1
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De I, Weidenhausen J, Concha N, Müller CW. Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy. PLoS One 2024; 19:e0307850. [PMID: 39226277 PMCID: PMC11371216 DOI: 10.1371/journal.pone.0307850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 07/12/2024] [Indexed: 09/05/2024] Open
Abstract
DNMT1 is an essential DNA methyltransferase that catalyzes the transfer of methyl groups to CpG islands in DNA and generates a prominent epigenetic mark. The catalytic activity of DNMT1 relies on its conformational plasticity and ability to change conformation from an auto-inhibited to an activated state. Here, we present four cryo-EM reconstructions of apo DNMT1 and DNTM1: non-productive DNA, DNTM1: H3Ub2-peptide, DNTM1: productive DNA complexes. Our structures demonstrate the flexibility of DNMT1's N-terminal regulatory domains during the transition from an apo 'auto-inhibited' to a DNA-bound 'non-productive' and finally a DNA-bound 'productive' state of DNMT1. Furthermore, we address the regulation of DNMT1's methyltransferase activity by a DNMT1-selective small-molecule inhibitor and ubiquitinated histone H3. We observe that DNMT1 binds DNA in a 'non-productive' state despite the presence of the inhibitor and present the cryo-EM reconstruction of full-length DNMT1 in complex with a di-ubiquitinated H3 peptide analogue. Taken together, our results provide structural insights into the reaction cycle of DNMT1.
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Affiliation(s)
- Inessa De
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Jonas Weidenhausen
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Nestor Concha
- GlaxoSmithKline, Collegeville, PA, United States of America
| | - Christoph W. Müller
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
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2
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Balder P, Jones C, Coward K, Yeste M. Sperm chromatin: Evaluation, epigenetic signatures and relevance for embryo development and assisted reproductive technology outcomes. Eur J Cell Biol 2024; 103:151429. [PMID: 38905808 DOI: 10.1016/j.ejcb.2024.151429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 06/07/2024] [Accepted: 06/07/2024] [Indexed: 06/23/2024] Open
Abstract
Sperm chromatin is distinct from somatic cell chromatin, as a result of extensive remodeling during the final stages of spermatogenesis. In this process, the majority of histones is replaced with protamines. The chromatin is consequently highly condensed and inert, which facilitates protection of the DNA. The sperm epigenomic landscape is shaped by histone retention, histone and protamine modification, DNA methylation, and RNAs. In recent years, sperm chromatin integrity and its epigenetic marks have been increasingly studied, and the constitution of sperm chromatin is steadily being uncovered. This growing body of research prompts assessment of the frequently overlooked involvement of sperm in fertility and embryonic development. Moreover, numerous endogenous and exogenous factors are known to affect sperm chromatin, which may in turn impact the reproductive success. Concerns have been raised about the effects of assisted reproductive technology (ART) on the sperm epigenome, embryonic development and offspring health. This review examines the structure and epigenetic signatures of sperm chromatin in the context of fertility and early embryonic development. Additionally, sperm chromatin evaluation and causes of aberrant integrity are outlined. Building on the knowledge discussed in the current review, future research should aim to elucidate the intricate relationship between all aspects of sperm chromatin and embryo development. This could lead to the uncovering of new targets for treating infertility, as well as the acquisition of much needed insights into the possible reciprocal association between ART and sperm chromatin integrity.
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Affiliation(s)
- Pauline Balder
- Nuffield Department of Women's and Reproductive Health, Level 3, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK; The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Celine Jones
- Nuffield Department of Women's and Reproductive Health, Level 3, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Kevin Coward
- Nuffield Department of Women's and Reproductive Health, Level 3, Women's Centre, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| | - Marc Yeste
- Biotechnology of Animal and Human Reproduction (TechnoSperm), Institute of Food and Agricultural Technology, University of Girona, Girona ES-17003, Spain; Unit of Cell Biology, Department of Biology, Faculty of Sciences, University of Girona, Girona ES-17003, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona ES-08010, Spain.
