101
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Oxidative stress in sperm affects the epigenetic reprogramming in early embryonic development. Epigenetics Chromatin 2018; 11:60. [PMID: 30333056 PMCID: PMC6192351 DOI: 10.1186/s13072-018-0224-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 09/17/2018] [Indexed: 12/27/2022] Open
Abstract
Background Reactive oxygen species (ROS)-induced oxidative stress is well known to play a major role in male infertility. Sperm are sensitive to ROS damaging effects because as male germ cells form mature sperm they progressively lose the ability to repair DNA damage. However, how oxidative DNA lesions in sperm affect early embryonic development remains elusive. Results Using cattle as model, we show that fertilization using sperm exposed to oxidative stress caused a major developmental arrest at the time of embryonic genome activation. The levels of DNA damage response did not directly correlate with the degree of developmental defects. The early cellular response for DNA damage, γH2AX, is already present at high levels in zygotes that progress normally in development and did not significantly increase at the paternal genome containing oxidative DNA lesions. Moreover, XRCC1, a factor implicated in the last step of base excision repair (BER) pathway, was recruited to the damaged paternal genome, indicating that the maternal BER machinery can repair these DNA lesions induced in sperm. Remarkably, the paternal genome with oxidative DNA lesions showed an impairment of zygotic active DNA demethylation, a process that previous studies linked to BER. Quantitative immunofluorescence analysis and ultrasensitive LC–MS-based measurements revealed that oxidative DNA lesions in sperm impair active DNA demethylation at paternal pronuclei, without affecting 5-hydroxymethylcytosine (5hmC), a 5-methylcytosine modification that has been implicated in paternal active DNA demethylation in mouse zygotes. Thus, other 5hmC-independent processes are implicated in active DNA demethylation in bovine embryos. The recruitment of XRCC1 to damaged paternal pronuclei indicates that oxidative DNA lesions drive BER to repair DNA at the expense of DNA demethylation. Finally, this study highlighted striking differences in DNA methylation dynamics between bovine and mouse zygotes that will facilitate the understanding of the dynamics of DNA methylation in early development. Conclusions The data demonstrate that oxidative stress in sperm has an impact not only on DNA integrity but also on the dynamics of epigenetic reprogramming, which may harm the paternal genetic and epigenetic contribution to the developing embryo and affect embryo development and embryo quality. Electronic supplementary material The online version of this article (10.1186/s13072-018-0224-y) contains supplementary material, which is available to authorized users.
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102
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Hrit J, Goodrich L, Li C, Wang BA, Nie J, Cui X, Martin EA, Simental E, Fernandez J, Liu MY, Nery JR, Castanon R, Kohli RM, Tretyakova N, He C, Ecker JR, Goll M, Panning B. OGT binds a conserved C-terminal domain of TET1 to regulate TET1 activity and function in development. eLife 2018; 7:34870. [PMID: 30325306 PMCID: PMC6214653 DOI: 10.7554/elife.34870] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 10/15/2018] [Indexed: 12/11/2022] Open
Abstract
TET enzymes convert 5-methylcytosine to 5-hydroxymethylcytosine and higher oxidized derivatives. TETs stably associate with and are post-translationally modified by the nutrient-sensing enzyme OGT, suggesting a connection between metabolism and the epigenome. Here, we show for the first time that modification by OGT enhances TET1 activity in vitro. We identify a TET1 domain that is necessary and sufficient for binding to OGT and report a point mutation that disrupts the TET1-OGT interaction. We show that this interaction is necessary for TET1 to rescue hematopoetic stem cell production in tet mutant zebrafish embryos, suggesting that OGT promotes TET1’s function during development. Finally, we show that disrupting the TET1-OGT interaction in mouse embryonic stem cells changes the abundance of TET2 and 5-methylcytosine, which is accompanied by alterations in gene expression. These results link metabolism and epigenetic control, which may be relevant to the developmental and disease processes regulated by these two enzymes.
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Affiliation(s)
- Joel Hrit
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States.,TETRAD Graduate Program, University of California San Francisco, San Francisco, United States
| | - Leeanne Goodrich
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States.,TETRAD Graduate Program, University of California San Francisco, San Francisco, United States
| | - Cheng Li
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Program in Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology (BCMB Allied program), Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States
| | - Bang-An Wang
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States
| | - Ji Nie
- Department of Chemistry, Howard Hughes Medical Institute, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.,Institute for Biophysical Dynamics, University of Chicago, Chicago, United States
| | - Xiaolong Cui
- Department of Chemistry, Howard Hughes Medical Institute, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.,Institute for Biophysical Dynamics, University of Chicago, Chicago, United States
| | - Elizabeth Allene Martin
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States.,TETRAD Graduate Program, University of California San Francisco, San Francisco, United States
| | - Eric Simental
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States.,TETRAD Graduate Program, University of California San Francisco, San Francisco, United States
| | - Jenna Fernandez
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, United States
| | - Monica Yun Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Joseph R Nery
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States
| | - Rosa Castanon
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States
| | - Rahul M Kohli
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, United States
| | - Chuan He
- Department of Chemistry, Howard Hughes Medical Institute, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.,Institute for Biophysical Dynamics, University of Chicago, Chicago, United States
| | - Joseph R Ecker
- Genomic Analysis Laboratory and Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, United States
| | - Mary Goll
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Barbara Panning
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States
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103
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Li J, Liang W, Li Y, Qian W. APURINIC/APYRIMIDINIC ENDONUCLEASE2 and ZINC FINGER DNA 3'-PHOSPHOESTERASE Play Overlapping Roles in the Maintenance of Epigenome and Genome Stability. THE PLANT CELL 2018; 30:1954-1970. [PMID: 30135084 PMCID: PMC6181018 DOI: 10.1105/tpc.18.00287] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/19/2018] [Accepted: 08/22/2018] [Indexed: 05/21/2023]
Abstract
Base excision repair (BER) is essential for active DNA demethylation and DNA damage repair in mammals and plants. Here, we provide genetic and biochemical evidence that APURINIC/APYRIMIDINIC ENDONUCLEASE2 (APE2) plays overlapping roles with ZINC FINGER DNA 3'-PHOSPHOESTERASE (ZDP) in active DNA demethylation and DNA damage repair in Arabidopsis thaliana Simultaneous mutation of APE2 and ZDP causes DNA hypermethylation at more than 2000 loci, most of which are not hypermethylated in ape2 or zdp single mutants. The zdp and ape2 single mutants exhibit normal development, but the zdp ape2 double mutants display pleiotropic developmental defects and are supersensitive to the DNA alkylating reagent methyl methanesulfonate. The gradual accumulation of DNA lesions in the zdp ape2 seedlings is accompanied by constitutive activation of the DNA damage response and alteration of the cell cycle. Interestingly, knockout of the key DNA demethylase REPRESSOR OF SILENCING1 reduces the magnitude of DNA lesion accumulation and the DNA damage response in the zdp ape2 mutants, suggesting that a proportion of the DNA damage in the zdp ape2 mutants arises from incomplete active DNA demethylation. Lastly, we find that APE2 has 3'-phosphatase activity and strong 3'-5' exonuclease activity in vitro. Together, our results suggest that APE2 and ZDP, two BER proteins, play overlapping roles in the maintenance of epigenome and genome stability in plants.
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Affiliation(s)
- Jinchao Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenjie Liang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
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104
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Lanata CM, Chung SA, Criswell LA. DNA methylation 101: what is important to know about DNA methylation and its role in SLE risk and disease heterogeneity. Lupus Sci Med 2018; 5:e000285. [PMID: 30094041 PMCID: PMC6069928 DOI: 10.1136/lupus-2018-000285] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 06/25/2018] [Indexed: 12/20/2022]
Abstract
SLE is a complex autoimmune disease that results from the interplay of genetics, epigenetics and environmental exposures. DNA methylation is an epigenetic mechanism that regulates gene expression and tissue differentiation. Among all the epigenetic modifications, DNA methylation perturbations have been the most widely studied in SLE. It mediates processes relevant to SLE, including lymphocyte development, X-chromosome inactivation and the suppression of endogenous retroviruses. The establishment of most DNA methylation marks occurs in utero; however, a small percentage of epigenetic marks are dynamic and can change throughout a person’s lifetime and in relation to exposures. In this review, we discuss the current understanding of the biology of DNA methylation and its regulators, the measurement and interpretation of methylation marks, the effects of genetics on DNA methylation and the role of environmental exposures with relevance to SLE. We also summarise research findings associated with SLE disease risk and heterogeneity. The robust finding of hypomethylation of interferon-responsive genes in patients with SLE and new associations beyond interferon-responsive genes such as cell-specific methylation abnormalities are described. We also discuss methylation changes associated with lupus nephritis, autoantibody status and disease activity. Lastly, we explore future research directions, emphasising the need for longitudinal studies, cell tissue and context-specific profiling, as well as integrative approaches. With new technologies, DNA methylation perturbations could be targeted and edited, offering novel therapeutic approaches.
