Preface xi
Christoph GRUNAU and Stéphane MAURY
Chapter 1 A Brief Conceptual History of Epigenetics, and More Besides 1
Arnaud POCHEVILLE
1.1 Introduction 1
1.2 The birth of the term: from epigenesis to pangenesis 3
1.3 From pangene to classical gene 7
1.4 Classical epigenetics 11
1.5 Molecular epigenetics 12
1.6 Epigenetics without knowing it, or Mr Jourdain's epigenetics 15
1.7 Post-genomic epigenetics: epigenomics 19
1.8 Developmental, ecological and evolutionary epigenetics 25
1.9 Epigenetics and ethics 29
1.10 Conclusion 29
1.11 References 32
Chapter 2 Molecular Players of Epigenetic Information 61
Natacha BIES ETHEVE, Séverine CHAMBEYRON and Frédéric BANTIGNIES
2.1 Introduction 61
2.2 DNA methylation 63
2.2.1 The different types of DNA methylation 63
2.2.2 DNA demethylation 64
2.2.3 The effects of DNA methylation 65
2.3 Histone modifications 68
2.3.1 The nucleosome 68
2.3.2 Histone marks 69
2.3.3 Histone marks and their function 71
2.3.4 Histone mark complexes 73
2.3.5 Links between DNA methylation and histone modification 74
2.4 Chromatin topology 75
2.4.1 Epigenetic landscapes 75
2.4.2 From nucleosome to chromosome territories 76
2.4.3 Focus on topologically associating domains 77
2.5 Regulatory RNAs 80
2.5.1 Regulatory RNAs, from discovery to biogenesis 80
2.5.2 Modes of action of regulatory RNAs on the establishment of epigenetic marks 84
2.6 Conclusion 88
2.7 References 88
Chapter 3 Epigenetics and Transposable Elements 95
Clémentine VITTE, Séverine CHAMBEYRON and Cristina VIEIRA
3.1 Introduction 95
3.2 TEs in genomes 96
3.2.1 Discovery and classification 96
3.2.2 Abundance and location of TEs in genomes 99
3.2.3 Transposition control 101
3.3 Impact of TEs on phenotype 103
3.3.1 Genetic impact 103
3.3.2 Epigenetic impact 107
3.3.3 Local spreading of epigenetic marks 109
3.4 The effect of TE in adaptation and evolution 110
3.5 Conclusion 112
3.6 References 113
Chapter 4 Epigenetics: The Same for all Species? 117
Clémentine VITTE and Nicolas NÈGRE
4.1 Universal epigenetic mechanisms? 117
4.2 Origin of the various chromatin components 118
4.2.1 Origin of DNA 118
4.2.2 Origin of small RNAs 119
4.2.3 Origin of DNA methylation 120
4.2.4 Origin of chromatin 121
4.3 Evolution of epigenetic systems 121
4.4 Example of the evolution of DNA methylation in different groups of organisms 122
4.5 Which model organisms for epigenetics? 125
4.6 References 126
Chapter 5 Epigenome Modifications as a Therapeutic and Research Tool 129
Nelia LUVIANO, Francesco CALZAFERRI and Marie LOPEZ
5.1 Introduction 129
5.2 Epigenetic modification strategies 130
5.2.1 Epigenetic ligands 130
5.2.2 Epigenetic engineering 133
5.3 Epigenetic modification targeting DNA methylation 139
5.3.1 DNMT inhibitors 139
5.3.2 dCas9-based technology to edit DNA methylation 141
5.3.3 Examples of DNA methylation modifications 142
5.4 Epigenetic modification of histone epigenetic marks 144
5.4.1 Inhibitors of histone-targeting epigenetic marks 146
5.4.2 dCas9-based technology to edit post-translational histone modifications 146
5.5 dCas9-based technology to edit nuclear architecture 147
5.6 dCas9 fused to transcription factors 149
5.7 dCas13-based technology to edit RNA modifications 150
5.8 Conclusion 151
5.9 References 152
Chapter 6 Epigenetics and Stress 161
Raphaëlle CHAIX and Natacha BIES ETHEVE
6.1 Impact of environmental constraints on epigenetic marks in animals and humans 161
6.1.1 From psychosocial stress to epigenetic profiles 162
6.1.2 An epigenetic clock running faster 163
6.1.3 The intergenerational cost of stress exposure 165
6.1.4 "De-stress" the epigenome? 166
6.2 Impact of environmental stress on epigenetic marks in plants 167
6.2.1 Effects of abiotic factors on epigenetic marks in plants 167
6.2.2 Effects of biotic stresses on epigenetic marks and plant defense mechanisms 172
6.3 Conclusion 179
6.4 References 179
Chapter 7 Phenotypic Plasticity, Epigenetics and Adaptability 189
Patricia GIBERT, Cristina VIEIRA and Frédéric BRUNET
7.1 Introduction 189