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3
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Prasasya RD, Caldwell BA, Liu Z, Wu S, Leu NA, Fowler JM, Cincotta SA, Laird DJ, Kohli RM, Bartolomei MS. Iterative oxidation by TET1 is required for reprogramming of imprinting control regions and patterning of mouse sperm hypomethylated regions. Dev Cell 2024; 59:1010-1027.e8. [PMID: 38569549 PMCID: PMC11042979 DOI: 10.1016/j.devcel.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 12/07/2023] [Accepted: 02/29/2024] [Indexed: 04/05/2024]
Abstract
Ten-eleven translocation (TET) enzymes iteratively oxidize 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC), 5-formylcytosine, and 5-carboxylcytosine to facilitate active genome demethylation. Whether these bases are required to promote replication-coupled dilution or activate base excision repair during mammalian germline reprogramming remains unresolved due to the inability to decouple TET activities. Here, we generated two mouse lines expressing catalytically inactive TET1 (Tet1-HxD) and TET1 that stalls oxidation at 5hmC (Tet1-V). Tet1 knockout and catalytic mutant primordial germ cells (PGCs) fail to erase methylation at select imprinting control regions and promoters of meiosis-associated genes, validating the requirement for the iterative oxidation of 5mC for complete germline reprogramming. TET1V and TET1HxD rescue most hypermethylation of Tet1-/- sperm, suggesting the role of TET1 beyond its oxidative capability. We additionally identify a broader class of hypermethylated regions in Tet1 mutant mouse sperm that depend on TET oxidation for reprogramming. Our study demonstrates the link between TET1-mediated germline reprogramming and sperm methylome patterning.
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Affiliation(s)
- Rexxi D Prasasya
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Blake A Caldwell
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhengfeng Liu
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Songze Wu
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - N Adrian Leu
- Department of Biomedical Sciences, Center for Animal Transgenesis and Germ Cell Research, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Johanna M Fowler
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven A Cincotta
- Department of Obstetrics, Gynecology and Reproductive Science, Center for Reproductive Sciences, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 84143, USA
| | - Diana J Laird
- Department of Obstetrics, Gynecology and Reproductive Science, Center for Reproductive Sciences, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 84143, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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4
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Kriukienė E, Tomkuvienė M, Klimašauskas S. 5-Hydroxymethylcytosine: the many faces of the sixth base of mammalian DNA. Chem Soc Rev 2024; 53:2264-2283. [PMID: 38205583 DOI: 10.1039/d3cs00858d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Epigenetic phenomena play a central role in cell regulatory processes and are important factors for understanding complex human disease. One of the best understood epigenetic mechanisms is DNA methylation. In the mammalian genome, cytosines (C) in CpG dinucleotides were long known to undergo methylation at the 5-position of the pyrimidine ring (mC). Later it was found that mC can be oxidized to 5-hydroxymethylcytosine (hmC) or even further to 5-formylcytosine (fC) and to 5-carboxylcytosine (caC) by the action of 2-oxoglutarate-dependent dioxygenases of the TET family. These findings unveiled a long elusive mechanism of active DNA demethylation and bolstered a wave of studies in the area of epigenetic regulation in mammals. This review is dedicated to critical assessment of recent data on biochemical and chemical aspects of the formation and conversion of hmC in DNA, analytical techniques used for detection and mapping of this nucleobase in mammalian genomes as well as epigenetic roles of hmC in DNA replication, transcription, cell differentiation and human disease.
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Affiliation(s)
- Edita Kriukienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Miglė Tomkuvienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
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5
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Wei A, Zhang H, Qiu Q, Fabyanic EB, Hu P, Wu H. 5-hydroxymethylcytosines regulate gene expression as a passive DNA demethylation resisting epigenetic mark in proliferative somatic cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559662. [PMID: 37808741 PMCID: PMC10557716 DOI: 10.1101/2023.09.26.559662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Enzymatic erasure of DNA methylation in mammals involves iterative 5-methylcytosine (5mC) oxidation by the ten-eleven translocation (TET) family of DNA dioxygenase proteins. As the most abundant form of oxidized 5mC, the prevailing model considers 5-hydroxymethylcytosine (5hmC) as a key nexus in active DNA demethylation that can either indirectly facilitate replication-dependent depletion of 5mC by inhibiting maintenance DNA methylation machinery (UHRF1/DNMT1), or directly be iteratively oxidized to 5-formylcytosine (5fC) and 5-carboxycytosine (5caC) and restored to cytosine (C) through thymine DNA glycosylase (TDG)-mediated 5fC/5caC excision repair. In proliferative somatic cells, to what extent TET-dependent removal of 5mC entails indirect DNA demethylation via 5hmC-induced replication-dependent dilution or direct iterative conversion of 5hmC to 5fC/5caC is unclear. Here we leverage a catalytic processivity stalling variant of human TET1 (TET1.var: T1662E) to decouple the stepwise generation of 5hmC from subsequent 5fC/5caC generation, excision and repair. By using a CRISPR/dCas9-based epigenome-editing platform, we demonstrate that 5fC/5caC excision repair (by wild-type TET1, TET1.wt), but not 5hmC generation alone (by TET1.var), is requisite for robust restoration of unmodified cytosines and reversal of somatic silencing of the methylation-sensitive, germline-specific RHOXF2B gene promoter. Furthermore, integrated whole-genome multi-modal epigenetic sequencing reveals that hemi-hydroxymethylated CpG dyads predominantly resist replication-dependent depletion of 5mC on the opposing strand in TET1.var-expressing cells. Notably, TET1.var-mediated 5hmC generation is sufficient to induce similar levels of differential gene expression (compared to TET1.wt) without inducing major changes in unmodified cytosine profiles across the genome. Our study suggests 5hmC alone plays a limited role in driving replication-dependent DNA demethylation in the presence of functional DNMT1/UHRF1 mechanisms, but can regulate gene expression as a bona fide epigenetic mark in proliferative somatic cells.