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Affiliation(s)
- Cristina M Lanata
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Sharon A Chung
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Lindsey A Criswell
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, California, USA
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105
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Murín R, Abdalla M, Murínová N, Hatok J, Dobrota D. The metabolism of 5-methylcytosine residues in DNA. Physiol Res 2018. [PMID: 29527909 DOI: 10.33549/physiolres.933550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The fundamental biochemical processes of 5-methylcytosine (5-mC) synthesis, maintenance, conversion and removal determine the time and spatial pattern of DNA methylation. This has a strong effect on a plethora of physiological aspects of cellular metabolism. While the presence of 5-mC within the promoter region can silence gene expression, its derivative - 5-hydroxymethylcytosine exerts an opposite effect. Dysregulations in the metabolism of 5-mC lead to an altered DNA methylation pattern which is linked with a disrupted epigenome, and are considered to play a significant part in the etiology of several human diseases. A summary of recent knowledge about the molecular processes participating in DNA methylation pattern shaping is provided here.
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Affiliation(s)
- R Murín
- Department of Medical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic.
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106
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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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107
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Someya K, Nakatsukasa H, Ito M, Kondo T, Tateda KI, Akanuma T, Koya I, Sanosaka T, Kohyama J, Tsukada YI, Takamura-Enya T, Yoshimura A. Improvement of Foxp3 stability through CNS2 demethylation by TET enzyme induction and activation. Int Immunol 2018; 29:365-375. [PMID: 29048538 PMCID: PMC5890887 DOI: 10.1093/intimm/dxx049] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/05/2017] [Indexed: 12/12/2022] Open
Abstract
Since induced regulatory T cells (iTregs) can be produced in a large quantity in vitro, these cells are expected to be clinically useful to induce immunological tolerance in various immunological diseases. Foxp3 (Forkhead box P3) expression in iTregs is, however, unstable due to the lack of demethylation of the CpG island in the conserved non-coding sequence 2 (CNS2) of the Foxp3 locus. To facilitate the demethylation of CNS2, we over-expressed the catalytic domain (CD) of the ten-eleven translocation (TET) protein, which catalyzes the steps of the iterative demethylation of 5-methylcytosine. TET-CD over-expression in iTregs resulted in partial demethylation of CNS2 and stable Foxp3 expression. We also discovered that TET expression was enhanced under low oxygen (5%) culture conditions, which facilitated CNS2 DNA demethylation and stabilization of Foxp3 expression in a TET2- and TET3-dependent manner. In combination with vitamin C treatment, which has been reported to enhance TET catalytic activity, iTregs generated under low oxygen conditions retained more stable Foxp3 expression in vitro and in vivo and exhibited stronger suppression activity in a colitis model compared with untreated iTregs. Our data indicate that the induction and activation of TET enzymes in iTregs would be an effective method for Treg-mediated adoptive immunotherapy.
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Affiliation(s)
| | | | - Minako Ito
- Department of Microbiology and Immunology
| | | | | | | | - Ikuko Koya
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Tsukasa Sanosaka
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Jun Kohyama
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yu-Ichi Tsukada
- Advanced Biological Information Research Division, Inamori Frontier Research Center, Kyushu University, Fukuoka, Fukuoka 819-0395, Japan
| | - Takeji Takamura-Enya
- Department of Applied Chemistry, Kanagawa Institute of Technology, Shimo-Ogino 1030, Atsugi-shi 243-0292, Japan
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108
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Champroux A, Cocquet J, Henry-Berger J, Drevet JR, Kocer A. A Decade of Exploring the Mammalian Sperm Epigenome: Paternal Epigenetic and Transgenerational Inheritance. Front Cell Dev Biol 2018; 6:50. [PMID: 29868581 PMCID: PMC5962689 DOI: 10.3389/fcell.2018.00050] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 04/18/2018] [Indexed: 12/12/2022] Open
Abstract
The past decade has seen a tremendous increase in interest and progress in the field of sperm epigenetics. Studies have shown that chromatin regulation during male germline development is multiple and complex, and that the spermatozoon possesses a unique epigenome. Its DNA methylation profile, DNA-associated proteins, nucleo-protamine distribution pattern and non-coding RNA set up a unique epigenetic landscape which is delivered, along with its haploid genome, to the oocyte upon fertilization, and therefore can contribute to embryogenesis and to the offspring health. An emerging body of compelling data demonstrates that environmental exposures and paternal lifestyle can change the sperm epigenome and, consequently, may affect both the embryonic developmental program and the health of future generations. This short review will attempt to provide an overview of what is currently known about sperm epigenome and the existence of transgenerational epigenetic inheritance of paternally acquired traits that may contribute to the offspring phenotype.
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Affiliation(s)
- Alexandre Champroux
- GReD, Laboratoire “Génétique, Reproduction and Développement,” UMR Centre National de la Recherche Scientifique 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Julie Cocquet
- INSERM U1016, Institut Cochin, Centre National de la Recherche Scientifique UMR8104, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Joëlle Henry-Berger
- GReD, Laboratoire “Génétique, Reproduction and Développement,” UMR Centre National de la Recherche Scientifique 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Joël R. Drevet
- GReD, Laboratoire “Génétique, Reproduction and Développement,” UMR Centre National de la Recherche Scientifique 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ayhan Kocer
- GReD, Laboratoire “Génétique, Reproduction and Développement,” UMR Centre National de la Recherche Scientifique 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
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109
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Nishio K, Belle R, Katoh T, Kawamura A, Sengoku T, Hanada K, Ohsawa N, Shirouzu M, Yokoyama S, Suga H. Thioether Macrocyclic Peptides Selected against TET1 Compact Catalytic Domain Inhibit TET1 Catalytic Activity. Chembiochem 2018; 19:979-985. [PMID: 29665240 DOI: 10.1002/cbic.201800047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Indexed: 12/29/2022]
Abstract
The ten-eleven translocation (TET) protein family, consisting of three isoforms (TET1/2/3), have been found in mammalian cells and have a crucial role in 5-methylcytosine demethylation in genomic DNA through the catalysis of oxidation reactions assisted by 2-oxoglutarate (2OG). DNA methylation/demethylation contributes to the regulation of gene expression at the transcriptional level, and recent studies have revealed that TET1 is highly elevated in malignant cells of various diseases and related to malignant alteration. TET1 inhibitors based on a scaffold of thioether macrocyclic peptides, which have been discovered by the random nonstandard peptide integrated discovery (RaPID) system, are reported. The affinity-based selection was performed against the TET1 compact catalytic domain (TET1CCD) to yield thioether macrocyclic peptides. These peptides exhibited inhibitory activity of the TET1 catalytic domain (TET1CD), with an IC50 value as low as 1.1 μm. One of the peptides, TiP1, was also able to inhibit TET1CD over TET2CD with tenfold selectivity, although it was likely to target the 2OG binding site; this provides a good starting point to develop more selective inhibitors.
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Affiliation(s)
- Kosuke Nishio
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Roman Belle
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Akane Kawamura
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Welcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Toru Sengoku
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Kazuharu Hanada
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Noboru Ohsawa
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mikako Shirouzu
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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110
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Arsenic-containing hydrocarbons: effects on gene expression, epigenetics, and biotransformation in HepG2 cells. Arch Toxicol 2018; 92:1751-1765. [PMID: 29602950 DOI: 10.1007/s00204-018-2194-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/20/2018] [Indexed: 01/29/2023]
Abstract
Arsenic-containing hydrocarbons (AsHCs), a subgroup of arsenolipids found in fish and algae, elicit substantial toxic effects in various human cell lines and have a considerable impact on cellular energy levels. The underlying mode of action, however, is still unknown. The present study analyzes the effects of two AsHCs (AsHC 332 and AsHC 360) on the expression of 44 genes covering DNA repair, stress response, cell death, autophagy, and epigenetics via RT-qPCR in human liver (HepG2) cells. Both AsHCs affected the gene expression, but to different extents. After treatment with AsHC 360, flap structure-specific endonuclease 1 (FEN1) as well as xeroderma pigmentosum group A complementing protein (XPA) and (cytosine-5)-methyltransferase 3A (DNMT3A) showed time- and concentration-dependent alterations in gene expression, thereby indicating an impact on genomic stability. In the subsequent analysis of epigenetic markers, within 72 h, neither AsHC 332 nor AsHC 360 showed an impact on the global DNA methylation level, whereas incubation with AsHC 360 increased the global DNA hydroxymethylation level. Analysis of cell extracts and cell media by HPLC-mass spectrometry revealed that both AsHCs were considerably biotransformed. The identified metabolites include not only the respective thioxo-analogs of the two AsHCs, but also several arsenic-containing fatty acids and fatty alcohols, contributing to our knowledge of biotransformation mechanisms of arsenolipids.
