Transposable Elements and Genome Evolution: (ISTE Consignment)

Since their discovery by Barbara McClintock in the mid-20th century, the importance of transposable elements in shaping the architecture, function and evolution of genomes has gradually been unveiled. These DNA sequences populate nearly all genomes and are viewed as genomic parasites. They are mobile, capable of proliferating within genomes and also commonly travel between species. These elements are mutagenic and are responsible for several human genetic disorders, but they also constitute a major source of genetic diversity. Some insertions have beneficial effects for the host and are selected for, giving rise to significant evolutionary innovations. Their dynamics within genomes are intricate, as are their interactions with other genome components. To limit their proliferation, the genome has evolved sophisticated defense mechanisms. While researchers commonly use these elements as genetic tools, their identification in newly sequenced genomes remains a challenge due not only to their extensive diversity, but also their large copy numbers.

Table of Contents:
Acknowledgments xiii Aurélie HUA-VAN and Pierre CAPY Introduction xv Aurélie HUA-VAN and Pierre CAPY Chapter 1. Transposable Elements in Eukaryotes 1 Aurélie HUA-VAN 1.1. Introduction 1 1.2. Classification, structure and transposition mechanism 2 1.2.1. Class I 4 1.2.2. Class II 7 1.2.3. Autonomous, non-autonomous and relics 10 1.3. Abundance, diversity and distribution 10 1.4. Origins of transposable elements and evolutionary relationships with other genetic elements 12 1.5. Genomic impact 14 1.5.1. Genome size 15 1.5.2. Genome structure 15 1.5.3. Genome function and evolution 16 1.6. References 17 Chapter 2. Prokaryotic Transposable Elements 21 Alessandro M. VARANI, Karen E. ROSS and Mick CHANDLER 2.1. Introduction 21 2.1.1. Historical 21 2.1.2. Relationship between IS and transposons 22 2.1.3. The prokaryotic TE landscape 23 2.2. Transposases: the enzymes driving transposition 25 2.2.1. DDE enzymes 25 2.2.2. HUH enzymes 27 2.3. Insertion sequences 28 2.3.1. Overview 28 2.3.2. Impact 29 2.3.3. IS diversity 30 2.3.4. IS-related elements: tIS, MITEs and MICs 30 2.4. Transposons (Tn) 32 2.4.1. Compound transposons 32 2.4.2. Pseudocompound transposons, targeted insertion and translocatable units (TU) 33 2.4.3. Unit transposons with DDE transposases 34 2.4.4. Transposon using CRISPR components 45 2.4.5. Mobile elements which move using site-specific recombinases 46 2.5. Conclusion 52 2.6. References 53 Chapter 3. Transposable Elements and Human Diseases 61 Benoît CHÉNAIS 3.1. The moving parts of the human genome 61 3.2. TE insertion and its impact on the genome and gene expression 64 3.2.1. Chromosomal rearrangements 64 3.2.2. Modification of gene structure and expression by TE insertion 66 3.2.3. Escaping epigenetic control 68 3.3. TE involvement in human cancers 69 3.3.1. Inserting LINE-1 69 3.3.2. Insertion of Alu sequences and chromosomal recombination 70 3.3.3. Epigenetic alterations due to TE and cancer 72 3.4. Involvement of TEs in noncancerous pathologies 72 3.4.1. Implications of TE in hemoglobinopathies 72 3.4.2. Implications of TEs in metabolic diseases or diseases linked to metabolic genes 73 3.4.3. Implications of TEs in neurological diseases 76 3.4.4. Implications of TE in various other diseases 77 3.4.5. Link between TE and common diseases 78 3.5. The role of stress and environmental pollution in TE mobility 79 3.5.1. Epigenetic alterations caused by environmental pollutants 79 3.5.2. Methylation and mobility of LINE-1 elements in response to environmental stresses 80 3.5.3. Influence of occupational and psychosocial stresses on the mobility of LINE-1 elements 81 3.6. Conclusion 82 3.7. References 82 Chapter 4. The Silencing Mechanisms Inhibiting Transposable Element Activity in Somatic and Germ Cells 91 Chantal VAURY 4.1. Introduction 91 4.2. Silencing of transposable elements in somatic tissues 92 4.2.1. Mechanisms that ensure deposition of epigenetic hallmarks at TEs 92 4.2.2. Inheritance of the epigenetic state of TEs through cell division 95 4.2.3. Influence of environmental stresses on TE control in somatic cells 96 4.3. Silencing of transposable elements in the germline 97 4.3.1. The piRNA pathway in ovarian germ cells 97 4.3.2. Additional strategies used to silence TEs in the germline 100 4.4. The specific case of somatic cells surrounding the germline 102 4.5. Transmission of silencing through generations 103 4.6. Environmental stresses and their influence on TEs 105 4.7. Conclusion 107 4.8. References 107 Chapter 5. Transposable Elements and Adaptation 115 Marta CORONADO-ZAMORA and Josefa GONZÁLEZ 5.1. Transposable elements are mobile genomic sequences 115 5.1.1. Transposable elements are diverse genomic sequences 116 5.1.2. Transposable elements generate different types of mutations 117 5.2. Transposable elements and insecticide resistance 119 5.2.1. Transposable elements and metabolic resistance 120 5.2.2. Target resistance and transposable elements 123 5.3. Transposable elements