Transposable Elements and Genome Evolution

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.

• Acknowledgments xiiiAurélie HUA-VAN and Pierre CAPYIntroduction xvAurélie HUA-VAN and Pierre CAPYChapter 1. Transposable Elements in Eukaryotes 1Aurélie HUA-VAN1.1. Introduction 11.2. Classification, structure and transposition mechanism 21.2.1. Class I 41.2.2. Class II 71.2.3. Autonomous, non-autonomous and relics 101.3. Abundance, diversity and distribution 101.4. Origins of transposable elements and evolutionary relationships with other genetic elements 121.5. Genomic impact 141.5.1. Genome size 151.5.2. Genome structure 151.5.3. Genome function and evolution 161.6. References 17Chapter 2. Prokaryotic Transposable Elements 21Alessandro M. VARANI, Karen E. ROSS and Mick CHANDLER2.1. Introduction 212.1.1. Historical 212.1.2. Relationship between IS and transposons 222.1.3. The prokaryotic TE landscape 232.2. Transposases: the enzymes driving transposition 252.2.1. DDE enzymes 252.2.2. HUH enzymes 272.3. Insertion sequences 282.3.1. Overview 282.3.2. Impact 292.3.3. IS diversity 302.3.4. IS-related elements: tIS, MITEs and MICs 302.4. Transposons (Tn) 322.4.1. Compound transposons 322.4.2. Pseudocompound transposons, targeted insertion and translocatable units (TU) 332.4.3. Unit transposons with DDE transposases 342.4.4. Transposon using CRISPR components 452.4.5. Mobile elements which move using site-specific recombinases 462.5. Conclusion 522.6. References 53Chapter 3. Transposable Elements and Human Diseases 61Benoît CHÉNAIS3.1. The moving parts of the human genome 613.2. TE insertion and its impact on the genome and gene expression 643.2.1. Chromosomal rearrangements 643.2.2. Modification of gene structure and expression by TE insertion 663.2.3. Escaping epigenetic control 683.3. TE involvement in human cancers 693.3.1. Inserting LINE-1 693.3.2. Insertion of Alu sequences and chromosomal recombination 703.3.3. Epigenetic alterations due to TE and cancer 723.4. Involvement of TEs in noncancerous pathologies 723.4.1. Implications of TE in hemoglobinopathies 723.4.2. Implications of TEs in metabolic diseases or diseases linked to metabolic genes 733.4.3. Implications of TEs in neurological diseases 763.4.4. Implications of TE in various other diseases 773.4.5. Link between TE and common diseases 783.5. The role of stress and environmental pollution in TE mobility 793.5.1. Epigenetic alterations caused by environmental pollutants 793.5.2. Methylation and mobility of LINE-1 elements in response to environmental stresses 803.5.3. Influence of occupational and psychosocial stresses on the mobility of LINE-1 elements 813.6. Conclusion 823.7. References 82Chapter 4. The Silencing Mechanisms Inhibiting Transposable Element Activity in Somatic and Germ Cells 91Chantal VAURY4.1. Introduction 914.2. Silencing of transposable elements in somatic tissues 924.2.1. Mechanisms that ensure deposition of epigenetic hallmarks at TEs 924.2.2. Inheritance of the epigenetic state of TEs through cell division 954.2.3. Influence of environmental stresses on TE control in somatic cells 964.3. Silencing of transposable elements in the germline 974.3.1. The piRNA pathway in ovarian germ cells 974.3.2. Additional strategies used to silence TEs in the germline 1004.4. The specific case of somatic cells surrounding the germline 1024.5. Transmission of silencing through generations 1034.6. Environmental stresses and their influence on TEs 1054.7. Conclusion 1074.8. References 107Chapter 5. Transposable Elements and Adaptation 115Marta CORONADO-ZAMORA and Josefa GONZÁLEZ5.1. Transposable elements are mobile genomic sequences 1155.1.1. Transposable elements are diverse genomic sequences 1165.1.2. Transposable elements generate different types of mutations 1175.2. Transposable elements and insecticide resistance 1195.2.1. Transposable elements and metabolic resistance 1205.2.2. Target resistance and transposable elements 1235.3. Transposable elements and the immune response 1255.4. Transposable elements and environmental shock response 1265.5. Conclusion 1305.6. Acknowledgments 1305.7. References 131Chapter 6. Domestication (Exaptation) of