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EPIGENETICS IN AQUACULTURE
This essential guide will allow you to understand how new developments in our knowledge of epigenetic mechanisms and epigenetic inheritance can be applied to improve aquaculture production and aquatic resource management and conservation.
Epigenetics is the study of heritable changes in gene expression that are independent of alterations in the nucleotide sequence. It integrates genomic and environmental influences to shape the phenotype. Epigenetics is a field with particular relevance to aquaculture and aquatic organisms, since it underpins acclimatory responses to diverse and changing environments and inheritance of desired phenotypes.
Epigenetics in Aquaculture provides a comprehensive introduction to epigenetics, epigenetic mechanisms, epigenetic inheritance, and research methods. It also provides the current state of the art on research and development on epigenetics in the major functions of aquatic organisms in the framework of aquaculture production. The fact that aquaculture is the fastest-growing sector of food production makes the book especially timely.
Readers will also find:
- Detailed treatment of subjects including aquatic faunal reproduction, sex determination, growth regulation, nutritional programming, disease resistance, stress response and much more
- Survey of current research lacunae and the projected future of the discipline
- An authorial team of internationally renowned experts
Epigenetics in Aquaculture is a valuable reference for researchers, biologists and advanced students in any area of marine science, oceanography, aquaculture, environmental science, and food production.
