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Lawir DF, Soza-Ried C, Iwanami N, Siamishi I, Bylund GO, O Meara C, Sikora K, Kanzler B, Johansson E, Schorpp M, Cauchy P, Boehm T. Antagonistic interactions safeguard mitotic propagation of genetic and epigenetic information in zebrafish. Commun Biol 2024; 7:31. [PMID: 38182651 PMCID: PMC10770094 DOI: 10.1038/s42003-023-05692-3] [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: 05/24/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024] Open
Abstract
The stability of cellular phenotypes in developing organisms depends on error-free transmission of epigenetic and genetic information during mitosis. Methylation of cytosine residues in genomic DNA is a key epigenetic mark that modulates gene expression and prevents genome instability. Here, we report on a genetic test of the relationship between DNA replication and methylation in the context of the developing vertebrate organism instead of cell lines. Our analysis is based on the identification of hypomorphic alleles of dnmt1, encoding the DNA maintenance methylase Dnmt1, and pole1, encoding the catalytic subunit of leading-strand DNA polymerase epsilon holoenzyme (Pole). Homozygous dnmt1 mutants exhibit genome-wide DNA hypomethylation, whereas the pole1 mutation is associated with increased DNA methylation levels. In dnmt1/pole1 double-mutant zebrafish larvae, DNA methylation levels are restored to near normal values, associated with partial rescue of mutant-associated transcriptional changes and phenotypes. Hence, a balancing antagonism between DNA replication and maintenance methylation buffers against replicative errors contributing to the robustness of vertebrate development.
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Affiliation(s)
- Divine-Fondzenyuy Lawir
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Cristian Soza-Ried
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Norimasa Iwanami
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Iliana Siamishi
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Göran O Bylund
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Connor O Meara
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Katarzyna Sikora
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Bioinformatic Unit, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Benoît Kanzler
- Transgenic Mouse Core Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Erik Johansson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Michael Schorpp
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Pierre Cauchy
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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2
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Ross SE, Vázquez-Marín J, Gert KRB, González-Rajal Á, Dinger ME, Pauli A, Martínez-Morales JR, Bogdanovic O. Evolutionary conservation of embryonic DNA methylome remodelling in distantly related teleost species. Nucleic Acids Res 2023; 51:9658-9671. [PMID: 37615576 PMCID: PMC10570028 DOI: 10.1093/nar/gkad695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/28/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
Methylation of cytosines in the CG context (mCG) is the most abundant DNA modification in vertebrates that plays crucial roles in cellular differentiation and identity. After fertilization, DNA methylation patterns inherited from parental gametes are remodelled into a state compatible with embryogenesis. In mammals, this is achieved through the global erasure and re-establishment of DNA methylation patterns. However, in non-mammalian vertebrates like zebrafish, no global erasure has been observed. To investigate the evolutionary conservation and divergence of DNA methylation remodelling in teleosts, we generated base resolution DNA methylome datasets of developing medaka and medaka-zebrafish hybrid embryos. In contrast to previous reports, we show that medaka display comparable DNA methylome dynamics to zebrafish with high gametic mCG levels (sperm: ∼90%; egg: ∼75%), and adoption of a paternal-like methylome during early embryogenesis, with no signs of prior DNA methylation erasure. We also demonstrate that non-canonical DNA methylation (mCH) reprogramming at TGCT tandem repeats is a conserved feature of teleost embryogenesis. Lastly, we find remarkable evolutionary conservation of DNA methylation remodelling patterns in medaka-zebrafish hybrids, indicative of compatible DNA methylation maintenance machinery in far-related teleost species. Overall, these results suggest strong evolutionary conservation of DNA methylation remodelling pathways in teleosts, which is distinct from the global DNA methylome erasure and reestablishment observed in mammals.
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Affiliation(s)
- Samuel E Ross
- Garvan Institute of Medical Research, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Javier Vázquez-Marín
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Krista R B Gert
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030, Vienna, Austria
| | - Álvaro González-Rajal
- Garvan Institute of Medical Research, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Juan Ramon Martínez-Morales
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Ozren Bogdanovic
- Garvan Institute of Medical Research, Sydney, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
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3
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Wang W, Yang Y, Tan S, Zhou T, Liu Y, Tian C, Bao L, Xing D, Su B, Wang J, Zhang Y, Liu S, Shi H, Gao D, Dunham R, Liu Z. Genomic imprinting-like monoallelic paternal expression determines sex of channel catfish. SCIENCE ADVANCES 2022; 8:eadc8786. [PMID: 36542716 PMCID: PMC9770954 DOI: 10.1126/sciadv.adc8786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
The X and Y chromosomes of channel catfish have the same gene contents. Here, we report allelic hypermethylation of the X chromosome within the sex determination region (SDR). Accordingly, the X-borne hydin-1 gene was silenced, whereas the Y-borne hydin-1 gene was expressed, making monoallelic expression of hydin-1 responsible for sex determination, much like genomic imprinting. Treatment with a methylation inhibitor, 5-aza-dC, erased the epigenetic marks within the SDR and caused sex reversal of genetic females into phenotypic males. After the treatment, hydin-1 and six other genes related to cell cycle control and proliferative growth were up-regulated, while three genes related to female sex differentiation were down-regulated in genetic females, providing additional support for epigenetic sex determination in catfish. This mechanism of sex determination provides insights into the plasticity of genetic sex determination in lower vertebrates and its connection with temperature sex determination where DNA methylation is broadly involved.
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Affiliation(s)
- Wenwen Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Yujia Yang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Suxu Tan
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Yang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Changxu Tian
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Lisui Bao
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - De Xing
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Baofeng Su
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Jinhai Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Yu Zhang
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Huitong Shi
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Dongya Gao
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, USA
| | - Rex Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, USA
| | - Zhanjiang Liu
- Department of Biology, College of Arts and Sciences, Syracuse University, Syracuse, NY, USA
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4
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Fellous A, Wegner KM, John U, Mark FC, Shama LNS. Windows of opportunity: Ocean warming shapes temperature-sensitive epigenetic reprogramming and gene expression across gametogenesis and embryogenesis in marine stickleback. GLOBAL CHANGE BIOLOGY 2022; 28:54-71. [PMID: 34669228 DOI: 10.1111/gcb.15942] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/23/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Rapid climate change is placing many marine species at risk of local extinction. Recent studies show that epigenetic mechanisms (e.g. DNA methylation, histone modifications) can facilitate both within and transgenerational plasticity to cope with changing environments. However, epigenetic reprogramming (erasure and re-establishment of epigenetic marks) during gamete and early embryo development may hinder transgenerational epigenetic inheritance. Most of our knowledge about reprogramming stems from mammals and model organisms, whereas the prevalence and extent of reprogramming among non-model species from wild populations is rarely investigated. Moreover, whether reprogramming dynamics are sensitive to changing environmental conditions is not well known, representing a key knowledge gap in the pursuit to identify mechanisms underlying links between parental exposure to changing climate patterns and environmentally adapted offspring phenotypes. Here, we investigated epigenetic reprogramming (DNA methylation/hydroxymethylation) and gene expression across gametogenesis and embryogenesis of marine stickleback (Gasterosteus aculeatus) under three ocean warming scenarios (ambient, +1.5 and +4°C). We found that parental acclimation to ocean warming led to dynamic and temperature-sensitive reprogramming throughout offspring development. Both global methylation/hydroxymethylation and expression of genes involved in epigenetic modifications were strongly and differentially affected by the increased warming scenarios. Comparing transcriptomic profiles from gonads, mature gametes and early embryonic stages showed sex-specific accumulation and temperature sensitivity of several epigenetic actors. DNA methyltransferase induction was primarily maternally inherited (suggesting maternal control of remethylation), whereas induction of several histone-modifying enzymes was shaped by both parents. Importantly, massive, temperature-specific changes to the epigenetic landscape occurred in blastula, a critical stage for successful embryo development, which could, thus, translate to substantial consequences for offspring phenotype resilience in warming environments. In summary, our study identified key stages during gamete and embryo development with temperature-sensitive reprogramming and epigenetic gene regulation, reflecting potential 'windows of opportunity' for adaptive epigenetic responses under future climate change.
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Affiliation(s)
- Alexandre Fellous
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, List, Germany
| | - K Mathias Wegner
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, List, Germany
| | - Uwe John
- Ecological Chemistry Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Felix C Mark
- Integrative Ecophysiology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Lisa N S Shama
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, List, Germany
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5
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Robinson PC, Littler HR, Lange A, Santos EM. Developmental exposure window influences silver toxicity but does not affect the susceptibility to subsequent exposures in zebrafish embryos. Histochem Cell Biol 2020; 154:579-595. [PMID: 33083906 PMCID: PMC7609441 DOI: 10.1007/s00418-020-01933-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2020] [Indexed: 01/07/2023]
Abstract
Silver is a non-essential, toxic metal widespread in freshwaters and capable of causing adverse effects to wildlife. Its toxic effects have been studied in detail but less is known about how sensitivity varies during development and whether pre-exposures affect tolerance upon re-exposure. We address these knowledge gaps using the zebrafish embryo (Danio rerio) model to investigate whether exposures encompassing stages of development prior to mid-blastula transition, when chorion hardening and epigenetic reprogramming occur, result in greater toxicity compared to those initiated after this period. We conducted exposures to silver initiated at 0.5 h post fertilisation (hpf) and 4 hpf to determine if toxicity differed. In parallel, we exposed embryos to the methylation inhibitor 5-azacytidine as a positive control. Toxicity increased when exposures started from 0.5 hpf compared to 4 hpf and LC50 were significantly lower by 1.2 and 7.6 times for silver and 5-azacyitidine, respectively. We then investigated whether pre-exposure to silver during early development (from 0.5 or 4 hpf) affected the outcome of subsequent exposures during the larvae stage, and found no alterations in toxicity compared to naïve larvae. Together, these data demonstrate that during early development zebrafish embryos are more sensitive to silver when experiments are initiated at the one-cell stage, but that pre-exposures do not influence the outcome of subsequent exposures, suggesting that no long-lasting memory capable of influencing future susceptibility was maintained under our experimental conditions. The finding that toxicity is greater for exposures initiated at the one-cell stage has implications for designing testing systems to assess chemical toxicity.
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Affiliation(s)
- Paige C Robinson
- Biosciences, College of Life and Environmental Sciences, Geoffrey Pope Building, University of Exeter, Exeter, EX4 4QD, UK.
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe, Weymouth, DT4 8UB, Dorset, UK.
| | - Hannah R Littler
- Biosciences, College of Life and Environmental Sciences, Geoffrey Pope Building, University of Exeter, Exeter, EX4 4QD, UK
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, The Nothe, Weymouth, DT4 8UB, Dorset, UK
| | - Anke Lange
- Biosciences, College of Life and Environmental Sciences, Geoffrey Pope Building, University of Exeter, Exeter, EX4 4QD, UK
| | - Eduarda M Santos
- Biosciences, College of Life and Environmental Sciences, Geoffrey Pope Building, University of Exeter, Exeter, EX4 4QD, UK.
- Sustainable Aquaculture Futures, University of Exeter, Exeter, EX4 4QD, UK.
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6
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Mu X, Chen X, Liu J, Yuan L, Wang D, Qian L, Qian Y, Shen G, Huang Y, Li X, Li Y, Lin X. A multi-omics approach reveals molecular mechanisms by which phthalates induce cardiac defects in zebrafish (Danio rerio). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 265:113876. [PMID: 32806432 DOI: 10.1016/j.envpol.2019.113876] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 12/16/2019] [Accepted: 12/22/2019] [Indexed: 06/11/2023]
Abstract
The potential risks of phthalates affecting human and animal health as well as the environment are emerging as serious concerns worldwide. However, the mechanism by which phthalates induce developmental effects is under debate. Herein, we found that embryonic exposure of zebrafish to di-(2-ethylhexyl) phthalate (DEHP) and di-butyl phthalate (DBP) increased the rate of heart defects including abnormal heart rate and pericardial edema. Changes in the transcriptional profile demonstrated that genes involved in the development of the heart, such as tbx5b, nppa, ctnt, my17, cmlc1, were significantly altered by DEHP and DBP at 50 μg/L, which agreed with the abnormal cardiac outcomes. Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) further showed that significant hypomethylation of nppa and ctnt was identified after DEHP and DBP exposure, which was consistent with the up-regulation of these genes. Notably, hypermethylation on the promoter region (<1 kb) of tbx5b was found after DEHP and DBP exposure, which might be responsible for its decrease in transcription. In conclusion, phthalates have the potential to induce cardiac birth defects, which might be associated with the transcriptional regulation of the involved developmental factors such as tbx5b. These findings would contribute to understand the molecular pathways that mediated the cardiac defects caused by phthalates.