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111
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112
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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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113
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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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Hardwick JS, Lane AN, Brown T. Epigenetic Modifications of Cytosine: Biophysical Properties, Regulation, and Function in Mammalian DNA. Bioessays 2018; 40. [DOI: 10.1002/bies.201700199] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/13/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Jack S. Hardwick
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
| | - Andrew N. Lane
- Department of Toxicology and Cancer Biology; University of Kentucky; 789 S. Limestone St. Lexington KY 40536 USA
| | - Tom Brown
- Chemistry Research Laboratory; Department of Chemistry; University of Oxford; 12 Mansfield Road Oxford OX1 3TA UK
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Spallotta F, Cencioni C, Atlante S, Garella D, Cocco M, Mori M, Mastrocola R, Kuenne C, Guenther S, Nanni S, Azzimato V, Zukunft S, Kornberger A, Sürün D, Schnütgen F, von Melchner H, Di Stilo A, Aragno M, Braspenning M, van Criekinge W, De Blasio MJ, Ritchie RH, Zaccagnini G, Martelli F, Farsetti A, Fleming I, Braun T, Beiras-Fernandez A, Botta B, Collino M, Bertinaria M, Zeiher AM, Gaetano C. Stable Oxidative Cytosine Modifications Accumulate in Cardiac Mesenchymal Cells From Type2 Diabetes Patients. Circ Res 2018; 122:31-46. [DOI: 10.1161/circresaha.117.311300] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 11/10/2017] [Accepted: 11/16/2017] [Indexed: 12/17/2022]
Abstract
Rationale:
Human cardiac mesenchymal cells (CMSCs) are a therapeutically relevant primary cell population. Diabetes mellitus compromises CMSC function as consequence of metabolic alterations and incorporation of stable epigenetic changes.
Objective:
To investigate the role of α-ketoglutarate (αKG) in the epimetabolic control of DNA demethylation in CMSCs.
Methods and Results:
Quantitative global analysis, methylated and hydroxymethylated DNA sequencing, and gene-specific GC methylation detection revealed an accumulation of 5-methylcytosine, 5-hydroxymethylcytosine, and 5-formylcytosine in the genomic DNA of human CMSCs isolated from diabetic donors. Whole heart genomic DNA analysis revealed iterative oxidative cytosine modification accumulation in mice exposed to high-fat diet (HFD), injected with streptozotocin, or both in combination (streptozotocin/HFD). In this context, untargeted and targeted metabolomics indicated an intracellular reduction of αKG synthesis in diabetic CMSCs and in the whole heart of HFD mice. This observation was paralleled by a compromised TDG (thymine DNA glycosylase) and TET1 (ten–eleven translocation protein 1) association and function with TET1 relocating out of the nucleus. Molecular dynamics and mutational analyses showed that αKG binds TDG on Arg275 providing an enzymatic allosteric activation. As a consequence, the enzyme significantly increased its capacity to remove G/T nucleotide mismatches or 5-formylcytosine. Accordingly, an exogenous source of αKG restored the DNA demethylation cycle by promoting TDG function, TET1 nuclear localization, and TET/TDG association. TDG inactivation by CRISPR/Cas9 knockout or TET/TDG siRNA knockdown induced 5-formylcytosine accumulation, thus partially mimicking the diabetic epigenetic landscape in cells of nondiabetic origin. The novel compound (S)-2-[(2,6-dichlorobenzoyl)amino]succinic acid (AA6), identified as an inhibitor of αKG dehydrogenase, increased the αKG level in diabetic CMSCs and in the heart of HFD and streptozotocin mice eliciting, in HFD, DNA demethylation, glucose uptake, and insulin response.
Conclusions:
Restoring the epimetabolic control of DNA demethylation cycle promises beneficial effects on cells compromised by environmental metabolic changes.
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Affiliation(s)
- Francesco Spallotta
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Chiara Cencioni
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Sandra Atlante
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Davide Garella
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Mattia Cocco
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Mattia Mori
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Raffaella Mastrocola
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Carsten Kuenne
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Stefan Guenther
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Simona Nanni
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Valerio Azzimato
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Sven Zukunft
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Angela Kornberger
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Duran Sürün
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Frank Schnütgen
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Harald von Melchner
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Antonella Di Stilo
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Manuela Aragno
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Maarten Braspenning
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Wim van Criekinge
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Miles J. De Blasio
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Rebecca H. Ritchie
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Germana Zaccagnini
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Fabio Martelli
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Antonella Farsetti
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Ingrid Fleming
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Thomas Braun
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Andres Beiras-Fernandez
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Bruno Botta
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Massimo Collino
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Massimo Bertinaria
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Andreas M. Zeiher
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Carlo Gaetano
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
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116
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Lejart A, Salbert G, Huet S. Cytosine hydroxymethylation by TET enzymes: From the control of gene expression to the regulation of DNA repair mechanisms, and back. AIMS BIOPHYSICS 2018. [DOI: 10.3934/biophy.2018.3.182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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117
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Muñoz-López Á, Summerer D. Recognition of Oxidized 5-Methylcytosine Derivatives in DNA by Natural and Engineered Protein Scaffolds. CHEM REC 2017; 18:105-116. [PMID: 29251421 DOI: 10.1002/tcr.201700088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Indexed: 12/14/2022]
Abstract
Methylation of genomic cytosine to 5-methylcytosine is a central regulatory element of mammalian gene expression with important roles in development and disease. 5-methylcytosine can be actively reversed to cytosine via oxidation to 5-hydroxymethyl-, 5-formyl-, and 5-carboxylcytosine by ten-eleven-translocation dioxygenases and subsequent base excision repair or replication-dependent dilution. Moreover, the oxidized 5-methylcytosine derivatives are potential epigenetic marks with unique biological roles. Key to a better understanding of these roles are insights into the interactions of the nucleobases with DNA-binding protein scaffolds: Natural scaffolds involved in transcription, 5-methylcytosine-reading and -editing as well as general chromatin organization can be selectively recruited or repulsed by oxidized 5-methylcytosines, forming the basis of their biological functions. Moreover, designer protein scaffolds engineered for the selective recognition of oxidized 5-methylcytosines are valuable tools to analyze their genomic levels and distribution. Here, we review recent structural and functional insights into the molecular recognition of oxidized 5-methylcytosine derivatives in DNA by selected protein scaffolds.
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Affiliation(s)
- Álvaro Muñoz-López
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund
| | - Daniel Summerer
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund
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118
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Kitsera N, Allgayer J, Parsa E, Geier N, Rossa M, Carell T, Khobta A. Functional impacts of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine at a single hemi-modified CpG dinucleotide in a gene promoter. Nucleic Acids Res 2017; 45:11033-11042. [PMID: 28977475 PMCID: PMC5737506 DOI: 10.1093/nar/gkx718] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 08/08/2017] [Indexed: 12/19/2022] Open
Abstract
Enzymatic oxidation of 5-methylcytosine (5-mC) in the CpG dinucleotides to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxycytosine (5-caC) has central role in the process of active DNA demethylation and epigenetic reprogramming in mammals. However, it is not known whether the 5-mC oxidation products have autonomous epigenetic or regulatory functions in the genome. We used an artificial upstream promoter constituted of one cAMP response element (CRE) to measure the impact of 5-mC in a hemi-methylated CpG on the promoter activity and further explored the consequences of 5-hmC, 5-fC, and 5-caC in the same system. All modifications induced mild impairment of the CREB transcription factor binding to the consensus 5'-TGACGTCA-3' CRE sequence. The decrease of the gene expression by 5-mC or 5-hmC was proportional to the impairment of CREB binding and had a steady character over at least 48 h. In contrast, promoters containing single 5-fC or 5-caC underwent further progressive loss of activity, up to an almost complete repression. This decline was dependent on the thymine-DNA glycosylase (TDG). The results thus indicate that 5-fC and 5-caC can provide a signal for perpetuation and enhancement of the repressed transcriptional state by a mechanism that requires base excision repair.
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Affiliation(s)
- Nataliya Kitsera
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz 55131, Germany
| | - Julia Allgayer
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, Mainz 55128, Germany
| | - Edris Parsa
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Nadine Geier
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz 55131, Germany
| | - Martin Rossa
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Andriy Khobta
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz 55131, Germany.,Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, Mainz 55128, Germany
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119
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Valentini E, Zampieri M, Malavolta M, Bacalini MG, Calabrese R, Guastafierro T, Reale A, Franceschi C, Hervonen A, Koller B, Bernhardt J, Slagboom PE, Toussaint O, Sikora E, Gonos ES, Breusing N, Grune T, Jansen E, Dollé MET, Moreno-Villanueva M, Sindlinger T, Bürkle A, Ciccarone F, Caiafa P. Analysis of the machinery and intermediates of the 5hmC-mediated DNA demethylation pathway in aging on samples from the MARK-AGE Study. Aging (Albany NY) 2017; 8:1896-1922. [PMID: 27587280 PMCID: PMC5076444 DOI: 10.18632/aging.101022] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/15/2016] [Indexed: 12/22/2022]
Abstract
Gradual changes in the DNA methylation landscape occur throughout aging virtually in all human tissues. A widespread reduction of 5-methylcytosine (5mC), associated with highly reproducible site-specific hypermethylation, characterizes the genome in aging. Therefore, an equilibrium seems to exist between general and directional deregulating events concerning DNA methylation controllers, which may underpin the age-related epigenetic changes. In this context, 5mC-hydroxylases (TET enzymes) are new potential players. In fact, TETs catalyze the stepwise oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), driving the DNA demethylation process based on thymine DNA glycosylase (TDG)-mediated DNA repair pathway. The present paper reports the expression of DNA hydroxymethylation components, the levels of 5hmC and of its derivatives in peripheral blood mononuclear cells of age-stratified donors recruited in several European countries in the context of the EU Project 'MARK-AGE'. The results provide evidence for an age-related decline of TET1, TET3 and TDG gene expression along with a decrease of 5hmC and an accumulation of 5caC. These associations were independent of confounding variables, including recruitment center, gender and leukocyte composition. The observed impairment of 5hmC-mediated DNA demethylation pathway in blood cells may lead to aberrant transcriptional programs in the elderly.