and the immune response 125 5.4. Transposable elements and environmental shock response 126 5.5. Conclusion 130 5.6. Acknowledgments 130 5.7. References 131 Chapter 6. Domestication (Exaptation) of Transposable Elements 135 Christopher ELLISON 6.1. Introduction 135 6.2. Host genes derived from transposons 137 6.2.1. Repeated domestication of transposases 137 6.2.2. Repeated domestication of envelope genes 140 6.3. TEs can disperse noncoding regulatory sequences across the genome 141 6.4. TEs form structural components of the genome 143 6.4.1. Transposons function in centromere specification 143 6.4.2. Transposons act as telomeres in Drosophila 144 6.5. Summary 145 6.6. References 145 Chapter 7. Horizontal Transfers and Transposable Elements 149 Emmanuelle LERAT 7.1. Introduction 149 7.2. Mechanisms and prerequisites for horizontal transfers of transposable elements 152 7.2.1. Direct transmission 152 7.2.2. Transmission by a viral vector 153 7.2.3. Transmission via host–pathogen interactions 155 7.2.4. Factors for successful horizontal transfer of transposable elements 156 7.3. Bioinformatics methods for detecting horizontal transfer of transposable elements 157 7.3.1. HTdetect 158 7.3.2. VHICA 159 7.4. Documented examples of horizontal transfers of transposable elements 160 7.5. The impact of horizontal transfers of transposable elements 163 7.5.1. Adaptation and creation of gene novelties 163 7.5.2. The appearance of new species 164 7.6. Conclusion 165 7.7. References 165 Chapter 8. Genome Invasion Dynamics 175 Arnaud LE ROUZIC and Aurélie HUA-VAN 8.1. The lifecycle of transposable elements 175 8.2. Transposable elements as parasites of sexual reproduction 177 8.2.1. Amplification 177 8.2.2. The selfish DNA model 177 8.3. Limiting the spread 178 8.3.1. Natural selection 179 8.3.2. Transposition regulation 181 8.4. Long-term evolution 182 8.4.1. Interactions between TE copies 182 8.4.2. Selection on TE sequences 183 8.5. The intriguing case of asexuals 183 8.6. Transposable element genomics 185 8.6.1. Transposition rates obtained in the lab 185 8.6.2. Comparative genomics of assembled genomes 186 8.6.3. Population genomics 187 8.7. Conclusion 188 8.8. References 189 Chapter 9. The Ecology of Transposable Elements 193 Pierre CAPY, Christian BIÉMONT and Cristina VIEIRA 9.1. Introduction 193 9.1.1. Lifecycle of a transposable element 193 9.1.2. Variability in the number of copies 196 9.1.3. What does the genome represent for a transposable element? 197 9.2. Cellular, population and specific dynamics 198 9.2.1. The dynamics of transposable elements vary from cell to cell 198 9.2.2. Interactions between groups of transposable elements within a genome 199 9.2.3. Transposable element environment and activity 200 9.2.4. Scales of structuring: from the copy to the ecosystem 201 9.3. The "genome ecology" approach 204 9.3.1. Ecological niche theory 205 9.3.2. Neutralist theory of biodiversity 206 9.3.3. Comments 210 9.4. Conclusion 210 9.5. References 211 Chapter 10. Transposable Elements as Tools 223 Chengyi SONG and Zoltán IVICS 10.1. Introduction 223 10.2. Development of DNA transposons as genetic tools 226 10.2.1. Discovery and de novo engineering of genetic tools based on active DNA transposons 10.2.2. DNA transposons popularly applied as genetic tools 227 10.2.3. Insertion preference and cargo capacity of DNA transposons 230 10.3. DNA transposons as efficient gene transfer tools applied in important model organisms 232 10.4. Insertional mutagenesis based on engineered transposons 233 10.5. Application of transposons in human gene therapy 237 10.5.1. Gene therapy in vivo 238 10.5.2. Ex vivo cell engineering with transposons 239 10.5.3. Induced pluripotent stem cell reprogramming with transposons 240 10.6. Transposase as an excision tool 241 10.7. Toward specific gene targeting by fusing transposases with other nucleases 242 10.8. Conclusion 243 10.9. References 244 Chapter 11. Genomic Characterization of Transposable Elements: Databases and Software 255 Gabriel DA LUZ WALLAU 11.1. Introduction 255 11.2. Databases 256 11.3. Search strategies for transposable element characterization. 260 11.4. Nature of input sequences 263 11.4.1. Raw reads 263 11.4.2. Draft or complete genome assembly 263 11.5. Population genomics of transposable elements 264 11.6. How to evaluate the most suitable database and TE/MGEs search strategy for your study? 267 11.7. Acknowledgments 268 11.8. References 268 List of Authors 273 Index 275

About the Author :
Aurélie Hua-Van is Professor of Biology at Paris-Saclay University, France. She teaches in various domains such as genetics, evolution, life origin and bioinformatics. Her research focuses on eukaryotic transposable elements evolution and dynamics, through experimental evolution and genomics. Pierre Capy is a former Professor of Biology at Paris-Saclay University, France. He taught evolutionary biology, quantitative genetics and genome plasticity, and always tried to create bridges between ecology and molecular biology. It is within this context that his research on transposable elements is placed.