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Affiliation(s)
- Xiyan Mu
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China.
| | - Xiaofeng Chen
- College of Sciences, China Agricultural University, People's Republic of China
| | - Jia Liu
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
| | - Lilai Yuan
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
| | - Donghui Wang
- College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Le Qian
- College of Sciences, China Agricultural University, People's Republic of China
| | - Yu Qian
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
| | - Gongming Shen
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
| | - Ying Huang
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
| | - Xuxing Li
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
| | - Yingren Li
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
| | - Xiangming Lin
- Fishery Resource and Environment Research Center, Chinese Academy of Fishery Sciences, Beijing, People's Republic of China
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7
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Transgenerational inheritance of impaired larval T cell development in zebrafish. Nat Commun 2020; 11:4505. [PMID: 32908148 PMCID: PMC7481223 DOI: 10.1038/s41467-020-18289-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
Evidence for transgenerational inheritance of epigenetic information in vertebrates is scarce. Aberrant patterns of DNA methylation in gametes may set the stage for transmission into future generations. Here, we describe a viable hypomorphic allele of dnmt1 in zebrafish that causes widespread demethylation of CpG dinucleotides in sperm and somatic tissues. We find that homozygous mutants are essentially normal, with the exception of drastically impaired lymphopoiesis, affecting both larval and adult phases of T cell development. The phenotype of impaired larval (but not adult) T cell development is transmitted to subsequent generations by genotypically wildtype fish. We further find that about 200 differentially methylated regions in sperm DNA of transmitting and non-transmitting males, including hypermethylated sites associated with runx3 and rptor genes, whose reduced activities are associated with impaired larval T cell development. Our results indicate a particular sensitivity of larval T cell development to transgenerationally inherited epimutations. Evidence for transgenerational inheritance of epigenetic information in vertebrates is scarce. Here the authors report that homozygous dnmt1 mutant zebrafish are essentially normal, with the exception of impaired lymphopoiesis, with impaired larval (but not adult) T cell development being transmitted to subsequent generations by genotypically wildtype fish.
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8
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Tung A, Levin M. Extra-genomic instructive influences in morphogenesis: A review of external signals that regulate growth and form. Dev Biol 2020; 461:1-12. [PMID: 31981561 DOI: 10.1016/j.ydbio.2020.01.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/21/2020] [Accepted: 01/21/2020] [Indexed: 12/18/2022]
Abstract
Embryonic development and regeneration accomplish a remarkable feat: individual cells work together to create or repair complex anatomical structures. What is the source of the instructive signals that specify these invariant and robust organ-level outcomes? The most frequently studied source of morphogenetic control is the host genome and its transcriptional circuits. However, it is now apparent that significant information affecting patterning also arrives from outside of the body. Both biotic and physical factors, including temperature and various molecular signals emanating from pathogens, commensals, and conspecific organisms, affect developmental outcomes. Here, we review examples in which anatomical patterning decisions are strongly impacted by lateral signals that originate from outside of the zygotic genome. The endogenous pathways targeted by these influences often show transgenerational effects, enabling them to shape the evolution of anatomies even faster than traditional Baldwin-type assimilation. We also discuss recent advances in the biophysics of morphogenetic controls and speculate on additional sources of important patterning information which could be exploited to better understand the evolution of bodies and to design novel approaches for regenerative medicine.
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Affiliation(s)
- Angela Tung
- Department of Biology and Allen Discovery Center at Tufts University, Medford, MA, USA
| | - Michael Levin
- Department of Biology and Allen Discovery Center at Tufts University, Medford, MA, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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9
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Akdogan-Ozdilek B, Duval KL, Goll MG. Chromatin dynamics at the maternal to zygotic transition: recent advances from the zebrafish model. F1000Res 2020; 9. [PMID: 32528656 PMCID: PMC7262572 DOI: 10.12688/f1000research.21809.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2020] [Indexed: 01/02/2023] Open
Abstract
Early animal development is characterized by intense reorganization of the embryonic genome, including large-scale changes in chromatin structure and in the DNA and histone modifications that help shape this structure. Particularly profound shifts in the chromatin landscape are associated with the maternal-to-zygotic transition, when the zygotic genome is first transcribed and maternally loaded transcripts are degraded. The accessibility of the early zebrafish embryo facilitates the interrogation of chromatin during this critical window of development, making it an important model for early chromatin regulation. Here, we review our current understanding of chromatin dynamics during early zebrafish development, highlighting new advances as well as similarities and differences between early chromatin regulation in zebrafish and other species.
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Affiliation(s)
| | | | - Mary G Goll
- Department of Genetics, University of Georgia, Athens, GA, USA
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10
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Balasubramanian S, Raghunath A, Perumal E. Role of epigenetics in zebrafish development. Gene 2019; 718:144049. [DOI: 10.1016/j.gene.2019.144049] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023]
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11
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Jorgensen BG, Ro S. Role of DNA Methylation in the Development and Differentiation of Intestinal Epithelial Cells and Smooth Muscle Cells. J Neurogastroenterol Motil 2019; 25:377-386. [PMID: 31327220 PMCID: PMC6657918 DOI: 10.5056/jnm19077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022] Open
Abstract
The mammalian intestine contains many different cell types but is comprised of 2 main cell types: epithelial cells and smooth muscle cells. Recent in vivo and in vitro evidence has revealed that various alterations to the DNA methylation apparatus within both of these cell types can result in a variety of cellular phenotypes including modified differentiation status, apoptosis, and uncontrolled growth. Methyl groups added to cytosines in regulatory genomic regions typically act to repress associated gene transcription. Aberrant DNA methylation patterns are often found in cells with abnormal growth/differentiation patterns, including those cells involved in burdensome intestinal pathologies including inflammatory bowel diseases and intestinal pseudo-obstructions. The altered methylation patterns being observed in various cell cultures and DNA methyltransferase knockout models indicate an influential connection between DNA methylation and gastrointestinal cells’ development and their response to environmental signaling. As these modified DNA methylation levels are found in a number of pathological gastrointestinal conditions, further investigations into uncovering the causative nature, and controlled regulation, of this epigenetic modification is of great interest.
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Affiliation(s)
- Brian G Jorgensen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, USA
| | - Seungil Ro
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, USA
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12
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Reinardy HC, Pedersen KB, Nahrgang J, Frantzen M. Effects of mine tailings exposure on early life stages of atlantic cod. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2019; 38:1446-1454. [PMID: 30901098 PMCID: PMC6851963 DOI: 10.1002/etc.4415] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/27/2018] [Accepted: 03/12/2019] [Indexed: 05/16/2023]
Abstract
In Norway, mine tailings waste can be deposited by coastal submarine dispersal. Mine tailings slurry includes fine particles <10 µm with elevated levels of metals (e.g., copper, iron) from residual mineral ore. Prolonged suspension of small particles in the water column may bring them into contact with locally spawned pelagic fish eggs, including Atlantic cod, Gadus morhua. Newly fertilized cod embryos were exposed to suspended mine tailings particles up to 3.2 mg/L in flow-through aquaria for a total of 21 d. Significantly more particles adhered to the surface of the chorion from the high treatment after 11-d exposure, and dissolved Cu concentrations increased in the water (up to 0.36 ± 0.06 µg/L). There was no adverse effect on embryo mortality but an 8% elevation in larval mortality. There were no differences with treatment on timing of hatching, embryo and larva morphometrics, abnormalities, or cardiac activity. There was a treatment-dependent up-regulation of stress marker genes (hspa8, cyp1c1) but no indication of metal-induced activation of metallothionien (mt gene transcription). Transcription markers for DNA and histone methyltransferases did show treatment-related up-regulation, indicative of altered methylation in larvae when developmental methylation patterns are determined, indicating some level of chronic toxicity that may have longer-term effects. Environ Toxicol Chem 2019;38:1446-1454. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.
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Affiliation(s)
- Helena C. Reinardy
- Department of Arctic TechnologyUniversity Centre in SvalbardLongyearbyenSvalbardNorway
| | | | - Jasmine Nahrgang
- Department of Arctic and Marine BiologyUiT The Arctic University of NorwayTromsøNorway
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13
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Fellous A, Earley RL, Silvestre F. Identification and expression of mangrove rivulus (Kryptolebias marmoratus) histone deacetylase (HDAC) and lysine acetyltransferase (KAT) genes. Gene 2019; 691:56-69. [DOI: 10.1016/j.gene.2018.12.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/14/2018] [Accepted: 12/14/2018] [Indexed: 12/17/2022]
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Rajshekar S, Yao J, Arnold PK, Payne SG, Zhang Y, Bowman TV, Schmitz RJ, Edwards JR, Goll M. Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome. eLife 2018; 7:39658. [PMID: 30484769 PMCID: PMC6261255 DOI: 10.7554/elife.39658] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 11/04/2018] [Indexed: 12/13/2022] Open
Abstract
Pericentromeric satellite repeats are enriched in 5-methylcytosine (5mC). Loss of 5mC at these sequences is common in cancer and is a hallmark of Immunodeficiency, Centromere and Facial abnormalities (ICF) syndrome. While the general importance of 5mC is well-established, the specific functions of 5mC at pericentromeres are less clear. To address this deficiency, we generated a viable animal model of pericentromeric hypomethylation through mutation of the ICF-gene ZBTB24. Deletion of zebrafish zbtb24 caused a progressive loss of 5mC at pericentromeres and ICF-like phenotypes. Hypomethylation of these repeats triggered derepression of pericentromeric transcripts and activation of an interferon-based innate immune response. Injection of pericentromeric RNA is sufficient to elicit this response in wild-type embryos, and mutation of the MDA5-MAVS dsRNA-sensing machinery blocks the response in mutants. These findings identify activation of the innate immune system as an early consequence of pericentromeric hypomethylation, implicating derepression of pericentromeric transcripts as a trigger of autoimmunity. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter). Cells package DNA into structures called chromosomes. When cells divide, each chromosome duplicates, and a structure called a centromere initially holds the copies together. The sequences of DNA on either side of the centromeres are often highly repetitive. In backboned animals, this DNA normally also has extra chemical modifications called methyl groups attached to it. The role that these methyl groups play in this region is not known, although in other DNA regions they often stop the DNA being ‘transcribed’ into molecules of RNA. The cells of people who have a rare human genetic disorder called ICF syndrome, lack the methyl groups near the centromere. The methyl groups may also be lost in old and cancerous cells. Researchers often use ‘model’ animals to investigate the effects of DNA modifications. But, until now, there were no animal models that lose methyl groups from the DNA around centromeres in the same way as seen in ICF syndrome. Rajshekar et al. have developed a new zebrafish model for ICF syndrome that loses the methyl groups around its centromeres over time. Studying the cells of these zebrafish showed that when the methyl groups are missing, the cell starts to transcribe the DNA sequences around the centromeres. The resulting RNA molecules appear to be mistaken by the cell for viral RNA. They activate immune sensors that normally detect RNA viruses, which triggers an immune response. The new zebrafish model can now be used in further studies to help researchers to understand the key features of ICF syndrome. Future work could also investigate whether the loss of methyl groups around the centromeres plays a role in other diseases where the immune system attacks healthy tissues.