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Affiliation(s)
- Elisabetta Valentini
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy.,Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Michele Zampieri
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy.,Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Marco Malavolta
- National Institute of Health and Science on Aging (INRCA), Nutrition and Ageing Centre, Scientific and Technological Research Area, 60100 Ancona, Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40126, Italy.,CIG-Interdepartmental Center "L. Galvani", Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Roberta Calabrese
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy.,Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Tiziana Guastafierro
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy.,Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Anna Reale
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40126, Italy.,CIG-Interdepartmental Center "L. Galvani", Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Antti Hervonen
- The School of Medicine, The University of Tampere, 33014 Tampere, Finland
| | - Bernhard Koller
- Department for Internal Medicine, University Teaching Hospital Hall in Tirol, Tirol, Austria
| | | | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Olivier Toussaint
- University of Namur, Research Unit on Cellular Biology, Namur B-5000, Belgium
| | - Ewa Sikora
- Laboratory of the Molecular Bases of Ageing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Efstathios S Gonos
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, Athens, Greece
| | - Nicolle Breusing
- Institute of Nutritional Medicine (180c), University of Hohenheim, 70599 Stuttgart, Gemany
| | - Tilman Grune
- German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany
| | - Eugène Jansen
- Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | - Martijn E T Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | - María Moreno-Villanueva
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Thilo Sindlinger
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Fabio Ciccarone
- Department of Biology, University of Rome "Tor Vergata", 00133 Rome, Italy.,Shared senior authorship
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy.,Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy.,Shared senior authorship
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120
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Ellison EM, Bradley-Whitman MA, Lovell MA. Single-Base Resolution Mapping of 5-Hydroxymethylcytosine Modifications in Hippocampus of Alzheimer's Disease Subjects. J Mol Neurosci 2017; 63:185-197. [PMID: 28866733 PMCID: PMC5909840 DOI: 10.1007/s12031-017-0969-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/23/2017] [Indexed: 12/19/2022]
Abstract
Epigenetic modifications to cytosine have been shown to regulate transcription in cancer, embryonic development, and recently neurodegeneration. While cytosine methylation studies are now common in neurodegenerative research, hydroxymethylation studies are rare, particularly genome-wide mapping studies. As an initial study to analyze 5-hydroxymethylcytosine (5-hmC) in the Alzheimer's disease (AD) genome, reduced representation hydroxymethylation profiling (RRHP) was used to analyze more than 2 million sites of possible modification in hippocampal DNA of sporadic AD and normal control subjects. Genes with differentially hydroxymethylated regions were filtered based on previously published microarray data for altered gene expression in hippocampal DNA of AD subjects. Our data show significant pathways for altered levels of 5-hmC in the hippocampus of AD subjects compared to age-matched normal controls involved in signaling, energy metabolism, cell function, gene expression, protein degradation, and cell structure and stabilization. Overall, our data suggest a possible role for the dysregulation of epigenetic modifications to cytosine in late stage AD.
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Affiliation(s)
| | - Melissa A Bradley-Whitman
- Sanders-Brown Center on Aging, University of Kentucky, 135 Sanders-Brown Center on Aging, 800 South Limestone S, Lexington, KY, 40536, USA
| | - Mark A Lovell
- Department of Chemistry, University of Kentucky, Lexington, KY, USA.
- Sanders-Brown Center on Aging, University of Kentucky, 135 Sanders-Brown Center on Aging, 800 South Limestone S, Lexington, KY, 40536, USA.
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121
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Slyvka A, Mierzejewska K, Bochtler M. Nei-like 1 (NEIL1) excises 5-carboxylcytosine directly and stimulates TDG-mediated 5-formyl and 5-carboxylcytosine excision. Sci Rep 2017; 7:9001. [PMID: 28827588 PMCID: PMC5566547 DOI: 10.1038/s41598-017-07458-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/26/2017] [Indexed: 01/01/2023] Open
Abstract
Thymine DNA glycosylase (TDG) and Nei-like 1 (NEIL1) have both been implicated in the base excision repair step of active DNA demethylation. The robust glycosylase activity of TDG on DNA substrates containing 5-formylcytosine (5fC) or 5-carboxylcytosine (5caC) is universally accepted, but the mode of action of NEIL1 is still debated. Based on genetic experiments, it has been suggested that NEIL1 acts redundantly with TDG and excises 5fC and 5caC directly. However, this result has been disputed, and it was suggested instead that NEIL1 is recruited by the monofunctional TDG for the 2′-deoxyribose excision step. Using purified human NEIL1 and its catalytically impaired P2T and E3Q variants as controls, we detect NEIL1 activity on 5caC, but not a 5fC containing dsDNA substrate. We confirm direct NEIL1 TDG binding and NEIL1 mediated 2′-deoxyribose excision downstream of TDG glycosylase activity. NEIL1 acts not only downstream of TDG, but also enhances TDG activity on 5fC or 5caC containing DNA. NEIL1 mediated enhancement of the TDG glycosylase activity is substrate specific and does not occur for dsDNA with a T/G mismatch.
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Affiliation(s)
- Anton Slyvka
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Karolina Mierzejewska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland. .,Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Pawinskiego 5a, 02-106, Warsaw, Poland.
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122
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Abstract
The physiological identity of every cell is maintained by highly specific transcriptional networks that establish a coherent molecular program that is in tune with nutritional conditions. The regulation of cell-specific transcriptional networks is accomplished by an epigenetic program via chromatin-modifying enzymes, whose activity is directly dependent on metabolites such as acetyl-coenzyme A, S-adenosylmethionine, and NAD+, among others. Therefore, these nuclear activities are directly influenced by the nutritional status of the cell. In addition to nutritional availability, this highly collaborative program between epigenetic dynamics and metabolism is further interconnected with other environmental cues provided by the day-night cycles imposed by circadian rhythms. Herein, we review molecular pathways and their metabolites associated with epigenetic adaptations modulated by histone- and DNA-modifying enzymes and their responsiveness to the environment in the context of health and disease.
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123
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Genome Stability by DNA Polymerase β in Neural Progenitors Contributes to Neuronal Differentiation in Cortical Development. J Neurosci 2017; 37:8444-8458. [PMID: 28765330 DOI: 10.1523/jneurosci.0665-17.2017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 07/06/2017] [Accepted: 07/27/2017] [Indexed: 01/21/2023] Open
Abstract
DNA repair is crucial for genome stability in the developing cortex, as somatic de novo mutations cause neurological disorders. However, how DNA repair contributes to neuronal development is largely unknown. To address this issue, we studied the spatiotemporal roles of DNA polymerase β (Polβ), a key enzyme in DNA base excision repair pathway, in the developing cortex using distinct forebrain-specific conditional knock-out mice, Emx1-Cre/Polβ fl/fl and Nex-Cre/Polβ fl/fl mice. Polβ expression was absent in both neural progenitors and postmitotic neurons in Emx1-Cre/Polβ fl/fl mice, whereas only postmitotic neurons lacked Polβ expression in Nex-Cre/Polβ fl/fl mice. We found that DNA double-strand breaks (DSBs) were frequently detected during replication in cortical progenitors of Emx1-Cre/Polβ fl/fl mice. Increased DSBs remained in postmitotic cells, which resulted in p53-mediated neuronal apoptosis. This neuronal apoptosis caused thinning of the cortical plate, although laminar structure was normal. In addition, accumulated DSBs also affected growth of corticofugal axons but not commissural axons. These phenotypes were not observed in Nex-Cre/Polβ fl/fl mice. Moreover, cultured Polβ-deficient neural progenitors exhibited higher sensitivity to the base-damaging agent methylmethanesulfonate, resulting in enhanced DSB formation. Similar damage was found by vitamin C treatment, which induces TET1-mediated DNA demethylation via 5-hydroxymethylcytosine. Together, genome stability mediated by Polβ-dependent base excision repair is crucial for the competence of neural progenitors, thereby contributing to neuronal differentiation in cortical development.SIGNIFICANCE STATEMENT DNA repair is crucial for development of the nervous system. However, how DNA polymerase β (Polβ)-dependent DNA base excision repair pathway contributes to the process is still unknown. We found that loss of Polβ in cortical progenitors rather than postmitotic neurons led to catastrophic DNA double-strand breaks (DSBs) during replication and p53-mediated neuronal apoptosis, which resulted in thinning of the cortical plate. The DSBs also affected corticofugal axon growth in surviving neurons. Moreover, induction of base damage and DNA demethylation intermediates in the genome increased DSBs in cultured Polβ-deficient neural progenitors. Thus, genome stability by Polβ-dependent base excision repair in neural progenitors is required for the viability and differentiation of daughter neurons in the developing nervous system.