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Table of Contents
Cover
Title Page
Copyright Page
Dedication Page
About the Editors
List of Contributors
Preface
Acknowledgments
Part I: Theoretical and Practical Bases of Epigenetics in Aquaculture
1 The Potential Role of Epigenetics in Aquaculture: Insights from Different Taxa to Diverse Teleosts
1.1 Introduction
1.2 Key Players of Epigenetics
1.3 Divergent Epigenetic Mechanisms from Different Taxa to Diverse Teleosts
1.4 The Roles and Applications of Epigenetics
1.5 Conclusion and Perspectives
Acknowledgments
References
2 Transcriptional Epigenetic Mechanisms in Aquatic Species
2.1 Epigenetic Mechanisms as Modulators of Transcription
2.2 Transcriptional Epigenetic Mechanisms in Aquatic Species
2.3 Modulation of Biological Functions by Transcriptional Epigenetic Mechanisms in Aquaculture Species of Interest
2.4 Conclusions and Perspectives
Acknowledgments
References
3 Epigenetic Regulation of Gene Expression by Noncoding RNAs
3.1 General Introduction
3.2 Major Types of ncRNAs
3.3 Roles of ncRNA in Key Processes of Teleosts
3.4 ncRNAs as Biomarkers and Future Perspectives
Acknowledgments
References
4 Epigenetic Inheritance in Aquatic Organisms
4.1 Introduction
4.2 Epigenetic Reprogramming of Embryo and Germline Cells
4.3 Heritable Effects of Environmental Stress
4.4 Past Exposure and Future Phenotypic Consequences in Aquatic Species
4.5 Conclusions and Perspectives
References
5 Environmental Epigenetics in Fish: Response to Climate Change Stressors
5.1 Overview of Climate Change and Environmental Stressors
5.2 Epigenetic Response to Climate Change
5.3 Conclusions and Future Perspectives
Acknowledgments
References
6 Analytical Methods and Tools to Study the Epigenome
6.1 Introduction
6.2 Recommendations for Choosing a Method to Study the Epigenome
6.3 Methods and Tools to Analyze Epigenetic Modifications
6.4 Bioinformatics Analysis
6.5 Databases and Other Public Resources
6.6 Conclusions and Outlook
Acknowledgments
References
Part II: Epigenetics Insights from Major Aquatic Groups
7 Epigenetics in Sexual Maturation and Gametes of Fish
7.1 Introduction
7.2 Epigenetics During Spermatogenesis and Oogenesis
7.3 Epigenetic Changes in the Gametes Triggered by Environmental Constraints
7.4 Conclusion
Acknowledgments
References
8 Epigenetics in Sex Determination and Differentiation of Fish
8.1 Introduction
8.2 Epigenetics and Sex Chromosome Evolution
8.3 Epigenetics and Sex Determination
8.4 Epigenetic Regulation of Sex Differentiation in Gonochoristic Species and Sex Change in Hermaphrodites
8.5 Transgenerational Epigenetic Sex Reversal
8.6 Conclusions and Future Perspectives
Acknowledgments
References
9 Epigenetics in Fish Growth
9.1 Myogenesis in Teleosts
9.2 Skeletogenesis in Teleosts
9.3 Epigenetic Regulation of Sexually Dimorphic Growth
9.4 Epigenetic Control of the Skeleton in Teleosts
9.5 Mitochondrial Epigenetics
9.6 Conclusion
Acknowledgments
References
10 Epigenetics in Fish Nutritional Programming
10.1 Epigenetic Basis of Nutritional Programming
10.2 Nutritional Programming
10.3 Key Nutrients and Metabolites for Epigenetic Mechanisms
10.4 Case Examples
10.5 Conclusions and Perspectives for Nutritional Programming in Aquaculture
Acknowledgments
References
11 Microbiome, Epigenetics and Fish Health Interactions in Aquaculture
11.1 Introduction
11.2 The Fish Microbiome in Aquaculture
11.3 Microbiome‐Epigenome Interactions
11.4 Gaps in Knowledge and Future Research Avenues
11.5 Conclusions
References
12 Epigenetics of Stress in Farmed Fish
12.1 Introduction
12.2 Stress and Stress Response
12.3 Is There an Epigenetics of Stress in Cultured Fish?
12.4 The Neuroepigenetics of Stress: Fishing with Mammalian Models
12.5 Epigenetic Biomonitoring of Stress
12.6 Conclusions
Acknowledgments
References
13 Epigenetics in Hybridization and Polyploidization of Aquatic Animals
13.1 Hybridizing and Hybridization
13.2 Polyploidy and Polyploidization
13.3 Epigenetic Changes and Effects During Hybridization and Polyploidization in Aquatic Animals
13.4 Association of Epigenetic Changes with Heterosis
13.5 Conclusions and Future Perspectives
Acknowledgments
References
14 Epigenetics in Aquatic Toxicology
14.1 Introduction
14.2 Epigenetic Endpoints in Aquatic Toxicology Studies
14.3 Epigenetics During Early Development Related to Toxicology
14.4 Multigenerational and Transgenerational Toxicology
14.5 Epigenetics in Ecological Risk Assessment
14.6 Rapid Evolution
14.7 Epigenetics in Aquaculture
14.8 Conclusion and Perspectives
References
15 Epigenetics in Mollusks
15.1 Introduction
15.2 DNA Modifications in Mollusk Species
15.3 Chromatin Conformation and Histone Modifications/Variants in Mollusks
15.4 Noncoding RNAs in Mollusks
15.5 Epigenetic Responses to Environmental Fluctuations in Mollusks
15.6 Mechanisms of Meiotic Epigenetic Inheritance in Mollusks and Their Impact in Evolution
15.7 Perspectives
15.8 General Conclusions
References
16 Epigenetics in Crustaceans
16.1 Introduction
16.2 Epigenetics Research with Brine Shrimps and Copepods
16.3 Epigenetics Research with Water Fleas
16.4 Epigenetics Research with Amphipods
16.5 Epigenetics Research with Freshwater Crayfish
16.6 Epigenetics Research with Shrimps and Crabs
16.7 State of the Art of Epigenetics Research in Crustaceans
16.8 Potential Application of Epigenetics in Crustacean Aquaculture
References
17 Epigenetics in Algae
17.1 Introduction: What Are Algae
17.2 Algae Epigenetics
17.3 Environmental Stress Alters Microalgae Epigenomes
17.4 Conclusions and Perspectives
References
Part III: Implementation of Epigenetics in Aquaculture
18 Development of Epigenetic Biomarkers in Aquatic Organisms
18.1 Biomarkers
18.2 Epigenetic Biomarkers
18.3 Development of Epigenetic Biomarkers
18.4 Epigenetic Biomarkers in Aquatic Organisms and their Applications in Aquaculture
18.5 Future Perspectives
18.6 Concluding Remarks
Acknowledgments
References
19 Genetics and Epigenetics in Aquaculture Breeding
19.1 Overview
19.2 Breeding in Aquaculture and Evolution of Genetic Markers
19.3 Epigenetics and Missing Heritability
19.4 Transgenerational Inheritance of Epigenetic Marks
19.5 Epigenetic Marks – Possible Biomarkers to Improve Breeding
19.6 Association Analysis and Search for Epigenetic Biomarkers
19.7 Concluding Remarks
References
20 Epigenetics in Aquaculture
20.1 Introduction
20.2 Knowledge Gaps
20.3 Challenges
20.4 Prospects
Acknowledgments
References
Index-Species
Index-Subjects
End User License Agreement
List of Tables
Chapter 1
Table 1.1 Differences and similarities in DNA methylation and related key p...
Table 1.2 Comparative outcomes resulting from the gene knockout of cytosine...
Table 1.3 Change of nutrition‐/muscle‐related epigenetic markers in relatio...
Chapter 2
Table 2.1 A simplified overview of key molecular epigenetic mechanisms and ...
Table 2.2 Fish species for which epigenetic mechanisms have been studied.
Table 2.3 Invertebrate species for which epigenetic mechanisms have been st...
Chapter 3
Table 3.1 Most commonly used databases and software programs.
Chapter 4
Table 4.1 Epigenetic inheritance of environmentally induced effects in fish...
Chapter 5
Table 5.1 Effects of environmental stressors and epigenetic/phenotypic chan...
Chapter 6
Table 6.1 Classification of epigenetic methods according to the type of mod...
Table 6.2 Comparison of common methods for assessing epigenetic modificatio...
Chapter 7
Table 7.1 Impact of external factors on the epigenetic profile of fish gona...
Chapter 16
Table 16.1 Crustaceans produced in world aquaculture for human consumption....
Chapter 17
Table 17.1 DNA methylation in microalgae species.
Table 17.2 Top‐Down Mass. Spectrometry characterization of
C. reinhardtii
h...
Table 17.3 Reverse BLAST was used to identify chromatin‐modifying enzymes fo...
List of Illustrations
Chapter 1
Figure 1.1 Phylogenetic epigenetics showing the common and divergent epigene...
Figure 1.2 Environment (internal vs. external) where fertilization and early...
Figure 1.3 Genetic and epigenetic effects of parents across generations. Off...
Chapter 2
Figure 2.1 DNA methylation landscape of vertebrate and invertebrate genomes....
Figure 2.2 Histone modifications (a) and simplified diagram of chromatin sta...
Figure 2.3 Key players that contribute to create, read, and erase specific e...
Figure 2.4 Epigenetic modifications linking environmental cues with physiolo...
Chapter 3
Figure 3.1 Overview of epigenetic regulation of gene expression. Arrows and ...
Figure 3.2 Overview of PubMed publications comprising sncRNA work and sncRNA...
Figure 3.3 Schematic overview of RNA types divided into noncoding and coding...
Figure 3.4 Five different types of the genomic organization of miRNA genes....
Figure 3.5 Summary of analysis pipeline from data acquisition to sncRNA expr...
Figure 3.6 Bioanalyzer files presenting total RNA extractions from four diff...
Figure 3.7 Categories of lncRNA. lncRNAs are classified according to their g...
Figure 3.8 Different types of lncRNA regulatory roles during gene expression...
Figure 3.9 miRNA abundance during early teleost development. (a) Total read ...
Figure 3.10 Overview of reported miRNAs involved in teleost development embr...
Figure 3.11 5S/18S abundance in the gonads. (a) Total RNA electropherograms ...
Figure 3.12 sncRNA size distribution from teleost developmental stages and g...
Figure 3.13 Target sites of miR‐19a Zhao et al. [200], miR‐148 Chu et al. [1...
Figure 3.14 Schematic overview of miRs acting in toll‐like receptor (TLR) si...
Figure 3.15 Schematic overview of miRs acting on the NOD‐like receptor (NLR)...
Figure 3.16 Schematic overview of miRs acting in the RLR signaling pathway. ...
Chapter 4
Figure 4.1 A schematic showing gene–environment interactions and emergence o...
Figure 4.2 Schematic showing life history stages sensitive to external stres...
Figure 4.3 DNA methylation reprogramming model during embryogenesis (left pa...
Figure 4.4 Initial exposure and generations of the exposed organisms in mice...
Figure 4.5 Environmental stressors cause somatic effects in the exposed orga...
Figure 4.6 Hypothetical cumulative transgenerational effects of BPA or EE2 e...
Figure 4.7 Design of transgenerational laboratory experiments in fish. Expos...
Figure 4.8 Environmental stressors (biotic and abiotic) can induce adaptive ...
Chapter 5
Figure 5.1 A summary of environmental stress on sex differentiation in fish....
Chapter 6
Figure 6.1 Common detection methods used to assess cytosine methylation. (a)...
Figure 6.2 Common bisulfite‐based techniques coupled to NGS. (a) Reduced rep...
Figure 6.3 Common detection methods used to study histone PTMs. (a) Chromati...
Chapter 7
Figure 7.1 DNA methylation dynamics in fish PGCs and gametes. (a) Percentage...
Chapter 8
Figure 8.1 Sex chromosome and autosome fusions create multiple sex chromosom...
Figure 8.2 Sex reversal in Chinese tongue sole (
Cynoglossus semilaevis
). (a)...
Figure 8.3 Differentially methylated and differentially expressed genes in t...
Figure 8.4 Transgenerational epigenetic inheritance of sexual reversal in Ch...
Figure 8.5 Dosage compensation of the Z chromosome in neomale testes. (a) Me...
Chapter 9
Figure 9.1 The process of myofiber formation in vertebrates. The muscle regu...
