1
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Scelfo A, Barra V, Abdennur N, Spracklin G, Busato F, Salinas-Luypaert C, Bonaiti E, Velasco G, Bonhomme F, Chipont A, Tijhuis AE, Spierings DC, Guérin C, Arimondo P, Francastel C, Foijer F, Tost J, Mirny L, Fachinetti D. Tunable DNMT1 degradation reveals DNMT1/DNMT3B synergy in DNA methylation and genome organization. J Cell Biol 2024; 223:e202307026. [PMID: 38376465 PMCID: PMC10876481 DOI: 10.1083/jcb.202307026] [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: 07/06/2023] [Revised: 11/20/2023] [Accepted: 01/15/2024] [Indexed: 02/21/2024] Open
Abstract
DNA methylation (DNAme) is a key epigenetic mark that regulates critical biological processes maintaining overall genome stability. Given its pleiotropic function, studies of DNAme dynamics are crucial, but currently available tools to interfere with DNAme have limitations and major cytotoxic side effects. Here, we present cell models that allow inducible and reversible DNAme modulation through DNMT1 depletion. By dynamically assessing whole genome and locus-specific effects of induced passive demethylation through cell divisions, we reveal a cooperative activity between DNMT1 and DNMT3B, but not of DNMT3A, to maintain and control DNAme. We show that gradual loss of DNAme is accompanied by progressive and reversible changes in heterochromatin, compartmentalization, and peripheral localization. DNA methylation loss coincides with a gradual reduction of cell fitness due to G1 arrest, with minor levels of mitotic failure. Altogether, this system allows DNMTs and DNA methylation studies with fine temporal resolution, which may help to reveal the etiologic link between DNAme dysfunction and human disease.
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Affiliation(s)
- Andrea Scelfo
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR 144, Paris, France
| | - Viviana Barra
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR 144, Paris, France
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - Nezar Abdennur
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA, USA
- Department of Systems Biology, UMass Chan Medical School, Worcester, MA, USA
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - George Spracklin
- Department of Systems Biology, UMass Chan Medical School, Worcester, MA, USA
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Florence Busato
- Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Université Paris-Saclay, Evry, France
| | | | - Elena Bonaiti
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR 144, Paris, France
| | | | - Frédéric Bonhomme
- Epigenetic Chemical Biology, Institut Pasteur, CNRS UMR n°3523 Chem4Life, Université Paris Cité, Paris, France
| | - Anna Chipont
- Cytometry Platform, Institut Curie, Paris, France
| | - Andréa E. Tijhuis
- European Research Institute for the Biology of Ageing, University Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Diana C.J. Spierings
- European Research Institute for the Biology of Ageing, University Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Coralie Guérin
- Cytometry Platform, Institut Curie, Paris, France
- Université Paris Cité, INSERM, Paris, France
| | - Paola Arimondo
- Epigenetic Chemical Biology, Institut Pasteur, CNRS UMR n°3523 Chem4Life, Université Paris Cité, Paris, France
| | | | - Floris Foijer
- European Research Institute for the Biology of Ageing, University Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Jӧrg Tost
- Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Université Paris-Saclay, Evry, France
| | - Leonid Mirny
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, Sorbonne Université, CNRS, UMR 144, Paris, France
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2
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Feng Q, Duan H, Zhou X, Wang Y, Zhang J, Zhang H, Chen G, Bao X. DNA Methyltransferase 3A: A Significant Target for the Discovery of Inhibitors as Potent Anticancer Drugs. Mini Rev Med Chem 2024; 24:507-520. [PMID: 37642180 DOI: 10.2174/1389557523666230825100246] [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: 04/20/2023] [Revised: 06/27/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023]
Abstract
DNA methyltransferase (DNMT) is a conserved family of Cytosine methylases, which plays a crucial role in the regulation of Epigenetics. They have been considered promising therapeutic targets for cancer. Among the DNMT family, mutations in the DNMT3A subtype are particularly important in hematologic malignancies. The development of specific DNMT3A subtype inhibitors to validate the therapeutic potential of DNMT3A in certain diseases is a significant task. In this review, we summarized the small molecule inhibitors of DNMT3A discovered in recent years and their inhibitory activities, and classified them based on their inhibitory mechanisms.
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Affiliation(s)
- Qixun Feng
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Honggao Duan
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Xinglong Zhou
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Yuning Wang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Jinda Zhang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Haoge Zhang
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Guoliang Chen
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Xuefei Bao
- Key Laboratory of Structure-Based Drugs Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
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3
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Sun S, Liu Q, Wang Z, Huang YY, Sublette M, Dwork A, Rosoklija G, Ge Y, Galfalvy H, Mann JJ, Haghighi F. Functional Architecture of Brain and Blood Transcriptome Delineate Biological Continuity Between Suicidal Ideation and Suicide. RESEARCH SQUARE 2023:rs.3.rs-2958575. [PMID: 37398042 PMCID: PMC10312911 DOI: 10.21203/rs.3.rs-2958575/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Human genetic studies indicate that suicidal ideation and behavior are both heritable. Most studies have examined associations between aberrant gene expression and suicide behavior, but behavior risk is linked to severity of suicidal ideation. Through a gene network approach, this study investigates how gene co-expression patterns are associated with suicidal ideation and severity using RNA-seq data in peripheral blood from 46 live participants with elevated suicidal ideation and 46 with no ideation. Associations with presence and severity of suicidal ideation were found within 18 and 3 co-expressed modules respectively (p < 0.05), not explained by severity of depression. Suicidal ideation presence and severity-related gene modules with enrichment of genes involved in defense against microbial infection, inflammation, and adaptive immune response were identified, and tested using RNA-seq data from postmortem brain that revealed gene expression differences in suicide decedents vs. non-suicides in white matter, but not gray matter. Findings support a role of brain and peripheral blood inflammation in suicide risk, showing that suicidal ideation presence and severity is associated with an inflammatory signature detectable in blood and brain, indicating a biological continuity between ideation and suicidal behavior that may underlie a common heritability.
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4
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Ngan KCH, Hoenig SM, Kwok HS, Lue NZ, Gosavi PM, Tanner DA, Garcia EM, Lee C, Liau BB. Activity-based CRISPR scanning uncovers allostery in DNA methylation maintenance machinery. eLife 2023; 12:80640. [PMID: 36762644 PMCID: PMC9946446 DOI: 10.7554/elife.80640] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 02/03/2023] [Indexed: 02/11/2023] Open
Abstract
Allostery enables dynamic control of protein function. A paradigmatic example is the tightly orchestrated process of DNA methylation maintenance. Despite the fundamental importance of allosteric sites, their identification remains highly challenging. Here, we perform CRISPR scanning on the essential maintenance methylation machinery-DNMT1 and its partner UHRF1-with the activity-based inhibitor decitabine to uncover allosteric mechanisms regulating DNMT1. In contrast to non-covalent DNMT1 inhibition, activity-based selection implicates numerous regions outside the catalytic domain in DNMT1 function. Through computational analyses, we identify putative mutational hotspots in DNMT1 distal from the active site that encompass mutations spanning a multi-domain autoinhibitory interface and the uncharacterized BAH2 domain. We biochemically characterize these mutations as gain-of-function, exhibiting increased DNMT1 activity. Extrapolating our analysis to UHRF1, we discern putative gain-of-function mutations in multiple domains, including key residues across the autoinhibitory TTD-PBR interface. Collectively, our study highlights the utility of activity-based CRISPR scanning for nominating candidate allosteric sites, and more broadly, introduces new analytical tools that further refine the CRISPR scanning framework.
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Affiliation(s)
- Kevin Chun-Ho Ngan
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - Samuel M Hoenig
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Hui Si Kwok
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - Nicholas Z Lue
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - Pallavi M Gosavi
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - David A Tanner
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Emma M Garcia
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - Ceejay Lee
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States,Broad Institute of MIT and HarvardCambridgeUnited States
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5
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DNA Methyltransferases: From Evolution to Clinical Applications. Int J Mol Sci 2022; 23:ijms23168994. [PMID: 36012258 PMCID: PMC9409253 DOI: 10.3390/ijms23168994] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is an epigenetic mark that living beings have used in different environments. The MTases family catalyzes DNA methylation. This process is conserved from archaea to eukaryotes, from fertilization to every stage of development, and from the early stages of cancer to metastasis. The family of DNMTs has been classified into DNMT1, DNMT2, and DNMT3. Each DNMT has been duplicated or deleted, having consequences on DNMT structure and cellular function, resulting in a conserved evolutionary reaction of DNA methylation. DNMTs are conserved in the five kingdoms of life: bacteria, protists, fungi, plants, and animals. The importance of DNMTs in whether methylate or not has a historical adaptation that in mammals has been discovered in complex regulatory mechanisms to develop another padlock to genomic insurance stability. The regulatory mechanisms that control DNMTs expression are involved in a diversity of cell phenotypes and are associated with pathologies transcription deregulation. This work focused on DNA methyltransferases, their biology, functions, and new inhibitory mechanisms reported. We also discuss different approaches to inhibit DNMTs, the use of non-coding RNAs and nucleoside chemical compounds in recent studies, and their importance in biological, clinical, and industry research.
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6
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DNMT1 regulates the timing of DNA methylation by DNMT3 in an enzymatic activity-dependent manner in mouse embryonic stem cells. PLoS One 2022; 17:e0262277. [PMID: 34986190 PMCID: PMC8730390 DOI: 10.1371/journal.pone.0262277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/21/2021] [Indexed: 01/01/2023] Open
Abstract
DNA methylation (DNAme; 5-methylcytosine, 5mC) plays an essential role in mammalian development, and the 5mC profile is regulated by a balance of opposing enzymatic activities: DNA methyltransferases (DNMTs) and Ten-eleven translocation dioxygenases (TETs). In mouse embryonic stem cells (ESCs), de novo DNAme by DNMT3 family enzymes, demethylation by the TET-mediated conversion of 5mC to 5-hydroxymethylation (5hmC), and maintenance of the remaining DNAme by DNMT1 are actively repeated throughout cell cycles, dynamically forming a constant 5mC profile. Nevertheless, the detailed mechanism and physiological significance of this active cyclic DNA modification in mouse ESCs remain unclear. Here by visualizing the localization of DNA modifications on metaphase chromosomes and comparing whole-genome methylation profiles before and after the mid-S phase in ESCs lacking Dnmt1 (1KO ESCs), we demonstrated that in 1KO ESCs, DNMT3-mediated remethylation was interrupted during and after DNA replication. This results in a marked asymmetry in the distribution of 5hmC between sister chromatids at mitosis, with one chromatid being almost no 5hmC. When introduced in 1KO ESCs, the catalytically inactive form of DNMT1 (DNMT1CI) induced an increase in DNAme in pericentric heterochromatin and the DNAme-independent repression of IAPEz, a retrotransposon family, in 1KO ESCs. However, DNMT1CI could not restore the ability of DNMT3 to methylate unmodified dsDNA de novo in S phase in 1KO ESCs. Furthermore, during in vitro differentiation into epiblasts, 1KO ESCs expressing DNMT1CI showed an even stronger tendency to differentiate into the primitive endoderm than 1KO ESCs and were readily reprogrammed into the primitive streak via an epiblast-like cell state, reconfirming the importance of DNMT1 enzymatic activity at the onset of epiblast differentiation. These results indicate a novel function of DNMT1, in which DNMT1 actively regulates the timing and genomic targets of de novo methylation by DNMT3 in an enzymatic activity-dependent and independent manner, respectively.