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Affiliation(s)
- Srivarsha Rajshekar
- Program in Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, United States.,Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Institute of Bioinformatics, University of Georgia, Athens, United States
| | - Jun Yao
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Paige K Arnold
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Sara G Payne
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, United States
| | - Yinwen Zhang
- Institute of Bioinformatics, University of Georgia, Athens, United States
| | - Teresa V Bowman
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, New York, United States
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Georgia, United States
| | - John R Edwards
- Department of Medicine, Center for Pharmacogenomics, Washington University in St. Louis School of Medicine, Missouri, United States
| | - Mary Goll
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Department of Genetics, University of Georgia, Georgia, United States
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Fellous A, Labed‐Veydert T, Locrel M, Voisin A, Earley RL, Silvestre F. DNA methylation in adults and during development of the self-fertilizing mangrove rivulus, Kryptolebias marmoratus. Ecol Evol 2018; 8:6016-6033. [PMID: 29988456 PMCID: PMC6024129 DOI: 10.1002/ece3.4141] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 03/18/2018] [Accepted: 04/04/2018] [Indexed: 12/18/2022] Open
Abstract
In addition to genetic variation, epigenetic mechanisms such as DNA methylation might make important contributions to heritable phenotypic diversity in populations. However, it is often difficult to disentangle the contributions of genetic and epigenetic variation to phenotypic diversity. Here, we investigated global DNA methylation and mRNA expression of the methylation-associated enzymes during embryonic development and in adult tissues of one natural isogenic lineage of mangrove rivulus fish, Kryptolebias marmoratus. Being the best-known self-fertilizing hermaphroditic vertebrate affords the opportunity to work with genetically identical individuals to examine, explicitly, the phenotypic effects of epigenetic variance. Using the LUminometric Methylation Assay (LUMA), we described variable global DNA methylation at CpG sites in adult tissues, which differed significantly between hermaphrodite ovotestes and male testes (79.6% and 87.2%, respectively). After fertilization, an immediate decrease in DNA methylation occurred to 15.8% in gastrula followed by re-establishment to 70.0% by stage 26 (liver formation). Compared to zebrafish, at the same embryonic stages, this reprogramming event seems later, deeper, and longer. Furthermore, genes putatively encoding DNA methyltransferases (DNMTs), Ten-Eleven Translocation (TET), and MeCP2 proteins showed specific regulation in adult gonad and brain, and also during early embryogenesis. Their conserved domains and expression profiles suggest that these proteins play important roles during reproduction and development. This study raises questions about mangrove rivulus' peculiar reprogramming period in terms of epigenetic transmission and physiological adaptation of individuals to highly variable environments. In accordance with the general-purpose genotype model, epigenetic mechanisms might allow for the expression of diverse phenotypes among genetically identical individuals. Such phenotypes might help to overcome environmental challenges, making the mangrove rivulus a valuable vertebrate model for ecological epigenetic studies. The mangrove rivulus, Kryptolebias marmoratus, is the best-known self-fertilizing hermaphroditic vertebrate that allows to work with genetically identical individuals to examine, explicitly, the phenotypic effects of epigenetic variance. The reprogramming event is later, more dramatic and longer than in other described vertebrates. High evolutionary conservation and expression patterns of DNMT, TET, and MeCP2 proteins in K. marmoratus suggest biological roles for each member in gametogenesis and development.
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Affiliation(s)
- Alexandre Fellous
- Laboratory of Evolutionary and Adaptive PhysiologyInstitute of Life, Earth and EnvironmentUniversity of NamurNamurBelgium
| | - Tiphaine Labed‐Veydert
- Laboratory of Evolutionary and Adaptive PhysiologyInstitute of Life, Earth and EnvironmentUniversity of NamurNamurBelgium
| | - Mélodie Locrel
- Laboratory of Evolutionary and Adaptive PhysiologyInstitute of Life, Earth and EnvironmentUniversity of NamurNamurBelgium
| | - Anne‐Sophie Voisin
- Laboratory of Evolutionary and Adaptive PhysiologyInstitute of Life, Earth and EnvironmentUniversity of NamurNamurBelgium
| | - Ryan L. Earley
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
| | - Frederic Silvestre
- Laboratory of Evolutionary and Adaptive PhysiologyInstitute of Life, Earth and EnvironmentUniversity of NamurNamurBelgium
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16
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Gore AV, Tomins KA, Iben J, Ma L, Castranova D, Davis AE, Parkhurst A, Jeffery WR, Weinstein BM. An epigenetic mechanism for cavefish eye degeneration. Nat Ecol Evol 2018; 2:1155-1160. [PMID: 29807993 PMCID: PMC6023768 DOI: 10.1038/s41559-018-0569-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 05/02/2018] [Indexed: 12/23/2022]
Abstract
Coding and non-coding mutations in DNA contribute significantly to phenotypic variability during evolution. However, less is known about the role of epigenetics in this process. Although previous studies have identified eye development genes associated with the loss-of-eyes phenotype in the Pachón blind cave morph of the Mexican tetra Astyanax mexicanus, no inactivating mutations have been found in any of these genes. Here, we show that excess DNA methylation-based epigenetic silencing promotes eye degeneration in blind cave A. mexicanus. By performing parallel analyses in A. mexicanus cave and surface morphs, and in the zebrafish Danio rerio, we have discovered that DNA methylation mediates eye-specific gene repression and globally regulates early eye development. The most significantly hypermethylated and downregulated genes in the cave morph are also linked to human eye disorders, suggesting that the function of these genes is conserved across vertebrates. Our results show that changes in DNA methylation-based gene repression can serve as an important molecular mechanism generating phenotypic diversity during development and evolution.
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Affiliation(s)
- Aniket V Gore
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
| | - Kelly A Tomins
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - James Iben
- Molecular Genomics Laboratory, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Li Ma
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Daniel Castranova
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Andrew E Davis
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Amy Parkhurst
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - William R Jeffery
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Brant M Weinstein
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
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Jessop P, Ruzov A, Gering M. Developmental Functions of the Dynamic DNA Methylome and Hydroxymethylome in the Mouse and Zebrafish: Similarities and Differences. Front Cell Dev Biol 2018; 6:27. [PMID: 29616219 PMCID: PMC5869911 DOI: 10.3389/fcell.2018.00027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 03/05/2018] [Indexed: 12/25/2022] Open
Abstract
5-methylcytosine (5mC) is the best understood DNA modification and is generally believed to be associated with repression of gene expression. Over the last decade, sequentially oxidized forms of 5mC (oxi-mCs) have been discovered within the genomes of vertebrates. Their discovery was accompanied by that of the ten-eleven translocation (TET) methylcytosine dioxygenases, the enzymes that catalyze the formation of the oxi-mCs. Although a number of studies performed on different vertebrate models and embryonic stem cells demonstrated that both TET enzymes and oxi-mCs are likely to be important for several developmental processes it is currently unclear whether their developmental roles are conserved among vertebrates. Here, we summarize recent developments in this field suggesting that biological roles of TETs/oxi-mCs may significantly differ between mice and zebrafish. Thus, although the role of TET proteins in late organogenesis has been documented for both these systems; unlike in mice the enzymatic oxidation of 5mC does not seem to be involved in zygotic reprogramming or gastrulation in zebrafish. Our analysis may provide an insight into the general principles of epigenetic regulation of animal development and cellular differentiation.
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Affiliation(s)
- Peter Jessop
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Alexey Ruzov
- Division of Cancer and Stem Cells, Centre for Biomolecular Sciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Martin Gering
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
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Paredes JF, Lopez-Olmeda JF, Muñoz-Cueto JA, Sánchez-Vázquez F. Circadian expression of DNA methylation and demethylation genes in zebrafish gonads. Chronobiol Int 2018; 35:920-932. [PMID: 29509082 DOI: 10.1080/07420528.2018.1440403] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
This research aimed at investigating the light synchronization and endogenous origin of daily expression rhythms of eight key genes involved in epigenetic mechanisms (DNA methylation and demethylation) in zebrafish gonads. To this end, 84 zebrafish were distributed into six tanks, each one containing 14 fish (7 males and 7 females). Animals were subjected to 12 h light:12 h dark cycles (LD, lights on at ZT0 h) and fed randomly three times a day during the light phase. Locomotor activity rhythms were recorded in each tank for 20 days to test their synchronization to light. Then, zebrafish were fasted for one day and gonad samples were collected every 4 h during a 24 h cycle (ZT2, 6, 10, 14, 18, and 22 h). The results revealed that most of the epigenetic genes investigated exhibited a significant daily rhythm. DNA methylation genes (dnmt4, dnmt5, dnmt7) exhibited a daily rhythm of expression with a nocturnal acrophase (ZT14:01~ZT22:17 h), except for dnmt7 in males (ZT2:25 h). Similarly, all DNA demethylation genes (tet2, tdg, mb4, gadd45aa, and apobec2b) revealed the existence of statistically significant daily rhythms, except for gadd45aa in females. In females, tdg, mb4, and apobec2b presented a nocturnal peak (ZT14:20 ~ ZT22:04 h), whereas the tet2 acrophase was diurnal (ZT4:02 h). In males, tet2, tdg, and gadd45aa had nocturnal acrophases (ZT18:26~ZT21:31 h), whereas mb4 and apobec2b displayed diurnal acrophases (ZT5:28 and ZT4:02 h, respectively). To determine the endogenous nature of gene expression rhythms, another experiment was performed: 12 groups of 14 fish (7 males and 7 females) were kept in complete darkness (DD) and sampled every 4 h during a 48 h cycle (CT2, 6, 10, 14, 18, 22, 26, 30, 34, 38, 42, and 46 h). Under DD, most of the genes (7 out of 8) presented circadian rhythmicity with different endogenous periodicities (tau), suggesting that the epigenetic mechanisms of DNA methylation and demethylation in the gonads follow an internal control, functioning as part of the translation network linking the environment into somatic signals in fish reproduction.
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Affiliation(s)
| | - Jose Fernando Lopez-Olmeda
- b Department of Physiology, Faculty of Biology , University of Murcia , Murcia , Spain.,c Kalrsruhe Institute of Technology , Institute of Toxicology and Genetics , Eggenstein , Germany
| | - Jose A Muñoz-Cueto
- d Department of Biology, Faculty of Marine and Environmental Sciences, Faculty of Marine and Environmental Sciences , University of Cadiz , Cádiz , Spain.,e CACYTMAR , Research Institutes , Puerto Real , Spain
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Subbanna S, Nagre NN, Shivakumar M, Joshi V, Psychoyos D, Kutlar A, Umapathy NS, Basavarajappa BS. CB1R-Mediated Activation of Caspase-3 Causes Epigenetic and Neurobehavioral Abnormalities in Postnatal Ethanol-Exposed Mice. Front Mol Neurosci 2018; 11:45. [PMID: 29515368 PMCID: PMC5826222 DOI: 10.3389/fnmol.2018.00045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 02/02/2018] [Indexed: 12/15/2022] Open
Abstract
Alcohol exposure can affect brain development, leading to long-lasting behavioral problems, including cognitive impairment, which together is defined as fetal alcohol spectrum disorder (FASD). However, the fundamental mechanisms through which this occurs are largely unknown. In this study, we report that the exposure of postnatal day 7 (P7) mice to ethanol activates caspase-3 via cannabinoid receptor type-1 (CB1R) in neonatal mice and causes a reduction in methylated DNA binding protein (MeCP2) levels. The developmental expression of MeCP2 in mice is closely correlated with synaptogenesis and neuronal maturation. It was shown that ethanol treatment of P7 mice enhanced Mecp2 mRNA levels but reduced protein levels. The genetic deletion of CB1R prevented, and administration of a CB1R antagonist before ethanol treatment of P7 mice inhibited caspase-3 activation. Additionally, it reversed the loss of MeCP2 protein, cAMP response element binding protein (CREB) activation, and activity-regulated cytoskeleton-associated protein (Arc) expression. The inhibition of caspase-3 activity prior to ethanol administration prevented ethanol-induced loss of MeCP2, CREB activation, epigenetic regulation of Arc expression, long-term potentiation (LTP), spatial memory deficits and activity-dependent impairment of several signaling molecules, including MeCP2, in adult mice. Collectively, these results reveal that the ethanol-induced CB1R-mediated activation of caspase-3 degrades the MeCP2 protein in the P7 mouse brain and causes long-lasting neurobehavioral deficits in adult mice. This CB1R-mediated instability of MeCP2 during active synaptic maturation may disrupt synaptic circuit maturation and lead to neurobehavioral abnormalities, as observed in this animal model of FASD.