Figure 9.2 Transverse 3D section of the mid trunk during somitogenesis in fi...
Figure 9.3 Nile tilapia mitochondrial genome and its 5mC methylation map. Th...
Chapter 10
Figure 10.1 Critical windows for nutritional programming and alterations in ...
Figure 10.2 Broodstock nutrition and potential long‐term effects in offsprin...
Figure 10.3 Key nutrients and metabolites influencing epigenetic mechanisms....
Chapter 11
Figure 11.1 Number of articles published on the microbiome or epigenome for ...
Figure 11.2 Relative abundance of different bacterial taxa in the gut microb...
Figure 11.3 Schematic representation of the different host‐related extrinsic...
Figure 11.4 Challenges and opportunities for aquaculture of epigenetic progr...
Chapter 12
Figure 12.1 Stress responses induced by common aquaculture stressors and ass...
Figure 12.2 Genes considered relevant candidates for epigenetic studies in f...
Chapter 13
Figure 13.1 Schematic diagram of hybridizing, hybridization, polyploidy, and...
Figure 13.2 Epigenetic changes during hybridization and polyploidization in ...
Chapter 14
Figure 14.1 Articles published within the last 42 years with search terms re...
Figure 14.2 Schematic diagram of epigenetic mechanisms involved in aquatic t...
Figure 14.3 Bar graph depicting the differential methylation relative to con...
Figure 14.4 (a) Hypermethylation of histone lysine residues in the presence ...
Figure 14.5 Long noncoding RNA characteristics in large yellow croaker. (a) ...
Figure 14.6 True transgenerational exposure occurs in the F2 and F3 generati...
Chapter 15
Figure 15.1 Impact of DNA methylation during the development of the cupped o...
Figure 15.2 Histone modifications during the development of the cupped oyste...
Figure 15.3 Examples of NcRNAs mechanisms in the pearl oyster
P. fucata
. (a)...
Figure 15.4 Epigenetic mechanisms' interaction in the memory formation of
Ap
...
Figure 15.5 Epigenetic response to climate change and habitat features in mo...
Figure 15.6 Epigenetic response in acclimatization in mollusks. (a) Heat map...
Figure 15.7 Examples of epigenetic response to chemical pollution in mollusk...
Figure 15.8 Epigenetic modifications in response to
Schistosoma mansoni
infe...
Figure 15.9 Epigenetic mechanisms in multigenerational effects in mollusks. ...
Chapter 16
Figure 16.1 Stimulation and transgenerational inheritance of trained immunit...
Figure 16.2 Transgenerational inheritance of phloroglucinol‐induced resistan...
Figure 16.3 DNA methylation in
Daphnia
water fleas and age‐ and sex‐related ...
Figure 16.4 Changes of epigenetic signatures and chromatin structure in
Daph
...
Figure 16.5 DNA methylation in marbled crayfish (
Procambarus virginalis)
. (a...
Figure 16.6 Dynamics of DNA methylation during the life cycle of marbled cra...
Figure 16.7 Genetic uniformity and phenotypic and epigenetic diversity in ma...
Figure 16.8 Comparison of fecundity, DNA content, and DNA methylation betwee...
Figure 16.9 Survival and alterations of heart rate and DNA methylation in sh...
Figure 16.10 Expression of sex‐determining
CFSH
gene and associated DNA meth...
Chapter 17
Figure 17.1 Images of model algae species. (a)
Chlamydomonas reinhardtii
,...
Figure 17.2 The tree of life can be modeled in several different ways, but i...
Figure 17.3 Harmful algal blooms occur when algae rapidly proliferate, consu...
Figure 17.4 DNA methylation in the CpG context for all algae species measure...
Figure 17.5 Histone PTMs identified in
P. tricornutum
(upper) and
Thalassios
...
Chapter 18
Figure 18.1 General systematic procedure for epigenetic biomarker (EB) devel...
Figure 18.2 Main categories of machine learning (ML) methods. For all three ...
Figure 18.3 Supervised ML methods for key traits and processes of aquatic or...
Figure 18.4 Basic concepts for ML. (a) Workflow for building the optimal mod...
Figure 18.5 Development and application of epigenetic biomarkers in aquatic ...
Figure 18.6 Candidate transgenerational epigenetic biomarkers (EBs) for high...
Chapter 19
Figure 19.1 The compound annual growth rate for aquaculture, poultry, pig, s...
Figure 19.2 Diagram depicting the transmission of various inherited elements...
Chapter 20
Figure 20.1 Some of the internal factors (above the fish) and external facto...
Figure 20.2 Major stages (in uppercase) and processes (in lowercase) of the ...
Figure 20.3 Epigenetic integration in aquaculture. First, selection for epig...
Figure 20.4 Identification of an epigenetic marker with both prognostic and ...
Figure 20.5 Development of epigenetic markers to aid in broodstock selection...
Guide
Cover Page
Title Page
Copyright Page
Dedication Page
About the Editors
List of Contributors
Preface
Acknowledgments
Table of Contents
Begin Reading
Index-Species
Index
Wiley End User License Agreement
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Epigenetics in Aquaculture
Edited by
Francesc Piferrer
Institute of Marine Sciences (ICM)
Spanish National Research Council (CSIC)
Barcelona, Spain
Han‐Ping Wang
Ohio Center for Aquaculture Research and Development
The Ohio State University
Piketon, Ohio, USA
This edition first published 2023© 2023 John Wiley & Sons Ltd
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The right of Francesc Piferrer and Han‐ping Wang to be identified as the editorial material in this work has been asserted in accordance with law.
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Library of Congress Cataloging‐in‐Publication DataNames: Piferrer, Francesc, 1960– editor. | Wang, Han‐Ping, 1958– editor.Title: Epigenetics in aquaculture / [edited by] Francesc Piferrer, CSIC, Institute of Marine Sciences, Barcelona, Spain, Han‐Ping Wang, Ohio Center for Aquaculture Research and Development, The Ohio State University, Piketon, Ohio, USA.Description: First edition. | Chichester, West Sussex, UK ; Hoboken : John Wiley & Sons Ltd., 2023. | Includes bibliographical references and index.Identifiers: LCCN 2023000224 (print) | LCCN 2023000225 (ebook) | ISBN 9781119821915 (Hardback) | ISBN 9781119821922 (adobe pdf) | ISBN 9781119821939 (epub)Subjects: LCSH: Aquacultural biotechnology. | Epigenetics.Classification: LCC SH136.B56 P54 2023 (print) | LCC SH136.B56 (ebook) | DDC 639.8–dc23/eng/20230215LC record available at https://lccn.loc.gov/2023000224LC ebook record available at https://lccn.loc.gov/2023000225
Cover Design: WileyCover Image: © Alisles/Adobe Stock Photos; Adobe Express; phonlamaiphoto/Adobe Stock Photos; issaronow/Adobe Stock Photos; Ahmed.yosri/Wikimedia Common
Dedication
Dedicated to Marta Burcet, for her affection and love – Francesc Piferrer.