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7
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mRNA Expressions of Methylation Related Enzymes and Duration of Thermal Conditioning in Chicks. J Poult Sci 2022; 59:90-95. [PMID: 35125918 PMCID: PMC8791769 DOI: 10.2141/jpsa.0210029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/15/2021] [Indexed: 11/21/2022] Open
Abstract
DNA methylation regulates gene expression by modifying the nucleosome structure of DNA, without altering the gene sequence. It has been reported that DNA methylation reactions are catalyzed by several enzymes. In chickens, thermal conditioning treatment affects the central DNA methylation levels. The purpose of this study was to clarify the changes in DNA methylation and demethylation factors during thermal conditioning in the hypothalamus of 3-day-old chicks. Male chicks (3-days old) were exposed to 40±0.5°C as a thermal conditioning treatment for 1, 2, 6, 9, or 12 h. The control chicks were kept in a thermoneutral zone (30±0.2°C). After thermal conditioning, the mRNA levels of DNA methyltransferase (DNMT)-1, -3a, -3b, and ten-eleven translocation (TET)-1, -2, and -3 in the hypothalamus were measured by q-PCR. The mRNA levels of DNMT-3a and TET-1 were increased by thermal conditioning. Moreover, the expression level of TET-1 increased with the loading time of the thermal conditioning. The gene expressions of DNMT-1, DNMT-3b, TET-2, and TET-3 were not affected by thermal conditioning. Since DNMT-3a is a catalyst for de-novo DNA methylation and TET-1 catalyzes the oxidation of methylated cytosine, it is suggested that the thermal conditioning increased the activation of DNA methylation and demethylation factors, which occur in the hypothalamus of neonatal chicks.
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8
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Tajima S, Suetake I, Takeshita K, Nakagawa A, Kimura H, Song J. Domain Structure of the Dnmt1, Dnmt3a, and Dnmt3b DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:45-68. [PMID: 36350506 PMCID: PMC11025882 DOI: 10.1007/978-3-031-11454-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In mammals, three major DNA methyltransferases, Dnmt1, Dnmt3a, and Dnmt3b, have been identified. Dnmt3a and Dnmt3b are responsible for establishing DNA methylation patterns produced through their de novo-type DNA methylation activity in implantation stage embryos and during germ cell differentiation. Dnmt3-like (Dnmt3l), which is a member of the Dnmt3 family but does not possess DNA methylation activity, was reported to be indispensable for global methylation in germ cells. Once the DNA methylation patterns are established, maintenance-type DNA methyltransferase Dnmt1 faithfully propagates them to the next generation via replication. All Dnmts possess multiple domains. For instance, Dnmt3a and Dnmt3b each contain a Pro-Trp-Trp-Pro (PWWP) domain that recognizes the histone H3K36me2/3 mark, an Atrx-Dnmt3-Dnmt3l (ADD) domain that recognizes unmodified histone H3 tail, and a catalytic domain that methylates CpG sites. Dnmt1 contains an N-terminal independently folded domain (NTD) that interacts with a variety of regulatory factors, a replication foci-targeting sequence (RFTS) domain that recognizes the histone H3K9me3 mark and H3 ubiquitylation, a CXXC domain that recognizes unmodified CpG DNA, two tandem Bromo-Adjacent-homology (BAH1 and BAH2) domains that read the H4K20me3 mark with BAH1, and a catalytic domain that preferentially methylates hemimethylated CpG sites. In this chapter, the structures and functions of these domains are described.
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Affiliation(s)
- Shoji Tajima
- Institute for Protein Research, Osaka University, Osaka, Japan.
| | - Isao Suetake
- Department of Nutritional Sciences, Faculty of Nutritional Sciences, Nakamura Gakuen University, Fukuoka, Japan
| | | | - Atsushi Nakagawa
- Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hironobu Kimura
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Jikui Song
- Department of Biochemistry, University of California Riverside, Riverside, CA, USA.
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9
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Jurkowska RZ, Jeltsch A. Enzymology of Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:69-110. [DOI: 10.1007/978-3-031-11454-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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10
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Polverino A, Sorrentino P, Pesoli M, Mandolesi L. Nutrition and cognition across the lifetime: an overview on epigenetic mechanisms. AIMS Neurosci 2021; 8:448-476. [PMID: 34877399 PMCID: PMC8611190 DOI: 10.3934/neuroscience.2021024] [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: 04/22/2021] [Accepted: 07/12/2021] [Indexed: 12/28/2022] Open
Abstract
The functioning of our brain depends on both genes and their interactions with environmental factors. The close link between genetics and environmental factors produces structural and functional cerebral changes early on in life. Understanding the weight of environmental factors in modulating neuroplasticity phenomena and cognitive functioning is relevant for potential interventions. Among these, nutrition plays a key role. In fact, the link between gut and brain (the gut-brain axis) is very close and begins in utero, since the Central Nervous System (CNS) and the Enteric Nervous System (ENS) originate from the same germ layer during the embryogenesis. Here, we investigate the epigenetic mechanisms induced by some nutrients on the cognitive functioning, which affect the cellular and molecular processes governing our cognitive functions. Furthermore, epigenetic phenomena can be positively affected by specific healthy nutrients from diet, with the possibility of preventing or modulating cognitive impairments. Specifically, we described the effects of several nutrients on diet-dependent epigenetic processes, in particular DNA methylation and histones post-translational modifications, and their potential role as therapeutic target, to describe how some forms of cognitive decline could be prevented or modulated from the early stages of life.
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Affiliation(s)
- Arianna Polverino
- Institute of Diagnosis and Treatment Hermitage Capodimonte, Naples, Italy.,Department of Motor and Wellness Sciences, University of Naples "Parthenope", Naples, Italy
| | - Pierpaolo Sorrentino
- Institut de Neurosciences des Systèmes, Aix-Marseille University, Marseille, France.,Institute of Applied Sciences and Intelligent Systems, National Research Council, Pozzuoli, Italy
| | - Matteo Pesoli
- Department of Motor and Wellness Sciences, University of Naples "Parthenope", Naples, Italy
| | - Laura Mandolesi
- Department of Humanities Studies, University of Naples Federico II, Naples, Italy
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11
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Sugita E, Hayashi K, Hishikawa A, Itoh H. Epigenetic Alterations in Podocytes in Diabetic Nephropathy. Front Pharmacol 2021; 12:759299. [PMID: 34630127 PMCID: PMC8497789 DOI: 10.3389/fphar.2021.759299] [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] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/13/2021] [Indexed: 01/19/2023] Open
Abstract
Recently, epigenetic alterations have been shown to be involved in the pathogenesis of diabetes and its complications. Kidney podocytes, which are glomerular epithelial cells, are important cells that form a slit membrane—a barrier for proteinuria. Podocytes are terminally differentiated cells without cell division or replenishment abilities. Therefore, podocyte damage is suggested to be one of the key factors determining renal prognosis. Recent studies, including ours, suggest that epigenetic changes in podocytes are associated with chronic kidney disease, including diabetic nephropathy. Furthermore, the association between DNA damage repair and epigenetic changes in diabetic podocytes has been demonstrated. Detection of podocyte DNA damage and epigenetic changes using human samples, such as kidney biopsy and urine-derived cells, may be a promising strategy for estimating kidney damage and renal prognoses in patients with diabetes. Targeting epigenetic podocyte changes and associated DNA damage may become a novel therapeutic strategy for preventing progression to end-stage renal disease (ESRD) and provide a possible prognostic marker in diabetic nephropathy. This review summarizes recent advances regarding epigenetic changes, especially DNA methylation, in podocytes in diabetic nephropathy and addresses detection of these alterations in human samples. Additionally, we focused on DNA damage, which is increased under high-glucose conditions and associated with the generation of epigenetic changes in podocytes. Furthermore, epigenetic memory in diabetes is discussed. Understanding the role of epigenetic changes in podocytes in diabetic nephropathy may be of great importance considering the increasing diabetic nephropathy patient population in an aging society.
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Affiliation(s)
- Erina Sugita
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Kaori Hayashi
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Akihito Hishikawa
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Hiroshi Itoh
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
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12
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Qin W, Scicluna BP, van der Poll T. The Role of Host Cell DNA Methylation in the Immune Response to Bacterial Infection. Front Immunol 2021; 12:696280. [PMID: 34394088 PMCID: PMC8358789 DOI: 10.3389/fimmu.2021.696280] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Host cells undergo complex transcriptional reprogramming upon infection. Epigenetic changes play a key role in the immune response to bacteria, among which DNA modifications that include methylation have received much attention in recent years. The extent of DNA methylation is well known to regulate gene expression. Whilst historically DNA methylation was considered to be a stable epigenetic modification, accumulating evidence indicates that DNA methylation patterns can be altered rapidly upon exposure of cells to changing environments and pathogens. Furthermore, the action of proteins regulating DNA methylation, particularly DNA methyltransferases and ten-eleven translocation methylcytosine dioxygenases, may be modulated, at least in part, by bacteria. This review discusses the principles of DNA methylation, and recent insights about the regulation of host DNA methylation during bacterial infection.
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Affiliation(s)
- Wanhai Qin
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Brendon P Scicluna
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Tom van der Poll
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Division of Infectious Diseases, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
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13
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Kausar S, Abbas MN, Cui H. A review on the DNA methyltransferase family of insects: Aspect and prospects. Int J Biol Macromol 2021; 186:289-302. [PMID: 34237376 DOI: 10.1016/j.ijbiomac.2021.06.205] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/22/2021] [Accepted: 06/30/2021] [Indexed: 12/11/2022]
Abstract
The DNA methyltransferase family contains a conserved set of DNA-modifying enzymatic proteins. They are responsible for epigenetic gene modulation, such as transcriptional silencing, transcription activation, and post-transcriptional modulation. Recent research has revealed that the canonical DNA methyltransferases (DNMTs) biological roles go beyond their traditional functions of establishing and maintaining DNA methylation patterns. Although a complete DNA methylation toolkit is absent in most insect orders, recent evidence indicates the de novo DNA methylation and maintenance function remain conserved. Studies using various molecular approaches provided evidence that DNMTs are multi-functional proteins. However, still in-depth studies on their biological role lack due to the least studied area in insects. Here, we review the DNA methylation toolkit of insects, focusing on recent research on various insect orders, which exhibit DNA methylation at different levels, and for which DNMTs functional studies have become available in recent years. We survey research on the potential roles of DNMTs in the regulation of gene transcription in insect species. DNMTs participate in different physiological processes by interacting with other epigenetic factors. Future studies on insect's DNMTs will benefit to understand developmental processes, responses to various stimuli, and adaptability of insects to different environmental conditions.