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Affiliation(s)
- Shivakumar Subbanna
- Division of Analytical Psychopharmacology, Nathan Kline Institute for Psychiatric Research, New York, NY, United States
| | - Nagaraja N. Nagre
- Division of Analytical Psychopharmacology, Nathan Kline Institute for Psychiatric Research, New York, NY, United States
| | - Madhu Shivakumar
- Division of Analytical Psychopharmacology, Nathan Kline Institute for Psychiatric Research, New York, NY, United States
| | - Vikram Joshi
- Division of Analytical Psychopharmacology, Nathan Kline Institute for Psychiatric Research, New York, NY, United States
| | - Delphine Psychoyos
- Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, United States
| | - Abdullah Kutlar
- Center for Blood Disorders, Augusta University, Augusta, GA, United States
| | | | - Balapal S. Basavarajappa
- Division of Analytical Psychopharmacology, Nathan Kline Institute for Psychiatric Research, New York, NY, United States
- New York State Psychiatric Institute, New York, NY, United States
- Department of Psychiatry, College of Physicians & Surgeons, Columbia University, New York, NY, United States
- Department of Psychiatry, New York University Langone Medical Center, New York, NY, United States
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20
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Ribas L, Vanezis K, Imués MA, Piferrer F. Treatment with a DNA methyltransferase inhibitor feminizes zebrafish and induces long-term expression changes in the gonads. Epigenetics Chromatin 2017; 10:59. [PMID: 29216900 PMCID: PMC5721477 DOI: 10.1186/s13072-017-0168-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 11/30/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The role of epigenetic modifications such as DNA methylation during vertebrate sexual development is far from being clear. Using the zebrafish model, we tested the effects of one of the most common DNA methyltransferase (dnmt) inhibitor, 5-aza-2'-deoxycytidine (5-aza-dC), which is approved for the treatment of acute myeloid leukaemia and is under active investigation for the treatment of solid tumours. Several dose-response experiments were carried out during two periods, including not only the very first days of development (0-6 days post-fertilization, dpf), as done in previous studies, but also, and as a novelty, the period of gonadal development (10-30 dpf). RESULTS Early treatment with 5-aza-dC altered embryonic development, delayed hatching and increased teratology and mortality, as expected. The most striking result, however, was an increase in the number of females, suggesting that alterations induced by 5-aza-dC treatment can affect sexual development as well. Results were confirmed when treatment coincided with gonadal development. In addition, we also found that the adult gonadal transcriptome of 5-aza-dC-exposed females included significant changes in the expression of key reproduction-related genes (e.g. cyp11a1, esr2b and figla), and that several pro-female-related pathways such as the Fanconi anaemia or the Wnt signalling pathways were downregulated. Furthermore, an overall inhibition of genes implicated in epigenetic regulatory mechanisms (e.g. dnmt1, dicer, cbx4) was also observed. CONCLUSIONS Taken together, our results indicate that treatment with a DNA methylation inhibitor can also alter the sexual development in zebrafish, with permanent alterations of the adult gonadal transcriptome, at least in females. Our results show the importance of DNA methylation for proper control of sexual development, open new avenues for the potential control of sex ratios in fish (aquaculture, population control) and call attention to possibly hidden long-term effects of dnmt therapy when used, for example, in the treatment of prepuberal children affected by some types of cancer.
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Affiliation(s)
- Laia Ribas
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Passeig Marítim, 37-45, 08003, Barcelona, Spain
| | - Konstantinos Vanezis
- Imperial Centre for Translational and Experimental Medicine, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Marco Antonio Imués
- Departamento de Recursos Hidrobiológicos, Universidad de Nariño, Torobajo, Pasto, Colombia
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Passeig Marítim, 37-45, 08003, Barcelona, Spain.
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21
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Madakashira B, Corbett L, Zhang C, Paoli P, Casement JW, Mann J, Sadler KC, Mann DA. Variant Histone H2afv reprograms DNA methylation during early zebrafish development. Epigenetics 2017; 12:811-824. [PMID: 29099280 PMCID: PMC5739095 DOI: 10.1080/15592294.2017.1359382] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The DNA methylome is re-patterned during discrete phases of vertebrate development. In zebrafish, there are 2 waves of global DNA demethylation and re-methylation: the first occurs before gastrulation when the parental methylome is changed to the zygotic pattern and the second occurs after formation of the embryonic body axis, during organ specification. The occupancy of the histone variant H2A.Z and regions of DNA methylation are generally anti-correlated, and it has been proposed that H2A.Z restricts the boundaries of highly methylated regions. While many studies have described the dynamics of methylome changes during early zebrafish development, the factors involved in establishing the DNA methylation landscape in zebrafish embryos have not been identified. We test the hypothesis that the zebrafish ortholog of H2A.Z (H2afv) restricts DNA methylation during development. We find that, in control embryos, bulk genome methylation decreases after gastrulation, with a nadir at the bud stage, and peaks during mid-somitogenesis; by 24 hours post -fertilization, total DNA methylation levels return to those detected in gastrula. Early zebrafish embryos depleted of H2afv have significantly more bulk DNA methylation during somitogenesis, suggesting that H2afv limits methylation during this stage of development. H2afv deficient embryos are small, with multisystemic abnormalities. Genetic interaction experiments demonstrate that these phenotypes are suppressed by depletion of DNA methyltransferase 1 (Dnmt1). This work demonstrates that H2afv is essential for global DNA methylation reprogramming during early vertebrate development and that embryonic development requires crosstalk between H2afv and Dnmt1.
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Affiliation(s)
- Bhavani Madakashira
- a Program in Biology , New York University Abu Dhabi , Abu Dhabi , United Arab Emirates
| | - Laura Corbett
- b Fibrosis Group , Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne , NE24HH
| | - Chi Zhang
- a Program in Biology , New York University Abu Dhabi , Abu Dhabi , United Arab Emirates
| | - Pier Paoli
- b Fibrosis Group , Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne , NE24HH
| | - John W Casement
- c Bioinformatics Support Unit, Faculty of Medical Sciences , Newcastle University , Newcastle Upon Tyne , NE24HH
| | - Jelena Mann
- b Fibrosis Group , Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne , NE24HH
| | - Kirsten C Sadler
- a Program in Biology , New York University Abu Dhabi , Abu Dhabi , United Arab Emirates.,d Department of Medicine/Division of Liver Diseases, Department of Developmental and Regenerative Biology , Icahn School of Medicine at Mount Sinai , New York , New York
| | - Derek A Mann
- b Fibrosis Group , Institute of Cellular Medicine, Newcastle University , Newcastle upon Tyne , NE24HH
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Kupsco A, Dasgupta S, Nguyen C, Volz DC. Dynamic Alterations in DNA Methylation Precede Tris(1,3-dichloro-2-propyl)phosphate-Induced Delays in Zebrafish Epiboly. ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS 2017; 4:367-373. [PMID: 28993812 PMCID: PMC5630170 DOI: 10.1021/acs.estlett.7b00332] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Tris(1,3-dichloro-2-propyl)phosphate (TDCIPP) is an organophosphate flame retardant that impacts zebrafish epiboly - an effect that may be associated with genome-wide hypomethylation. Using zebrafish as a model, the objectives of this study were to (1) quantify concentration-dependent impacts of TDCIPP on epiboly; (2) determine whether co-exposure with folic acid (FA) - a methyl donor - mitigates TDCIPP-induced impacts; and (3) using ten previously identified TDCIPP-susceptible loci, rely on bisulfite amplicon sequencing (BSAS) to monitor CpG methylation dynamics across multiple TDCIPP concentrations in the presence or absence of FA. Embryos were exposed to TDCIPP from 0.75 h post-fertilization (hpf) to 2, 4, 6, or 24 hpf in the presence or absence of 1 mM FA. Although TDCIPP delayed epiboly up to 3 h by 6 hpf and induced malformations by 24 hpf, FA was unable to mitigate TDCIPP-induced effects at all stages evaluated. Moreover, while no differences in global methylation were detected using a 5-methylcytosine (5-mC) DNA ELISA, BSAS revealed that TDCIPP-induced effects on CpG methylation were dependent on concentration and developmental stage, and that early effects on methylation do not persist despite continuous exposure. Our findings demonstrate that TDCIPP delays zebrafish epiboly, a phenotype that is preceded by complex, dynamic alterations in DNA methylation.
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23
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Carvan MJ, Kalluvila TA, Klingler RH, Larson JK, Pickens M, Mora-Zamorano FX, Connaughton VP, Sadler-Riggleman I, Beck D, Skinner MK. Mercury-induced epigenetic transgenerational inheritance of abnormal neurobehavior is correlated with sperm epimutations in zebrafish. PLoS One 2017; 12:e0176155. [PMID: 28464002 PMCID: PMC5413066 DOI: 10.1371/journal.pone.0176155] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 04/06/2017] [Indexed: 01/10/2023] Open
Abstract
Methylmercury (MeHg) is a ubiquitous environmental neurotoxicant, with human exposures predominantly resulting from fish consumption. Developmental exposure of zebrafish to MeHg is known to alter their neurobehavior. The current study investigated the direct exposure and transgenerational effects of MeHg, at tissue doses similar to those detected in exposed human populations, on sperm epimutations (i.e., differential DNA methylation regions [DMRs]) and neurobehavior (i.e., visual startle and spontaneous locomotion) in zebrafish, an established human health model. F0 generation embryos were exposed to MeHg (0, 1, 3, 10, 30, and 100 nM) for 24 hours ex vivo. F0 generation control and MeHg-exposed lineages were reared to adults and bred to yield the F1 generation, which was subsequently bred to the F2 generation. Direct exposure (F0 generation) and transgenerational actions (F2 generation) were then evaluated. Hyperactivity and visual deficit were observed in the unexposed descendants (F2 generation) of the MeHg-exposed lineage compared to control. An increase in F2 generation sperm epimutations was observed relative to the F0 generation. Investigation of the DMRs in the F2 generation MeHg-exposed lineage sperm revealed associated genes in the neuroactive ligand-receptor interaction and actin-cytoskeleton pathways being effected, which correlate to the observed neurobehavioral phenotypes. Developmental MeHg-induced epigenetic transgenerational inheritance of abnormal neurobehavior is correlated with sperm epimutations in F2 generation adult zebrafish. Therefore, mercury can promote the epigenetic transgenerational inheritance of disease in zebrafish, which significantly impacts its environmental health considerations in all species including humans.
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Affiliation(s)
- Michael J. Carvan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
- * E-mail:
| | - Thomas A. Kalluvila
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Rebekah H. Klingler
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Jeremy K. Larson
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Matthew Pickens
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Francisco X. Mora-Zamorano
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | | | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, United States of America
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, United States of America
| | - Michael K. Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, United States of America
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24
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Kamstra JH, Sales LB, Aleström P, Legler J. Differential DNA methylation at conserved non-genic elements and evidence for transgenerational inheritance following developmental exposure to mono(2-ethylhexyl) phthalate and 5-azacytidine in zebrafish. Epigenetics Chromatin 2017; 10:20. [PMID: 28413451 PMCID: PMC5389146 DOI: 10.1186/s13072-017-0126-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/04/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Exposure to environmental stressors during development may lead to latent and transgenerational adverse health effects. To understand the role of DNA methylation in these effects, we used zebrafish as a vertebrate model to investigate heritable changes in DNA methylation following chemical-induced stress during early development. We exposed zebrafish embryos to non-embryotoxic concentrations of the biologically active phthalate metabolite mono(2-ethylhexyl) phthalate (MEHP, 30 µM) and the DNA methyltransferase 1 inhibitor 5-azacytidine (5AC, 10 µM). Direct, latent and transgenerational effects on DNA methylation were assessed using global, genome-wide and locus-specific DNA methylation analyses. RESULTS Following direct exposure in zebrafish embryos from 0 to 6 days post-fertilization, genome-wide analysis revealed a multitude of differentially methylated regions, strongly enriched at conserved non-genic elements for both compounds. Pathways involved in adipogenesis were enriched with the putative obesogenic compound MEHP. Exposure to 5AC resulted in enrichment of pathways involved in embryonic development and transgenerational effects on larval body length. Locus-specific methylation analysis of 10 differentially methylated sites revealed six of these loci differentially methylated in sperm sampled from adult zebrafish exposed during development to 5AC, and in first and second generation larvae. With MEHP, consistent changes were found at 2 specific loci in first and second generation larvae. CONCLUSIONS Our results suggest a functional role for DNA methylation on cis-regulatory conserved elements following developmental exposure to compounds. Effects on these regions are potentially transferred to subsequent generations.