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Affiliation(s)
- Alex Wei
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Hongjie Zhang
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Qi Qiu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Emily B. Fabyanic
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - Peng Hu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
- Present address: College Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104
- Lead contact
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6
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Wang T, Fowler JM, Liu L, Loo CE, Luo M, Schutsky EK, Berríos KN, DeNizio JE, Dvorak A, Downey N, Montermoso S, Pingul BY, Nasrallah M, Gosal WS, Wu H, Kohli RM. Direct enzymatic sequencing of 5-methylcytosine at single-base resolution. Nat Chem Biol 2023; 19:1004-1012. [PMID: 37322153 PMCID: PMC10763687 DOI: 10.1038/s41589-023-01318-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 03/17/2023] [Indexed: 06/17/2023]
Abstract
5-methylcytosine (5mC) is the most important DNA modification in mammalian genomes. The ideal method for 5mC localization would be both nondestructive of DNA and direct, without requiring inference based on detection of unmodified cytosines. Here we present direct methylation sequencing (DM-Seq), a bisulfite-free method for profiling 5mC at single-base resolution using nanogram quantities of DNA. DM-Seq employs two key DNA-modifying enzymes: a neomorphic DNA methyltransferase and a DNA deaminase capable of precise discrimination between cytosine modification states. Coupling these activities with deaminase-resistant adapters enables accurate detection of only 5mC via a C-to-T transition in sequencing. By comparison, we uncover a PCR-related underdetection bias with the hybrid enzymatic-chemical TET-assisted pyridine borane sequencing approach. Importantly, we show that DM-Seq, unlike bisulfite sequencing, unmasks prognostically important CpGs in a clinical tumor sample by not confounding 5mC with 5-hydroxymethylcytosine. DM-Seq thus offers an all-enzymatic, nondestructive, faithful and direct method for the reading of 5mC alone.
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Affiliation(s)
- Tong Wang
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Johanna M Fowler
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christian E Loo
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Meiqi Luo
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emily K Schutsky
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Kiara N Berríos
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Jamie E DeNizio
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Ashley Dvorak
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Nick Downey
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Saira Montermoso
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Bianca Y Pingul
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - MacLean Nasrallah
- Department of Pathology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Hao Wu
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
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7
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Yano N, Fedulov AV. Targeted DNA Demethylation: Vectors, Effectors and Perspectives. Biomedicines 2023; 11:biomedicines11051334. [PMID: 37239005 DOI: 10.3390/biomedicines11051334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Aberrant DNA hypermethylation at regulatory cis-elements of particular genes is seen in a plethora of pathological conditions including cardiovascular, neurological, immunological, gastrointestinal and renal diseases, as well as in cancer, diabetes and others. Thus, approaches for experimental and therapeutic DNA demethylation have a great potential to demonstrate mechanistic importance, and even causality of epigenetic alterations, and may open novel avenues to epigenetic cures. However, existing methods based on DNA methyltransferase inhibitors that elicit genome-wide demethylation are not suitable for treatment of diseases with specific epimutations and provide a limited experimental value. Therefore, gene-specific epigenetic editing is a critical approach for epigenetic re-activation of silenced genes. Site-specific demethylation can be achieved by utilizing sequence-dependent DNA-binding molecules such as zinc finger protein array (ZFA), transcription activator-like effector (TALE) and clustered regularly interspaced short palindromic repeat-associated dead Cas9 (CRISPR/dCas9). Synthetic proteins, where these DNA-binding domains are fused with the DNA demethylases such as ten-eleven translocation (Tet) and thymine DNA glycosylase (TDG) enzymes, successfully induced or enhanced transcriptional responsiveness at targeted loci. However, a number of challenges, including the dependence on transgenesis for delivery of the fusion constructs, remain issues to be solved. In this review, we detail current and potential approaches to gene-specific DNA demethylation as a novel epigenetic editing-based therapeutic strategy.