7.2 Experimental approach to PP 191
7.2.1 What is a reaction norm? 191
7.2.2 How can we study PP? 192
7.2.3 Which traits should be considered? 193
7.3 Molecular mechanisms of PP 194
7.4 Evolution of PP 195
7.5 Evolution through PP 197
7.6 Conclusion 200
7.7 References 201
Chapter 8 Epigenetics and Climate Change: The Example of Forest Ecosystems 205
Stéphane MAURY and Christophe PLOMION
8.1 Introduction: an ecological crisis on an unprecedented scale 205
8.2 Forests and climate change: from current situation to challenges 209
8.2.1 The role of forests and trees in ecosystems 209
8.2.2 Adapting trees to their environment 210
8.3 Epigenetics as a source of flexibility in trees in a context of GC 216
8.3.1 Intra-individual epigenetic variation: mosaicism, plasticity, memory and priming 216
8.3.2 Population epigenetic variation and tree adaptation 222
8.3.3 The promise of epigenetics for the improvement, management and conservation of genetic resources in forest trees 225
8.4 Conclusion 232
8.5 Acknowledgements 232
8.6 References 233
Chapter 9 Epigenetics and Crop Improvement 239
Julie LECLERCQ, Dominique THIS and Patrice THIS
9.1 Introduction 239
9.2 Defining agricultural transition objectives and challenges 240
9.2.1 Rice and production in marginal areas 240
9.2.2 Grapevines and terroir in the face of climate change 240
9.2.3 Common breeding objectives for agriculture in transition 241
9.3 The contribution of (epi)genetics to the definition of traits of agronomic interest and the construction of ideotypes 244
9.3.1 Importance of epigenetic phenomena in the modulation of traits and adaptive plasticity in plants 244
9.3.2 Seeking phenotypic diversity for traits of interest: the question of heritability 246
9.3.3 Epigenetics as a source of new diversity for plant improvement 248
9.4 The role of epigenetics in current selection schemes 248
9.4.1 Development and characterization of recombinant populations 248
9.4.2 Development of epigenetic marks 251
9.4.3 Quantitative epigenetics: identifying loci of agronomic interest 252
9.4.4 Marker-assisted selection, genomics, phenomics and epigenomics 253
9.5 The final stages before a new variety is labeled 254
9.5.1 Obtaining basic material (seeds or seedlings) 254
9.5.2 Plant variety certificate 255
9.5.3 Verification of agronomic value (in rice fields or terroir) 256
9.6 Development of new varieties without sexual crossing 256
9.6.1 Transgenesis or cisgenesis in a favorable chromatin context 256
9.6.2 Epigenomic and epibreeding editing 257
9.7 Legislation and marketing of varietal innovations resulting from epigenetic variations 259
9.8 Conclusion and prospects 260
9.9 References 260
Chapter 10 Epigenetics and Livestock Improvement 265
Vincent COUSTHAM and Frédérique PITEL
10.1 Introduction 265
10.2 Genetic selection issues and epigenetic improvement levers 266
10.2.1 Genetic X Epigenetic Interactions 267
10.2.2 Selection importance 268
10.3 Early phenotype programming 268
10.3.1 Nutritional programming 269
10.3.2 Thermal conditioning 272
10.4 Transgenerational epigenetic effects 274
10.5 Conclusion 275
10.6 References 275
Chapter 11 Epigenetics in Evolution 281
Christoph GRUNAU and Alexandra WEYRICH
11.1 Evolution, Environments and Inheritance 281
11.1.1 Don't be too rigid - plasticity is also important 284
11.1.2 Bringing everything together 287
11.2 Conclusions and further readings 289
11.3 References 289
Chapter 12 Epigenetics and Society: Epigenetics in the French Press 291
Michel DUBOIS, Catherine GUASPARE and Séverine LOUVEL
12.1 Introduction 291
12.2 Data and methodology 293
12.3 Epigenetics press 294
12.4 Words and categories 296
12.5 A look at epigenetics in the French press 300
12.5.1 The relationship between epigenetics and genetics 300
12.5.2 Epigenetics and health 301
12.5.3 Consumer epigenetics 302
12.5.4 Epigenetics and environmental exposure 304
12.6 Discussion: the appeal and visibility of epigenetics 306
12.7 Conclusion 307
12.8 References 308
List of Authors 311
Index 315