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124
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Rahimoff R, Kosmatchev O, Kirchner A, Pfaffeneder T, Spada F, Brantl V, Müller M, Carell T. 5-Formyl- and 5-Carboxydeoxycytidines Do Not Cause Accumulation of Harmful Repair Intermediates in Stem Cells. J Am Chem Soc 2017; 139:10359-10364. [PMID: 28715893 DOI: 10.1021/jacs.7b04131] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
5-Formyl-dC (fdC) and 5-carboxy-dC (cadC) are newly discovered bases in the mammalian genome that are supposed to be substrates for base excision repair (BER) in the framework of active demethylation. The bases are recognized by the monofunctional thymine DNA glycosylase (Tdg), which cleaves the glycosidic bond of the bases to give potentially harmful abasic sites (AP-sites). Because of the turnover of fdC and cadC during cell state transitions, it is an open question to what extent such harmful AP-sites may accumulate during these processes. Here, we report the development of a new reagent that in combination with mass spectrometry (MS) allows us to quantify the levels of AP-sites. This combination also allowed the quantification of β-elimination (βE) products, which are repair intermediates of bifunctional DNA glycosylases. In combination with feeding of isotopically labeled nucleosides, we were able to trace the intermediates back to their original nucleobases. We show that, while the steady-state levels of fdC and cadC are substantially increased in Tdg-deficient cells, those of both AP- and βE-sites are unaltered. The levels of the detected BER intermediates are 1 and 2 orders of magnitude lower than those of cadC and fdC, respectively. Thus, neither the presence of fdC nor that of cadC in stem cells leads to the accumulation of harmful AP- and βE-site intermediates.
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Affiliation(s)
- René Rahimoff
- Center for Integrated Protein Science at the Department of Chemistry, LMU Munich , Butenandtstrasse 5-13, Munich 81377, Germany
| | - Olesea Kosmatchev
- Center for Integrated Protein Science at the Department of Chemistry, LMU Munich , Butenandtstrasse 5-13, Munich 81377, Germany
| | - Angie Kirchner
- Center for Integrated Protein Science at the Department of Chemistry, LMU Munich , Butenandtstrasse 5-13, Munich 81377, Germany
| | - Toni Pfaffeneder
- Center for Integrated Protein Science at the Department of Chemistry, LMU Munich , Butenandtstrasse 5-13, Munich 81377, Germany
| | - Fabio Spada
- Center for Integrated Protein Science at the Department of Chemistry, LMU Munich , Butenandtstrasse 5-13, Munich 81377, Germany
| | - Victor Brantl
- Center for Integrated Protein Science at the Department of Chemistry, LMU Munich , Butenandtstrasse 5-13, Munich 81377, Germany
| | - Markus Müller
- Center for Integrated Protein Science at the Department of Chemistry, LMU Munich , Butenandtstrasse 5-13, Munich 81377, Germany
| | - Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry, LMU Munich , Butenandtstrasse 5-13, Munich 81377, Germany
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125
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Klungland A, Robertson AB. Oxidized C5-methyl cytosine bases in DNA: 5-Hydroxymethylcytosine; 5-formylcytosine; and 5-carboxycytosine. Free Radic Biol Med 2017; 107:62-68. [PMID: 27890639 DOI: 10.1016/j.freeradbiomed.2016.11.038] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/17/2016] [Accepted: 11/23/2016] [Indexed: 01/31/2023]
Abstract
Recent reports suggest that the Tet enzyme family catalytically oxidize 5-methylcytosine in mammalian cells. The oxidation of 5-methylcytosine can result in three chemically distinct species - 5-hydroxymethylcytsine, 5-formylcytosine, and 5-carboxycytosine. While the base excision repair machinery processes 5-formylcytosine and 5-carboxycytosine rapidly, 5-hydroxymethylcytosine is stable under physiological conditions. As a stable modification 5-hydroxymethylcytosine has a broad range of functions, from stem cell pluriopotency to tumorigenesis. The subsequent oxidation products, 5-formylcytosine and 5-carboxycytosine, are suggested to be involved in an active DNA demethylation pathway. This review provides an overview of the biochemistry and biology of 5-methylcytosine oxidation products.
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Affiliation(s)
- Arne Klungland
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Norway; Institute of Basic Medical Sciences, University of Oslo, PO Box 1018 Blindern, N-0315 Oslo, Norway
| | - Adam B Robertson
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Norway.
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126
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D'Errico M, Parlanti E, Pascucci B, Fortini P, Baccarini S, Simonelli V, Dogliotti E. Single nucleotide polymorphisms in DNA glycosylases: From function to disease. Free Radic Biol Med 2017; 107:278-291. [PMID: 27932076 DOI: 10.1016/j.freeradbiomed.2016.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/25/2016] [Accepted: 12/02/2016] [Indexed: 02/08/2023]
Abstract
Oxidative stress is associated with a growing number of diseases that span from cancer to neurodegeneration. Most oxidatively induced DNA base lesions are repaired by the base excision repair (BER) pathway which involves the action of various DNA glycosylases. There are numerous genome wide studies attempting to associate single-nucleotide polymorphisms (SNPs) with predispositions to various types of disease; often, these common variants do not have significant alterations in their biochemical function and do not exhibit a convincing phenotype. Nevertheless several lines of evidence indicate that SNPs in DNA repair genes may modulate DNA repair capacity and contribute to risk of disease. This overview provides a convincing picture that SNPs of DNA glycosylases that remove oxidatively generated DNA lesions are susceptibility factors for a wide disease spectrum that includes besides cancer (particularly lung, breast and gastrointestinal tract), cochlear/ocular disorders, myocardial infarction and neurodegenerative disorders which can be all grouped under the umbrella of oxidative stress-related pathologies.
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Affiliation(s)
- Mariarosaria D'Errico
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
| | - Eleonora Parlanti
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Barbara Pascucci
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Salaria, Km 29,300, 00016 Monterotondo Stazione, Rome, Italy
| | - Paola Fortini
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Sara Baccarini
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Valeria Simonelli
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Eugenia Dogliotti
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
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Golson ML, Kaestner KH. Epigenetics in formation, function, and failure of the endocrine pancreas. Mol Metab 2017; 6:1066-1076. [PMID: 28951829 PMCID: PMC5605720 DOI: 10.1016/j.molmet.2017.05.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/16/2017] [Accepted: 05/22/2017] [Indexed: 01/17/2023] Open
Abstract
Background Epigenetics, in the broadest sense, governs all aspects of the life of any multicellular organism, as it controls how differentiated cells arrive at their unique phenotype during development and differentiation, despite having a uniform (with some exceptions such as T-cells and germ cells) genetic make-up. The endocrine pancreas is no exception. Transcriptional regulators and epigenetic modifiers shape the differentiation of the five major endocrine cell types from their common precursor in the fetal pancreatic bud. Beyond their role in cell differentiation, interactions of the organism with the environment are also often encoded into permanent or semi-permanent epigenetic marks and affect cellular behavior and organismal health. Epigenetics is defined as any heritable – at least through one mitotic cell division – change in phenotype or trait that is not the result of a change in genomic DNA sequence, and it forms the basis that mediates the environmental impact on diabetes susceptibility and islet function. Scope of review We will summarize the impact of epigenetic regulation on islet cell development, maturation, function, and pathophysiology. We will briefly recapitulate the major epigenetic marks and their relationship to gene activity, and outline novel strategies to employ targeted epigenetic modifications as a tool to improve islet cell function. Major conclusions The improved understanding of the epigenetic underpinnings of islet cell differentiation, function and breakdown, as well as the development of innovative tools for their manipulation, is key to islet cell biology and the discovery of novel approaches to therapies for islet cell failure.