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Affiliation(s)
- Naohiro Yano
- Department of Surgery, Rhode Island Hospital, Alpert Medical School of Brown University, 593 Eddy Street, Providence, RI 02903, USA
| | - Alexey V Fedulov
- Department of Surgery, Rhode Island Hospital, Alpert Medical School of Brown University, 593 Eddy Street, Providence, RI 02903, USA
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8
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Turpin M, Salbert G. 5-methylcytosine turnover: Mechanisms and therapeutic implications in cancer. Front Mol Biosci 2022; 9:976862. [PMID: 36060265 PMCID: PMC9428128 DOI: 10.3389/fmolb.2022.976862] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/26/2022] [Indexed: 12/04/2022] Open
Abstract
DNA methylation at the fifth position of cytosine (5mC) is one of the most studied epigenetic mechanisms essential for the control of gene expression and for many other biological processes including genomic imprinting, X chromosome inactivation and genome stability. Over the last years, accumulating evidence suggest that DNA methylation is a highly dynamic mechanism driven by a balance between methylation by DNMTs and TET-mediated demethylation processes. However, one of the main challenges is to understand the dynamics underlying steady state DNA methylation levels. In this review article, we give an overview of the latest advances highlighting DNA methylation as a dynamic cycling process with a continuous turnover of cytosine modifications. We describe the cooperative actions of DNMT and TET enzymes which combine with many additional parameters including chromatin environment and protein partners to govern 5mC turnover. We also discuss how mathematical models can be used to address variable methylation levels during development and explain cell-type epigenetic heterogeneity locally but also at the genome scale. Finally, we review the therapeutic implications of these discoveries with the use of both epigenetic clocks as predictors and the development of epidrugs that target the DNA methylation/demethylation machinery. Together, these discoveries unveil with unprecedented detail how dynamic is DNA methylation during development, underlying the establishment of heterogeneous DNA methylation landscapes which could be altered in aging, diseases and cancer.
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Affiliation(s)
- Marion Turpin
- Sp@rte Team, UMR6290 CNRS, Institute of Genetics and Development of Rennes, Rennes, France
- University of Rennes 1, Rennes, France
| | - Gilles Salbert
- Sp@rte Team, UMR6290 CNRS, Institute of Genetics and Development of Rennes, Rennes, France
- University of Rennes 1, Rennes, France
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9
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Weirath NA, Hurben AK, Chao C, Pujari SS, Cheng T, Liu S, Tretyakova NY. Small Molecule Inhibitors of TET Dioxygenases: Bobcat339 Activity Is Mediated by Contaminating Copper(II). ACS Med Chem Lett 2022; 13:792-798. [PMID: 35586434 PMCID: PMC9109264 DOI: 10.1021/acsmedchemlett.1c00677] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/12/2022] [Indexed: 12/12/2022] Open
Abstract
Ten eleven translocation (TET) dioxygenases 1-3 are non-heme Fe(II) and α-ketoglutarate dependent enzymes that catalyze oxidation of 5-methylcytosine (5mC) in DNA to hydroxymethyl-C, formyl-C, and carboxy-C. This typically leads to gene activation and epigenetic remodeling. Most known inhibitors of TET are α-ketoglutarate mimics that may interfere with other α-ketoglutarate dependent enzymes. Recently, a novel cytosine-based inhibitor of TET, Bobcat339, was reported to have mid-μM inhibitory activity against TET1 and TET2. The molecule is now sold as a TET inhibitor by several vendors. We independently prepared Bobcat339 in our laboratory and observed that it had minimal inhibitory activity against human TET1 and TET2 via a quantitative LC-ESI-MS/MS assay. Furthermore, the inhibitory activity of commercial Bobcat339 preparations was directly correlated with Cu(II) content. We therefore conclude that Bobcat339 alone is not capable of inhibiting TET enzymes at the reported concentrations, and that its activity is enhanced by contaminating Cu(II).
