Function and Evolution of Repeated DNA Sequences

Guy-Franck Richard is a research director at Institut Pasteur, France. He also leads a team within the CNRS unit Génétique des génomes. His research focuses on the stability and evolution of repeated DNA sequences in eukaryotic organisms.

• Foreword xiiiBernard DUJONIntroduction xvGuy-Franck RICHARDChapter 1 Whole-Genome Duplications, a Source of Redundancy at the Entire-Genome Scale 1Elise PAREY and Camille BERTHELOT1.1 Prevalence of polyploids in the tree of life 21.1.1 Whole duplications in eukaryotes 21.1.2 Polyploidies in prokaryotic organisms 61.1.3 Polyploid cells in normal and pathological physiology 71.2 Mechanisms for the appearance of whole-genome duplications 71.2.1 Non-separation of chromosomes after replication 71.2.2 Autopolyploidization, a perfect genome redundancy 91.2.3 Allopolyploidization, an overlapping of genomes of similar species 91.3 Cellular consequences of whole-genome duplications 111.3.1 Disruption of cell and nucleus organization 111.3.2 Modifications in the expression of genes and transposons 131.3.3 Unstable meiosis 151.4 Rediploidization: evolutionary reduction in genetic redundancy 161.4.1 Resolution of meiosis by karyotype rearrangement 161.4.2 Evolutionary divergence of duplicated sequences 181.4.3 Bias and dominance during rediploidization 201.4.4 Incomplete and lineage-specific rediploidizations 211.5 Functions and evolution of duplicated genes 221.5.1 Redundancy and subfunctionalization 231.5.2 Neofunctionalization and evolutionary innovations 241.5.3 Gene repertoire bias 261.5.4 Regulatory blocks and splitting of regulatory regions 291.6 Whole-genome duplications and evolutionary diversification 321.6.1 Association with geological crises 321.6.2 Evolutionary speciations and radiations 331.7 Perspectives and conclusions 341.8 References 35Chapter 2 Segmental Duplications and CNVs: Adaptive Potential of Structural Polymorphism 47Patricia BALARESQUE and Franklin DELEHELLE2.1 The multiple facets of genetic polymorphism 482.2 From Segmental Duplications to Copy Number Variants: terminology 492.3 SDs: a general overview 492.3.1 Background 492.3.2 SDs: more than a category of sequences, superstructures 502.3.3 SD and CNV: study biases related to the attractiveness of subjects as well as to the technological developments of the moment 512.3.4 SD: characteristics in human and non-human primates 522.4 Methodologies for detecting structural variation in genomes 532.4.1 In vitro methods 542.4.2 Methods on reads 542.4.3 Post-assembly methods 542.5 The molecular mechanisms at the origin of structural variation 562.5.1 Homologous recombination mechanisms 562.5.2 Non-homologous recombination mechanisms 572.6 Regions rich in SDs/LCRs favor the creation of CNVs: insertions/duplications, deletions and inversions 582.6.1 Insertions/duplications and deletions 582.6.2 Inversions 602.7 From SDs to CNVs in humans and primates 612.7.1 General overview 612.7.2 Delineating regions of interest 612.7.3 Heterogeneity in the distribution of intra- and interchromosomal SDs 622.7.4 Intrachromosomal and interchromosomal SDs: what do they teach us about the evolutionary history and origin of SDs? 622.7.5 Intra- and interchromosomal SDs: the specific case of sex chromosomes 662.7.6 SDs: an association with specific sequences? 662.8 SDs in little-studied species: general genomic profiles 662.8.1 Twelve genomes under study 682.8.2 Distribution and characteristics of SDs in genomes 702.9 SD content: impact of a duplicated environment on sequences that make up the SDs 702.9.1 SDs and non-coding sequences: the case of microsatellites 712.9.2 SDs and coding genes: the fate of genes in SDs 722.10 SDs and epigenetic modifications 752.11 The adaptive potential of SDs: between the benefit of innovation and the cost of pathology 782.11.1 The organism’s defense: immune system 792.11.2 Nutrient/food assimilation 802.11.3 Sensory perception of the environment 802.11.4 Neurological processes 822.11.5 Reproduction and the X and Y chromosomes: true SD concentrates 832.12 SDs and associated CNVs: their roles in species adaptation to changes in environments 862.12.1 SDs: a link between genomic architecture, adaptive potential and environmental changes? 862.12.2 Adaptation to global environmental stress 862.12.3 Adaptation to nutrient-poor surroundings 882.12.4 Adaptation to low and high temperatures 882.12.5 Heavy-metal adaptation 892.12.6 Antibiotics and drugs 902.12.7 Pesticide resistance 902.12.8 Domestication and post-domestication of plant and animal species 912.12.9 Competition and evolutionary success: invasive species and hybridization 932.13 Conclusion 942.14 Glossary of terms 952.15 References 96Chapter 3 Transposable Elements: Parasites that Shape Genome Evolution 117Amandine BONNET, Karine CASIER, Clément CARRÉ, Laure TEYSSET and Pascale LESAGE3.1 Transposable elements in eukaryotic genomes 1173.1.1 TEs: essential components of eukaryotic genomes 1183.1.2 Acquisition of new TEs by horizontal transfer 1193.2 Classification of TEs and transposition mechanisms 1203.2.1 Class I retrotransposons 1203.2.2 Class II DNA transposons 1233.3 TE self-regulation 1233.3.1 