To my grandboy Harrison Wang, who arrived in the world with this book and brings us so much laughter and energy, and his parents, Alan Wang and Kathy Zhang, for their understanding of the influences of parental care, nutrition, and other environmental factors on offspring’s early development and beyond – Han‐Ping Wang.
About the Editors
Francesc Piferrer obtained his PhD in biology in 1990 and currently is research professor and deputy‐director at the Institute of Marine Sciences (CSIC) in Barcelona. His traditional field of research is sexual development in fish. He has made relevant contributions to our understanding of how genetic, epigenetic, and environmental factors determine whether an animal will differentiate as male or female. In the last years, he has been studying environmental influences on the establishment of epimutations and the contribution of epigenetic inheritance to enable animals to cope with a changing environment. He is significantly contributing to the integration of epigenetics in aquaculture research. His lab developed the world’s first epigenetic test to predict sex and the first epigenetic clock in fish. He organized the first epigenetics session in an international aquaculture conference. Dr. Piferrer has been the principal investigator in numerous research projects and contracts with companies, having signed two patents. He is the editor of 2 previous books and the author of more than 160 articles in indexed journals and has directed 14 doctoral theses. He has carried out management tasks at the Catalan Society of Biology and the Spanish Ministry of Science and Innovation and provided advice to the European Commission and the Council of Europe. He was awarded the XII Jacumar Prize for the Best Aquaculture Research in 2013 and the Research Award of the Official College of Biologists in 2020. In 2019, he became a full member of the Royal Academy of Sciences and Arts of Barcelona.
Dr. Han‐Ping Wang is principal scientist/research professor and director of the Ohio Center for Aquaculture Research and Development at The Ohio State University (OSU). He has provided leadership as project director for about 75 research projects in the areas of breeding, genetics, sex control, and epigenetics in fish and aquaculture. He was the first to achieve success in controlled breeding and culture of Reeves shad, and in developing large‐scale populations of all‐male bluegill, all‐female yellow perch, and superior perch strains. He also completed whole genome sequencing of these two species. Dr. Wang has published more than 170 papers in prestigious international journals and proceedings as a principal author or corresponding author and three books, including this book and Sex Control in Aquaculture. Dr. Wang has advised more than 30 PhD students and post‐doctoral researchers and organized and chaired 2 international conferences. He has served as a member of the US Department of Agriculture (USDA)‐NCRAC Research and Technical Committee and a research review panellist of the USDA and the US National Oceanic and Atmospheric Administration (NOAA). Dr. Wang has been awarded approximately $11 million grants for his research and outreach. He has won 6 S&T Achievement Awards, and 10 “best paper” and other professional awards from national and international agencies.
List of Contributors
Anne‐Catrin AdamFeed and Nutrition, Institute of Marine Research (IMR)Bergen, Norway
Dafni AnastasiadiThe New Zealand Institute for Plant and Food Research Limited, Nelson Research Centre, Nelson, New Zealand
Ishrat AnkaBiosciences Department, Faculty of Science and Engineering, Swansea University, Swansea, UK
Jana AsselmanLaboratory for Environmental Toxicology and Aquatic Ecology, Ghent University, Ghent, Belgium
Anne BeemelmannsInstitut de Biologie Intégrative et des Systèmes (IBIS)Université Laval, Québec City, Quebec, Canada
Ramji K. BhandariDepartment of Biology, University of North Carolina Greensboro, Greensboro, NC, USA
Susanne M. BranderCoastal Oregon Marine Experiment Station, Department of Fisheries, Wildlife, and Conservation SciencesOregon State University, Newport, OR, USA
Sofia ConsuegraBiosciences Department, Faculty of Science and Engineering, Swansea University, Swansea, UK
Marit EspeFeed and Nutrition, Institute of Marine Research (IMR)Bergen, Norway
Manon FalletMan‐Technology‐Environment Research Centre (MTM)School of Science and Technology, Örebro UniversityÖrebro, Sweden
Bo FengYellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
Jorge M.O. FernandesFaculty of Biosciences and Aquaculture, Nord UniversityBodø, Norway
Ignacio FernándezCentro Oceanográfico de Vigo, Instituto Español de Oceanografía (IEO‐CSIC), Spanish National Research Council, Vigo, Spain
Paulo GavaiaCentro de Ciências do Mar (CCMAR) and Department of Biomedical Sciences and Medicine, Universidade do Algarve, Faro, Portugal
Jian‐Fang GuiState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Wuhan, China
Bruno GuinandInstitut des Sciences de l’Evolution de MontpellierUniversity of Montpellier, CNRS, IRD, EPHEMontpellier, France
María Paz HerráezDepartment of Molecular Biology, Faculty of Biology and Environmental Sciences, Universidad de LeónLeón, Spain
Timothy A. HoreDepartment of Anatomy, University of OtagoDunedin, New Zealand
Sara J. HuttonDepartment of Environmental and Molecular ToxicologyOregon State University, Corvallis, OR, USA
Ioannis KonstantinidisFaculty of Biosciences and Aquaculture, Nord UniversityBodø, Norway
Catherine LabbéINRAE, Department of Fish Physiology and GenomicsCampus de Beaulieu, Rennes, France
Audrey LaurentINRAE, Department of Fish Physiology and GenomicsCampus de Beaulieu, Rennes, France
Qian LiuYellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
Marta Lombó AlonsoDepartment of Molecular Biology, Faculty of Biology and Environmental Sciences, Universidad de LeónLeón, SpainDipartimento Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
Wenxiu MaYellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
Shokouoh Makvandi‐NejadDepartment of Immunology and Virology, Norwegian Veterinary Institute, Ås, Norway
Jan A. MennigenDepartment of Biology, University of Ottawa, OttawaOntario, Canada
Hooman MoghadamBreeding and Genetics, Benchmark Genetics Norway ASBergen, Norway
Laia Navarro‐MartínInstitute of Environmental Assessment and Water Research, IDAEA‐CSIC, Spanish National Research Council (CSIC), Barcelona, Spain
Artem V. NedoluzhkoFaculty of Biosciences and Aquaculture, Nord UniversityBodø, NorwayPaleogenomics Laboratory, European University at Saint Petersburg, Saint Petersburg, Russia
Oscar Ortega‐RecaldeDepartment of Anatomy, University of Otago, DunedinNew Zealand
Francesc PiferrerInstitute of Marine Sciences, Spanish National Research Council (CSIC), Barcelona, Spain
Takaya SaitoFeed and Nutrition, Institute of Marine Research (IMR)Bergen, Norway
Athanasios SamarasDepartment of Biology, University of Crete, HeraklionCrete, Greece
Elena SarropoulouInstitute of Marine Biology, Biotechnology, and Aquaculture, Hellenic Centre for Marine ResearchHraklion, Crete, Greece
Changwei ShaoYellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
Zhi‐Gang ShenCollege of Fisheries, Huazhong Agricultural UniversityWuhan, China
Kaja H. SkjærvenFeed and Nutrition, Institute of Marine Research (IMR)Bergen, Norway
Christina R. SteadmanEarth & Environmental Sciences Division, Climate, Ecology & Environment Group, Los Alamos National laboratory, Los Alamos, NM, USA
Lili TangYellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
Günter VogtFaculty of Biosciences, University of HeidelbergHeidelberg, Germany
Rune WaagbøFeed and Nutrition, Institute of Marine Research (IMR)Bergen, Norway
Han‐Ping WangOhio Center for Aquaculture Research and DevelopmentThe Ohio State University South CentersPiketon, OH, USA
Qian WangYellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
Tamsyn Uren WebsterBiosciences Department, Faculty of Science and Engineering, Swansea University, Swansea, UK
Yue YuCollege of Fisheries, Huazhong Agricultural University, Wuhan, China
Xiaona ZhaoYellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
Li ZhouState Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Wuhan, China
Preface
Aquaculture is the fastest food production sector in the world and prospects are that this position will be maintained for years to come. According to data from the Food and Agriculture Organization (FAO) of the United Nations, in 2020 global aquaculture production reached a record of 122.6 million tons worth USD 281.5 billion. Animals accounted for 87.5 million tons while algae comprised 35.1 million tons. However, aquaculture must become more sustainable to meet the growing demand for aquatic foods of an ever‐increasing human population. Thus, improved aquaculture production requires further technical innovations, including more focus on breeding programs, feed utilization, well‐being, and disease control. Similar to any other food production system, aquaculture is about producing the phenotypes with superior value. In this endeavor, new advances on our understanding of the epigenetic regulation of the phenotype have the potential to play an increasing role in achieving aquaculture production sustainability.