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Affiliation(s)
- Jorke H. Kamstra
- Faculty of Veterinary Medicine, Department of Basic Sciences and Aquatic Medicine, CoE CERAD, Norwegian University of Life Sciences, P.O. Box 8146 Dep., 0033 Oslo, Norway
| | - Liana Bastos Sales
- Institute for Environmental Studies, VU University Amsterdam, Amsterdam, The Netherlands
| | - Peter Aleström
- Faculty of Veterinary Medicine, Department of Basic Sciences and Aquatic Medicine, CoE CERAD, Norwegian University of Life Sciences, P.O. Box 8146 Dep., 0033 Oslo, Norway
| | - Juliette Legler
- Institute for Environmental Studies, VU University Amsterdam, Amsterdam, The Netherlands
- Institute for Environment, Health and Societies, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
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25
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Dorts J, Falisse E, Schoofs E, Flamion E, Kestemont P, Silvestre F. DNA methyltransferases and stress-related genes expression in zebrafish larvae after exposure to heat and copper during reprogramming of DNA methylation. Sci Rep 2016; 6:34254. [PMID: 27731414 PMCID: PMC5059630 DOI: 10.1038/srep34254] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/08/2016] [Indexed: 12/23/2022] Open
Abstract
DNA methylation, a well-studied epigenetic mark, is important for gene regulation in adulthood and for development. Using genetic and epigenetic approaches, the present study aimed at evaluating the effects of heat stress and copper exposure during zebrafish early embryogenesis when patterns of DNA methylation are being established, a process called reprogramming. Embryos were exposed to 325 μg Cu/L from fertilization (<1 h post fertilization - hpf) to 4 hpf at either 26.5 °C or 34 °C, followed by incubation in clean water at 26.5 °C till 96 hpf. Significant increased mortality rates and delayed hatching were observed following exposure to combined high temperature and Cu. Secondly, both stressors, alone or in combination, significantly upregulated the expression of de novo DNA methyltransferase genes (dnmt3) along with no differences in global cytosine methylation level. Finally, Cu exposure significantly increased the expression of metallothionein (mt2) and heat shock protein (hsp70), the latter being also increased following exposure to high temperature. These results highlighted the sensitivity of early embryogenesis and more precisely of the reprogramming period to environmental challenges, in a realistic situation of combined stressors.
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Affiliation(s)
- Jennifer Dorts
- Research Unit in Environmental and Evolutionary Biology, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Elodie Falisse
- Research Unit in Environmental and Evolutionary Biology, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Emilie Schoofs
- Research Unit in Environmental and Evolutionary Biology, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Enora Flamion
- Research Unit in Environmental and Evolutionary Biology, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Patrick Kestemont
- Research Unit in Environmental and Evolutionary Biology, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
| | - Frédéric Silvestre
- Research Unit in Environmental and Evolutionary Biology, University of Namur, Rue de Bruxelles 61, B-5000 Namur, Belgium
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Volz DC, Leet JK, Chen A, Stapleton H, Katiyar N, Kaundal R, Yu Y, Wang Y. Tris(1,3-dichloro-2-propyl)phosphate Induces Genome-Wide Hypomethylation within Early Zebrafish Embryos. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:10255-63. [PMID: 27574916 PMCID: PMC5080636 DOI: 10.1021/acs.est.6b03656] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Tris(1,3-dichloro-2-propyl)phosphate (TDCIPP) is a high-production volume organophosphate-based plasticizer and flame retardant widely used within the United States. Using zebrafish as a model, the objectives of this study were to determine whether (1) TDCIPP inhibits DNA methyltransferase (DNMT) within embryonic nuclear extracts; (2) uptake of TDCIPP from 0.75 h postfertilization (hpf, 2-cell) to 2 hpf (64-cell) or 6 hpf (shield stage) leads to impacts on the early embryonic DNA methylome; and (3) TDCIPP-induced impacts on cytosine methylation are localized to CpG islands within intergenic regions. Within this study, 5-azacytidine (5-azaC, a DNMT inhibitor) was used as a positive control. Although 5-azaC significantly inhibited zebrafish DNMT, TDCIPP did not affect DNMT activity in vitro at concentrations as high as 500 μM. However, rapid embryonic uptake of 5-azaC and TDCIPP from 0.75 to 2 hpf resulted in chemical- and chromosome-specific alterations in cytosine methylation at 2 hpf. Moreover, TDCIPP exposure predominantly resulted in hypomethylation of positions outside of CpG islands and within intragenic (exon) regions of the zebrafish genome. Overall, these findings provide the foundation for monitoring DNA methylation dynamics within zebrafish as well as identifying potential associations among TDCIPP exposure, adverse health outcomes, and DNA methylation status within human populations.
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Affiliation(s)
- David C. Volz
- Department
of Environmental Sciences, University of
California, Riverside, Riverside, California 92521, United States
- D. C. Volz. Phone: (951)
827-4450; Fax: (951) 827-3993; E-mail:
| | - Jessica K. Leet
- Department
of Environmental Health Sciences, University
of South Carolina, Columbia, South Carolina 29208, United States
| | - Albert Chen
- Division
of Environmental Sciences and Policy, Duke
University, Durham, North Carolina 27708, United States
| | - Heather
M. Stapleton
- Division
of Environmental Sciences and Policy, Duke
University, Durham, North Carolina 27708, United States
| | - Neerja Katiyar
- Bioinformatics
Facility, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California 92521, United States
| | - Rakesh Kaundal
- Bioinformatics
Facility, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California 92521, United States
| | - Yang Yu
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521, United States
| | - Yinsheng Wang
- Department
of Chemistry, University of California,
Riverside, Riverside, California 92521, United States
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Dasmahapatra AK, Khan IA. Modulation of DNA methylation machineries in Japanese rice fish (Oryzias latipes) embryogenesis by ethanol and 5-azacytidine. Comp Biochem Physiol C Toxicol Pharmacol 2016; 179:174-83. [PMID: 26510680 DOI: 10.1016/j.cbpc.2015.10.011] [Citation(s) in RCA: 8] [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: 09/14/2015] [Revised: 10/09/2015] [Accepted: 10/22/2015] [Indexed: 01/20/2023]
Abstract
As a sequel of our investigations on the impact of epigenome in inducing fetal alcohol spectrum disorder (FASD) phenotypes in Japanese rice fish, we have investigated on several DNA methylation machinery genes including DNA methyl transferase 3ba (dnmt3ba) and methyl binding proteins (MBPs), namely, mbd1b, mbd3a, mbd3b, and mecp2 at the transcription level. Studies were made during normal development, from 0day post fertilization (dpf) to hatching, and also exposing the fertilized eggs to ethanol or a DNMT inhibitor, 5-azacytidine (5-azaC). We observed that during development, all these genes followed distinct expression patterns, generally high mRNA copies in early phases (0-1dpf) and significantly low mRNA copies prior to or after hatching. Ethanol (100-500mM, 0-2dpf) was unable to alter any of these mRNAs in 2dpf; additional four day (2-6dpf) maintenance of these embryos in ethanol-free environment, on 6dpf, was also unable to establish any significant difference in these mRNA levels in comparison with the corresponding controls. However, continuous exposure of fertilized eggs in 300mM ethanol, 0-6dpf, showed significantly high mRNA copies only in MBPs (mbd1b, mbd3a, mbd3b, mecp2). 5-azaC (2mM) on 2dpf was able to enhance only mbd3b mRNA. Removal of 5-azaC and maintenance of these embryos in clean medium, 2-6dpf, showed significantly enhanced mbd3b and mecp2 mRNAs compared to corresponding controls on 6dpf. Our studies showed that in Japanese rice fish embryogenesis both ethanol and 5-azaC have the potential to specifically modulate the developmental rhythm of DNA methylation machineries.
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Affiliation(s)
- Asok K Dasmahapatra
- National Center for Natural Product Research, School of Pharmacy, University of Mississippi, University, MS 38677, USA; Department of BioMolecular Sciences, Division of Pharmacology, School of Pharmacy, University of Mississippi, University, MS 38677, USA.
| | - Ikhlas A Khan
- National Center for Natural Product Research, School of Pharmacy, University of Mississippi, University, MS 38677, USA; Department of BioMolecular Sciences, Division of Pharmacognosy, School of Pharmacy, University of Mississippi, University, MS 38677, USA
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Kamstra JH, Aleström P, Kooter JM, Legler J. Zebrafish as a model to study the role of DNA methylation in environmental toxicology. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:16262-16276. [PMID: 25172464 DOI: 10.1007/s11356-014-3466-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 08/14/2014] [Indexed: 06/03/2023]
Abstract
Environmental epigenetics is a rapidly growing field which studies the effects of environmental factors such as nutrition, stress, and exposure to compounds on epigenetic gene regulation. Recent studies have shown that exposure to toxicants in vertebrates is associated with changes in DNA methylation, a major epigenetic mechanism affecting gene transcription. Zebra fish, a well-known model in toxicology and developmental biology, are emerging as a model species in environmental epigenetics despite their evolutionary distance to rodents and humans. In this review, recent insights in DNA methylation during zebra fish development are discussed and compared to mammalian models in order to evaluate zebra fish as a model to study the role of DNA methylation in environmental toxicology. Differences exist in DNA methylation reprogramming during early development, whereas in later developmental stages, tissue distribution of both 5-methylcytosine and 5-hydroxymethylcytosine seems more conserved between species, as well as basic DNA (de)methylation mechanisms. All DNA methyl transferases identified so far in mammals are present in zebra fish, as well as a number of major demethylation pathways. However, zebra fish appear to lack some methylation pathways present in mammals, such as parental imprinting. Several studies report effects on DNA methylation in zebra fish following exposure to environmental contaminants, such as arsenic, benzo[a]pyrene, and tris(1,3-dichloro-2-propyl)phosphate. Though more research is needed to examine heritable effects of contaminant exposure on DNA methylation, recent data suggests the usefulness of the zebra fish as a model in environmental epigenetics.
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Affiliation(s)
- Jorke H Kamstra
- Institute for Environmental Studies, VU University Amsterdam, 1081 HV, Amsterdam, The Netherlands.
| | - Peter Aleström
- Faculty of Veterinary Medicine and Biosciences, Dept. of Basic Science and Aquatic Medicine, Norwegian University of Life Sciences, 0033, Oslo, Norway.
| | - Jan M Kooter
- Department of Molecular Cell Biology, Section Genetics, VU University Amsterdam, 1081 HV, Amsterdam, The Netherlands.
| | - Juliette Legler
- Institute for Environmental Studies, VU University Amsterdam, 1081 HV, Amsterdam, The Netherlands.
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Torres-Núñez E, Cal L, Suárez-Bregua P, Gómez-Marin C, Moran P, Gómez-Skarmeta JL, Rotllant J. Matricellular protein SPARC/osteonectin expression is regulated by DNA methylation in its core promoter region. Dev Dyn 2015; 244:693-702. [PMID: 25728805 DOI: 10.1002/dvdy.24267] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/03/2015] [Accepted: 02/16/2015] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND SPARC/osteonectin is an evolutionarily conserved matricellular protein that modulates cell-matrix interaction and cell function. In all vertebrates, SPARC is dynamically expressed during embryogenesis. However, the precise function of SPARC and the regulatory elements required for its expression in particular during early embryogenesis are largely unknown. RESULTS The present study was undertaken to explore the molecular mechanisms that regulate sparc gene expression by in vivo functional characterization of the sparc promoter and identification of possible putative regulatory elements that govern basal promoter activity. We report here transient expression analyses of eGFP expression from transgenic zebrafish containing a Sparc-iTol2-eGFP-BAC and/or 7.25 kb-sparc-Tol2-eGFP constructs. eGFP expression was specifically found in the notochord, otic vesicle, fin fold, intermediate cell mass, and olfactory placode of BAC and Tol2 transposon vectors injected embryos. Deletion analysis revealed that promoter activity resides in the unique 5'-untranslated intronic region. Computer-based analysis revealed a putative CpG island immediately proximal to the translation start site within the intron sequence. Global inhibition of methylation with 5-Aza-2-deoxycytidine promoted sparc expression in association with decreasing CpG methylation. CONCLUSIONS Taken together, these data identify a contributory role for DNA methylation in regulating sparc expression in zebrafish embryogenesis.