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Affiliation(s)
- Maria L Golson
- University of Pennsylvania, Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Philadelphia, PA, USA
| | - Klaus H Kaestner
- University of Pennsylvania, Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Philadelphia, PA, USA
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128
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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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129
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5-Formylcytosine does not change the global structure of DNA. Nat Struct Mol Biol 2017; 24:544-552. [PMID: 28504696 DOI: 10.1038/nsmb.3411] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/13/2017] [Indexed: 01/14/2023]
Abstract
The mechanism by which the recently identified DNA modification 5-formylcytosine (fC) is recognized by epigenetic writer and reader proteins is not known. Recently, an unusual DNA structure, F-DNA, has been proposed as the basis for enzyme recognition of clusters of fC. We used NMR and X-ray crystallography to compare several modified DNA duplexes with unmodified analogs and found that in the crystal state the duplexes all belong to the A family, whereas in solution they are all members of the B family. We found that, contrary to previous findings, fC does not significantly affect the structure of DNA, although there are modest local differences at the modification sites. Hence, global conformation changes are unlikely to account for the recognition of this modified base, and our structural data favor a mechanism that operates at base-pair resolution for the recognition of fC by epigenome-modifying enzymes.
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130
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Genome-wide profiling of DNA 5-hydroxymethylcytosine during rat Sertoli cell maturation. Cell Discov 2017; 3:17013. [PMID: 28529766 PMCID: PMC5423031 DOI: 10.1038/celldisc.2017.13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/24/2017] [Indexed: 01/04/2023] Open
Abstract
Sertoli cells have dual roles during the cells' lifetime. In the juvenile mammal, Sertoli cells proliferate and create the structure of the testis, and during puberty they cease to proliferate and take on the adult role of supporting germ cells through spermatogenesis. Accordingly, many genes expressed in Sertoli cells during testis formation are repressed during spermatogenesis. 5-Hydroxymethylcytosine (5hmC) is a DNA modification enzymatically generated from 5mC and present in all investigated mammalian tissues at varying levels. Using mass spectrometry and immunofluorescence staining we identified a substantial Sertoli cell-specific global 5hmC increase during rat puberty. Chemical labeling, pull-down and sequencing of 5hmC-containing genomic DNA from juvenile and adult rat Sertoli cells revealed that genes that lose or gain 5hmC belong to different functional pathways and mirror the functions of the cells in the two different states. Loss of 5hmC is associated with genes involved in development and cell structure, whereas gain of 5hmC is associated with genes involved in cellular pathways pertaining to the function of the adult Sertoli cells. This redistribution during maturation shows that 5hmC is a dynamic nucleotide modification, correlated to gene expression.
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131
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Pan F, Wingo TS, Zhao Z, Gao R, Makishima H, Qu G, Lin L, Yu M, Ortega JR, Wang J, Nazha A, Chen L, Yao B, Liu C, Chen S, Weeks O, Ni H, Phillips BL, Huang S, Wang J, He C, Li GM, Radivoyevitch T, Aifantis I, Maciejewski JP, Yang FC, Jin P, Xu M. Tet2 loss leads to hypermutagenicity in haematopoietic stem/progenitor cells. Nat Commun 2017; 8:15102. [PMID: 28440315 PMCID: PMC5414116 DOI: 10.1038/ncomms15102] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 02/27/2017] [Indexed: 12/12/2022] Open
Abstract
TET2 is a dioxygenase that catalyses multiple steps of 5-methylcytosine oxidation. Although TET2 mutations frequently occur in various types of haematological malignancies, the mechanism by which they increase risk for these cancers remains poorly understood. Here we show that Tet2-/- mice develop spontaneous myeloid, T- and B-cell malignancies after long latencies. Exome sequencing of Tet2-/- tumours reveals accumulation of numerous mutations, including Apc, Nf1, Flt3, Cbl, Notch1 and Mll2, which are recurrently deleted/mutated in human haematological malignancies. Single-cell-targeted sequencing of wild-type and premalignant Tet2-/- Lin-c-Kit+ cells shows higher mutation frequencies in Tet2-/- cells. We further show that the increased mutational burden is particularly high at genomic sites that gained 5-hydroxymethylcytosine, where TET2 normally binds. Furthermore, TET2-mutated myeloid malignancy patients have significantly more mutational events than patients with wild-type TET2. Thus, Tet2 loss leads to hypermutagenicity in haematopoietic stem/progenitor cells, suggesting a novel TET2 loss-mediated mechanism of haematological malignancy pathogenesis.
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Affiliation(s)
- Feng Pan
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1011 NW 15th Street, Room 411, Gautier Building, MC R629, Miami, Florida 33136, USA.,Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.,Department of Biological Sciences, Florida International University, Miami, Florida 33199, USA
| | - Thomas S Wingo
- Departments of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30307, USA.,Neurology, Emory University School of Medicine, Atlanta, Georgia 30307, USA.,Division of Neurology, Department of Veterans Affairs Medical Center, Atlanta, Georgia 30033, USA
| | - Zhigang Zhao
- Department of Hematology and Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Rui Gao
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1011 NW 15th Street, Room 411, Gautier Building, MC R629, Miami, Florida 33136, USA
| | - Hideki Makishima
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Guangbo Qu
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1011 NW 15th Street, Room 411, Gautier Building, MC R629, Miami, Florida 33136, USA.,Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Li Lin
- Departments of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30307, USA
| | - Miao Yu
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA
| | - Janice R Ortega
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033, USA
| | - Jiapeng Wang
- Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Aziz Nazha
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Li Chen
- Departments of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30307, USA
| | - Bing Yao
- Departments of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30307, USA
| | - Can Liu
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1011 NW 15th Street, Room 411, Gautier Building, MC R629, Miami, Florida 33136, USA
| | - Shi Chen
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1011 NW 15th Street, Room 411, Gautier Building, MC R629, Miami, Florida 33136, USA
| | - Ophelia Weeks
- Department of Biological Sciences, Florida International University, Miami, Florida 33199, USA
| | - Hongyu Ni
- Department of Pathology, University of Illinois at Chicago, Chicago, Illinois 60607, USA
| | - Brittany Lynn Phillips
- Department of Biochemistry and Pharmacology, Emory University School of Medicine, Atlanta, Georgia 30307, USA
| | - Suming Huang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Jianlong Wang
- Department of Developmental and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, USA
| | - Guo-Min Li
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, California 90033, USA
| | - Tomas Radivoyevitch
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Iannis Aifantis
- Howard Hughes Medical Institute and Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,NYU Cancer Institute and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Feng-Chun Yang
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1011 NW 15th Street, Room 411, Gautier Building, MC R629, Miami, Florida 33136, USA.,Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
| | - Peng Jin
- Departments of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30307, USA
| | - Mingjiang Xu
- Department of Biochemistry and Molecular Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1011 NW 15th Street, Room 411, Gautier Building, MC R629, Miami, Florida 33136, USA.,Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA
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132
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Sakaki M, Ebihara Y, Okamura K, Nakabayashi K, Igarashi A, Matsumoto K, Hata K, Kobayashi Y, Maehara K. Potential roles of DNA methylation in the initiation and establishment of replicative senescence revealed by array-based methylome and transcriptome analyses. PLoS One 2017; 12:e0171431. [PMID: 28158250 PMCID: PMC5291461 DOI: 10.1371/journal.pone.0171431] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 01/20/2017] [Indexed: 01/01/2023] Open
Abstract
Cellular senescence is classified into two groups: replicative and premature senescence. Gene expression and epigenetic changes are reported to differ between these two groups and cell types. Normal human diploid fibroblast TIG-3 cells have often been used in cellular senescence research; however, their epigenetic profiles are still not fully understood. To elucidate how cellular senescence is epigenetically regulated in TIG-3 cells, we analyzed the gene expression and DNA methylation profiles of three types of senescent cells, namely, replicatively senescent, ras-induced senescent (RIS), and non-permissive temperature-induced senescent SVts8 cells, using gene expression and DNA methylation microarrays. The expression of genes involved in the cell cycle and immune response was commonly either down- or up-regulated in the three types of senescent cells, respectively. The altered DNA methylation patterns were observed in replicatively senescent cells, but not in prematurely senescent cells. Interestingly, hypomethylated CpG sites detected on non-CpG island regions ("open sea") were enriched in immune response-related genes that had non-CpG island promoters. The integrated analysis of gene expression and methylation in replicatively senescent cells demonstrated that differentially expressed 867 genes, including cell cycle- and immune response-related genes, were associated with DNA methylation changes in CpG sites close to the transcription start sites (TSSs). Furthermore, several miRNAs regulated in part through DNA methylation were found to affect the expression of their targeted genes. Taken together, these results indicate that the epigenetic changes of DNA methylation regulate the expression of a certain portion of genes and partly contribute to the introduction and establishment of replicative senescence.