The term “epigenetics” was coined by Conrad Waddington in the 1940s, but with a meaning different from how it is understood today. Initially, it was essentially related to what today is understood as the field of developmental biology and how the phenotype comes into being. However, the modern concept of epigenetics, i.e., “the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence,” arose in the mid‐1990s and around the turn of this century. The field has largely benefited especially from the advancements made after the sequence of the human genome, the characterization of the regulatory elements, and all emerging technologies to interrogate different aspects of the genome and epigenome.
Epigenetics is now considered one of the “hot topics” in biology. Epigenetic modifications or “marks” can be easily identified, and they constitute therapeutic approaches for the treatment of an increasing number of diseases. Thus, there is a lot of research ongoing in the epigenetics of cancer, for example.
There are three very important aspects to take into account when dealing with epigenetics. First, epigenetics integrates genomic and environmental influences to bring about the phenotype. Second, there is a fraction of the phenotypic variance that cannot be explained solely on genetic variation, but that can be explained by taking into account epigenetic variation. Third, epigenetic changes can be inherited and thus passed from parents to offspring into the following generations. Combined, this has prompted the implementation of epigenetic research, not only in ecology and evolution for its contribution to adaptation to new environments, but also into agriculture and livestock for improved food production. Consequently, recently there has been both a clear interest in marine epigenetics and in the application of epigenetics in aquaculture. One of the main reasons is that aquatic organisms are quite susceptible to environmental cues since, for example, temperature in a cold‐blooded animal influences growth rates more strongly than in a warm‐blooded animal. Further, in contrast to mammals, fishes seem to have less reprogramming and erasing of epigenetic marks after fertilization, thus facilitating epigenetic transmission of environmental influences to the next generation. Thus, there is a lot of interest for the application of epigenetics in aquaculture. However, and to the best of our knowledge, there are currently no books that address this need.
“Epigenetics in Aquaculture” consists of 20 chapters and is arranged into three parts: Part I: Theoretical and practical bases of epigenetics in aquaculture; Part II: Epigenetics insights from major aquatic groups; and Part III: Implementation of epigenetics in aquaculture. All chapters are written by top specialists with ample experience and at the forefront in their respective research fields.
Part I contains six chapters (Chapters 1–6) and provides the necessary background to understand what epigenetics is about and what are the major mechanisms and phenomena. The first chapter covers the overall roles and the diversity of epigenetic mechanisms across major taxa and provides insights into their potential applications in aquaculture and aquatic animals. The following two chapters are devoted to the three main epigenetic mechanisms regulating gene expression, namely, DNA methylation, histone modifications, and non‐coding RNAs. The next two chapters are devoted to two key aspects of epigenetics. One explains how epigenetic modifications can be inherited across different generations, a hot topic in different areas of biology, and the other elucidates the role of epigenetics in integrating environmental cues as a powerful mechanism in the adaptation and the basis of organismal plastic responses to rapid environmental change. The last chapter of Part I presents the currently available methods to analyze the epigenetic modifications including the latest developments, as well as some basic resources for the bioinformatics analysis of the data. It also explains how to choose among the different approaches based on the type of question that one aims to answer.
Part II contains 11 chapters (Chapters 7–17) and constitutes the bulk of the book. These chapters explore the roles of epigenetic regulatory mechanisms in key biological process and their relevance for aquatic production. The first two chapters deal with epigenetic sex determination and differentiation as well as the dynamics of epigenetic marks during gametogenesis and early development. The following two chapters are devoted to growth, with one focusing on skeletal muscle and the other emphasizing nutritional programming. The next two chapters of Part II are devoted to the epigenetics of stress response, immune response, and the emerging topic of the role of the microbiome in shaping epigenetic responses of the host. Additionally, one chapter is focused on epigenetics in hybridization and polyploidy and another on how epigenetics can contribute to explain organismal responses to toxins present in the aquatic environment. Many of the above‐cited chapters of Part II focus on fish, where considerable work has been carried out so far. Thus, this part ends with three chapters dedicated to the epigenetics of other taxa that are also very important for aquaculture production, namely mollusks, crustaceans, and algae, where interesting discoveries related to similarities and differences with the situation in vertebrates are being made.
Finally, Part III includes the final three chapters (Chapters 18–20), dealing with the actual integration of epigenetics into aquaculture practice. For this, the development of biomarkers and their applications in aquaculture is discussed. Particular attention is then paid on the integration of epigenetic selection into current genetic breeding programs. The final chapter identifies knowledge gaps, discusses challenges that must be overcome, and outlines future prospects on the application of epigenetics in aquaculture. In addition to tables, figures, and abundant bibliography, each chapter contains a glossary of terms used with pertinent definitions.
Thus, this book provides an update on the state‐of‐the‐art on the knowledge of epigenetic regulatory mechanisms in major taxa of aquatic organisms including algae, crustaceans, mollusks, and fish and how this new knowledge can be applied to increase aquaculture production. It covers both basic and applied aspects of epigenetics related to reproduction, development, growth, nutrition, and disease of aquatic species, which we hope will benefit the aquatic scientific community and the aquaculture sector.