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Affiliation(s)
- Nicholas A. Weirath
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, Minnesota 55455, United States
| | - Alexander K. Hurben
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, Minnesota 55455, United States
| | - Christopher Chao
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, Minnesota 55455, United States
| | - Suresh S. Pujari
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, Minnesota 55455, United States
| | - Tao Cheng
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, Minnesota 55912, United States
| | - Shujun Liu
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, Minnesota 55912, United States
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, Minnesota 55455, United States
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10
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DNA Demethylation in the Processes of Repair and Epigenetic Regulation Performed by 2-Ketoglutarate-Dependent DNA Dioxygenases. Int J Mol Sci 2021; 22:ijms221910540. [PMID: 34638881 PMCID: PMC8508711 DOI: 10.3390/ijms221910540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/05/2022] Open
Abstract
Site-specific DNA methylation plays an important role in epigenetic regulation of gene expression. Chemical methylation of DNA, including the formation of various methylated nitrogenous bases, leads to the formation of genotoxic modifications that impair DNA functions. Despite the fact that different pathways give rise to methyl groups in DNA, the main pathway for their removal is oxidative demethylation, which is catalyzed by nonheme Fe(II)/α-ketoglutarate–dependent DNA dioxygenases. DNA dioxygenases share a common catalytic mechanism of the oxidation of the alkyl groups on nitrogenous bases in nucleic acids. This review presents generalized data on the catalytic mechanism of action of DNA dioxygenases and on the participation of typical representatives of this superfamily, such as prokaryotic enzyme AlkB and eukaryotic enzymes ALKBH1–8 and TET1–3, in both processes of direct repair of alkylated DNA adducts and in the removal of an epigenetic mark (5-methylcytosine).
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11
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Wang T, Loo CE, Kohli RM. Enzymatic approaches for profiling cytosine methylation and hydroxymethylation. Mol Metab 2021; 57:101314. [PMID: 34375743 PMCID: PMC8829811 DOI: 10.1016/j.molmet.2021.101314] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/26/2021] [Accepted: 08/03/2021] [Indexed: 12/20/2022] Open
Abstract
Background In mammals, modifications to cytosine bases, particularly in cytosine-guanine (CpG) dinucleotide contexts, play a major role in shaping the epigenome. The canonical epigenetic mark is 5-methylcytosine (5mC), but oxidized versions of 5mC, including 5-hydroxymethylcytosine (5hmC), are now known to be important players in epigenomic dynamics. Understanding the functional role of these modifications in gene regulation, normal development, and pathological conditions requires the ability to localize these modifications in genomic DNA. The classical approach for sequencing cytosine modifications has involved differential deamination via the chemical sodium bisulfite; however, bisulfite is destructive, limiting its utility in important biological or clinical settings where detection of low frequency populations is critical. Additionally, bisulfite fails to resolve 5mC from 5hmC. Scope of review To summarize how enzymatic rather than chemical approaches can be leveraged to localize and resolve different cytosine modifications in a non-destructive manner. Major conclusions Nature offers a suite of enzymes with biological roles in cytosine modification in organisms spanning from bacteriophages to mammals. These enzymatic activities include methylation by DNA methyltransferases, oxidation of 5mC by TET family enzymes, hypermodification of 5hmC by glucosyltransferases, and the generation of transition mutations from cytosine to uracil by DNA deaminases. Here, we describe how insights into the natural reactivities of these DNA-modifying enzymes can be leveraged to convert them into powerful biotechnological tools. Application of these enzymes in sequencing can be accomplished by relying on their natural activity, exploiting their ability to discriminate between cytosine modification states, reacting them with functionalized substrate analogs to introduce chemical handles, or engineering the DNA-modifying enzymes to take on new reactivities. We describe how these enzymatic reactions have been combined and permuted to localize DNA modifications with high specificity and without the destructive limitations posed by chemical methods for epigenetic sequencing. Chemical sequencing methods damage DNA and can confound cytosine modifications. DNA modifying enzymes offer non-destructive and selective biotechnological tools. DNA deaminases, methyltransferases, oxygenases and glucosyltransferases can be used. Permuting enzymes with various activities can reveal distinct cytosine states. Engineered enzymes utilizing unnatural co-substrates expand sequencing scope.
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Affiliation(s)
- Tong Wang
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christian E Loo
- Graduate Group in Biochemistry and Molecular 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; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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12
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Abstract
T lymphocytes undergo carefully orchestrated programming during development in the thymus and subsequently during differentiation in the periphery. This intricate specification allows for cell-type and context-specific transcriptional programs that regulate immune responses to infection and malignancy. Epigenetic changes, including histone modifications and covalent modification of DNA itself through DNA methylation, are now recognized to play a critical role in these cell-fate decisions. DNA methylation is mediated primarily by the actions of the DNA methyltransferase (DNMT) and ten-eleven-translocation (TET) families of epigenetic enzymes. In this review, we discuss the role of DNA methylation and its enzymatic regulators in directing the development and differentiation of CD4+ and CD8+ T-cells.