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Affiliation(s)
- Saima Kausar
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Muhammad Nadeem Abbas
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China.
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14
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Haggerty C, Kretzmer H, Riemenschneider C, Kumar AS, Mattei AL, Bailly N, Gottfreund J, Giesselmann P, Weigert R, Brändl B, Giehr P, Buschow R, Galonska C, von Meyenn F, Pappalardi MB, McCabe MT, Wittler L, Giesecke-Thiel C, Mielke T, Meierhofer D, Timmermann B, Müller FJ, Walter J, Meissner A. Dnmt1 has de novo activity targeted to transposable elements. Nat Struct Mol Biol 2021; 28:594-603. [PMID: 34140676 PMCID: PMC8279952 DOI: 10.1038/s41594-021-00603-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 05/10/2021] [Indexed: 02/06/2023]
Abstract
DNA methylation plays a critical role during development, particularly in repressing retrotransposons. The mammalian methylation landscape is dependent on the combined activities of the canonical maintenance enzyme Dnmt1 and the de novo Dnmts, 3a and 3b. Here, we demonstrate that Dnmt1 displays de novo methylation activity in vitro and in vivo with specific retrotransposon targeting. We used whole-genome bisulfite and long-read Nanopore sequencing in genetically engineered methylation-depleted mouse embryonic stem cells to provide an in-depth assessment and quantification of this activity. Utilizing additional knockout lines and molecular characterization, we show that the de novo methylation activity of Dnmt1 depends on Uhrf1, and its genomic recruitment overlaps with regions that enrich for Uhrf1, Trim28 and H3K9 trimethylation. Our data demonstrate that Dnmt1 can catalyze DNA methylation in both a de novo and maintenance context, especially at retrotransposons, where this mechanism may provide additional stability for long-term repression and epigenetic propagation throughout development.
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Affiliation(s)
- Chuck Haggerty
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Christina Riemenschneider
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Abhishek Sampath Kumar
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexandra L Mattei
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Nina Bailly
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Judith Gottfreund
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken, Germany
| | - Pay Giesselmann
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Raha Weigert
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Björn Brändl
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Christian-Albrechts-Universität zu Kiel, Department of Psychiatry and Psychotherapy, Kiel, Germany
| | - Pascal Giehr
- Institute of Food, Nutrition and Health, ETH Zurich, Schwerzenbach, Switzerland
| | - René Buschow
- Microscopy and Cryo-electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Christina Galonska
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Spatial Transcriptomics, Part of 10x Genomics Inc, Stockholm, Sweden
| | | | | | - Michael T McCabe
- Epigenetics Research Unit, Oncology R&D, GlaxoSmithKline, Collegeville, PA, USA
| | - Lars Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Claudia Giesecke-Thiel
- Flow Cytometry Joint Facilities Scientific Service, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - David Meierhofer
- Mass Spectrometry Joint Facilities Scientific Service, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Franz-Josef Müller
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Christian-Albrechts-Universität zu Kiel, Department of Psychiatry and Psychotherapy, Kiel, Germany
| | - Jörn Walter
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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15
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Das AB, Seddon AR, O'Connor KM, Hampton MB. Regulation of the epigenetic landscape by immune cell oxidants. Free Radic Biol Med 2021; 170:131-149. [PMID: 33444713 DOI: 10.1016/j.freeradbiomed.2020.12.453] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/21/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022]
Abstract
Excessive production of microbicidal oxidants by neutrophils can damage host tissue. The short-term response of cells to oxidative stress is well understood, but the mechanisms behind long-term consequences require further clarification. Epigenetic pathways mediate cellular adaptation, and are therefore a potential target of oxidative stress. Indeed, there is evidence that many proteins and metabolites involved in epigenetic pathways are redox sensitive. In this review we provide an overview of the epigenetic landscape and discuss the potential for redox regulation. Using this information, we highlight specific examples where neutrophil oxidants react with epigenetic pathway components. We also use published data from redox proteomics to map out known intersections between oxidative stress and epigenetics that may signpost helpful directions for future investigation. Finally, we discuss the role neutrophils play in adaptive pathologies with a focus on tumour initiation and progression. We hope this information will stimulate further discourse on the emerging field of redox epigenomics.
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Affiliation(s)
- Andrew B Das
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Annika R Seddon
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Karina M O'Connor
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
| | - Mark B Hampton
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
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16
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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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17
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Rastogi A, Lin X, Lombard B, Loew D, Tirichine L. Probing the evolutionary history of epigenetic mechanisms: what can we learn from marine diatoms. AIMS GENETICS 2021. [DOI: 10.3934/genet.2015.3.173] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
AbstractRecent progress made on epigenetic studies revealed the conservation of epigenetic features in deep diverse branching species including Stramenopiles, plants and animals. This suggests their fundamental role in shaping species genomes across different evolutionary time scales. Diatoms are a highly successful and diverse group of phytoplankton with a fossil record of about 190 million years ago. They are distantly related from other super-groups of Eukaryotes and have retained some of the epigenetic features found in mammals and plants suggesting their ancient origin. Phaeodactylum tricornutum and Thalassiosira pseudonana, pennate and centric diatoms, respectively, emerged as model species to address questions on the evolution of epigenetic phenomena such as what has been lost, retained or has evolved in contemporary species. In the present work, we will discuss how the study of non-model or emerging model organisms, such as diatoms, helps understand the evolutionary history of epigenetic mechanisms with a particular focus on DNA methylation and histone modifications.
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Affiliation(s)
- Achal Rastogi
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d’Ulm 75005 Paris, France
| | - Xin Lin
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d’Ulm 75005 Paris, France
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, China
| | - Bérangère Lombard
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d’Ulm 75248 Cedex 05 Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d’Ulm 75248 Cedex 05 Paris, France
| | - Leïla Tirichine
- Ecology and Evolutionary Biology Section, Institut de Biologie de l'École Normale Supérieure (IBENS), CNRS UMR8197 INSERM U1024, 46 rue d’Ulm 75005 Paris, France
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18
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Parveen N, Dhawan S. DNA Methylation Patterning and the Regulation of Beta Cell Homeostasis. Front Endocrinol (Lausanne) 2021; 12:651258. [PMID: 34025578 PMCID: PMC8137853 DOI: 10.3389/fendo.2021.651258] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/21/2021] [Indexed: 12/14/2022] Open
Abstract
Pancreatic beta cells play a central role in regulating glucose homeostasis by secreting the hormone insulin. Failure of beta cells due to reduced function and mass and the resulting insulin insufficiency can drive the dysregulation of glycemic control, causing diabetes. Epigenetic regulation by DNA methylation is central to shaping the gene expression patterns that define the fully functional beta cell phenotype and regulate beta cell growth. Establishment of stage-specific DNA methylation guides beta cell differentiation during fetal development, while faithful restoration of these signatures during DNA replication ensures the maintenance of beta cell identity and function in postnatal life. Lineage-specific transcription factor networks interact with methylated DNA at specific genomic regions to enhance the regulatory specificity and ensure the stability of gene expression patterns. Recent genome-wide DNA methylation profiling studies comparing islets from diabetic and non-diabetic human subjects demonstrate the perturbation of beta cell DNA methylation patterns, corresponding to the dysregulation of gene expression associated with mature beta cell state in diabetes. This article will discuss the molecular underpinnings of shaping the islet DNA methylation landscape, its mechanistic role in the specification and maintenance of the functional beta cell phenotype, and its dysregulation in diabetes. We will also review recent advances in utilizing beta cell specific DNA methylation patterns for the development of biomarkers for diabetes, and targeting DNA methylation to develop translational approaches for supplementing the functional beta cell mass deficit in diabetes.
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Affiliation(s)
| | - Sangeeta Dhawan
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, United States
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19
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Yang M, Barrios J, Yan J, Zhao W, Yuan S, Dong E, Ai X. Causal roles of stress kinase JNK2 in DNA methylation and binge alcohol withdrawal-evoked behavioral deficits. Pharmacol Res 2021; 164:105375. [PMID: 33316384 PMCID: PMC7867628 DOI: 10.1016/j.phrs.2020.105375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/20/2020] [Accepted: 12/06/2020] [Indexed: 11/27/2022]
Abstract
Excessive binge alcohol intake is a common drinking pattern in humans, especially during holidays. Cessation of the binge drinking often leads to aberrant withdrawal behaviors, as well as serious heart rhythm abnormalities (clinically diagnosed as Holiday Heart Syndrome (HHS)). In our HHS mouse model with well-characterized binge alcohol withdrawal (BAW)-induced heart phenotypes, BAW leads to anxiety-like behaviors and cognitive impairment. We have previously reported that stress-activated c-Jun NH(2)-terminal kinase (JNK) plays a causal role in BAW-induced heart phenotypes. In the HHS brain, we found that activation of JNK2 (but not JNK1 and JNK3) in the prefrontal cortex (PFC), but not hippocampus and amygdala, led to anxiety-like behaviors and impaired cognition. DNA methylation mediated by a crucial DNA methylation enzyme, DNA methyltransferase1 (DNMT1), is known to be critical in alcohol-associated behavioral deficits. In HHS mice, JNK2 in the PFC (but not hippocampus and amygdala) causally enhanced total genomic DNA methylation via increased DNMT1 expression, which was regulated by enhanced binding of JNK downstream transcriptional factor c-JUN to the DNMT1 promoter. JNK2-specific inhibition either by an inhibitor JNK2I or JNK2 knockout completely offset c-JUN-regulated DNMT1 upregulation and restored the level of DNA methylation in HHS PFC to the baseline levels seen in sham controls. Strikingly, either JNK2-specific inhibition or genetic JNK2 depletion or DNMT1 inhibition (by an inhibitor 5-Azacytidine) completely abolished BAW-evoked behavioral deficits. In conclusion, our studies revealed a novel mechanism by which JNK2 drives BAW-evoked behavioral deficits through a DNMT1-regulated DNA hypermethylation. JNK2 could be a novel therapeutic target for alcohol withdrawal treatment and/or prevention.