This book will be appealing to anyone interested in knowing all major aspects related to epigenetics, including mechanisms, inheritance, methodology, etc. Information contained within will be particularly useful to researchers working on epigenetics in aquatic animals and aquaculture, including basic aspects of fish and shellfish epigenetics, reproductive endocrinology, genetics, and evolutionary and environmental biology. It will also appeal to PhD and MSc students and biologists working in hatcheries or in breeding companies, who will all benefit from reading about epigenetics and the opportunities it can provide. More broadly, aquatic biologists, including fisheries managers and conservation biologists, will also benefit from clear and practical information in epigenetics. The epigenetic insights from fish, shellfish, and aquatic model species will attract readers from other disciplines as well, who might find inspiration in findings made on epigenetics of aquatic organisms.
Our previous book, “Sex Control in Aquaculture,” was based on knowledge accumulated after decades of applying sex control techniques to improve aquatic productivity. In contrast, the present book is based on research that is just a few years old because the study of epigenetics in aquatic organisms and its application in aquaculture is still in its infancy. Thus, a lot remains to be done. We hope that our efforts in providing a comprehensive picture of the current situation will be of much help and foster future research. The well‐known British zoologist D'Arcy Thompson (1860–1948) wrote in the preface of his most famous book “On Growth and Form” that “this book of mine has little need of preface, for indeed it is ‘all preface’ from beginning to end.” Given that the application to epigenetics into aquaculture is still in the first steps of a hopefully long and profitable journey, it could be stated that in a good way the same applies to the present book.
Francesc Piferrer and Han‐Ping Wang
Acknowledgments
We thank Bradford Sherman at The Ohio State University for the English editing of all chapters of this book. Thanks also go to Sarah Swanson and Hong Yao at The Ohio State University for their assistance in chapter coordination, format review, and reference/citation editing. We thank Hong Yao at The Ohio State University for designing the front cover of the book and Zhi‐Gang Shen at the Huazhong Agricultural University for helping with the indexes of this book. Special thanks go to all anonymous reviewers for their efforts in the peer review of the chapters and for their constructive comments that helped improve the quality of the book. We thank Rebecca Ralf, Stacey Woods and Vinitha Kannaperan at Wiley for their guidance throughout the production of this book.
Part ITheoretical and Practical Bases of Epigenetics in Aquaculture
1The Potential Role of Epigenetics in Aquaculture: Insights from Different Taxa to Diverse Teleosts
Han-Ping Wang1 and Zhi-Gang Shen2
1 Ohio Center for Aquaculture Research and Development, The Ohio State University South Centers, Piketon, OH, USA
2 College of Fisheries, Huazhong Agricultural University, Wuhan, China
1.1 Introduction
1.1.1 Concepts and Terminology
As aquaculture and livestock production and human demands increase, recent efforts have been focused on improving the production efficiency and health of agricultural animals and fish and their sustainability using advanced approaches. One of the recent approaches has been the application of sequencing technologies, genotype analysis, and genome editing for genetic improvement programs. Although great advancement has been achieved through genetic selection in animals, including those used in aquaculture, genetics can only elucidate part of the phenotypic variability of economic traits to researchers and breeders. Recent research strongly supports the view that epigenetic modifications contribute to additional layers of variation that could facilitate the improvement of different aspects of production, including reproduction, health, growth and nutrition, and overall sustainability of agricultural and aquacultural animals.
The concept of “epigenetics” was originally proposed based on advances in plant research in 1942 by Conrad H. Waddington, indicating the effect of the environment on the development of phenotypes at that time [1, 2]. Epigenetics has evolved considerably since then and is now implicated as the event of molecular modifications that are heritable and in control of the genome activity and gene expression modulation leading to phenotypic variations without changing the DNA base sequence [3, 4]. In other words, epigenetics is the set of heritable marks (including DNA methylation, chromatin remodeling, posttranslational histone changes, noncoding RNAs, and other molecules) on the genome that can modify gene expression without changing the DNA sequence content [5]. These epigenetic marks are able to transmit messages through mitosis by mediating gene expression [6]. The epigenome, or the set of epigenetic modifications of the genome of a given cell, has a dynamic role throughout the lifetime as it mediates genetic and environmental interaction [7, 8]. The general terminology of epigenetics is listed in Box 1.1.
1.1.2 Epigenetic Mechanisms and Phenomena
Genetics deals with the inheritance of information encoded by the DNA nucleotide sequence and its variants, which can have severe consequences as seen in genetically inherited diseases [9]. In contrast, epigenetic mechanisms modulate chromatin packaging and gene expression by adding or removing chemical tags to/from DNA and histones without altering the DNA sequence. Environmental exposures acting on enzymes can alter the epigenetic signatures, which can be transmitted to the next generation, without directly changing epigenetic signatures. In the process of DNA methylation and DNA demethylation, DNMTs (DNA methyltransferases) add methyl groups to cytosine residues, and TET (ten‐eleven‐translocation) proteins actively catalyze the oxidation of 5mC (5‐methylcytosine) to 5hmC (5‐hydroxymethylcytosine) for demethylation; demethylation also occurs passively through cell division without de novo methylation; DNA hypomethylation and hypermethylation play an essential role in gene transcription and transcriptional repression respectively [10, 11].
Box 1.1 General Glossary of Epigenetics
CpG sites: Regions of DNA where guanine follows a cytosine nucleotide. In vertebrates, cytosines at CpG dinucleotides constitute the principal target of DNA methylation, while cytosine methylation takes place in other sequence contexts in invertebrates. CpG sites occur with high frequency in genomic regions called CpG islands.
DNA methylation: The adding of methyl groups to the DNA molecule, usually on a cytosine of cytosine‐guanine dinucleotides, as a means of chemical DNA modification.
Epigenetic modifications: Chromatin and DNA modifications that affect genome function without alterations in the underlying DNA sequence.
Epimutation: A heritable change resulting in an alteration in gene expression but not affecting the DNA‐coding sequence. Epimutations take place when methyl groups are added or removed from DNA or when changes are made to histones that bind to the DNA in chromosomes.
Histone modification: A covalent posttranslational alteration of histone proteins such as lysine acetylation, methylation, serine phosphorylation, arginine methylation, etc.
Noncoding RNA: A generic term for functional RNA molecules including miRNA, siRNA, piRNA, and lncRNA, which are not translated into proteins that can regulate gene expression at both transcriptional and posttranscriptional levels.
Phenotypic plasticity: The capacity of a genotype to generate various phenotypes in response to different environmental changes.
Transgenerational epigenetic inheritance: The epigenetic effect on the phenotype that can be transmitted to subsequent generations of cells or organisms without leading to changes in DNA base sequences.
For histone methylation, HATs (histone acetyltransferases) add acetyl groups to lysine residues within the N‐terminal end of histones, causing local chromatin decondensation that allows transcriptional activation to occur [10, 12, 13]. HDACs (histone deacetylases) remove the acetyl group’s chromatin condensation and repress gene regions transcriptionally [10, 14], whereas HMTs (histone methyltransferases) add methyl groups to lysine and arginine residues and HDMs (histone demethylases) remove methyl groups. Different from DNA methylation, whether histone methylation activity is associated with activation or repression of gene expression is dependent on the amino acid methylation position and extent [10, 15, 16]. The detailed roles of these key players in epigenetics are described in the section later.