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Affiliation(s)
- Eva Torres-Núñez
- Aquatic Molecular Pathobiology Lab, Instituto de Investigaciones Marinas (IIM-CSIC), Vigo, Spain
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30
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Kamstra JH, Løken M, Aleström P, Legler J. Dynamics of DNA hydroxymethylation in zebrafish. Zebrafish 2015; 12:230-7. [PMID: 25751297 DOI: 10.1089/zeb.2014.1033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
During embryonic development in mammals, most of the methylated cytosines in the paternal genome are converted to 5-hydroxymethyldeoxycytidine (hmC), as part of DNA methylation reprogramming. Recent data also suggest tissue-specific functional roles of hmC, perhaps as an epigenetic mark. However, limited data are available on the levels and tissue distribution in zebrafish. In this study, we used high-performance liquid chromatography mass spectrometry to quantify hmC and 5-methyldeoxycytidine (mC) in zebrafish during development and in different tissues of the adult fish. Low levels of mC were found at 0.5 hours postfertilization (hpf) (1-2 cell stage) (1.9%), and increased to 8.4% by 96 hpf, with similar levels observed in different adult tissues. No hmC was detected up to 12 hpf, but levels increased during development from 24 up to 96 hpf (0.23%). In tissues, the highest levels of hmC were found in the brain (0.49%), intermediate levels in muscle (0.13%), liver (0.08%), and intestine (0.06%) and low levels in testis (0.01%), with an inverse correlation between hmC and mC. Our results indicate similar tissue distribution and levels of hmC between zebrafish and mammals, but distinct differences during embryonic development. Although more research is needed, these results support the use of zebrafish as an alternative model in the elucidation of tissue-specific functions of hmC.
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Affiliation(s)
- Jorke H Kamstra
- 1 Institute for Environmental Studies, VU University Amsterdam , Amsterdam, the Netherlands
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31
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Liu X, Jia X, Yuan H, Ma K, Chen Y, Jin Y, Deng M, Pan W, Chen S, Chen Z, de The H, Zon LI, Zhou Y, Zhou J, Zhu J. DNA methyltransferase 1 functions through C/ebpa to maintain hematopoietic stem and progenitor cells in zebrafish. J Hematol Oncol 2015; 8:15. [PMID: 25886310 PMCID: PMC4372312 DOI: 10.1186/s13045-015-0115-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/24/2015] [Indexed: 12/13/2022] Open
Abstract
Background DNA methyltransferase 1 (Dnmt1) regulates expression of many critical genes through maintaining parental DNA methylation patterns on daughter DNA strands during mitosis. It is essential for embryonic development and diverse biological processes, including maintenance of hematopoietic stem and progenitor cells (HSPCs). However, the precise molecular mechanism of how Dnmt1 is involved in HSPC maintenance remains unexplored. Methods An N-ethyl-N-nitrosourea (ENU)-based genetic screening was performed to identify putative mutants with defects in definitive HSPCs during hematopoiesis in zebrafish. The expression of hematopoietic markers was analyzed via whole mount in situ hybridization assay (WISH). Positional cloning approach was carried out to identify the gene responsible for the defective definitive hematopoiesis in the mutants. Analyses of the mechanism were conducted by morpholino-mediated gene knockdown, mRNA injection rescue assays, anti-phosphorylated histone H3 (pH3) immunostaining and TUNEL assay, quantitative real-time PCR, and bisulfite sequencing analysis. Results A heritable mutant line with impaired HSPCs of definitive hematopoiesis was identified. Positional cloning demonstrated that a stop codon mutation was introduced in dnmt1 which resulted in a predicted truncated Dnmt1 lacking the DNA methylation catalytic domain. Molecular analysis revealed that expression of CCAAT/enhancer-binding protein alpha (C/ebpa) was upregulated, which correlated with hypomethylation of CpG islands in the regulation regions of cebpa gene in Dnmt1 deficient HSPCs. Overexpression of a transcriptional repressive SUMO-C/ebpa fusion protein could rescue hematological defects in the dnmt1 mutants. Finally, dnmt1 and cebpa double null embryos exhibited no obvious abnormal hematopoiesis indicated that the HSPC defects triggered by dnmt1 mutation were C/ebpa dependent. Conclusions Dnmt1 is required for HSPC maintenance via cebpa regulation during definitive hematopoiesis in zebrafish. Electronic supplementary material The online version of this article (doi:10.1186/s13045-015-0115-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaohui Liu
- CNRS-LIA124, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xiaoe Jia
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, 200031, China.
| | - Hao Yuan
- CNRS-LIA124, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Ke Ma
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, 200031, China.
| | - Yi Chen
- Laboratory of Development and Diseases, State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yi Jin
- Laboratory of Development and Diseases, State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Min Deng
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, 200031, China.
| | - Weijun Pan
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences & Shanghai Jiao Tong University School of Medicine, Shanghai, 200031, China.
| | - Saijuan Chen
- CNRS-LIA124, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Zhu Chen
- CNRS-LIA124, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hugues de The
- CNRS-LIA124, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Equipe Labellisée No. 11 Ligue Nationale Contre le Cancer, Hôpital St. Louis, Université de Paris 7/INSERM/CNRS UMR 944/7212, 75475, Paris, France.
| | - Leonard I Zon
- Stem Cell Program, Hematology/Oncology Program at Children's Hospital Boston, Harvard Medical School, Boston, MA, 02114, USA.
| | - Yi Zhou
- Stem Cell Program, Hematology/Oncology Program at Children's Hospital Boston, Harvard Medical School, Boston, MA, 02114, USA.
| | - Jun Zhou
- CNRS-LIA124, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jun Zhu
- CNRS-LIA124, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Equipe Labellisée No. 11 Ligue Nationale Contre le Cancer, Hôpital St. Louis, Université de Paris 7/INSERM/CNRS UMR 944/7212, 75475, Paris, France.
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32
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Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos. Nat Commun 2015; 6:6315. [PMID: 25697895 PMCID: PMC4339225 DOI: 10.1038/ncomms7315] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 01/19/2015] [Indexed: 01/09/2023] Open
Abstract
DNA methylation undergoes dynamic changes during development and cell differentiation. Recent genome-wide studies discovered that tissue-specific differentially methylated regions (DMRs) often overlap tissue-specific distal cis-regulatory elements. However, developmental DNA methylation dynamics of the majority of the genomic CpGs outside gene promoters and CpG islands has not been extensively characterized. Here we generate and compare comprehensive DNA methylome maps of zebrafish developing embryos. From these maps we identify thousands of developmental stage-specific DMRs (dsDMR) across zebrafish developmental stages. The dsDMRs contain evolutionarily conserved sequences, are associated with developmental genes, and are marked with active enhancer histone post-translational modifications. Their methylation pattern correlates much stronger than promoter methylation with expression of putative target genes. When tested in vivo using a transgenic zebrafish assay, 20 out of 20 selected candidate dsDMRs exhibit functional enhancer activities. Our data suggest that developmental enhancers are a major target of DNA methylation changes during embryogenesis.
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33
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Nagre NN, Subbanna S, Shivakumar M, Psychoyos D, Basavarajappa BS. CB1-receptor knockout neonatal mice are protected against ethanol-induced impairments of DNMT1, DNMT3A, and DNA methylation. J Neurochem 2015; 132:429-442. [PMID: 25487288 DOI: 10.1111/jnc.13006] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 12/21/2022]
Abstract
The significant consequences of ethanol use during pregnancy are neurobehavioral abnormalities involving hippocampal and neocortex malfunctions that cause learning and memory deficits collectively named fetal alcohol spectrum disorder. However, the molecular mechanisms underlying these abnormalities are still poorly understood and therefore warrant systematic research. Here, we document novel epigenetic abnormalities in the mouse model of fetal alcohol spectrum disorder. Ethanol treatment of P7 mice, which induces activation of caspase 3, impaired DNA methylation through reduced DNA methyltransferases (DNMT1 and DNMT3A) levels. Inhibition of caspase 3 activity, before ethanol treatment, rescued DNMT1, DNMT3A proteins as well as DNA methylation levels. Blockade of histone methyltransferase (G9a) activity or cannabinoid receptor type-1 (CB1R), prior to ethanol treatment, which, respectively, inhibits or prevents activation of caspase 3, rescued the DNMT1 and DNMT3A proteins and DNA methylation. No reduction of DNMT1 and DNMT3A proteins and DNA methylation was found in P7 CB1R null mice, which exhibit no ethanol-induced activation of caspase 3. Together, these data demonstrate that ethanol-induced activation of caspase 3 impairs DNA methylation through DNMT1 and DNMT3A in the neonatal mouse brain, and such impairments are absent in CB1R null mice. Epigenetic events mediated by DNA methylation may be one of the essential mechanisms of ethanol teratogenesis. Schematic mechanism of action by which ethanol impairs DNA methylation. Studies have demonstrated that ethanol has the capacity to bring epigenetic changes to contribute to the development of fetal alcohol spectrum disorder (FASD). However, the mechanisms are not well studied. P7 ethanol induces the activation of caspase 3 and impairs DNA methylation through reduced DNA methyltransferases (DNMT1 and DNMT3A) proteins (→). The inhibition or genetic ablation of cannabinoid receptor type-1 or inhibition of histone methyltransferase (G9a) by Bix (-----) or inhibition of caspase 3 activation by Q- quinoline-Val-Asp(Ome)-CH2-O-phenoxy (Q-VD-OPh) () rescue loss of DNMT1, DNMT3A as well as DNA methylation. Hence, the putative DNMT1/DNMT3A/DNA methylation mechanism may have a potential regulatory role in FASD.
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Affiliation(s)
- Nagaraja N Nagre
- Division of Analytical Psychopharmacology, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
| | - Shivakumar Subbanna
- Division of Analytical Psychopharmacology, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
| | - Madhu Shivakumar
- Division of Analytical Psychopharmacology, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
| | - Delphine Psychoyos
- Institute of Biosciences and Technology, Houston, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Balapal S Basavarajappa
- Division of Analytical Psychopharmacology, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA.,New York State Psychiatric Institute, College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA.,Department of Psychiatry, College of Physicians & Surgeons, Columbia University, New York, NY 10032, USA
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Shimoda N, Hirose K, Kaneto R, Izawa T, Yokoi H, Hashimoto N, Kikuchi Y. No evidence for AID/MBD4-coupled DNA demethylation in zebrafish embryos. PLoS One 2014; 9:e114816. [PMID: 25536520 PMCID: PMC4275248 DOI: 10.1371/journal.pone.0114816] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 10/28/2014] [Indexed: 12/20/2022] Open
Abstract
The mechanisms responsible for active DNA demethylation remain elusive in Metazoa. A previous study that utilized zebrafish embryos provided a potent mechanism for active demethylation in which three proteins, AID, MBD4, and GADD45 are involved. We recently found age-dependent DNA hypomethylation in zebrafish, and it prompted us to examine if AID and MBD4 could be involved in the phenomenon. Unexpectedly, however, we found that most of the findings in the previous study were not reproducible. First, the injection of a methylated DNA fragment into zebrafish eggs did not affect either the methylation of genomic DNA, injected methylated DNA itself, or several loci tested or the expression level of aid, which has been shown to play a role in demethylation. Second, aberrant methylation was not observed at certain CpG islands following the injection of antisense morpholino oligonucleotides against aid and mbd4. Furthermore, we demonstrated that zebrafish MBD4 cDNA lacked a coding region for the methyl-CpG binding domain, which was assumed to be necessary for guidance to target regions. Taken together, we concluded that there is currently no evidence to support the proposed roles of AID and MBD4 in active demethylation in zebrafish embryos.
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Affiliation(s)
- Nobuyoshi Shimoda
- Department of Regenerative Medicine, National Institute for Longevity Sciences, National Center for Geriatrics and Gerontology, 35 Gengo, Morioka, Obu, Aichi 474-8522, Japan
- * E-mail:
| | - Kentaro Hirose
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Reiya Kaneto
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Toshiaki Izawa
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Hayato Yokoi
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumi-Dori Amamiya-Machi, Aoba-Ku, Sendai 981-8555, Japan
| | - Naohiro Hashimoto
- Department of Regenerative Medicine, National Institute for Longevity Sciences, National Center for Geriatrics and Gerontology, 35 Gengo, Morioka, Obu, Aichi 474-8522, Japan
| | - Yutaka Kikuchi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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Olsvik PA, Williams TD, Tung HS, Mirbahai L, Sanden M, Skjaerven KH, Ellingsen S. Impacts of TCDD and MeHg on DNA methylation in zebrafish (Danio rerio) across two generations. Comp Biochem Physiol C Toxicol Pharmacol 2014; 165:17-27. [PMID: 24878852 DOI: 10.1016/j.cbpc.2014.05.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/06/2014] [Accepted: 05/18/2014] [Indexed: 12/30/2022]
Abstract
This study aimed to investigate whether dioxin (TCDD) and methylmercury (MeHg) pose a threat to offspring of fish exposed to elevated concentrations of these chemicals via epigenetic-based mechanisms. Adult female zebrafish were fed diets added either 20 μg/kg 2,3,7,8 TCDD or 10 mg/kg MeHg for 47 days, or 10 mg/kg 5-aza-2'-deoxycytidine (5-AZA), a hypomethylating agent, for 32 days, and bred with unexposed males in clean water to produce F1 and F2 offspring. Global DNA methylation, promoter CpG island methylation and target gene transcription in liver of adult females and in 3 days post fertilization (dpf) F1 and F2 embryos were determined with HPLC, a novel CpG island tiling array containing 54,933 different probes and RT-qPCR, respectively. The results showed that chemical treatment had no significant effect on global DNA methylation levels in F1 (MeHg and TCDD) and F2 (MeHg) embryos and only a limited number of genes were identified with altered methylation levels at their promoter regions. CYP1A1 transcription, an established marker of TCDD exposure, was elevated 27-fold in F1 embryos compared to the controls, matching the high levels of CYP1A1 expression observed in F0 TCDD-treated females. This suggests that maternal transfer of TCDD is a significant route of exposure for the F1 offspring. In conclusion, the selected doses of TCDD and MeHg, two chemicals often found in high concentrations in fish, appear to have only modest effects on DNA methylation in F1 (MeHg and TCDD) and F2 (MeHg) embryos of treated F0 females.