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Affiliation(s)
- Mei Yang
- Department of Physiology & Biophysics, Rush University Medical Center, Chicago, IL, 60607, USA
| | - Jasson Barrios
- Department of Physiology & Biophysics, Rush University Medical Center, Chicago, IL, 60607, USA
| | - Jiajie Yan
- Department of Physiology & Biophysics, Rush University Medical Center, Chicago, IL, 60607, USA
| | - Weiwei Zhao
- Department of Physiology & Biophysics, Rush University Medical Center, Chicago, IL, 60607, USA
| | - Shengtao Yuan
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing, 210009, China
| | - Erbo Dong
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, IL, 60612, USA.
| | - Xun Ai
- Department of Physiology & Biophysics, Rush University Medical Center, Chicago, IL, 60607, USA.
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20
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Zhao C, Zhang N, Zhang Y, Tuersunjiang N, Gao S, Liu W, Zhang Y. A DNA methylation state transition model reveals the programmed epigenetic heterogeneity in human pre-implantation embryos. Genome Biol 2020; 21:277. [PMID: 33198783 PMCID: PMC7667739 DOI: 10.1186/s13059-020-02189-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/27/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND During mammalian early embryogenesis, expression and epigenetic heterogeneity emerge before the first cell fate determination, but the programs causing such determinate heterogeneity are largely unexplored. RESULTS Here, we present MethylTransition, a novel DNA methylation state transition model, for characterizing methylation changes during one or a few cell cycles at single-cell resolution. MethylTransition involves the creation of a transition matrix comprising three parameters that represent the probabilities of DNA methylation-modifying activities in order to link the methylation states before and after a cell cycle. We apply MethylTransition to single-cell DNA methylome data from human pre-implantation embryogenesis and elucidate that the DNA methylation heterogeneity that emerges at promoters during this process is largely an intrinsic output of a program with unique probabilities of DNA methylation-modifying activities. Moreover, we experimentally validate the effect of the initial DNA methylation on expression heterogeneity in pre-implantation mouse embryos. CONCLUSIONS Our study reveals the programmed DNA methylation heterogeneity during human pre-implantation embryogenesis through a novel mathematical model and provides valuable clues for identifying the driving factors of the first cell fate determination during this process.
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Affiliation(s)
- Chengchen Zhao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
| | - Naiqian Zhang
- School of Mathematics and Statistics, Shandong University at Weihai, Weihai, 264209 China
| | - Yalin Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, 200092 China
| | - Nuermaimaiti Tuersunjiang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, 200092 China
| | - Wenqiang Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, 200092 China
| | - Yong Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092 China
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21
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Zhang Y, Tian Y, Zhang H, Xu B, Chen H. Potential pathways of zinc deficiency-promoted tumorigenesis. Biomed Pharmacother 2020; 133:110983. [PMID: 33190036 DOI: 10.1016/j.biopha.2020.110983] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 12/11/2022] Open
Abstract
Zinc (Zn) is the second most abundant necessary trace element in the human body. It is reported that zinc deficiency (ZD) promotes many types of cancer progression through multiple signal pathways. It is well known that oxidative stress, DNA damage, DNA repair, cell cycle, cell apoptosis, metabolic alterations, microRNAs abnormal expression, and inflammation level are closely related to cancer development. Cumulative evidence suggests that ZD influences these biological functions. This review explores the latest advances in understanding the role of ZD in tumorigenesis. Fully comprehending the potential mechanisms of ZD-induced tumors may provide novel clues for prevention and clinical treatment of cancers.
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Affiliation(s)
- Yuting Zhang
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Yuyang Tian
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, PR China; Queen Mary School, Medical Department, Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Haowen Zhang
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, PR China; Queen Mary School, Medical Department, Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Baohua Xu
- Department of Experimental Animals, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, PR China; Jiangxi Key Laboratory of Experimental Animals, Nanchang University, Nanchang, Jiangxi, 330006, PR China
| | - Hongping Chen
- Department of Histology and Embryology, Medical College of Nanchang University, Nanchang, Jiangxi, 330006, PR China; Jiangxi Key Laboratory of Experimental Animals, Nanchang University, Nanchang, Jiangxi, 330006, PR China.
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22
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Rivera RM. Consequences of assisted reproductive techniques on the embryonic epigenome in cattle. Reprod Fertil Dev 2020; 32:65-81. [PMID: 32188559 DOI: 10.1071/rd19276] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Procedures used in assisted reproduction have been under constant scrutiny since their inception with the goal of improving the number and quality of embryos produced. However, invitro production of embryos is not without complications because many fertilised oocytes fail to become blastocysts, and even those that do often differ in the genetic output compared with their invivo counterparts. Thus only a portion of those transferred complete normal fetal development. An unwanted consequence of bovine assisted reproductive technology (ART) is the induction of a syndrome characterised by fetal overgrowth and placental abnormalities, namely large offspring syndrome; a condition associated with inappropriate control of the epigenome. Epigenetics is the study of chromatin and its effects on genetic output. Establishment and maintenance of epigenetic marks during gametogenesis and embryogenesis is imperative for the maintenance of cell identity and function. ARTs are implemented during times of vast epigenetic reprogramming; as a result, many studies have identified ART-induced deviations in epigenetic regulation in mammalian gametes and embryos. This review describes the various layers of epigenetic regulation and discusses findings pertaining to the effects of ART on the epigenome of bovine gametes and the preimplantation embryo.
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Affiliation(s)
- Rocío Melissa Rivera
- Division of Animal Science University of Missouri, Columbia, Missouri 65211, USA.
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23
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DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation. Nat Commun 2020; 11:3723. [PMID: 32709850 PMCID: PMC7381644 DOI: 10.1038/s41467-020-17531-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 07/06/2020] [Indexed: 01/07/2023] Open
Abstract
DNA methylation maintenance by DNMT1 is an essential process in mammals but molecular mechanisms connecting DNA methylation patterns and enzyme activity remain elusive. Here, we systematically analyzed the specificity of DNMT1, revealing a pronounced influence of the DNA sequences flanking the target CpG site on DNMT1 activity. We determined DNMT1 structures in complex with preferred DNA substrates revealing that DNMT1 employs flanking sequence-dependent base flipping mechanisms, with large structural rearrangements of the DNA correlating with low catalytic activity. Moreover, flanking sequences influence the conformational dynamics of the active site and cofactor binding pocket. Importantly, we show that the flanking sequence preferences of DNMT1 highly correlate with genomic methylation in human and mouse cells, and 5-azacytidine triggered DNA demethylation is more pronounced at CpG sites with flanks disfavored by DNMT1. Overall, our findings uncover the intricate interplay between CpG-flanking sequence, DNMT1-mediated base flipping and the dynamic landscape of DNA methylation.
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24
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Kinetics and mechanisms of mitotic inheritance of DNA methylation and their roles in aging-associated methylome deterioration. Cell Res 2020; 30:980-996. [PMID: 32581343 DOI: 10.1038/s41422-020-0359-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022] Open
Abstract
Mitotic inheritance of the DNA methylome is a challenging task for the maintenance of cell identity. Whether DNA methylation pattern in different genomic contexts can all be faithfully maintained is an open question. A replication-coupled DNA methylation maintenance model was proposed decades ago, but some observations suggest that a replication-uncoupled maintenance mechanism exists. However, the capacity and the underlying molecular events of replication-uncoupled maintenance are unclear. By measuring maintenance kinetics at the single-molecule level and assessing mutant cells with perturbation of various mechanisms, we found that the kinetics of replication-coupled maintenance are governed by the UHRF1-Ligase 1 and PCNA-DNMT1 interactions, whereas nucleosome occupancy and the interaction between UHRF1 and methylated H3K9 specifically regulate replication-uncoupled maintenance. Surprisingly, replication-uncoupled maintenance is sufficiently robust to largely restore the methylome when replication-coupled maintenance is severely impaired. However, solo-WCGW sites and other CpG sites displaying aging- and cancer-associated hypomethylation exhibit low maintenance efficiency, suggesting that although quite robust, mitotic inheritance of methylation is imperfect and that this imperfection may contribute to selective hypomethylation during aging and tumorigenesis.
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25
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Dahlet T, Argüeso Lleida A, Al Adhami H, Dumas M, Bender A, Ngondo RP, Tanguy M, Vallet J, Auclair G, Bardet AF, Weber M. Genome-wide analysis in the mouse embryo reveals the importance of DNA methylation for transcription integrity. Nat Commun 2020; 11:3153. [PMID: 32561758 PMCID: PMC7305168 DOI: 10.1038/s41467-020-16919-w] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 05/29/2020] [Indexed: 12/20/2022] Open
Abstract
Mouse embryos acquire global DNA methylation of their genome during implantation. However the exact roles of DNA methyltransferases (DNMTs) in embryos have not been studied comprehensively. Here we systematically analyze the consequences of genetic inactivation of Dnmt1, Dnmt3a and Dnmt3b on the methylome and transcriptome of mouse embryos. We find a strict division of function between DNMT1, responsible for maintenance methylation, and DNMT3A/B, solely responsible for methylation acquisition in development. By analyzing severely hypomethylated embryos, we uncover multiple functions of DNA methylation that is used as a mechanism of repression for a panel of genes including not only imprinted and germline genes, but also lineage-committed genes and 2-cell genes. DNA methylation also suppresses multiple retrotransposons and illegitimate transcripts from cryptic promoters in transposons and gene bodies. Our work provides a thorough analysis of the roles of DNA methyltransferases and the importance of DNA methylation for transcriptome integrity in mammalian embryos.
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Affiliation(s)
- Thomas Dahlet
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Andrea Argüeso Lleida
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Hala Al Adhami
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Michael Dumas
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Ambre Bender
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Richard P Ngondo
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
- IBMP, CNRS UPR2357, 67084, Strasbourg, France
| | - Manon Tanguy
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Judith Vallet
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Ghislain Auclair
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Anaïs F Bardet
- University of Strasbourg, Strasbourg, France
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France
| | - Michael Weber
- University of Strasbourg, Strasbourg, France.
- Biotechnology and Cell Signaling, CNRS UMR7242, 300 Bd Sébastien Brant, 67412, Illkirch, Cedex, France.