It is understood that ncRNAs also possess vital roles in the regulation of gene expression, particularly micro‐ (miRs) and long noncoding RNAs, which regulate important genetic programs through interaction with the coding genome. For example, interfering RNAs can assist in the recruitment of enzymes modifying chromatin to mediate transcription or promote the posttranscriptional degradation of transcripts [9].
1.2 Key Players of Epigenetics
1.2.1 DNMTs
In animals, DNA cytosine methylation takes place mainly in the CpG dinucleotides in the genome [17, 18], while in humans, approximately 70–80% of CpG dinucleotides are methylated, with 5mC enriched on transposons, satellite repeats, and intergenic regions [19]. 5mC discovered initially in tubercle bacillus and calf thymus DNA [20, 21] is now the main epigenetic modification identified in the genomes of plants and animals [19]. This modification is implicated in the suppressing transcription of transposable elements (TEs) [22] and maintaining chromosomal integrity [22, 23] with start site DNA methylation of promoters, enhancers, and transcription associated with coding regions' gene repression [24].
In mammals, three key members (DNMT1, DNMT2, and DNMT3) of DNA‐cytosine‐5‐methyltransferase enzymes, which catalyze the transfer of methyl groups to the 5‐position of cytosines, are responsible for establishing and maintaining the methylation patterns as key “writers” [25]. The DNMT1 preferentially methylates hemimethylated DNA [26, 27] to ensure the maintenance and propagation of methylation patterns through cell division [28]. Knocking out DNMT1 in mice leads to embryonic lethality during the developmental stage and dilution of DNA methylation during cell cycles [29]. During cell differentiation processes, the DNMT3a and DNMT3b are actively involved in the de novo methylation with different functions – the former is contributory to establishing the patterns of DNA methylation at maternally imprinted loci [30] and the latter is involved in methylation of CpG islands and pericentromeric repeats during inactivation of X‐chromosome [31]. Loss of germline function of DNMT3a and DNMT3b leads to an absence of methylation in spermatogonia, resulting in arrest in meiosis and infertility [10, 32–35] and embryonic lethality in mice [36]. In addition, the DNMT family has a cofactor, DNMT3l, which is instrumental in recruiting de novo methyltransferases to target sequences [30, 37]. A study shows that DNMT3l can serve as both a positive modulator of DNA methylation at gene bodies of housekeeping genes and a negative mediator at promoters of bivalent genes, during embryonic cell differentiation in a mouse [17, 38]. Like DNMTs, DNMT3l involvement in de novo DNA methylation is so important that a lack of DNMT3l causes infertility [39–43].
In contrast, DNMTs are not founded to be involved in DNA methylation in plants, and their non‐CpG methylation is typically targeted to TEs with modulation by siRNAs. The 5mC modification of plants takes place in multiple dinucleotide contexts, including CpG, CHH, and CHG. Instead, three other DNA methyltransferase enzymes, methyltransferase 1 (MET1) and chromomethylase 2 and 3 (CMT2 and CMT3) are responsible for these modifications. The enzyme DNA methylation “readers” that mediate gene expression include SUVH1 and SUVH3, which are the SU(VAR)3‐9 protein homologs [44, chapter 17]. Similarly, algae do not have mammalian DNMTs for DNA methylation [45, 46]. However, like animals, CpG methylation of TEs and gene bodies have also been reported in plants [17, 47–49].
Overall, DNA methylation distribution in fish is similar to mammals, with Dnmt1, Dnmt3a, and Dnmt3b involvement in CpG methylation and very little in non‐CpG sites. However, DNA methyltransferase isoforms are more expanded and DNA methylation machinery is more diversified in teleosts than mammals due to whole genome duplication and locus‐specific rearrangements [50–52]. Different mammalian paralogues of DNA methylation enzymes, Dnmt1, Dnmt3a, and Dnmt3b are identified in fish. For example, dnmt3aa and dnmt3ab have been found to mediate sex differentiation of zebrafish related to temperature [53] and gonadal dntm3aa plays an important role in gamete development through gonadal DNA methylation in tilapia [54]. Dnmts are also involved in the methylation related to muscle growth as evidenced in Atlantic cod (Gadus morhua), in which dnmt1 and dnmt3a are found to be associated with improving photoperiod‐stimulated growth [55]. In addition, higher percentages of CpG methylation were observed, and PGCs are predetermined by germplasm and not elicited via epigenetic mechanisms in fish when compared to mammals [56]. Furthermore, studies show that Dnmt3l is absent from fish genomes, which is also the case in bird and amphibian genomes. DNMT3L is a key cofactor for the relatively high methylation of mammalian sperm and the lack of Dnmt3l in fish suggests their low levels of methylation in sperm.
In summary, DNMTs play a crucial “writer” role in maintaining and propagating 5mC/cytosine methylation patterns through early development across taxa. Other than DNMT1, DNMT3a, and DNMT3b, mammals have a cofactor, DNMT3L. Knockout or deletion of DNMT1, DNMT3b, and DNMT3L in mice leads to embryonic lethality. DNMTs have not been found to be involved in DNA methylation in plants and algae. DNA methylation distribution in fish is similar to mammals but more diversified with more and different mammalian paralogues of DNA methylation enzymes. However, fish lack a Dnmt3l gene and the global hypomethylation of sperm DNA [57], the same as birds and amphibia. These specific features of the DNA methylation landscape in fish make them unique as model species for studying comparative DNA methylation patterns and early evolutionary fates of duplicated genes, including the determination of the mechanisms for dnmt3aa and dnmt3ab regulation of sex differentiation with temperature and identification of basic DNA methylation patterns in somatic and germ cells within lifecycle and between generations of aquatic species (Chapter 2). The related epigenetic research will benefit fish, the aquatic field, and the entire taxa in general.
1.2.2 TETs
In mammals, TETs (ten‐eleven translocations), including TET1, TET2, and TET3, play an important role as an “eraser” in DNA demethylation during early development and multiple adult somatic tissues [58]. The TET proteins contain a C‐terminal catalytic dioxygenase domain that can recognize CpG dinucleotides and bind to 5mC to perform oxidation reactions, producing 5hmC, 5fC (5‐formylcytosine), and 5caC (5‐carboxylcytosine) [29, 36, 59, 60]. These oxidized derivatives are then diluted during replication or replaced by unmethylated cytosines by the DNA repair machinery [61]. Thus, while the old 5mC patterns were being erased and new ones established right after fertilization during organogenesis and early development, TETs performed two waves of erasure process in mammalian genomes [62–64]. In mouse preimplantation embryos, demethylation of both parental genomes is likely to follow a TDG (thymine DNA glycosylase)‐independent pathway in spite of involving 5mC oxidation to 5fC/5caC [17, 65]. Depleting the three TET enzymes together leads to incorrect differentiation of embryonic stem cells [66], and gastrulation defects in mice highlight the importance of the 5mC derivatives for development and differentiation [67]. However, studies show that the experimental mice with knockout of individual TET1 or TET2 can survive [68–70], with TET1‐deleted mice showing a neurogenesis‐related phenotype [71, 72] and TET2 deficiency affecting hematopoietic stem cell (HSC) differentiation [70, 73, 74], and combined deletion unchanging organogenesis [75]. TET3 knockout leads only to neonatal lethality during mouse embryonic development [17, 76].