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Affiliation(s)
- Mizuho Sakaki
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya, Tokyo, Japan
- Department of Biomolecular Science, Graduate School of Science, Toho University, Funabashi, Chiba, Japan
| | - Yukiko Ebihara
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya, Tokyo, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Setagaya, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya, Tokyo, Japan
| | - Arisa Igarashi
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Setagaya, Tokyo, Japan
| | - Kenji Matsumoto
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Setagaya, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Setagaya, Tokyo, Japan
| | - Yoshiro Kobayashi
- Department of Biomolecular Science, Graduate School of Science, Toho University, Funabashi, Chiba, Japan
| | - Kayoko Maehara
- Department of Nutrition, Graduate School of Health Science, Kio University, Kitakatsuragi, Nara, Japan
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133
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Lin IH, Chen YF, Hsu MT. Correlated 5-Hydroxymethylcytosine (5hmC) and Gene Expression Profiles Underpin Gene and Organ-Specific Epigenetic Regulation in Adult Mouse Brain and Liver. PLoS One 2017; 12:e0170779. [PMID: 28125731 PMCID: PMC5268415 DOI: 10.1371/journal.pone.0170779] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/10/2017] [Indexed: 12/19/2022] Open
Abstract
Background DNA methylation is an epigenetic mechanism essential for gene regulation and vital for mammalian development. 5-hydroxymethylcytosine (5hmC) is the first oxidative product of the TET-mediated 5-methylcytosine (5mC) demethylation pathway. Aside from being a key intermediate in cytosine demethylation, 5hmC may have potential regulatory functions with emerging importance in mammalian biology. Methods Here, we investigate the global 5hmC enrichment in five brain structures, including cerebellum, cerebral cortex, hippocampus, hypothalamus and thalamus, as well as liver tissues from female and male adult mice by using chemical capture-based technique coupled with next-generation sequencing. At the same time, we carried out total RNA sequencing (RNA-seq) to analyze the transcriptomes of brain regions and liver tissues. Results Our results reveal preferential 5hmC enrichment in the gene bodies of expressed genes, and 5hmC levels of many protein-coding genes are positively correlated with RNA expression intensity. However, more than 75% of genes with low or no 5hmC enrichment are genes encode for mitochondrial proteins and ribosomal proteins despite being actively transcribed, implying different transcriptional regulation mechanisms of these housekeeping genes. Brain regions developed from the same embryonic structures have more similar 5hmC profiles. Also, the genic 5hmC enrichment pattern is highly tissue-specific, and 5hmC marks genes involving in tissue-specific biological processes. Sex chromosomes are mostly depleted of 5hmC, and the X inactive specific transcript (Xist) gene located on the X chromosome is the only gene to show sex-specific 5hmC enrichment. Conclusions This is the first report of the whole-genome 5hmC methylome of five major brain structures and liver tissues in mice of both sexes. This study offers a comprehensive resource for future work of mammalian cytosine methylation dynamics. Our findings offer additional evidence that suggests 5hmC is an active epigenetic mark stably maintained after the global reprogramming event during early embryonic development.
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Affiliation(s)
- I-Hsuan Lin
- VYM Genome Research Center, National Yang-Ming University, Taipei, Taiwan
- The Center of Translational Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yi-Fan Chen
- VYM Genome Research Center, National Yang-Ming University, Taipei, Taiwan
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Ming-Ta Hsu
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
- Chien-Tien Hsu Cancer Research Foundation, Taipei, Taiwan
- * E-mail:
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134
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Abstract
DNA methylation plays important roles in development and disease. Yet, only recently has the dynamic nature of this epigenetic mark via oxidation and DNA repair-mediated demethylation been recognized. A major conceptual challenge to the model that DNA methylation is reversible is the risk of genomic instability, which may come with widespread DNA repair activity. Here, we focus on recent advances in mechanisms of TET-TDG mediated demethylation and cellular strategies that avoid genomic instability. We highlight the recently discovered involvement of NEIL DNA glycosylases, which cooperate with TDG in oxidative demethylation to accelerate substrate turnover and promote the organized handover of harmful repair intermediates to maintain genome stability.
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Affiliation(s)
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany.,Division of Molecular Embryology, German Cancer Research Center-Zentrum für Molekulare Biologie der Universität Heidelberg (DKFZ-ZMBH) Alliance, Heidelberg, Germany
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135
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Bernstein D, Golson ML, Kaestner KH. Epigenetic control of β-cell function and failure. Diabetes Res Clin Pract 2017; 123:24-36. [PMID: 27918975 PMCID: PMC5250585 DOI: 10.1016/j.diabres.2016.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 11/15/2016] [Indexed: 12/21/2022]
Abstract
Type 2 diabetes is a highly heritable disease, but only ∼15% of this heritability can be explained by known genetic variant loci. In fact, body mass index is more predictive of diabetes than any of the common risk alleles identified by genome-wide association studies. This discrepancy may be explained by epigenetic inheritance, whereby changes in gene regulation can be passed along to offspring. Epigenetic changes throughout an organism's lifetime, based on environmental factors such as chemical exposures, diet, physical activity, and age, can also affect gene expression and susceptibility to diabetes. Recently, novel genome-wide assays of epigenetic marks have resulted in a greater understanding of how genetics, epigenetics, and the environment interact in the development and inheritance of diabetes.
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Affiliation(s)
- Diana Bernstein
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria L Golson
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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136
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Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine. Nat Chem Biol 2016; 13:181-187. [PMID: 27918559 DOI: 10.1038/nchembio.2250] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 09/29/2016] [Indexed: 12/16/2022]
Abstract
Ten-eleven translocation (TET) enzymes catalyze stepwise oxidation of 5-methylcytosine (mC) to yield 5-hydroxymethylcytosine (hmC) and the rarer bases 5-formylcytosine (fC) and 5-carboxylcytosine (caC). Stepwise oxidation obscures how each individual base forms and functions in epigenetic regulation, and prompts the question of whether TET enzymes primarily serve to generate hmC or are adapted to produce fC and caC as well. By mutating a single, conserved active site residue in human TET2, Thr1372, we uncovered enzyme variants that permit oxidation to hmC but largely eliminate fC and caC. Biochemical analyses, combined with molecular dynamics simulations, elucidated an active site scaffold that is required for wild-type (WT) stepwise oxidation and that, when perturbed, explains the mutants' hmC-stalling phenotype. Our results suggest that the TET2 active site is shaped to enable higher-order oxidation and provide the first TET variants that could be used to probe the biological functions of hmC separately from fC and caC.
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137
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Kim R, Sheaffer KL, Choi I, Won KJ, Kaestner KH. Epigenetic regulation of intestinal stem cells by Tet1-mediated DNA hydroxymethylation. Genes Dev 2016; 30:2433-2442. [PMID: 27856615 PMCID: PMC5131782 DOI: 10.1101/gad.288035.116] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/21/2016] [Indexed: 12/02/2022]
Abstract
Here, Kim et al. provide novel insights into the epigenomic changes that occur during intestinal stem cell development and differentiation. They demonstrate that Tet1-mediated DNA hydroxymethylation plays a critical role in the epigenetic regulation of the Wnt pathway in intestinal stem and progenitor cells and consequently in the self-renewal of the intestinal epithelium. Methylated cytosines are associated with gene silencing. The ten-eleven translocation (TET) hydroxylases, which oxidize methylated cytosines to 5-hydroxymethylcytosine (5hmC), are essential for cytosine demethylation. Gene silencing and activation are critical for intestinal stem cell (ISC) maintenance and differentiation, but the potential role of TET hydroxylases in these processes has not yet been examined. Here, we generated genome-wide maps of the 5hmC mark in ISCs and their differentiated progeny. Genes with high levels of hydroxymethylation in ISCs are strongly associated with Wnt signaling and developmental processes. We found Tet1 to be the most abundantly expressed Tet gene in ISCs; therefore, we analyzed intestinal development in Tet1-deficient mice and determined that these mice are growth-retarded, exhibit partial postnatal lethality, and have significantly reduced numbers of proliferative cells in the intestinal epithelium. In addition, the Tet1-deficient intestine displays reduced organoid-forming capacity. In the Tet1-deficient crypt, decreased expression of Wnt target genes such as Axin2 and Lgr5 correlates with lower 5hmC levels at their promoters. These data demonstrate that Tet1-mediated DNA hydroxymethylation plays a critical role in the epigenetic regulation of the Wnt pathway in intestinal stem and progenitor cells and consequently in the self-renewal of the intestinal epithelium.
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Affiliation(s)
- Rinho Kim
- Department of Genetics, Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Karyn L Sheaffer
- Department of Genetics, Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Inchan Choi
- Department of Genetics, Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kyoung-Jae Won
- Department of Genetics, Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Klaus H Kaestner
- Department of Genetics, Center for Molecular Studies in Digestive and Liver Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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138
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Bochtler M, Kolano A, Xu GL. DNA demethylation pathways: Additional players and regulators. Bioessays 2016; 39:1-13. [PMID: 27859411 DOI: 10.1002/bies.201600178] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DNA demethylation can occur passively by "dilution" of methylation marks by DNA replication, or actively and independently of DNA replication. Direct conversion of 5-methylcytosine (5mC) to cytosine (C), as originally proposed, does not occur. Instead, active DNA methylation involves oxidation of the methylated base by ten-eleven translocations (TETs), or deamination of the methylated or a nearby base by activation induced deaminase (AID). The modified nucleotide, possibly together with surrounding nucleotides, is then replaced by the BER pathway. Recent data clarify the roles and the regulation of well-known enzymes in this process. They identify base excision repair (BER) glycosylases that may cooperate with or replace thymine DNA glycosylase (TDG) in the base excision step, and suggest possible involvement of DNA damage repair pathways other than BER in active DNA demethylation. Here, we review these new developments.