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Brito S, Lee MG, Bin BH, Lee JS. Zinc and Its Transporters in Epigenetics. Mol Cells 2020; 43:323-330. [PMID: 32274919 PMCID: PMC7191051 DOI: 10.14348/molcells.2020.0026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/25/2020] [Accepted: 04/04/2020] [Indexed: 12/19/2022] Open
Abstract
Epigenetic events like DNA methylation and histone modification can alter heritable phenotypes. Zinc is required for the activity of various epigenetic enzymes, such as DNA methyltransferases (DNMTs), histone acetyltransferases (HATs), histone deacetylases (HDACs), and histone demethylases, which possess several zinc binding sites. Thus, the dysregulation of zinc homeostasis can lead to epigenetic alterations. Zinc homeostasis is regulated by Zinc Transporters (ZnTs), Zrt- and Irt-like proteins (ZIPs), and the zinc storage protein metallothionein (MT). Recent advances revealed that ZIPs modulate epigenetics. ZIP10 deficiency was found to result in reduced HATs, confirming its involvement in histone acetylation for rigid skin barrier formation. ZIP13 deficiency, which is associated with Spondylocheirodysplastic Ehlers-Danlos syndrome (SCD-EDS), increases DNMT activity, leading to dysgenesis of dermis via improper gene expressions. However, the precise molecular mechanisms remain to be elucidated. Future molecular studies investigating the involvement of zinc and its transporters in epigenetics are warranted.
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Affiliation(s)
- Sofia Brito
- Department of Biological Sciences, Ajou University, Suwon 6499, Korea
- These authors contributed equally to this work
| | - Mi-Gi Lee
- Bio-Center, Gyeonggido Business and Science Accelerator, Suwon 169, Korea
- These authors contributed equally to this work
| | - Bum-Ho Bin
- Department of Biological Sciences, Ajou University, Suwon 6499, Korea
| | - Jong-Soo Lee
- Department of Biological Sciences, Ajou University, Suwon 6499, Korea
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Ali MM, Phillips SA, Mahmoud AM. HIF1α/TET1 Pathway Mediates Hypoxia-Induced Adipocytokine Promoter Hypomethylation in Human Adipocytes. Cells 2020; 9:cells9010134. [PMID: 31935962 PMCID: PMC7016890 DOI: 10.3390/cells9010134] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 12/28/2019] [Accepted: 01/03/2020] [Indexed: 12/22/2022] Open
Abstract
Obesity is associated with the accumulation of dysfunctional adipose tissue that secretes several pro-inflammatory cytokines (adipocytokines). Recent studies have presented evidence that adipose tissues in obese individuals and animal models are hypoxic, which may result in upregulation and stabilization of the hypoxia inducible factor HIF1α. Epigenetic mechanisms such as DNA methylation enable the body to respond to microenvironmental changes such as hypoxia and may represent a mechanistic link between obesity-associated hypoxia and upregulated inflammatory adipocytokines. The purpose of this study was to investigate the role of hypoxia in modifying adipocytokine DNA methylation and subsequently adipocytokine expression. We suggested that this mechanism is mediated via the DNA demethylase, ten-eleven translocation-1 (TET1), transcription of which has been shown to be induced by HIF1α. To this end, we studied the effect of hypoxia (2% O2) in differentiated subcutaneous human adipocytes in the presence or absence of HIF1α stabilizer (Dimethyloxalylglycine (DMOG), 500 μM), HIF1α inhibitor (methyl 3-[[2-[4-(2-adamantyl) phenoxy] acetyl] amino]-4-hydroxybenzoate, 30 μM), or TET1-specific siRNA. Subjecting the adipocytes to hypoxia significantly induced HIF1α and TET1 protein levels. Moreover, hypoxia induced global hydroxymethylation, reduced adipocytokine DNA promoter methylation, and induced adipocytokine expression. These effects were abolished by either HIF1α inhibitor or TET1 gene silencing. The major hypoxia-responsive adipocytokines were leptin, interleukin-1 (IL6), IL1β, tumor necrosis factor α (TNFα), and interferon γ (IFNγ). Overall, these data demonstrate an activation of the hydroxymethylation pathway mediated by TET1. This pathway contributes to promoter hypomethylation and gene upregulation of the inflammatory adipocytokines in adipocytes in response to hypoxia.
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Affiliation(s)
- Mohamed M. Ali
- Department of Physical Therapy and Integrative Physiology Laboratory, College of Applied Health Sciences, University of Illinois at Chicago, Chicago, IL 60612, USA;
| | - Shane A. Phillips
- Department of Physical Therapy and Integrative Physiology Laboratory, College of Applied Health Sciences and Division of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago, Chicago, IL 60612, USA;
| | - Abeer M. Mahmoud
- Department of Medicine, College of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
- Correspondence: ; Tel.: +1-312-355-8099
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Abstract
Depression is one of the most common psychiatric disorders affecting public health. Studies over the past years suggest that the methylations of some specific genes such as BDNF, SLC6A4, and NR3C1 play an important role in the development of depression. Recently, epigenetic evidences suggest that the expression levels of DNA methyltransferases differ in several brain areas including the prefrontal cortex, hippocampus, amygdala, and nucleus accumbens in depression patients and animal models, but the potential link between the expression levels of DNA methylatransferases and the methylations of specific genes needs further investigation to clarify the pathogenesis of depression.
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Affiliation(s)
- Zhenghao Duan
- Department of Human Anatomy, College of Basic Medical Sciences, China Medical University, Shenyang, China.,Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jie Lu
- Department of Human Anatomy, College of Basic Medical Sciences, China Medical University, Shenyang, China
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Mishima Y, Brueckner L, Takahashi S, Kawakami T, Otani J, Shinohara A, Takeshita K, Garvilles RG, Watanabe M, Sakai N, Takeshima H, Nachtegael C, Nishiyama A, Nakanishi M, Arita K, Nakashima K, Hojo H, Suetake I. Enhanced processivity of Dnmt1 by monoubiquitinated histone H3. Genes Cells 2019; 25:22-32. [DOI: 10.1111/gtc.12732] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Yuichi Mishima
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
| | - Laura Brueckner
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
| | - Saori Takahashi
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
| | - Toru Kawakami
- Laboratory of Organic Chemistry Institute for Protein Research Osaka University Suita Japan
| | - Junji Otani
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
| | - Akira Shinohara
- Laboratory of Genome‐Chromosome Function Institute for Protein Research Osaka University Suita Japan
| | | | | | - Mikio Watanabe
- Center for Twin Research Graduate School of Medicine Osaka University Suita Japan
| | - Norio Sakai
- Center for Twin Research Graduate School of Medicine Osaka University Suita Japan
| | - Hideyuki Takeshima
- Division of Epigenomics National Cancer Center Research Institute Tokyo Japan
| | - Charlotte Nachtegael
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
- Interuniversity Institute of Bioinformatics in Brussels Universite Libre de Bruxelles‐Vrije Universiteit Brussel Brussels Belgium
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology The Institute of Medical Science The University of Tokyo Tokyo Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology The Institute of Medical Science The University of Tokyo Tokyo Japan
| | - Kyohei Arita
- Graduate School of Medical Life Science Yokohama City University Yokohama Japan
| | - Kinichi Nakashima
- Department of Stem Cell Biology and Medicine Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Hironobu Hojo
- Laboratory of Organic Chemistry Institute for Protein Research Osaka University Suita Japan
| | - Isao Suetake
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
- Center for Twin Research Graduate School of Medicine Osaka University Suita Japan
- College of Nutrition Koshien University Takarazuka Japan
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Maric H, Supic G, Kandolf-Sekulovic L, Maric V, Mijuskovic Z, Radevic T, Rajovic M, Magic Z. DNMT1 and DNMT3B genetic polymorphisms affect the clinical course and outcome of melanoma patients. Melanoma Res 2019; 29:596-602. [PMID: 30950914 DOI: 10.1097/cmr.0000000000000612] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The aberrant DNA methylation plays a critical role in a number of different malignancies, including melanoma. DNA methylation is catalyzed by DNA methyltransferases (DNMTs), involved in methylation maintenance (DNMT1) and de novo DNA methylation (DNMT3A and DNMT3B). The current study investigated the association of genetic variants in the DNMT1 and DNMT3B with the clinicopathologic features and the clinical course of melanoma patients. In the present study, DNMT1 (rs2228612, rs2228611, and rs2114724) and DNMT3B (rs406193 and rs2424932) polymorphisms were examined in 123 melanoma patients. Single nucleotide polymorphisms were assessed using TaqMan SNPs Genotyping Assays according to the manufacturer's protocols. The carriers of the variant genotype of DNMT1 rs2228612 had poorer overall survival and recurrence-free survival, (P = 0.000 and 0.000, respectively), and an increased risk for adverse outcome [hazard ratio (HR) = 6.620, 95% confidence interval (CI): 2.214-19.791, P = 0.001]. DNMT1 rs2228612 was also associated with ulceration (P = 0.045), nodal status (P = 0.030), progression (P = 0. 007), and stage of disease (P = 0.003). Univariate analysis indicated that tumor-infiltrating lymphocytes could be a marker of good prognosis in melanoma patients (HR = 0.323, 95% CI: 0.127-0.855, P = 0.025), whereas the genotype distribution of the DNMT3B rs406193 polymorphism correlated significantly with the presence of tumor-infiltrating lymphocytes (P = 0.012). The multivariate analysis showed that the DNMT1 rs2228612 polymorphism (HR = 12.126, 95% CI: 2.345-62.715, P = 0.003) is an independent predictor of poor overall survival in melanoma patients. As expected, disease progression was also found to be an independent prognostic factor in melanoma patients (HR = 37.888, 95% CI: 3.615-397.062, P = 0.002). DNMT1 rs2228612 was found to be an independent predictor of poor overall survival in melanoma patients. DNMTs polymorphisms could serve as a potential target for novel therapeutic approaches.
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Affiliation(s)
- Helena Maric
- Second Surgery Clinic, University Hospital of Foca, Foca
| | | | | | - Veljko Maric
- Department of Surgery, Faculty of Medicine Foca, University of East Sarajevo, Lukavica, Serbia
| | | | | | - Milica Rajovic
- Clinic for Plastic and Reconstructive Surgery, Military Medical Academy, University of Defense, Belgrade
| | - Zvonko Magic
- Faculty of Medicine
- Institute for Medical Research
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Jara-Espejo M, Line SR. DNA G-quadruplex stability, position and chromatin accessibility are associated with CpG island methylation. FEBS J 2019; 287:483-495. [PMID: 31532882 DOI: 10.1111/febs.15065] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/22/2019] [Accepted: 09/16/2019] [Indexed: 01/06/2023]
Abstract
CpG islands (CGI) are genomic regions associated with gene promoters and involved in gene expression regulation. Despite their high CpG content and unlike bulk genomic DNA methylation pattern, these regions are usually hypomethylated. So far, the mechanisms controlling the CGI methylation patterning remain unclear. G-quadruplex (G4) structures can inhibit DNA methyltransferases 1 enzymatic activity, leading to CGI hypomethylation. Our aim was to analyse the association of G4 forming sequences (G4FS) and CGI methylation as well as to determine the intrinsic and extrinsic characteristics of G4FS that may modulate this phenomenon. Using methylation data from human embryonic stem cells (hESCs) and three hESC-derived populations, we showed that hypomethylated CpGs located inside CGI (CGI/CpG) tend to be associated with highly stable G4FS (Minimum free energy ≤ -30 kcal·mol-1 ). The association of highly stable G4FS and hypomethylation tend to be stronger when these structures are located at shorter distances (~ < 150 bp) from GCI/CpGs, when G4FS and CpGs are located within open chromatin and G4FS are inside CGI. Moreover, this association is not strongly influenced by the CpG content of CGI. Conversely, highly methylated CGI/CpG tend to be associated with low stability G4FS. Although CpGs inside CGIs without a G4FS tend to be more methylated, high stability G4FS within CGI neighbourhood were associated with decreased methylation. In summary, our data indicate that G4FS may act as protective cis elements against CGI methylation, and this effect seems to be influenced by the G4FS folding potential, its presence within CGI, CpG distance from G4FS and chromatin accessibility.