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Affiliation(s)
- Luis O Correa
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI
| | - Martha S Jordan
- Department of Pathology and Laboratory Medicine; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Shannon A Carty
- Department of Internal Medicine, Division of Hematology and Oncology; Rogel Cancer Center, University of Michigan, Ann Arbor, MI
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13
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Prasad R, Yen TJ, Bellacosa A. Active DNA demethylation-The epigenetic gatekeeper of development, immunity, and cancer. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e10033. [PMID: 36618446 PMCID: PMC9744510 DOI: 10.1002/ggn2.10033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 01/11/2023]
Abstract
DNA methylation is a critical process in the regulation of gene expression with dramatic effects in development and continually expanding roles in oncogenesis. 5-Methylcytosine was once considered to be an inherited and stably repressive epigenetic mark, which can be only removed by passive dilution during multiple rounds of DNA replication. However, in the past two decades, physiologically controlled DNA demethylation and deamination processes have been identified, thereby revealing the function of cytosine methylation as a highly regulated and complex state-not simply a static, inherited signature or binary on-off switch. Alongside these fundamental discoveries, clinical studies over the past decade have revealed the dramatic consequences of aberrant DNA demethylation. In this review we discuss DNA demethylation and deamination in the context of 5-methylcytosine as critical processes for physiological and physiopathological transitions within three states-development, immune maturation, and oncogenic transformation; and we describe the expanding role of DNA demethylating drugs as therapeutic agents in cancer.
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Affiliation(s)
- Rahul Prasad
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
| | - Timothy J. Yen
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
| | - Alfonso Bellacosa
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
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14
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Caldwell BA, Liu MY, Prasasya RD, Wang T, DeNizio JE, Leu NA, Amoh NYA, Krapp C, Lan Y, Shields EJ, Bonasio R, Lengner CJ, Kohli RM, Bartolomei MS. Functionally distinct roles for TET-oxidized 5-methylcytosine bases in somatic reprogramming to pluripotency. Mol Cell 2021; 81:859-869.e8. [PMID: 33352108 PMCID: PMC7897302 DOI: 10.1016/j.molcel.2020.11.045] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/01/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022]
Abstract
Active DNA demethylation via ten-eleven translocation (TET) family enzymes is essential for epigenetic reprogramming in cell state transitions. TET enzymes catalyze up to three successive oxidations of 5-methylcytosine (5mC), generating 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), or 5-carboxycytosine (5caC). Although these bases are known to contribute to distinct demethylation pathways, the lack of tools to uncouple these sequential oxidative events has constrained our mechanistic understanding of the role of TETs in chromatin reprogramming. Here, we describe the first application of biochemically engineered TET mutants that unlink 5mC oxidation steps, examining their effects on somatic cell reprogramming. We show that only TET enzymes proficient for oxidation to 5fC/5caC can rescue the reprogramming potential of Tet2-deficient mouse embryonic fibroblasts. This effect correlated with rapid DNA demethylation at reprogramming enhancers and increased chromatin accessibility later in reprogramming. These experiments demonstrate that DNA demethylation through 5fC/5caC has roles distinct from 5hmC in somatic reprogramming to pluripotency.
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Affiliation(s)
- Blake A Caldwell
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Monica Yun Liu
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rexxi D Prasasya
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tong Wang
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jamie E DeNizio
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - N Adrian Leu
- Department of Biomedical Sciences, School of Veterinary Medicine, Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nana Yaa A Amoh
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher Krapp
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yemin Lan
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emily J Shields
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Roberto Bonasio
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher J Lengner
- Department of Biomedical Sciences, School of Veterinary Medicine, Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
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15
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DeNizio JE, Dow BJ, Serrano JC, Ghanty U, Drohat AC, Kohli RM. TET-TDG Active DNA Demethylation at CpG and Non-CpG Sites. J Mol Biol 2021; 433:166877. [PMID: 33561435 DOI: 10.1016/j.jmb.2021.166877] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/02/2021] [Indexed: 11/24/2022]
Abstract
In mammalian genomes, cytosine methylation occurs predominantly at CG (or CpG) dinucleotide contexts. As part of dynamic epigenetic regulation, 5-methylcytosine (mC) can be erased by active DNA demethylation, whereby ten-eleven translocation (TET) enzymes catalyze the stepwise oxidation of mC to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxycytosine (caC), thymine DNA glycosylase (TDG) excises fC or caC, and base excision repair yields unmodified cytosine. In certain cell types, mC is also enriched at some non-CG (or CH) dinucleotides, however hmC is not. To provide biochemical context for the distribution of modified cytosines observed in biological systems, we systematically analyzed the activity of human TET2 and TDG for substrates in CG and CH contexts. We find that while TET2 oxidizes mC more efficiently in CG versus CH sites, this context preference can be diminished for hmC oxidation. Remarkably, TDG excision of fC and caC is only modestly dependent on CG context, contrasting its strong context dependence for thymine excision. We show that collaborative TET-TDG oxidation-excision activity is only marginally reduced for CA versus CG contexts. Our findings demonstrate that the TET-TDG-mediated demethylation pathway is not limited to CG sites and suggest a rationale for the depletion of hmCH in genomes rich in mCH.