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Affiliation(s)
- Matthias Bochtler
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Agnieszka Kolano
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Guo-Liang Xu
- Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
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139
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Abstract
5′-hydroxymethylcytosine (5hmC) is a variant of the common covalent epigenetic modification of DNA 5′-methylcytosine (5mC). Although the presence of this modified base in mammalian DNA has been recognized for several decades, it has recently gained center stage as a suspected intermediate in enzymatic active demethylation of 5mC. The role of 5hmC remains elusive in spite of a large body of studies. It is proposed that 5hmC is a variant of the 5mC epigenetic signal and is involved in epigenetic regulation of gene function. Recent data support a role for 5hmC in the activation of lineage-specific enhancers.
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Affiliation(s)
- Moshe Szyf
- Department of Pharmacology & Therapeutics, McGill University Medical School, 3655 Sir William Osler Promenade #1309, Montreal, QC, H3G 1Y6, Canada
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140
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Fraser R, Lin CJ. Epigenetic reprogramming of the zygote in mice and men: on your marks, get set, go! Reproduction 2016; 152:R211-R222. [PMID: 27601712 PMCID: PMC5097126 DOI: 10.1530/rep-16-0376] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/02/2016] [Indexed: 12/19/2022]
Abstract
Gametogenesis (spermatogenesis and oogenesis) is accompanied by the acquisition of gender-specific epigenetic marks, such as DNA methylation, histone modifications and regulation by small RNAs, to form highly differentiated, but transcriptionally silent cell-types in preparation for fertilisation. Upon fertilisation, extensive global epigenetic reprogramming takes place to remove the previously acquired epigenetic marks and produce totipotent zygotic states. It is the aim of this review to delineate the cellular and molecular events involved in maternal, paternal and zygotic epigenetic reprogramming from the time of gametogenesis, through fertilisation, to the initiation of zygotic genome activation for preimplantation embryonic development. Recent studies have begun to uncover the indispensable functions of epigenetic players during gametogenesis, fertilisation and preimplantation embryo development, and a more comprehensive understanding of these early events will be informative for increasing pregnancy success rates, adding particular value to assisted fertility programmes.
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Affiliation(s)
- Rupsha Fraser
- The University of EdinburghMRC Centre for Reproductive Health, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK
| | - Chih-Jen Lin
- The University of EdinburghMRC Centre for Reproductive Health, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, Scotland, UK
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141
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Drohat AC, Coey CT. Role of Base Excision "Repair" Enzymes in Erasing Epigenetic Marks from DNA. Chem Rev 2016; 116:12711-12729. [PMID: 27501078 DOI: 10.1021/acs.chemrev.6b00191] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Base excision repair (BER) is one of several DNA repair pathways found in all three domains of life. BER counters the mutagenic and cytotoxic effects of damage that occurs continuously to the nitrogenous bases in DNA, and its critical role in maintaining genomic integrity is well established. However, BER also performs essential functions in processes other than DNA repair, where it acts on naturally modified bases in DNA. A prominent example is the central role of BER in mediating active DNA demethylation, a multistep process that erases the epigenetic mark 5-methylcytosine (5mC), and derivatives thereof, converting them back to cytosine. Herein, we review recent advances in the understanding of how BER mediates this critical component of epigenetic regulation in plants and animals.
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Affiliation(s)
- Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| | - Christopher T Coey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
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142
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Abstract
5-methylcytosine (5mC) was long thought to be the only enzymatically created modified DNA base in mammalian cells. The discovery of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine as reaction products of the TET family 5mC oxidases has prompted extensive searches for proteins that specifically bind to these oxidized bases. However, only a few of such "reader" proteins have been identified and verified so far. In this review, we discuss potential biological functions of oxidized 5mC as well as the role the presumed reader proteins may play in interpreting the genomic signals of 5mC oxidation products.
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Affiliation(s)
- Jikui Song
- Department of Biochemistry, University of California Riverside, Riverside, CA, USA.
| | - Gerd P Pfeifer
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA.
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143
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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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144
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Mahfoudhi E, Talhaoui I, Cabagnols X, Della Valle V, Secardin L, Rameau P, Bernard OA, Ishchenko AA, Abbes S, Vainchenker W, Saparbaev M, Plo I. TET2-mediated 5-hydroxymethylcytosine induces genetic instability and mutagenesis. DNA Repair (Amst) 2016; 43:78-88. [DOI: 10.1016/j.dnarep.2016.05.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 04/28/2016] [Accepted: 05/23/2016] [Indexed: 02/04/2023]
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145
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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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146
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Liu MY, DeNizio JE, Schutsky EK, Kohli RM. The expanding scope and impact of epigenetic cytosine modifications. Curr Opin Chem Biol 2016; 33:67-73. [PMID: 27315338 DOI: 10.1016/j.cbpa.2016.05.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 12/11/2022]
Abstract
Chemical modifications to genomic DNA can expand and shape its coding potential. Cytosine methylation in particular has well-established roles in regulating gene expression and defining cellular identity. The discovery of TET family enzymes opened a major frontier beyond DNA methylation, revealing three oxidized forms of cytosine that could mediate DNA demethylation or encode independent epigenetic functions. Chemical biology has been instrumental in uncovering TET's intricate reaction mechanisms and scope of reactivity on a surprising variety of substrates. Moreover, innovative chemoenzymatic strategies have enabled sensitive detection of oxidized cytosine products in vitro and in vivo. We highlight key recent developments that demonstrate how chemical biology is advancing our understanding of the extended, dynamic epigenome.
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Affiliation(s)
- Monica Yun Liu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jamie E DeNizio
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emily K Schutsky
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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147
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Abstract
The AlkB gene that protects E.coli against methylation damage to DNA was identified more than 3 decades ago. 20 years later, the AlkB protein was shown to catalyze repair of methylated DNA base lesions by oxidative demethylation. Two human AlkB homologs were characterized with similar DNA repair activities and seven additional human AlkB homologs were identified based on sequence homology. All these dioxygenases, ALKBH1-8 and FTO, contain a conserved α-ketoglutarate/iron-dependent domain for methyl modifications and de-modifications. Well-designed research over the last 10 years has identified unforeseen substrate heterogeneity for the AlkB homologs, including novel reversible methyl modifications in RNA. The discoveries of RNA demethylation catalyzed by AlkB family enzymes initiated a new realm of gene expression regulation, although the understanding of precise endogenous activities and roles of these RNA demethylases are still undeveloped. It is worth mentioning that the AlkB mechanism and use of α-ketoglutarate have also emerged to be essential for many enzymes in epigenetic reprogramming that modify and de-modify methylated bases in DNA and methylated amino acids in histones.
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Affiliation(s)
- Endalkachew A Alemu
- Department of Microbiology, Division of Diagnostics and Intervention, Institute of Clinical Medicine, Oslo University Hospital, Rikshospitalet, Oslo NO-0027, Norway; Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo NO-0027, Norway
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
| | - Arne Klungland
- Department of Microbiology, Division of Diagnostics and Intervention, Institute of Clinical Medicine, Oslo University Hospital, Rikshospitalet, Oslo NO-0027, Norway; Department of Molecular Medicine, Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo NO-0027, Norway.
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148
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Schuermann D, Weber AR, Schär P. Active DNA demethylation by DNA repair: Facts and uncertainties. DNA Repair (Amst) 2016; 44:92-102. [PMID: 27247237 DOI: 10.1016/j.dnarep.2016.05.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pathways that control and modulate DNA methylation patterning in mammalian cells were poorly understood for a long time, although their importance in establishing and maintaining cell type-specific gene expression was well recognized. The discovery of proteins capable of converting 5-methylcytosine (5mC) to putative substrates for DNA repair introduced a novel and exciting conceptual framework for the investigation and ultimate discovery of molecular mechanisms of DNA demethylation. Against the prevailing notion that DNA methylation is a static epigenetic mark, it turned out to be dynamic and distinct mechanisms appear to have evolved to effect global and locus-specific DNA demethylation. There is compelling evidence that DNA repair, in particular base excision repair, contributes significantly to the turnover of 5mC in cells. By actively demethylating DNA, DNA repair supports the developmental establishment as well as the maintenance of DNA methylation landscapes and gene expression patterns. Yet, while the biochemical pathways are relatively well-established and reviewed, the biological context, function and regulation of DNA repair-mediated active DNA demethylation remains uncertain. In this review, we will thus summarize and critically discuss the evidence that associates active DNA demethylation by DNA repair with specific functional contexts including the DNA methylation erasure in the early embryo, the control of pluripotency and cellular differentiation, the maintenance of cell identity, and the nuclear reprogramming.
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Affiliation(s)
- David Schuermann
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland
| | - Alain R Weber
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland
| | - Primo Schär
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland.
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