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Affiliation(s)
- Manuel Jara-Espejo
- Department of Morphology, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, Brazil
| | - Sérgio Roberto Line
- Department of Morphology, Piracicaba Dental School, University of Campinas - UNICAMP, Piracicaba, Brazil
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Contribution of DNMT1 to Neuropathic Pain Genesis Partially through Epigenetically Repressing Kcna2 in Primary Afferent Neurons. J Neurosci 2019; 39:6595-6607. [PMID: 31182635 DOI: 10.1523/jneurosci.0695-19.2019] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/30/2019] [Accepted: 06/03/2019] [Indexed: 02/08/2023] Open
Abstract
Expressional changes of pain-associated genes in primary sensory neurons of DRG are critical for neuropathic pain genesis. DNA methyltransferase (DNMT)-triggered DNA methylation silences gene expression. We show here that DNMT1, a canonical maintenance methyltransferase, acts as the de novo DNMT and is required for neuropathic pain genesis likely through repressing at least DRG Kcna2 gene expression in male mice. Peripheral nerve injury upregulated DNMT1 expression in the injured DRG through the transcription factor cAMP response element binding protein-triggered transcriptional activation of Dnmt1 gene. Blocking this upregulation prevented nerve injury-induced DNA methylation within the promoter and 5'-untranslated region of Kcna2 gene, rescued Kcna2 expression and total Kv current, attenuated hyperexcitability in the injured DRG neurons, and alleviated nerve injury-induced pain hypersensitivities. Given that Kcna2 is a key player in neuropathic pain, our findings suggest that DRG DNMT1 may be a potential target for neuropathic pain management.SIGNIFICANCE STATEMENT In the present study, we reported that DNMT1, a canonical DNA maintenance methyltransferase, is upregulated via the activation of the transcription factor CREB in the injured DRG after peripheral nerve injury. This upregulation was responsible for nerve injury-induced de novo DNA methylation within the promoter and 5'-untranslated region of the Kcna2 gene, reductions in Kcna2 expression and Kv current and increases in neuronal excitability in the injured DRG. Since pharmacological inhibition or genetic knockdown of DRG DNMT1 alleviated nerve injury-induced pain hypersensitivities, DRG DNMT1 contributes to neuropathic pain genesis partially through repression of DRG Kcna2 gene expression.
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33
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Zhou J, Wu YC, Xiao BJ, Guo XD, Zheng QX, Wu B. Age-related Changes in the Global DNA Methylation Profile of Oligodendrocyte Progenitor Cells Derived from Rat Spinal Cords. Curr Med Sci 2019; 39:67-74. [PMID: 30868493 DOI: 10.1007/s11596-019-2001-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 12/27/2018] [Indexed: 01/12/2023]
Abstract
Demyelination of axons plays an important role in the pathology of many spinal cord diseases and injuries. Remyelination in demyelinated lesions is primarily performed by oligodendrocyte progenitor cells (OPCs), which generate oligodendrocytes in the developing and mature central nervous system. The efficiency of remyelination decreases with age. Many reports suggest that this decline in remyelination results from impaired OPC recruitment and differentiation during aging. Of the various molecular mechanisms involved in aging, changes in epigenetic modifications have received particular attention. Global DNA methylation is a major epigenetic modification that plays important roles in cellular senescence and organismal aging. Thus, we aimed to evaluate the dynamic changes in the global DNA methylation profiles of OPCs derived from rat spinal cords during the aging process. We separated and cultured OPCs from the spinal cords of neonatal, 4-month-old, and 16-month-old rats and investigated the age-related alterations of genomic DNA methylation levels by using quantitative colorimetric analysis. To determine the potential cause of dynamic changes in global DNA methylation, we further analyzed the activity of DNA methyltransferases (DNMTs) and the expression of DNMT1, DNMT3a, DNMT3b, TET1, TET2, TET3, MBD2, and MeCP2 in the OPCs from each group. Our results showed the genomic DNA methylation level and the activity of DNMTs from OPCs derived from rat spinal cords decreased gradually during aging, and OPCs from 16-month-old rats were characterized by global hypomethylation. During OPC aging, the mRNA and protein expression levels of DNMT3a, DNMT3b, and MeCP2 were significantly elevated; those of DNMT1 were significantly down-regulated; and no significant changes were observed in those for TET1, TET2, TET3, or MBD2. Our results indicated that global DNA hypomethylation in aged OPCs is correlated with DNMT1 downregulation. Together, these data provide important evidence for partly elucidating the mechanism of age-related impaired OPC recruitment and differentiation and assist in the development of new treatments for promoting efficient remyelination.
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Affiliation(s)
- Jing Zhou
- Department of General Surgery, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yong-Chao Wu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Bao-Jun Xiao
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiao-Dong Guo
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Qi-Xin Zheng
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Bin Wu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Ren W, Gao L, Song J. Structural Basis of DNMT1 and DNMT3A-Mediated DNA Methylation. Genes (Basel) 2018; 9:genes9120620. [PMID: 30544982 PMCID: PMC6316889 DOI: 10.3390/genes9120620] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 11/30/2018] [Accepted: 12/04/2018] [Indexed: 01/01/2023] Open
Abstract
DNA methylation, one of the major epigenetic mechanisms, plays critical roles in regulating gene expression, genomic stability and cell lineage commitment. The establishment and maintenance of DNA methylation in mammals is achieved by two groups of DNA methyltransferases (DNMTs): DNMT3A and DNMT3B, which are responsible for installing DNA methylation patterns during gametogenesis and early embryogenesis, and DNMT1, which is essential for propagating DNA methylation patterns during replication. Both groups of DNMTs are multi-domain proteins, containing a large N-terminal regulatory region in addition to the C-terminal methyltransferase domain. Recent structure-function investigations of the individual domains or large fragments of DNMT1 and DNMT3A have revealed the molecular basis for their substrate recognition and specificity, intramolecular domain-domain interactions, as well as their crosstalk with other epigenetic mechanisms. These studies highlight a multifaceted regulation for both DNMT1 and DNMT3A/3B, which is essential for the precise establishment and maintenance of lineage-specific DNA methylation patterns in cells. This review summarizes current understanding of the structure and mechanism of DNMT1 and DNMT3A-mediated DNA methylation, with emphasis on the functional cooperation between the methyltransferase and regulatory domains.
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Affiliation(s)
- Wendan Ren
- Department of Biochemistry, University of California, Riverside, CA 92521, USA.
| | - Linfeng Gao
- Environmental Toxicology Program, University of California, Riverside, CA 92521, USA.
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA 92521, USA.
- Environmental Toxicology Program, University of California, Riverside, CA 92521, USA.
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35
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Abstract
Codon usage depends on mutation bias, tRNA-mediated selection, and the need for high efficiency and accuracy in translation. One codon in a synonymous codon family is often strongly over-used, especially in highly expressed genes, which often leads to a high dN/dS ratio because dS is very small. Many different codon usage indices have been proposed to measure codon usage and codon adaptation. Sense codon could be misread by release factors and stop codons misread by tRNAs, which also contribute to codon usage in rare cases. This chapter outlines the conceptual framework on codon evolution, illustrates codon-specific and gene-specific codon usage indices, and presents their applications. A new index for codon adaptation that accounts for background mutation bias (Index of Translation Elongation) is presented and contrasted with codon adaptation index (CAI) which does not consider background mutation bias. They are used to re-analyze data from a recent paper claiming that translation elongation efficiency matters little in protein production. The reanalysis disproves the claim.
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36
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SanMiguel JM, Bartolomei MS. DNA methylation dynamics of genomic imprinting in mouse development. Biol Reprod 2018; 99:252-262. [PMID: 29462489 PMCID: PMC6044325 DOI: 10.1093/biolre/ioy036] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/31/2018] [Accepted: 02/07/2018] [Indexed: 01/05/2023] Open
Abstract
DNA methylation is an essential epigenetic mark crucial for normal mammalian development. This modification controls the expression of a unique class of genes, designated as imprinted, which are expressed monoallelically and in a parent-of-origin-specific manner. Proper parental allele-specific DNA methylation at imprinting control regions (ICRs) is necessary for appropriate imprinting. Processes that deregulate DNA methylation of imprinted loci cause disease in humans. DNA methylation patterns dramatically change during mammalian development: first, the majority of the genome, with the exception of ICRs, is demethylated after fertilization, and subsequently undergoes genome-wide de novo DNA methylation. Secondly, after primordial germ cells are specified in the embryo, another wave of demethylation occurs, with ICR demethylation occurring late in the process. Lastly, ICRs reacquire DNA methylation imprints in developing germ cells. We describe the past discoveries and current literature defining these crucial dynamics in relation to imprinted genes and the rest of the genome.
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Affiliation(s)
- Jennifer M SanMiguel
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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37
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Alvarez-Ponce D, Torres-Sánchez M, Feyertag F, Kulkarni A, Nappi T. Molecular evolution of DNMT1 in vertebrates: Duplications in marsupials followed by positive selection. PLoS One 2018; 13:e0195162. [PMID: 29621315 PMCID: PMC5886458 DOI: 10.1371/journal.pone.0195162] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/16/2018] [Indexed: 01/01/2023] Open
Abstract
DNA methylation is mediated by a conserved family of DNA methyltransferases (Dnmts). The human genome encodes three active Dnmts (Dnmt1, Dnmt3a and Dnmt3b), the tRNA methyltransferase Dnmt2, and the regulatory protein Dnmt3L. Despite their high degree of conservation among different species, genes encoding Dnmts have been duplicated and/or lost in multiple lineages throughout evolution, indicating that the DNA methylation machinery has some potential to undergo evolutionary change. However, little is known about the extent to which this machinery, or the methylome, varies among vertebrates. Here, we study the molecular evolution of Dnmt1, the enzyme responsible for maintenance of DNA methylation patterns after replication, in 79 vertebrate species. Our analyses show that all studied species exhibit a single copy of the DNMT1 gene, with the exception of tilapia and marsupials (tammar wallaby, koala, Tasmanian devil and opossum), each of which displays two apparently functional DNMT1 copies. Our phylogenetic analyses indicate that DNMT1 duplicated before the radiation of major marsupial groups (i.e., at least ~75 million years ago), thus giving rise to two DNMT1 copies in marsupials (copy 1 and copy 2). In the opossum lineage, copy 2 was lost, and copy 1 recently duplicated again, generating three DNMT1 copies: two putatively functional genes (copy 1a and 1b) and one pseudogene (copy 1ψ). Both marsupial copies (DNMT1 copies 1 and 2) are under purifying selection, and copy 2 exhibits elevated rates of evolution and signatures of positive selection, suggesting a scenario of neofunctionalization. This gene duplication might have resulted in modifications in marsupial methylomes and their dynamics.