Spatio-temporal regulation of TE expression 1243.3.2 Self-regulation of transposition efficiency 1253.3.3 Selective integration to better protect the genome 1253.4 TE restriction by the host 1293.4.1 Transcriptional repression of genomic copies 1293.4.2 TE transcripts: choice targets for multiple restrictions 1323.4.3 The Swiss knives of TE restriction: piRNAs 1343.4.4 Reverse transcription of retroelements: a key step to inhibit 1393.5 The impact of transposition events on genomes 1403.5.1 The structural and functional consequences of TE activity on the genome 1403.5.2 Pathologies associated with TE activity 1443.5.3 The impact of TEs on the evolution of the host 1483.6 Conclusion 1553.7 References 156Chapter 4 Insights Into the Evolutionary Diversity of Centromeres 181Nuria CORTES-SILVA, Aruni P SENARATNE and Ines A DRINNENBERG4.1 The centromere 1814.1.1 Definition and historical background 1814.1.2 Two main types of centromeric architectures 1834.2 Monocentromeres 1844.2.1 The diversity of monocentric architectures across fungi 1844.2.2 Animal and plant models contain long repetitive regional centromeres 1904.3 Holocentromeres 1924.3.1 Nematodes 1934.3.2 Plants 1954.3.3 Insects 1964.4 Open questions 1984.5 Acknowledgments 1984.6 References 198Chapter 5 Evolution and Functions of Telomeres 207Arturo LONDOÑO-VALLEJO5.1 Primary structure of telomeres 2075.1.1 Origin and evolution of telomeres 2105.1.2 Nucleoprotein structure of telomeres 2125.2 A telomere specific higher order structure: the T-loop 2155.2.1 Telomere replication, a fundamental mechanism for telomere maintenance 2155.3 Telomere lengthening mechanisms 2205.4 Telomere length homeostasis 2225.5 Telomeres and genome organization and function 2255.6 Cell senescence, aging and disease 2265.7 Conclusion 2275.8 Acknowledgments 2275.9 References 227Chapter 6 G-quadruplexes: Structure, Detection and Functions 239Emilia Puig LOMBARDI6.1 From guanine-guanine base-pairing to a secondary structure 2396.1.1 G-quartets 2396.1.2 Folding into a G-quadruplex structure 2416.2 The G4 structure: variations on a theme 2436.2.1 RNA G-quadruplexes (rG4) 2456.2.2 Exceptions to the rule(s): non-canonical G-quadruplexes 2456.3 Finding G-quadruplexes in a genome 2466.3.1 Experimental methods for G-quadruplex detection 2476.3.2 Computational methods 2506.4 Biological roles of G-quadruplexes 2576.4.1 First role attributed to quadruplexes: their formation intelomeres 2576.4.2 Predictions based on bioinformatic analyses 2596.5 Perspective: G-quadruplexes as anticancer therapeutic targets 2616.6 References 264Chapter 7 Satellite DNA, Microsatellites and Minisatellites 273Wilhelm VAYSSE–ZINKHÖFER and Guy-Franck RICHARD7.1 Satellite DNAs, origin and definition 2737.1.1 Minisatellites 2747.1.2 Microsatellites 2747.2 From semantics to biology 2757.2.1 Distribution of satellite DNAs in genomes 2757.2.2 Polymorphic genetic markers 2777.2.3 Trinucleotide repeat expansions 2817.2.4 Microsatellites regulate gene expression 2837.2.5 Minisatellites are important in cell adhesion 2857.2.6 Function of megasatellites 2877.2.7 Centromeric satellite DNA, complexity of structure–function studies 2887.3 The evolutionary mechanisms of tandem repeats 2897.3.1 Historical model of slippage during replication 2907.3.2 Slippage during DNA repair 2927.3.3 Repeat expansions and contractions during homologous recombination 2927.4 Microsatellites in human diseases 2977.4.1 Triplet repeat expansion disorders 2977.4.2 Colorectal cancers and the mismatch repair system 2987.4.3 Fragile sites 2997.5 De novo formation and evolution of tandem repeats 3007.5.1 Birth and death of microsatellites 3007.5.2 Formation of minisatellites 3047.6 Perspectives 3077.6.1 Inadequacy of software tools 3077.6.2 The importance of definitions in biology 3107.7 Acknowledgments 3117.8 References 311Chapter 8 CRISPR-Cas: An Adaptive Immune System 319Marie TOUCHON8.1 A brief history of the discovery of CRISPR-Cas systems 3198.2 General characteristics of CRISPR-Cas systems 3238.2.1 Diversity of repeats 3248.2.2 Diversity and origin of spacers 3258.2.3 Diversity and evolutionary classification of cas genes 3278.2.4 Origin of CRISPR-Cas systems 3298.3 Evolution of CRISPR-Cas systems 3308.3.1 Scattered distribution of CRISPR-Cas systems 3308.3.2 Massive transfer of CRISPR-Cas systems 3318.3.3 Commonly lost systems 3328.3.4 Evolutionary dynamics of CRISPR arrays 3338.4 An adaptive immune system 3348.4.1 A three-stage immune response 3348.4.2 Diversity of CRISPR-Cas molecular mechanisms 3378.4.3 Self- and none self-discrimination: avoiding self-targeting by CRISPR 3408.5 Phage escape mechanisms 3418.5.1 Genomic modifications 3418.5.2 Anti-CRISPR proteins 3438.6 Biological cost of CRISPR-Cas systems 3448.6.1 Cost of expression 3448.6.2 Cost of autoimmunity 3458.6.3 The genetic background of the host 3468.6.4 Limiting horizontal gene transfer 3478.6.5 Naïve and primed adaptation 3488.7 Importance in nature: impact of ecological factors 3498.7.1 Phage diversity – mutation rate 3498.7.2 Phage diversity – population size 3508.7.3 Infectious risk – alternative strategies 3508.8 Conclusions and perspectives 3518.9 References 353List of Authors 361Index 363