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Affiliation(s)
- Jamie E DeNizio
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, Philadelphia, PA 19147, USA; Department of Medicine, Department of Biochemistry & Biophysics, Perelman School of Medicine, Philadelphia, PA 19147, USA
| | - Blaine J Dow
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Juan C Serrano
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, Philadelphia, PA 19147, USA; Department of Medicine, Department of Biochemistry & Biophysics, Perelman School of Medicine, Philadelphia, PA 19147, USA
| | - Uday Ghanty
- Department of Medicine, Department of Biochemistry & Biophysics, Perelman School of Medicine, Philadelphia, PA 19147, USA
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Rahul M Kohli
- Department of Medicine, Department of Biochemistry & Biophysics, Perelman School of Medicine, Philadelphia, PA 19147, USA.
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16
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Ghanty U, Wang T, Kohli RM. Nucleobase Modifiers Identify TET Enzymes as Bifunctional DNA Dioxygenases Capable of Direct N‐Demethylation. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Uday Ghanty
- Department of Medicine Department of Biochemistry and Biophysics University of Pennsylvania Philadelphia PA 19104 USA
| | - Tong Wang
- Graduate Group in Biochemistry and Molecular Biophysics University of Pennsylvania Philadelphia PA 19104 USA
| | - Rahul M. Kohli
- Department of Medicine Department of Biochemistry and Biophysics University of Pennsylvania Philadelphia PA 19104 USA
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17
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Ghanty U, Wang T, Kohli RM. Nucleobase Modifiers Identify TET Enzymes as Bifunctional DNA Dioxygenases Capable of Direct N-Demethylation. Angew Chem Int Ed Engl 2020; 59:11312-11315. [PMID: 32271979 DOI: 10.1002/anie.202002751] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/26/2020] [Indexed: 02/04/2023]
Abstract
TET family enzymes are known for oxidation of the 5-methyl substituent on 5-methylcytosine (5mC) in DNA. 5mC oxidation generates the stable base 5-hydroxymethylcytosine (5hmC), starting an indirect, multi-step process that ends with reversion of 5mC to unmodified cytosine. While probing the nucleobase determinants of 5mC recognition, we discovered that TET enzymes are also proficient as direct N-demethylases of cytosine bases. We find that N-demethylase activity can be readily observed on substrates lacking a 5-methyl group and, remarkably, TET enzymes can be similarly proficient in either oxidation of 5mC or demethylation of N4-methyl substituents. Our results indicate that TET enzymes can act as both direct and indirect demethylases, highlight the active-site plasticity of these FeII /α-ketoglutarate-dependent dioxygenases, and suggest activity on unexplored substrates that could reveal new TET biology.
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Affiliation(s)
- Uday Ghanty
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Tong Wang
- Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rahul M Kohli
- Department of Medicine, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
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18
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Liu C, Cui X, Zhao BS, Narkhede P, Gao Y, Liu J, Dou X, Dai Q, Zhang LS, He C. DNA 5-Methylcytosine-Specific Amplification and Sequencing. J Am Chem Soc 2020; 142:4539-4543. [PMID: 32077696 DOI: 10.1021/jacs.9b12707] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
DNA 5-methylcytosine (5mC)-specific mapping has been hampered by severe DNA degradation and the presence of 5-hydroxymethylcytosine (5hmC) using the conventional bisulfite sequencing approach. Here, we present a 5mC-specific whole-genome amplification method (5mC-WGA), with which we achieved 5mC retention during DNA amplification from limited input down to 10 pg scale with limited interference from 5hmC signals, providing DNA 5mC methylome with high reproducibility and accuracy.