TETs possess an important role in response to numerous environmental stressors. Recent evidence shows that restricting maternal food during late gestation causes a reduced fetal and liver weight and fetal heart in goats, with a significant increase of TET1 and MBD2 (methyl‐CpG‐binding domain protein 2) expression in fetal heart and liver [77, 78]. Another study suggests that an adverse maternal environment downregulated TET1‐3 expression in the heart of male offspring of pregnant mice [77, 79]. Linking vitamins and TET function has also been evidenced. A study conducted by Chen et al. [80] revealed that TET1 effect on the reprogramming of embryonic fibroblast was mediated by vitamin C, leading to the induction of pluripotent stem cells in the mouse. These results suggest the possibility of applying nutritional intervention to control certain diseases. In terms of chemicals and pollutants, Feng et al. [81] found that repeated exposure of both mice and humans to cocaine‐recessed TET1 in the Nucleus accumbens and TET1 deficiency promoted the preference for cocaine in mice. Other studies suggested that global increases of 5hmC levels and TET1 activity were elevated by exposure to toxicants benzene and its metabolites, which can be found in cigarette smoke and petroleum products [77, 82, 83]. TET1 can be affected by radiation in different types of cells and tissues. Coulter et al. [84] and Kuhns et al. [85] found that TET1 depletion promoted ionizing radiation‐induced aberrant cell cycles and apoptosis processes. Another study showed that loss of TET1 resulted in augmented X‐ray‐induced deterioration and accumulated DNA damage and genomic instability of embryonic cells in mice. These results indicate that TETs are required for genomic stability, DNA damage repair, and cell cycle maintenance after radiation.
In plants, mammalian TET proteins and homologs have not been identified [86], although 5hmC and 5fC can be discernable in the DNA of several plants [87–89]. Some studies show that plants use a demethylation mechanism without 5mC enzymatic oxidation, and it is moved from the DNA by specific DNA glycosylases directly [17, 48, 90]; however, the roles of oxidized forms in 5mC are not clear yet in plants.
However, TET homologs have been identified in algae and fungi [91–93]. Recently, two studies show that a novel DNA modification C5‐glyceryl‐methylcytosine (5gmC) was catalyzed by algal TET homologue CMD1 from Chlamydomonas reinhardtii, using vitamin C as a co‐substrate [94, 95]. Also, a mushroom TET homolog CcTET from Coprinopsis cinerea was found to preferentially oxidize 5mC to 5fC, but not to 5hmC [17, 92, 95].
In teleosts, a few studies in zebrafish (Danio rerio) suggest that both the canonical TET‐TDG pathway [96, 97] and the AICDA/APOBEC (activation‐induced cytosine deaminases/apolipoprotein B mRNA editing complex) pathway are involved in demethylation activity and there is only one copy of tet1‐3 encoded in their genome as mammals (Chapter 2). There are seven tet and four tdg found in salmonids with duplicates of all tet genes following Ss4R [50, 52]. Overall, there is limited knowledge of the demethylation activity of both pathways in teleosts and more related research is needed.
In summary, evidence suggests that TET proteins play an important role in DNA demethylation during early development for differentiation and embryogenesis, and in responding to environmental stresses in vertebrates, including fish. TET1 absence causes DNA repair deficiency, severe DNA damage, and increased genomic instability. Although TET proteins and homologs have been found in algae and fungi [17, 91–93], this is not evidenced in plants [17, 86]. The tet1, tet2, tet3, and tet4 are identified in fish genomes due to specific whole genome duplication and locus‐specific rearrangements [51, 98, 99]. This specific feature of genome duplication is worth much attention for future research. The application of nutritional intervention could be a potential way to control certain diseases in aquatic species and aquaculture.
The epigenetic similarities and differences in the above key regulators and DNA methylation among terrestrial vertebrates, fish, and plants are listed in Table 1.1.
1.2.3 KMTs/KDMs
KMTs (histone lysine methyltransferases) and KDMs (histone lysine demethylases) are histone code writers and erasers that play a critical role in operating epigenetic control through histone modification [109–113]. In the past two decades, there have been many KMTs and KDMs and related biochemical properties and their regulation identified and investigated [114]. The activity of these histone modifiers needs to be in dynamic steadiness to balance epigenetic homeostasis. Evidence shows that alterations in histone lysine methylation possess an important role in the determination of neuronal development and differentiation, neuropsychiatric disorders, mental retardation, and behavioral changes in humans and animals [114] and lysine methylation balance is instrumental in the maintenance of genome integrity, gene regulation, and disease evasion [114–116].
Table 1.1 Differences and similarities in DNA methylation and related key payers among fish (exemplified by zebrafish), terrestrial vertebrates, and plants.
Source: Data from Youngson and Whitelaw [104] and Jessop et al. [108].
Terrestrial vertebrates
Fish
Plants
References
Presence of CpG methylation
CpG methylation
CpG methylation; very little in non‐CpG sites
Non‐CpG methylation targets to TEs and is commonly modulated by siRNAs
[
100
–
103
]
Timing of germline separation from somatic tissues
PGCs are obtained from the epiblast and appear in the posterior primitive streak during gastrulation; there is limited time for epigenetic alterations to be transmitted into the germline cells
PGCs are predetermined by germplasm and are not elicited via epigenetic mechanisms
There is no early separation of germline and soma, and the gametes obtained from vegetative tissue right before completing development
[104]
Targets of DNA methylation
In general, gene bodies are methylated, whereas CpG islands are often unmethylated
Same as other vertebrates
Methylation generally takes place on repetitive DNA elements and TEs
[105]
Methylation patterns
Typically, DNA methylation takes place globally in vertebrates and around 70–80% of cytosines in CpG dinucleotides are methylated
Same as other vertebrates
In general, there are mosaic DNA methylation patterns, which are characterized by domains of massively methylated DNA scattered with domains of free methylation
[
105
–
107
]
Genes involved in the cytosine methylation and oxidation pathway
Dnmt1, Dnmt3a, Dnmt3b, Dnmt3l, Uhrf1, Tet1, Tet2, Tet2, Tdg
dnmt1, dnmt3aa, dnmt3ab, dnmt3ba, dnmt3bb.1, dnmt3bb.2, dnmt3bb.3, Tet1, Tet2, Tet3,
Tet4
, Tdg.1, Tdg.2
[108]
Proteins involved in the cytosine methylation and oxidation pathway
