Epigenetics in Ecology and Evolution

Christoph Grunau is Professor of Biology at the Université de Perpignan Via Domitia, France, and Director of the "Host-Pathogen-Environment Interactions" laboratory. His research focuses on environmental epigenetics.Stéphane Maury is Professor of Plant Physiology and Epigenetics at the Université d'Orléans, France, in the "P2e" (Physiology Ecology Environment) laboratory (INRAE ECODIV Department). He coordinates a research team working on tree epigenetics in the context of climate change.

• Preface xiChristoph GRUNAU and Stéphane MAURYChapter 1 A Brief Conceptual History of Epigenetics, and More Besides 1Arnaud POCHEVILLE1.1 Introduction 11.2 The birth of the term: from epigenesis to pangenesis 31.3 From pangene to classical gene 71.4 Classical epigenetics 111.5 Molecular epigenetics 121.6 Epigenetics without knowing it, or Mr Jourdain’s epigenetics 151.7 Post-genomic epigenetics: epigenomics 191.8 Developmental, ecological and evolutionary epigenetics 251.9 Epigenetics and ethics 291.10 Conclusion 291.11 References 32Chapter 2 Molecular Players of Epigenetic Information 61Natacha BIES ETHEVE, Séverine CHAMBEYRON and Frédéric BANTIGNIES2.1 Introduction 612.2 DNA methylation 632.2.1 The different types of DNA methylation 632.2.2 DNA demethylation 642.2.3 The effects of DNA methylation 652.3 Histone modifications 682.3.1 The nucleosome 682.3.2 Histone marks 692.3.3 Histone marks and their function 712.3.4 Histone mark complexes 732.3.5 Links between DNA methylation and histone modification 742.4 Chromatin topology 752.4.1 Epigenetic landscapes 752.4.2 From nucleosome to chromosome territories 762.4.3 Focus on topologically associating domains 772.5 Regulatory RNAs 802.5.1 Regulatory RNAs, from discovery to biogenesis 802.5.2 Modes of action of regulatory RNAs on the establishment of epigenetic marks 842.6 Conclusion 882.7 References 88Chapter 3 Epigenetics and Transposable Elements 95Clémentine VITTE, Séverine CHAMBEYRON and Cristina VIEIRA3.1 Introduction 953.2 TEs in genomes 963.2.1 Discovery and classification 963.2.2 Abundance and location of TEs in genomes 993.2.3 Transposition control 1013.3 Impact of TEs on phenotype 1033.3.1 Genetic impact 1033.3.2 Epigenetic impact 1073.3.3 Local spreading of epigenetic marks 1093.4 The effect of TE in adaptation and evolution 1103.5 Conclusion 1123.6 References 113Chapter 4 Epigenetics: The Same for all Species? 117Clémentine VITTE and Nicolas NÈGRE4.1 Universal epigenetic mechanisms? 1174.2 Origin of the various chromatin components 1184.2.1 Origin of DNA 1184.2.2 Origin of small RNAs 1194.2.3 Origin of DNA methylation 1204.2.4 Origin of chromatin 1214.3 Evolution of epigenetic systems 1214.4 Example of the evolution of DNA methylation in different groups of organisms 1224.5 Which model organisms for epigenetics? 1254.6 References 126Chapter 5 Epigenome Modifications as a Therapeutic and Research Tool 129Nelia LUVIANO, Francesco CALZAFERRI and Marie LOPEZ5.1 Introduction 1295.2 Epigenetic modification strategies 1305.2.1 Epigenetic ligands 1305.2.2 Epigenetic engineering 1335.3 Epigenetic modification targeting DNA methylation 1395.3.1 DNMT inhibitors 1395.3.2 dCas9-based technology to edit DNA methylation 1415.3.3 Examples of DNA methylation modifications 1425.4 Epigenetic modification of histone epigenetic marks 1445.4.1 Inhibitors of histone-targeting epigenetic marks 1465.4.2 dCas9-based technology to edit post-translational histone modifications 1465.5 dCas9-based technology to edit nuclear architecture 1475.6 dCas9 fused to transcription factors 1495.7 dCas13-based technology to edit RNA modifications 1505.8 Conclusion 1515.9 References 152Chapter 6 Epigenetics and Stress 161Raphaëlle CHAIX and Natacha BIES ETHEVE6.1 Impact of environmental constraints on epigenetic marks in animals and humans 1616.1.1 From psychosocial stress to epigenetic profiles 1626.1.2 An epigenetic clock running faster 1636.1.3 The intergenerational cost of stress exposure 1656.1.4 “De-stress” the epigenome? 