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Affiliation(s)
- David Alvarez-Ponce
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
- * E-mail:
| | - María Torres-Sánchez
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, Madrid, Spain
| | - Felix Feyertag
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
| | - Asmita Kulkarni
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
| | - Taylen Nappi
- Department of Biology, University of Nevada, Reno, Nevada, United States of America
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38
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Caspase-9 CARD : core domain interactions require a properly formed active site. Biochem J 2018; 475:1177-1196. [PMID: 29500231 DOI: 10.1042/bcj20170913] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 12/20/2022]
Abstract
Caspase-9 is a critical factor in the initiation of apoptosis and as a result is tightly regulated by many mechanisms. Caspase-9 contains a Caspase Activation and Recruitment Domain (CARD), which enables caspase-9 to form a tight interaction with the apoptosome, a heptameric activating platform. The caspase-9 CARD has been thought to be principally involved in recruitment to the apoptosome, but its roles outside this interaction have yet to be uncovered. In this work, we show that the CARD is involved in physical interactions with the catalytic core of caspase-9 in the absence of the apoptosome; this interaction requires a properly formed caspase-9 active site. The active sites of caspases are composed of four extremely mobile loops. When the active-site loops are not properly ordered, the CARD and core domains of caspase-9 do not interact and behave independently, like loosely tethered beads. When the active-site loop bundle is properly ordered, the CARD domain interacts with the catalytic core, forming a single folding unit. Taken together, these findings provide mechanistic insights into a new level of caspase-9 regulation, prompting speculation that the CARD may also play a role in the recruitment or recognition of substrate.
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39
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Hervouet E, Peixoto P, Delage-Mourroux R, Boyer-Guittaut M, Cartron PF. Specific or not specific recruitment of DNMTs for DNA methylation, an epigenetic dilemma. Clin Epigenetics 2018; 10:17. [PMID: 29449903 PMCID: PMC5807744 DOI: 10.1186/s13148-018-0450-y] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/30/2018] [Indexed: 11/28/2022] Open
Abstract
Our current view of DNA methylation processes is strongly moving: First, even if it was generally admitted that DNMT3A and DNMT3B are associated with de novo methylation and DNMT1 is associated with inheritance DNA methylation, these distinctions are now not so clear. Secondly, since one decade, many partners of DNMTs have been involved in both the regulation of DNA methylation activity and DNMT recruitment on DNA. The high diversity of interactions and the combination of these interactions let us to subclass the different DNMT-including complexes. For example, the DNMT3L/DNMT3A complex is mainly related to de novo DNA methylation in embryonic states, whereas the DNMT1/PCNA/UHRF1 complex is required for maintaining global DNA methylation following DNA replication. On the opposite to these unspecific DNA methylation machineries (no preferential DNA sequence), some recently identified DNMT-including complexes are recruited on specific DNA sequences. The coexistence of both types of DNA methylation (un/specific) suggests a close cooperation and an orchestration between these systems to maintain genome and epigenome integrities. Deregulation of these systems can lead to pathologic disorders.
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Affiliation(s)
- Eric Hervouet
- INSERM unit 1098, University of Bourgogne Franche-Comté, Besançon, France.,EPIGENExp (EPIgenetics and GENe EXPression Technical Platform), Besançon, France
| | - Paul Peixoto
- INSERM unit 1098, University of Bourgogne Franche-Comté, Besançon, France.,EPIGENExp (EPIgenetics and GENe EXPression Technical Platform), Besançon, France
| | | | | | - Pierre-François Cartron
- 3INSERM unit S1232, University of Nantes, Nantes, France.,4Institut de cancérologie de l'Ouest, Nantes, France.,REpiCGO (Cancéropole Grand-Ouest), Nantes, France.,EpiSAVMEN Networks, Nantes, Région Pays de la Loire France
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40
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Ravichandran M, Jurkowska RZ, Jurkowski TP. Target specificity of mammalian DNA methylation and demethylation machinery. Org Biomol Chem 2018; 16:1419-1435. [DOI: 10.1039/c7ob02574b] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review here the molecular mechanisms employed by DNMTs and TET enzymes that are responsible for shaping the DNA methylation pattern of a mammalian cell.
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Affiliation(s)
| | | | - T. P. Jurkowski
- Universität Stuttgart
- Abteilung Biochemie
- Institute für Biochemie und Technische Biochemie
- Stuttgart D-70569
- Germany
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41
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DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants. Structure 2018; 26:85-95.e3. [DOI: 10.1016/j.str.2017.11.022] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 10/15/2017] [Accepted: 11/27/2017] [Indexed: 11/20/2022]
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42
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Hassanzadeh M, Kasymov R, Mahernia S, Adib M, Emperle M, Dukatz M, Bashtrykov P, Jeltsch A, Amanlou M. Discovery of Novel and Selective DNA Methyltransferase 1 Inhibitors by Pharmacophore and Docking-Based Virtual Screening. ChemistrySelect 2017. [DOI: 10.1002/slct.201701734] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Malihe Hassanzadeh
- Department of Medicinal Chemistry & Drug Design and Development Research Center; Faculty of Pharmacy; Tehran University of Medical Sciences; 16 Azar Ave. Tehran Iran
| | - Rustem Kasymov
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Shabnam Mahernia
- Department of Medicinal Chemistry & Drug Design and Development Research Center; Faculty of Pharmacy; Tehran University of Medical Sciences; 16 Azar Ave. Tehran Iran
| | - Mehdi Adib
- School of Chemistry; College of Science; University of Tehran; Tehran Iran
| | - Max Emperle
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Michael Dukatz
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Pavel Bashtrykov
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Albert Jeltsch
- Department of Biochemistry; Institute of Biochemistry and Technical Biochemistry; University Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Massoud Amanlou
- Department of Medicinal Chemistry & Drug Design and Development Research Center; Faculty of Pharmacy; Tehran University of Medical Sciences; 16 Azar Ave. Tehran Iran
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43
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Acetylation- and Methylation-Related Epigenetic Proteins in the Context of Their Targets. Genes (Basel) 2017; 8:genes8080196. [PMID: 28783137 PMCID: PMC5575660 DOI: 10.3390/genes8080196] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/19/2017] [Accepted: 07/31/2017] [Indexed: 12/19/2022] Open
Abstract
The nucleosome surface is covered with multiple modifications that are perpetuated by eight different classes of enzymes. These enzymes modify specific target sites both on DNA and histone proteins, and these modifications have been well identified and termed “epigenetics”. These modifications play critical roles, either by affecting non-histone protein recruitment to chromatin or by disturbing chromatin contacts. Their presence dictates the condensed packaging of DNA and can coordinate the orderly recruitment of various enzyme complexes for DNA manipulation. This genetic modification machinery involves various writers, readers, and erasers that have unique structures, functions, and modes of action. Regarding human disease, studies have mainly focused on the genetic mechanisms; however, alteration in the balance of epigenetic networks can result in major pathologies including mental retardation, chromosome instability syndromes, and various types of cancers. Owing to its critical influence, great potential lies in developing epigenetic therapies. In this regard, this review has highlighted mechanistic and structural interactions of the main epigenetic families with their targets, which will help to identify more efficient and safe drugs against several diseases.
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44
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Geyer KK, Niazi UH, Duval D, Cosseau C, Tomlinson C, Chalmers IW, Swain MT, Cutress DJ, Bickham-Wright U, Munshi SE, Grunau C, Yoshino TP, Hoffmann KF. The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni. PLoS Negl Trop Dis 2017; 11:e0005246. [PMID: 28510608 PMCID: PMC5433704 DOI: 10.1371/journal.pntd.0005246] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 12/10/2016] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The debilitating human disease schistosomiasis is caused by infection with schistosome parasites that maintain a complex lifecycle alternating between definitive (human) and intermediate (snail) hosts. While much is known about how the definitive host responds to schistosome infection, there is comparably less information available describing the snail's response to infection. METHODOLOGY/PRINCIPLE FINDINGS Here, using information recently revealed by sequencing of the Biomphalaria glabrata intermediate host genome, we provide evidence that the predicted core snail DNA methylation machinery components are associated with both intra-species reproduction processes and inter-species interactions. Firstly, methyl-CpG binding domain protein (Bgmbd2/3) and DNA methyltransferase 1 (Bgdnmt1) genes are transcriptionally enriched in gonadal compared to somatic tissues with 5-azacytidine (5-AzaC) treatment significantly inhibiting oviposition. Secondly, elevated levels of 5-methyl cytosine (5mC), DNA methyltransferase activity and 5mC binding in pigmented hybrid- compared to inbred (NMRI)- B. glabrata populations indicate a role for the snail's DNA methylation machinery in maintaining hybrid vigour or heterosis. Thirdly, locus-specific detection of 5mC by bisulfite (BS)-PCR revealed 5mC within an exonic region of a housekeeping protein-coding gene (Bg14-3-3), supporting previous in silico predictions and whole genome BS-Seq analysis of this species' genome. Finally, we provide preliminary evidence for parasite-mediated host epigenetic reprogramming in the schistosome/snail system, as demonstrated by the increase in Bgdnmt1 and Bgmbd2/3 transcript abundance following Bge (B. glabrata embryonic cell line) exposure to parasite larval transformation products (LTP). CONCLUSIONS/SIGNIFICANCE The presence of a functional DNA methylation machinery in B. glabrata as well as the modulation of these gene products in response to schistosome products, suggests a vital role for DNA methylation during snail development/oviposition and parasite interactions. Further deciphering the role of this epigenetic process during Biomphalaria/Schistosoma co-evolutionary biology may reveal key factors associated with disease transmission and, moreover, enable the discovery of novel lifecycle intervention strategies.