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Affiliation(s)
- Chang Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.,Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Xiaolong Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.,Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Boxuan Simen Zhao
- Department of Genetics, Stanford University, Stanford, California 94305, United States
| | - Pradnya Narkhede
- Department of Chemistry, University of Cambridge, Cambridge CB2 0SP, U.K
| | - Yawei Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jun Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.,Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Xiaoyang Dou
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.,Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Qing Dai
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.,Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Li-Sheng Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.,Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.,Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States
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19
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Pfeifer GP, Szabó PE, Song J. Protein Interactions at Oxidized 5-Methylcytosine Bases. J Mol Biol 2019:S0022-2836(19)30501-7. [PMID: 31401118 DOI: 10.1016/j.jmb.2019.07.039] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 12/19/2022]
Abstract
5-Methylcytosine (5mC), the major modified DNA base in mammalian cells, can be oxidized enzymatically to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) by the Ten-Eleven-Translocation (TET) family of proteins. Whereas 5fC and 5caC are recognized and removed by base excision repair proteins, the 5hmC base accumulates to substantial levels in certain cell types such as brain-derived neurons and is viewed as a relatively stable DNA base. As such, the existence of "reader" proteins that recognize 5hmC would be a logical assumption, and various searches have been undertaken to identify proteins that specifically bind to 5hmC and the other oxidized 5mC bases. However, the existence of definitive 5hmC "readers" has remained unclear and proteins interacting specifically with 5fC or 5caC are also very few. On the other hand, 5hmC is incapable of interacting with a number of proteins that recognize 5mC at CpG sequences, suggesting that 5hmC is an anti-reader modification that may serve to displace 5mC readers from DNA. In this review article, we discuss candidate proteins that may interact with oxidized 5mC bases.
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Affiliation(s)
- Gerd P Pfeifer
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
| | - Piroska E Szabó
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jikui Song
- Department of Biochemistry, University of California Riverside, Riverside, CA 92521, USA
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20
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Ma Y, Ma Y, Wen L, Lei H, Chen S, Wang X. Changes in DNA methylation and imprinting disorders in E9.5 mouse fetuses and placentas derived from vitrified eight-cell embryos. Mol Reprod Dev 2019; 86:404-415. [PMID: 30680835 DOI: 10.1002/mrd.23118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/08/2019] [Accepted: 01/20/2019] [Indexed: 01/21/2023]
Abstract
Vitrification is increasingly used in assisted reproductive technology (ART) laboratories worldwide, and potential vitrification-induced risks require further exploration. The effect of vitrification on changes in DNA methylation and imprinting disorders was investigated in E9.5 mouse fetuses and placentas. Fetus and placental tissues were collected from the natural mating (nautural conception [NC]) group, in vitro culture (IVC) group and vitrified embryo transfer (VET) group. The fetal crown-rump length at E9.5 in both the IVC (0.210 ± 0.059 mm) and VET (0.205 ± 0.048 mm) groups was significantly reduced compared with the NC group (0.288 ± 0.083 mm). The global methylation levels of fetuses were decreased in the IVC group compared with the NC group and it was increased after vitrification compared with IVC (p < 0.05), similar to what was observed in the NC group (p > 0.05). The changes could be attributed to the disorders of DNA methyltransferases and ten-eleven translocations. In the IVC and VET fetuses, a majority of maternally expressed genes were upregulated, which repressed fetal growth. Furthermore, vitrification led to a change in the methylation level of KvDMR1, which resulted in the disturbance of gene imprinting. According to our results, vitrification could contribute to increased methylation compared with IVC and contributes to a gene imprinting disorder rather than recovery. Despite the routine use of embryo vitrification in clinical settings, the effect that this procedure may have on genomic imprinting deserves much greater attention.
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Affiliation(s)
- Yuan Ma
- Department of Obstetrics and Gynecology, The Reproductive Medicine Center, Tangdu Hospital, Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Yefei Ma
- Department of Obstetrics and Gynecology, The Reproductive Medicine Center, Tangdu Hospital, Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Liang Wen
- Department of Obstetrics and Gynecology, The Reproductive Medicine Center, Tangdu Hospital, Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Hui Lei
- Department of Obstetrics and Gynecology, The Reproductive Medicine Center, Tangdu Hospital, Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Shuqiang Chen
- Department of Obstetrics and Gynecology, The Reproductive Medicine Center, Tangdu Hospital, Air Force Military Medical University, Xi'an, Shaanxi, China
| | - Xiaohong Wang
- Department of Obstetrics and Gynecology, The Reproductive Medicine Center, Tangdu Hospital, Air Force Military Medical University, Xi'an, Shaanxi, China
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