Transposable Elements 135Christopher ELLISON6.1. Introduction 1356.2. Host genes derived from transposons 1376.2.1. Repeated domestication of transposases 1376.2.2. Repeated domestication of envelope genes 1406.3. TEs can disperse noncoding regulatory sequences across the genome 1416.4. TEs form structural components of the genome 1436.4.1. Transposons function in centromere specification 1436.4.2. Transposons act as telomeres in Drosophila 1446.5. Summary 1456.6. References 145Chapter 7. Horizontal Transfers and Transposable Elements 149Emmanuelle LERAT7.1. Introduction 1497.2. Mechanisms and prerequisites for horizontal transfers of transposable elements 1527.2.1. Direct transmission 1527.2.2. Transmission by a viral vector 1537.2.3. Transmission via host–pathogen interactions 1557.2.4. Factors for successful horizontal transfer of transposable elements 1567.3. Bioinformatics methods for detecting horizontal transfer of transposable elements 1577.3.1. HTdetect 1587.3.2. VHICA 1597.4. Documented examples of horizontal transfers of transposable elements 1607.5. The impact of horizontal transfers of transposable elements 1637.5.1. Adaptation and creation of gene novelties 1637.5.2. The appearance of new species 1647.6. Conclusion 1657.7. References 165Chapter 8. Genome Invasion Dynamics 175Arnaud LE ROUZIC and Aurélie HUA-VAN8.1. The lifecycle of transposable elements 1758.2. Transposable elements as parasites of sexual reproduction 1778.2.1. Amplification 1778.2.2. The selfish DNA model 1778.3. Limiting the spread 1788.3.1. Natural selection 1798.3.2. Transposition regulation 1818.4. Long-term evolution 1828.4.1. Interactions between TE copies 1828.4.2. Selection on TE sequences 1838.5. The intriguing case of asexuals 1838.6. Transposable element genomics 1858.6.1. Transposition rates obtained in the lab 1858.6.2. Comparative genomics of assembled genomes 1868.6.3. Population genomics 1878.7. Conclusion 1888.8. References 189Chapter 9. The Ecology of Transposable Elements 193Pierre CAPY, Christian BIÉMONT and Cristina VIEIRA9.1. Introduction 1939.1.1. Lifecycle of a transposable element 1939.1.2. Variability in the number of copies 1969.1.3. What does the genome represent for a transposable element? 1979.2. Cellular, population and specific dynamics 1989.2.1. The dynamics of transposable elements vary from cell to cell 1989.2.2. Interactions between groups of transposable elements within a genome 1999.2.3. Transposable element environment and activity 2009.2.4. Scales of structuring: from the copy to the ecosystem 2019.3. The "genome ecology" approach 2049.3.1. Ecological niche theory 2059.3.2. Neutralist theory of biodiversity 2069.3.3. Comments 2109.4. Conclusion 2109.5. References 211Chapter 10. Transposable Elements as Tools 223Chengyi SONG and Zoltán IVICS10.1. Introduction 22310.2. Development of DNA transposons as genetic tools 22610.2.1. Discovery and de novo engineering of genetic tools based on active DNA transposons10.2.2. DNA transposons popularly applied as genetic tools 22710.2.3. Insertion preference and cargo capacity of DNA transposons 23010.3. DNA transposons as efficient gene transfer tools applied in important model organisms 23210.4. Insertional mutagenesis based on engineered transposons 23310.5. Application of transposons in human gene therapy 23710.5.1. Gene therapy in vivo 23810.5.2. Ex vivo cell engineering with transposons 23910.5.3. Induced pluripotent stem cell reprogramming with transposons 24010.6. Transposase as an excision tool 24110.7. Toward specific gene targeting by fusing transposases with other nucleases 24210.8. Conclusion 24310.9. References 244Chapter 11. Genomic Characterization of Transposable Elements: Databases and Software 255Gabriel DA LUZ WALLAU11.1. Introduction 25511.2. Databases 25611.3. Search strategies for transposable element characterization. 26011.4. Nature of input sequences 26311.4.1. Raw reads 26311.4.2. Draft or complete genome assembly 26311.5. Population genomics of transposable elements 26411.6. How to evaluate the most suitable database and TE/MGEs search strategy for your study? 26711.7. Acknowledgments 26811.8. References 268List of Authors 273Index 275