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Affiliation(s)
- Pål A Olsvik
- National Institute of Nutrition and Seafood Research, Nordnesboder 1-2, N-5005 Bergen, Norway.
| | - Timothy D Williams
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Hui-shan Tung
- National Institute of Nutrition and Seafood Research, Nordnesboder 1-2, N-5005 Bergen, Norway
| | - Leda Mirbahai
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Monica Sanden
- National Institute of Nutrition and Seafood Research, Nordnesboder 1-2, N-5005 Bergen, Norway
| | - Kaja H Skjaerven
- National Institute of Nutrition and Seafood Research, Nordnesboder 1-2, N-5005 Bergen, Norway
| | - Ståle Ellingsen
- National Institute of Nutrition and Seafood Research, Nordnesboder 1-2, N-5005 Bergen, Norway
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Skjærven KH, Hamre K, Penglase S, Finn RN, Olsvik PA. Thermal stress alters expression of genes involved in one carbon and DNA methylation pathways in Atlantic cod embryos. Comp Biochem Physiol A Mol Integr Physiol 2014; 173C:17-27. [PMID: 24641949 DOI: 10.1016/j.cbpa.2014.03.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 03/04/2014] [Accepted: 03/06/2014] [Indexed: 01/07/2023]
Abstract
One-carbon (1-C) metabolism is essential for normal embryonic development through its regulation of DNA methylation and cell proliferation. With consideration to the potential future anthropogenic oceanic warming, we studied the effects of both acute thermal stress and continuous thermal stress (10°C) during Atlantic cod embryo development on the expression levels of genes associated with the 1-C metabolism, including DNA methyltransferases. We conducted a phylogenetic analysis of vertebrate DNA methyltransferases to determine the number and similarity of DNMT found in Atlantic cod. This analysis revealed that Atlantic cod have one maintenance dnmt (dnmt1) and five de novo DNMTs (dnmt4, dnmt3, dnmt3b, dnmt3aa, dnmt3ab). Stage specific changes in expression levels occurred for all genes analyzed. The effect of acute thermal stress was evaluated during early development. Compared to controls these experiments showed significant alterations in expression levels of several genes, that in some instances were reversed at later stages of development. A significant effect of continuous thermal stress was found in gastrula embryos where lower mRNA expression levels of 1-C metabolism, de novo DNMTs and cell proliferation genes were detected. One exception was the maintenance DNMT, which was only sensitive to acute and not continuous thermal stress. DNA methylation status indicated that blastula embryos were hypomethylated compared to spermatozoa and late gastrula stages. In post-gastrula stage, however, continuous thermal stress resulted in a higher degree of DNA methylation compared to controls. These data reveal that the regulation of epigenetically important transcripts in the 1-C metabolism of Atlantic cod embryos is sensitive to thermal stress.
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Affiliation(s)
- Kaja H Skjærven
- National Institute of Nutrition and Seafood Research (NIFES), PO Box 2029 Nordnes, 5817 Bergen, Norway.
| | - Kristin Hamre
- National Institute of Nutrition and Seafood Research (NIFES), PO Box 2029 Nordnes, 5817 Bergen, Norway
| | - Samuel Penglase
- National Institute of Nutrition and Seafood Research (NIFES), PO Box 2029 Nordnes, 5817 Bergen, Norway; Institute of Biology, University of Bergen, PO Box 7803, 5020 Bergen, Norway
| | - Roderick Nigel Finn
- Institute of Biology, University of Bergen, PO Box 7803, 5020 Bergen, Norway; Institute of Marine Research, PO Box 1870 Nordnes, 5817 Bergen, Norway
| | - Pål A Olsvik
- National Institute of Nutrition and Seafood Research (NIFES), PO Box 2029 Nordnes, 5817 Bergen, Norway
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Zhang X, Li H, Qiu Q, Qi Y, Huang D, Zhang Y. 2,4-Dichlorophenol induces global DNA hypermethylation through the increase of S-adenosylmethionine and the upregulation of DNMTs mRNA in the liver of goldfish Carassius auratus. Comp Biochem Physiol C Toxicol Pharmacol 2014; 160:54-9. [PMID: 24316013 DOI: 10.1016/j.cbpc.2013.11.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 11/26/2013] [Accepted: 11/27/2013] [Indexed: 12/22/2022]
Abstract
Altered DNA methylation is associated with changes in gene expression, signal transduction and stress response after exposure to a wide range of exogenous compounds, and abnormal methylation is a major toxic effect induced by chemicals such as benzene and phenols. 2,4-Dichlorophenol (2,4-DCP), a derivative of phenol, has been classified as a priority pollutant by the US EPA due to its toxic effects on aquatic organisms. However, the effect of 2,4-DCP on DNA methylation and its potential mechanism in fish are rarely understood. The present study aims to figure out whether 2,4-DCP could impact DNA methylation and explore its potential mechanisms by measuring the global DNA methylation levels, S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) contents, the mRNA expression of DNA methyltransferase1 (DNMT1) and DNA methyltransferase3 (DNMT3) in the liver of goldfish Carassius auratus. DNA methylation levels were analyzed using high performance liquid chromatography (HPLC) and MspI/HpaII ethidium bromide assay, SAM and SAH contents were determined by HPLC, the mRNA expression of DNMT1 and DNMT3 was measured by quantitative-PCR (qPCR). The results showed that 2,4-DCP caused global DNA hypermethylation, elevated the methylation levels of CpG islands, increased the SAM and SAH contents, decreased the SAM/SAH ratio, and upregulated the mRNA expression of DNMT1 and DNMT3, while depletion of SAM with Na2SeO3 and inhibition of DNMTs activity with 5-aza-2'-deoxycytidine (5AdC) impaired 2,4-DCP-induced global DNA hypermethylation, suggesting that the increase of SAM contents and upregulation of the mRNA expression of DNMT1 and DNMT3 may play important roles in 2,4-DCP-induced global DNA hypermethylation process. Our report is the first one to show that short-term 2,4-DCP exposure caused the global DNA hypermethylation via altered SAM level and DNMTs expression in fish.
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Affiliation(s)
- Xiaoning Zhang
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Hui Li
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Qian Qiu
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yongmei Qi
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Dejun Huang
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Yingmei Zhang
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
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Williams TD, Mirbahai L, Chipman JK. The toxicological application of transcriptomics and epigenomics in zebrafish and other teleosts. Brief Funct Genomics 2014; 13:157-71. [DOI: 10.1093/bfgp/elt053] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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Analysis of DNA methylation reveals a partial reprogramming of the Müller glia genome during retina regeneration. Proc Natl Acad Sci U S A 2013; 110:19814-9. [PMID: 24248357 DOI: 10.1073/pnas.1312009110] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Upon retinal injury, zebrafish Müller glia (MG) transition from a quiescent supportive cell to a progenitor cell (MGPC). This event is accompanied by the induction of key transcription and pluripotency factors. Because somatic cell reprogramming during induced pluripotent stem cell generation is accompanied by changes in DNA methylation, especially in pluripotency factor gene promoters, we were interested in determining whether DNA methylation changes also underlie MG reprogramming following retinal injury. Consistent with this idea, we found that genes encoding components of the DNA methylation/demethylation machinery were induced in MGPCs and that manipulating MGPC DNA methylation with 5-aza-2'-deoxycytidine altered their properties. A comprehensive analysis of the DNA methylation landscape as MG reprogram to MGPCs revealed that demethylation predominates at early times, whereas levels of de novo methylation increase at later times. We found that these changes in DNA methylation were largely independent of Apobec2 protein expression. A correlation between promoter DNA demethylation and injury-dependent gene induction was noted. In contrast to induced pluripotent stem cell formation, we found that pluripotency factor gene promoters were already hypomethylated in quiescent MG and remained unchanged in MGPCs. Interestingly, these pluripotency factor promoters were also found to be hypomethylated in mouse MG. Our data identify a dynamic DNA methylation landscape as zebrafish MG transition to an MGPC and suggest that DNA methylation changes will complement other regulatory mechanisms to ensure gene expression programs controlling MG reprogramming are appropriately activated during retina regeneration.
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Hirose K, Shimoda N, Kikuchi Y. Transient reduction of 5-methylcytosine and 5-hydroxymethylcytosine is associated with active DNA demethylation during regeneration of zebrafish fin. Epigenetics 2013; 8:899-906. [PMID: 23880758 DOI: 10.4161/epi.25653] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Although dedifferentiation, transformation of differentiated cells into progenitor cells, is a critical step in the regeneration of amphibians and fish, the molecular mechanisms underlying this process, including epigenetic changes, remain unclear. Dot blot assays and immunohistochemical analyses revealed that, during regeneration of zebrafish fin, the levels of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are transiently reduced in blastema cells and cells adjacent to the amputation plane at 30 h post-amputation (hpa), and the level of 5mC, but not 5hmC, is almost restored by 72 hpa. We observed that the dedifferentiated cells showed reduced levels of 5mC and 5hmC independent of cell proliferation by 24 hpa. Furthermore, expressions of the proposed demethylation- and DNA repair-related genes were detected during fin regeneration. Taken together, our findings illustrate that the transient reduction of 5mC and 5hmC in dedifferentiated cells is associated with active demethylation during regeneration of zebrafish fin.
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Affiliation(s)
- Kentaro Hirose
- Department of Biological Science; Graduate School of Science; Hiroshima University; Hiroshima, Japan
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41
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Reprogramming the maternal zebrafish genome after fertilization to match the paternal methylation pattern. Cell 2013; 153:759-72. [PMID: 23663776 DOI: 10.1016/j.cell.2013.04.030] [Citation(s) in RCA: 270] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 03/11/2013] [Accepted: 04/16/2013] [Indexed: 11/23/2022]
Abstract
Early vertebrate embryos must achieve totipotency and prepare for zygotic genome activation (ZGA). To understand this process, we determined the DNA methylation (DNAme) profiles of zebrafish gametes, embryos at different stages, and somatic muscle and compared them to gene activity and histone modifications. Sperm chromatin patterns are virtually identical to those at ZGA. Unexpectedly, the DNA of many oocyte genes important for germline functions (i.e., piwil1) or early development (i.e., hox genes) is methylated, but the loci are demethylated during zygotic cleavage stages to precisely the state observed in sperm, even in parthenogenetic embryos lacking a replicating paternal genome. Furthermore, this cohort constitutes the genes and loci that acquire DNAme during development (i.e., ZGA to muscle). Finally, DNA methyltransferase inhibition experiments suggest that DNAme silences particular gene and chromatin cohorts at ZGA, preventing their precocious expression. Thus, zebrafish achieve a totipotent chromatin state at ZGA through paternal genome competency and maternal genome DNAme reprogramming.