1666.2 Impact of environmental stress on epigenetic marks in plants 1676.2.1 Effects of abiotic factors on epigenetic marks in plants 1676.2.2 Effects of biotic stresses on epigenetic marks and plant defense mechanisms 1726.3 Conclusion 1796.4 References 179Chapter 7 Phenotypic Plasticity, Epigenetics and Adaptability 189Patricia GIBERT, Cristina VIEIRA and Frédéric BRUNET7.1 Introduction 1897.2 Experimental approach to PP 1917.2.1 What is a reaction norm? 1917.2.2 How can we study PP? 1927.2.3 Which traits should be considered? 1937.3 Molecular mechanisms of PP 1947.4 Evolution of PP 1957.5 Evolution through PP 1977.6 Conclusion 2007.7 References 201Chapter 8 Epigenetics and Climate Change: The Example of Forest Ecosystems 205Stéphane MAURY and Christophe PLOMION8.1 Introduction: an ecological crisis on an unprecedented scale 2058.2 Forests and climate change: from current situation to challenges 2098.2.1 The role of forests and trees in ecosystems 2098.2.2 Adapting trees to their environment 2108.3 Epigenetics as a source of flexibility in trees in a context of GC 2168.3.1 Intra-individual epigenetic variation: mosaicism, plasticity, memory and priming 2168.3.2 Population epigenetic variation and tree adaptation 2228.3.3 The promise of epigenetics for the improvement, management and conservation of genetic resources in forest trees 2258.4 Conclusion 2328.5 Acknowledgements 2328.6 References 233Chapter 9 Epigenetics and Crop Improvement 239Julie LECLERCQ, Dominique THIS and Patrice THIS9.1 Introduction 2399.2 Defining agricultural transition objectives and challenges 2409.2.1 Rice and production in marginal areas 2409.2.2 Grapevines and terroir in the face of climate change 2409.2.3 Common breeding objectives for agriculture in transition 2419.3 The contribution of (epi)genetics to the definition of traits of agronomic interest and the construction of ideotypes 2449.3.1 Importance of epigenetic phenomena in the modulation of traits and adaptive plasticity in plants 2449.3.2 Seeking phenotypic diversity for traits of interest: the question of heritability 2469.3.3 Epigenetics as a source of new diversity for plant improvement 2489.4 The role of epigenetics in current selection schemes 2489.4.1 Development and characterization of recombinant populations 2489.4.2 Development of epigenetic marks 2519.4.3 Quantitative epigenetics: identifying loci of agronomic interest 2529.4.4 Marker-assisted selection, genomics, phenomics and epigenomics 2539.5 The final stages before a new variety is labeled 2549.5.1 Obtaining basic material (seeds or seedlings) 2549.5.2 Plant variety certificate 2559.5.3 Verification of agronomic value (in rice fields or terroir) 2569.6 Development of new varieties without sexual crossing 2569.6.1 Transgenesis or cisgenesis in a favorable chromatin context 2569.6.2 Epigenomic and epibreeding editing 2579.7 Legislation and marketing of varietal innovations resulting from epigenetic variations 2599.8 Conclusion and prospects 2609.9 References 260Chapter 10 Epigenetics and Livestock Improvement 265Vincent COUSTHAM and Frédérique PITEL10.1 Introduction 26510.2 Genetic selection issues and epigenetic improvement levers 26610.2.1 Genetic X Epigenetic Interactions 26710.2.2 Selection importance 26810.3 Early phenotype programming 26810.3.1 Nutritional programming 26910.3.2 Thermal conditioning 27210.4 Transgenerational epigenetic effects 27410.5 Conclusion 27510.6 References 275Chapter 11 Epigenetics in Evolution 281Christoph GRUNAU and Alexandra WEYRICH11.1 Evolution, Environments and Inheritance 28111.1.1 Don’t be too rigid – plasticity is also important 28411.1.2 Bringing everything together 28711.2 Conclusions and further readings 28911.3 References 289Chapter 12 Epigenetics and Society: Epigenetics in the French Press 291Michel DUBOIS, Catherine GUASPARE and Séverine LOUVEL12.1 Introduction 29112.2 Data and methodology 29312.3 Epigenetics press 29412.4 Words and categories 29612.5 A look at epigenetics in the French press 30012.5.1 The relationship between epigenetics and genetics 30012.5.2 Epigenetics and health 30112.5.3 Consumer epigenetics 30212.5.4 Epigenetics and environmental exposure 30412.6 Discussion: the appeal and visibility of epigenetics 30612.7 Conclusion 30712.8 References 308List of Authors 311Index 315