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Affiliation(s)
- Kathrin K. Geyer
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Umar H. Niazi
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - David Duval
- Université Perpignan Via Domitia, CNRS, IFREMER, Perpignan, France
| | - Céline Cosseau
- Université Perpignan Via Domitia, CNRS, IFREMER, Perpignan, France
| | - Chad Tomlinson
- Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Iain W. Chalmers
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Martin T. Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - David J. Cutress
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Utibe Bickham-Wright
- Department of Pathobiological Sciences, School of Veterinary Medicine University of Wisconsin, Madison, United States of America
| | - Sabrina E. Munshi
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
| | - Christoph Grunau
- Université Perpignan Via Domitia, CNRS, IFREMER, Perpignan, France
| | - Timothy P. Yoshino
- Department of Pathobiological Sciences, School of Veterinary Medicine University of Wisconsin, Madison, United States of America
| | - Karl F. Hoffmann
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais Campus, Aberystwyth, United Kingodm
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45
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He CC, Wang ZY, Tian K, Liu W, Li YB, Hong Y, Yu LX, Pang W, Jiang YG, Liu YQ. DNA methylation mechanism of intracellular zinc deficiency-induced injury in primary hippocampal neurons in the rat brain. Nutr Neurosci 2017; 21:478-486. [DOI: 10.1080/1028415x.2017.1312090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Cong-cong He
- College of Life Sciences, Nankai University, Tianjin 300071, China
- Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin 300050, China
| | - Zi-yu Wang
- Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin 300050, China
| | - Kun Tian
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Wei Liu
- Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin 300050, China
| | - Yi-bo Li
- Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin 300050, China
| | - Yan Hong
- Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin 300050, China
| | - Li-xia Yu
- Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin 300050, China
| | - Wei Pang
- Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin 300050, China
| | - Yu-gang Jiang
- Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin 300050, China
| | - Yan-qiang Liu
- College of Life Sciences, Nankai University, Tianjin 300071, China
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46
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Moody L, Chen H, Pan YX. Early-Life Nutritional Programming of Cognition-The Fundamental Role of Epigenetic Mechanisms in Mediating the Relation between Early-Life Environment and Learning and Memory Process. Adv Nutr 2017; 8:337-350. [PMID: 28298276 PMCID: PMC5347110 DOI: 10.3945/an.116.014209] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The perinatal period is a window of heightened plasticity that lays the groundwork for future anatomic, physiologic, and behavioral outcomes. During this time, maternal diet plays a pivotal role in the maturation of vital organs and the establishment of neuronal connections. However, when perinatal nutrition is either lacking in specific micro- and macronutrients or overloaded with excess calories, the consequences can be devastating and long lasting. The brain is particularly sensitive to perinatal insults, with several neurologic and psychiatric disorders having been linked to a poor in utero environment. Diseases characterized by learning and memory impairments, such as autism, schizophrenia, and Alzheimer disease, are hypothesized to be attributed in part to environmental factors, and evidence suggests that the etiology of these conditions may date back to very early life. In this review, we discuss the role of the early-life diet in shaping cognitive outcomes in offspring. We explore the endocrine and immune mechanisms responsible for these phenotypes and discuss how these systemic factors converge to change the brain's epigenetic landscape and regulate learning and memory across the lifespan. Through understanding the maternal programming of cognition, critical steps may be taken toward preventing and treating diseases that compromise learning and memory.
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Affiliation(s)
| | - Hong Chen
- Division of Nutritional Sciences,,Department of Food Science and Human Nutrition, and
| | - Yuan-Xiang Pan
- Division of Nutritional Sciences, .,Department of Food Science and Human Nutrition, and.,Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL
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47
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Chen Z, Li S, Subramaniam S, Shyy JYJ, Chien S. Epigenetic Regulation: A New Frontier for Biomedical Engineers. Annu Rev Biomed Eng 2017; 19:195-219. [PMID: 28301736 DOI: 10.1146/annurev-bioeng-071516-044720] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Gene expression in mammalian cells depends on the epigenetic status of the chromatin, including DNA methylation, histone modifications, promoter-enhancer interactions, and noncoding RNA-mediated regulation. The coordinated actions of these multifaceted regulations determine cell development, cell cycle regulation, cell state and fate, and the ultimate responses in health and disease. Therefore, studies of epigenetic modulations are critical for our understanding of gene regulation mechanisms at the molecular, cellular, tissue, and organ levels. The aim of this review is to provide biomedical engineers with an overview of the principles of epigenetics, methods of study, recent findings in epigenetic regulation in health and disease, and computational and sequencing tools for epigenetics analysis, with an emphasis on the cardiovascular system. This review concludes with the perspectives of the application of bioengineering to advance epigenetics and the utilization of epigenetics to translate bioengineering research into clinical medicine.
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Affiliation(s)
- Zhen Chen
- Department of Diabetes Complications and Metabolism, Beckman Research Institute, City of Hope, Duarte, California 91016; .,Department of Medicine, University of California at San Diego, La Jolla, California 92093; ,
| | - Shuai Li
- Department of Medicine, University of California at San Diego, La Jolla, California 92093; ,
| | - Shankar Subramaniam
- Department of Bioengineering and Institute of Engineering in Medicine, University of California at San Diego, La Jolla, California 92093; ,
| | - John Y-J Shyy
- Department of Medicine, University of California at San Diego, La Jolla, California 92093; ,
| | - Shu Chien
- Department of Medicine, University of California at San Diego, La Jolla, California 92093; , .,Department of Bioengineering and Institute of Engineering in Medicine, University of California at San Diego, La Jolla, California 92093; ,
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48
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Wang Y, Liu H, Sun Z. Lamarck rises from his grave: parental environment-induced epigenetic inheritance in model organisms and humans. Biol Rev Camb Philos Soc 2017; 92:2084-2111. [PMID: 28220606 DOI: 10.1111/brv.12322] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 01/12/2017] [Accepted: 01/18/2017] [Indexed: 12/12/2022]
Abstract
Organisms can change their physiological/behavioural traits to adapt and survive in changed environments. However, whether these acquired traits can be inherited across generations through non-genetic alterations has been a topic of debate for over a century. Emerging evidence indicates that both ancestral and parental experiences, including nutrition, environmental toxins, nurturing behaviour, and social stress, can have powerful effects on the physiological, metabolic and cellular functions in an organism. In certain circumstances, these effects can be transmitted across several generations through epigenetic (i.e. non-DNA sequence-based rather than mutational) modifications. In this review, we summarize recent evidence on epigenetic inheritance from parental environment-induced developmental and physiological alterations in nematodes, fruit flies, zebrafish, rodents, and humans. The epigenetic modifications demonstrated to be both susceptible to modulation by environmental cues and heritable, including DNA methylation, histone modification, and small non-coding RNAs, are also summarized. We particularly focus on evidence that parental environment-induced epigenetic alterations are transmitted through both the maternal and paternal germlines and exert sex-specific effects. The thought-provoking data presented here raise fundamental questions about the mechanisms responsible for these phenomena. In particular, the means that define the specificity of the response to parental experience in the gamete epigenome and that direct the establishment of the specific epigenetic change in the developing embryos, as well as in specific tissues in the descendants, remain obscure and require elucidation. More precise epigenetic assessment at both the genome-wide level and single-cell resolution as well as strategies for breeding at relatively sensitive periods of development and manipulation aimed at specific epigenetic modification are imperative for identifying parental environment-induced epigenetic marks across generations. Considering their diverse epigenetic architectures, the conservation and prevalence of the mechanisms underlying epigenetic inheritance in non-mammals require further investigation in mammals. Interpretation of the consequences arising from epigenetic inheritance on organisms and a better understanding of the underlying mechanisms will provide insight into how gene-environment interactions shape developmental processes and physiological functions, which in turn may have wide-ranging implications for human health, and understanding biological adaptation and evolution.
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Affiliation(s)
- Yan Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Huijie Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.,Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
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Abstract
Bioinformatic analysis can not only accelerate drug target identification and drug candidate screening and refinement, but also facilitate characterization of side effects and predict drug resistance. High-throughput data such as genomic, epigenetic, genome architecture, cistromic, transcriptomic, proteomic, and ribosome profiling data have all made significant contribution to mechanismbased drug discovery and drug repurposing. Accumulation of protein and RNA structures, as well as development of homology modeling and protein structure simulation, coupled with large structure databases of small molecules and metabolites, paved the way for more realistic protein-ligand docking experiments and more informative virtual screening. I present the conceptual framework that drives the collection of these high-throughput data, summarize the utility and potential of mining these data in drug discovery, outline a few inherent limitations in data and software mining these data, point out news ways to refine analysis of these diverse types of data, and highlight commonly used software and databases relevant to drug discovery.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Ottawa Institute of Systems Biology, Ottawa K1H 8M5, Canada
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50
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Papageorgiou DN, Karkoulia E, Amaral-Psarris A, Burda P, Kolodziej K, Demmers J, Bungert J, Stopka T, Strouboulis J. Distinct and overlapping DNMT1 interactions with multiple transcription factors in erythroid cells: Evidence for co-repressor functions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1515-1526. [PMID: 27693117 DOI: 10.1016/j.bbagrm.2016.09.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/14/2016] [Accepted: 09/26/2016] [Indexed: 01/14/2023]
Abstract
DNMT1 is the maintenance DNA methyltransferase shown to be essential for embryonic development and cellular growth and differentiation in many somatic tissues in mammals. Increasing evidence has also suggested a role for DNMT1 in repressing gene expression through interactions with specific transcription factors. Previously, we identified DNMT1 as an interacting partner of the TR2/TR4 nuclear receptor heterodimer in erythroid cells, implicated in the developmental silencing of fetal β-type globin genes in the adult stage of human erythropoiesis. Here, we extended this work by using a biotinylation tagging approach to characterize DNMT1 protein complexes in mouse erythroleukemic cells. We identified novel DNMT1 interactions with several hematopoietic transcription factors with essential roles in erythroid differentiation, including GATA1, GFI-1b and FOG-1. We provide evidence for DNMT1 forming distinct protein subcomplexes with specific transcription factors and propose the existence of a "core" DNMT1 complex with the transcription factors ZBP-89 and ZNF143, which is also present in non-hematopoietic cells. Furthermore, we identified the short (17a.a.) PCNA Binding Domain (PBD) located near the N-terminus of DNMT1 as being necessary for mediating interactions with the transcription factors described herein. Lastly, we provide evidence for DNMT1 serving as a co-repressor of ZBP-89 and GATA1 acting through upstream regulatory elements of the PU.1 and GATA1 gene loci.
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Affiliation(s)
- Dimitris N Papageorgiou
- Division of Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Elena Karkoulia
- Division of Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Alexandra Amaral-Psarris
- Division of Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece
| | - Pavel Burda
- Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Katarzyna Kolodziej
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jeroen Demmers
- Proteomics Center, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jörg Bungert
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Tomas Stopka
- Biocev, 1st Medical Faculty, Charles University, Prague, Czech Republic
| | - John Strouboulis
- Division of Molecular Oncology, Biomedical Sciences Research Center "Alexander Fleming", Vari, Greece.
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