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Alcohol modulates expression of DNA methyltranferases and methyl CpG-/CpG domain-binding proteins in murine embryonic fibroblasts. Reprod Toxicol 2013; 37:40-8. [PMID: 23395981 DOI: 10.1016/j.reprotox.2013.01.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 12/23/2012] [Accepted: 01/23/2013] [Indexed: 12/14/2022]
Abstract
Fetal alcohol syndrome (FAS), presenting with a constellation of neuro-/psychological, craniofacial and cardiac abnormalities, occurs frequently in offspring of women who consume alcohol during pregnancy, with a prevalence of 1-3 per 1000 livebirths. The present study was designed to test the hypothesis that alcohol alters global DNA methylation, and modulates expression of the DNA methyltransferases (DNMTs) and various methyl CpG-binding proteins. Murine embryonic fibroblasts (MEFs), utilized as an in vitro embryonic model system, demonstrated ∼5% reduction in global DNA methylation following exposure to 200mM ethanol. In addition, ethanol induced degradation of DNA methyltransferases (DNMT-1, DNMT-3a, and DNMT-3b), as well as the methyl CpG-binding proteins (MeCP-2, MBD-2 and MBD-3), in MEF cells by the proteasomal pathway. Such degradation could be completely rescued by pretreatment of MEF cells with the proteasomal inhibitor, MG-132. These data support a potential epigenetic molecular mechanism underlying the pathogenesis of FAS during mammalian development.
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Terriente J, Pujades C. Use of Zebrafish Embryos for Small Molecule Screening Related to Cancer. Dev Dyn 2013. [DOI: 10.1002/dvdy.23912] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Javier Terriente
- Department of Experimental and Health Sciences; Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona; PRBB; Barcelona; Spain
| | - Cristina Pujades
- Department of Experimental and Health Sciences; Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona; PRBB; Barcelona; Spain
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Martyniuk CJ, Alvarez S. Proteome analysis of the fathead minnow (Pimephales promelas) reproductive testes. J Proteomics 2012; 79:28-42. [PMID: 23234800 DOI: 10.1016/j.jprot.2012.11.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 10/31/2012] [Accepted: 11/17/2012] [Indexed: 11/28/2022]
Abstract
Proteomics is becoming more widely used as a tool in fish physiology and toxicology and can offer mechanistic insight into organism responses to environmental signals and stressors. Using a LTQ Orbitrap Velos MS/MS, we detected 1075 proteins in the reproductive testis of fathead minnow. Proteins localized to the testis included those with a role in spermatogenesis, DNA repair, gamete meiosis, and proteins that have methylation and phosporylation activity, which are important regulatory mechanisms required for sperm maturation. Enrichment analysis revealed that proteins involved in translation, excision DNA repair, and chromatin remodeling were significantly enriched in the testis (>25% protein coverage of the cellular pathways). Proteins involved in RNA metabolism, spliceosome assembly, metabolism, and DNA unwinding were localized to the testis, and the DEAD (Asp-Glu-Ala-Asp) box RNA-dependent helicase family was well represented in this reproductive tissue. Based upon common detected proteins and functional processes between FHMs and the more ancient sharks, other ray-finned fishes, and mammals, we hypothesize that biological processes involved in the testis (DNA unwinding, RNA processing, spliceosome assembly) have been conserved throughout vertebrate evolution. This study provides the foundation for more in depth proteomics studies investigating the effects of hormones and endocrine disruptors in the teleostean testes.
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Affiliation(s)
- Christopher J Martyniuk
- Canadian Rivers Institute and Department of Biology, University of New Brunswick, Saint John, New Brunswick, Canada E2L 4L5.
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Marandel L, Labbe C, Bobe J, Jammes H, Lareyre JJ, Le Bail PY. Do not put all teleosts in one net: focus on the sox2 and pou2 genes. Comp Biochem Physiol B Biochem Mol Biol 2012; 164:69-79. [PMID: 23142214 DOI: 10.1016/j.cbpb.2012.10.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 10/27/2012] [Accepted: 10/27/2012] [Indexed: 11/16/2022]
Abstract
The Pou2 and Sox2 proteins are major transcription factors for development and cell differentiation. In teleosts, the expression patterns of pou2 or sox2 are different between species from distant families, suggesting different regulatory mechanisms of gene expression. In this study, we assessed the divergences among teleosts, including within closely related species. The pou2 and sox2 gene expression patterns were characterised over several developmental stages in a cyprinid model, i.e., the goldfish, and the potential regulation sites of these genes within teleost conserved regions were localised. During embryonic development, differences in the expression patterns between the goldfish and other teleosts, including zebrafish, were observed for both genes. The in silico analysis of the 5' flanking regions of the pou2 gene showed high conservation within teleosts, whereas the sox2 sequence diverged in tetraodontiforms. Certain putative cis regulatory elements were common to all teleosts, whereas others were found only in cyprinids. The analysis of the DNA methylation patterns of the pou2 and sox2 upstream sequences revealed that the studied CpG sites remained hypomethylated at all stages of embryo development in both genes. In contrast, in the adult fin, the studied CpG sites were hypermethylated in pou2 but not in sox2, suggesting the existence of methylation-sensitive regions in pou2. Overall, although most similarities at the level of the gene regulatory sites were found within cyprinids, the expression pattern of pou2 or sox2 during development differs between cyprinids species.
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Affiliation(s)
- Lucie Marandel
- INRA, UR1037 Fish Physiology and Genomics, Biogenouest, Campus de Beaulieu, F-35000 Rennes, France
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McGee SP, Cooper EM, Stapleton HM, Volz DC. Early zebrafish embryogenesis is susceptible to developmental TDCPP exposure. ENVIRONMENTAL HEALTH PERSPECTIVES 2012; 120:1585-91. [PMID: 23017583 PMCID: PMC3556627 DOI: 10.1289/ehp.1205316] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 09/06/2012] [Indexed: 05/03/2023]
Abstract
BACKGROUND Chlorinated phosphate esters (CPEs) are widely used as additive flame retardants for low-density polyurethane foams and have frequently been detected at elevated concentrations within indoor environmental media. OBJECTIVES To begin characterizing the potential toxicity of CPEs on early vertebrate development, we examined the developmental toxicity of four CPEs used in polyurethane foam: tris(1,3-dichloro-2-propyl) phosphate (TDCPP), tris(2-chloroethyl) phosphate (TCEP), tris(1-chloro-2-propyl) phosphate (TCPP), and 2,2-bis(chloromethyl)propane-1,3-diyl tetrakis(2-chlorethyl) bis(phosphate) (V6). METHODS Using zebrafish as a model for vertebrate embryogenesis, we first screened the potential teratogenic effects of TDCPP, TCEP, TCPP, and V6 using a developmental toxicity assay. Based on these results, we focused on identification of susceptible windows of developmental TDCPP exposure as well as evaluation of uptake and elimination of TDCPP and bis(1,3-dichloro-2-propyl)phosphate (BDCPP, the primary metabolite) within whole embryos. Finally, because TDCPP-specific genotoxicity assays have, for the most part, been negative in vivo and because zygotic genome remethylation is a key biological event during cleavage, we investigated whether TDCPP altered the status of zygotic genome methylation during early zebrafish embryogenesis. RESULTS Overall, our findings suggest that the cleavage period during zebrafish embryogenesis is susceptible to TDCPP-induced delays in remethylation of the zygotic genome, a mechanism that may be associated with enhanced developmental toxicity following initiation of TDCPP exposure at the start of cleavage. CONCLUSIONS Our results suggest that further research is needed to better understand the effects of a widely used and detected CPE within susceptible windows of early vertebrate development.
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Affiliation(s)
- Sean P McGee
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, South Carolina 29208, USA
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Strobl-Mazzulla PH, Marini M, Buzzi A. Epigenetic landscape and miRNA involvement during neural crest development. Dev Dyn 2012; 241:1849-56. [PMID: 22972707 DOI: 10.1002/dvdy.23868] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2012] [Indexed: 11/06/2022] Open
Abstract
The neural crest (NC) is a multipotent, migratory cell population that arises from the dorsal neural fold of vertebrate embryos. NC cells migrate extensively and differentiate into a variety of tissues, including melanocytes, bone, and cartilage of the craniofacial skeleton, peripheral and enteric neurons, glia, and smooth muscle and endocrine cells. For several years, the gene regulatory network that orchestrates NC cells development has been extensively studied. However, we have recently begun to understand that epigenetic and posttranscriptional regulation, such as miRNAs, plays important roles in NC development. In this review, we focused on some of the most recent findings on chromatin-dependent mechanisms and miRNAs regulation during vertebrate NC cells development.
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Affiliation(s)
- Pablo H Strobl-Mazzulla
- Laboratory of Developmental Biology, Instituto de Investigaciones Biotecnológicas- Instituto Tecnológico de Chascomús, Chascomús, Argentina.
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Campos C, Valente LMP, Fernandes JMO. Molecular evolution of zebrafish dnmt3 genes and thermal plasticity of their expression during embryonic development. Gene 2012; 500:93-100. [PMID: 22450363 DOI: 10.1016/j.gene.2012.03.041] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 02/15/2012] [Accepted: 03/04/2012] [Indexed: 01/25/2023]
Abstract
DNA reprogramming by DNA (cytosine-5)-methyltransferases (dnmts) after fertilisation is a dynamic mechanism that is essential for early development. Amongst the three types of dnmt genes in vertebrates, dnmt3 is the one involved in de novo methylation and comprises three related genes, termed dnmt3a, dnmt3b and dnmt3L in mammals. Zebrafish (Danio rerio) has six dnmt3 paralogues, which have hitherto been termed dnmt3 to dnmt8. Bayesian inference of phylogeny and synteny analysis revealed that dnmt6 and dnmt8 are in fact duplicated dnmt3a genes, whereas the other paralogues are closely related to dnmt3b. Hence, we propose a revised nomenclature that more accurately reflects the relationship amongst zebrafish dnmt3 genes. Both dnmt3a genes were ubiquitously expressed in adult tissues, whilst the various dnmt3b paralogues were differentially expressed, with notably high expression levels in the gonads. The influence of embryonic temperature on dnmt3 expression was investigated, since it is known to have a significant impact in early development and a long-term effect on growth in some teleost species. Embryos were incubated at 23, 27 or 31°C and samples collected at six developmental stages from blastula until protruding mouth. Dnmt3 expression during early development was remarkably dynamic. In particular, mRNA levels of the two dnmt3a genes showed a marked increase throughout development and several significant differences in dnmt3a and dnmt3b transcript levels were found between temperatures at the same developmental point. Taken together, our data indicate that dnmt3 paralogues are diverging and that dnmt3a and dnmt3b may play different roles in thermal epigenetic regulation of gene expression during early development.
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Mudbhary R, Sadler KC. Epigenetics, development, and cancer: zebrafish make their mark.. ACTA ACUST UNITED AC 2011; 93:194-203. [PMID: 21671358 DOI: 10.1002/bdrc.20207] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Zebrafish embryos are an exceptional system for studying vertebrate development. Historically, studies using zebrafish to uncover key players in developmentally regulated gene expression have entailed detailed analysis of transcription factors. It is now apparent that epigenetic modifications of both DNA and histone tails are equally important in the regulation of gene expression during development. As such, blocking the function of key epigenetic modifiers impairs development, albeit with surprising tissue specificity. For instance, DNA methylation is an important epigenetic mark that is depleted in embryos lacking dnmt1 and uhrf1. These embryos display developmental defects in the eye, liver, pancreas, and larval lethality. Interestingly, human tumors derived from these same organs have aberrant changes in DNA methylation and altered expression of genes that are thought to contribute to formation of these cancers. These observations have provided a mechanistic basis for treating cancer with drugs that block the enzymes that facilitate DNA and histone modifications. Thus, it is important to understand the consequences of targeting these factors in a whole animal. We review the use of zebrafish for probing the genetic, cellular, and physiological response to alterations in the epigenome and highlight exciting data illustrating that epigenetic studies using zebrafish can inform and impact cancer biology.
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Affiliation(s)
- Raksha Mudbhary
- Division of Liver Diseases, Department of Medicine, Mount Sinai School of Medicine, New York, New York, USA
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Goll MG, Halpern ME. DNA methylation in zebrafish. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 101:193-218. [PMID: 21507352 DOI: 10.1016/b978-0-12-387685-0.00005-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
DNA methylation is crucial for normal development and cellular differentiation in many large-genome eukaryotes. The small tropical freshwater fish Danio rerio (zebrafish) has recently emerged as a powerful system for the study of DNA methylation, especially in the context of development. This review summarizes our current knowledge of DNA methylation in zebrafish and provides evidence for the general conservation of this system with mammals. In addition, emerging strategies are highlighted that use the fish model to address some of the key unanswered questions in DNA methylation research.
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Affiliation(s)
- Mary G Goll
- Developmental Biology Program, Sloan-Kettering Institute, New York, USA
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