopher S Nabel
- Department of Medicine, ‡Department of Biochemistry and Biophysics, and §Epigenetics Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Xing-Jun Cao
- Department of Medicine, ‡Department of Biochemistry and Biophysics, and §Epigenetics Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A Garcia
- Department of Medicine, ‡Department of Biochemistry and Biophysics, and §Epigenetics Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Rahul M Kohli
- Department of Medicine, ‡Department of Biochemistry and Biophysics, and §Epigenetics Program, Perelman School of Medicine, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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100
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Sanchez-Mut JV, Gräff J. Epigenetic Alterations in Alzheimer's Disease. Front Behav Neurosci 2015; 9:347. [PMID: 26734709 PMCID: PMC4681781 DOI: 10.3389/fnbeh.2015.00347] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 11/25/2015] [Indexed: 12/11/2022] Open
Abstract
Alzheimer’s disease (AD) is the major cause of dementia in Western societies. It progresses asymptomatically during decades before being belatedly diagnosed when therapeutic strategies have become unviable. Although several genetic alterations have been associated with AD, the vast majority of AD cases do not show strong genetic underpinnings and are thus considered a consequence of non-genetic factors. Epigenetic mechanisms allow for the integration of long-lasting non-genetic inputs on specific genetic backgrounds, and recently, a growing number of epigenetic alterations in AD have been described. For instance, an accumulation of dysregulated epigenetic mechanisms in aging, the predominant risk factor of AD, might facilitate the onset of the disease. Likewise, mutations in several enzymes of the epigenetic machinery have been associated with neurodegenerative processes that are altered in AD such as impaired learning and memory formation. Genome-wide and locus-specific epigenetic alterations have also been reported, and several epigenetically dysregulated genes validated by independent groups. From these studies, a picture emerges of AD as being associated with DNA hypermethylation and histone deacetylation, suggesting a general repressed chromatin state and epigenetically reduced plasticity in AD. Here we review these recent findings and discuss several technical and methodological considerations that are imperative for their correct interpretation. We also pay particular focus on potential implementations and theoretical frameworks that we expect will help to better direct future studies aimed to unravel the epigenetic participation in AD.
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Affiliation(s)
- Jose V Sanchez-Mut
- Neuroepigenetics Laboratory - UPGRAEFF, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
| | - Johannes Gräff
- Neuroepigenetics Laboratory - UPGRAEFF, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne Lausanne, Switzerland
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