http://www.loc.gov/mods/v3 http://www.loc.gov/standards/mods/v3/mods-3-2.xsd
Function and evolution of repeated DNA sequences
The genome of a living being is composed of DNA sequences with diverse origins. Beyond single-copy genes, whose product has a biological function that can be inferred by experimentation, certain DNA sequences, present in a large number of copies, escape the most refined approaches aimed at elucidating their precise role. The existence of what 20th century geneticists had already perceived (and wrongly described as "junk DNA"!) was confirmed by the sequencing of the first complex genomes, including that of Homo sapiens. A large part of what defines a living thing is not unique, but repeated, sometimes a very large number of times, increasing in complexity with successive duplications and multiplication. Understanding and defining the many functions of this myriad of repeated sequences, as well as their evolution through natural selection, has become one of the major challenges for 21st century genomics.
Foreword xiii Bernard DUJON -- Introduction xv Guy-Franck RICHARD -- Chapter 1 Whole-Genome Duplications, a Source of Redundancy at the Entire-Genome Scale 1 Elise PAREY and Camille BERTHELOT -- 1.1 Prevalence of polyploids in the tree of life -- 1.1.1 Whole duplications in eukaryotes -- 1.1.2 Polyploidies in prokaryotic organisms -- 1.1.3 Polyploid cells in normal and pathological physiology -- 1.2 Mechanisms for the appearance of whole-genome duplications -- 1.2.1 Non-separation of chromosomes after replication -- 1.2.2 Autopolyploidization, a perfect genome redundancy -- 1.2.3 Allopolyploidization, an overlapping of genomes of similar species -- 1.3 Cellular consequences of whole-genome duplications -- 1.3.1 Disruption of cell and nucleus organization -- 1.3.2 Modifications in the expression of genes and transposons -- 1.3.3 Unstable meiosis -- 1.4 Rediploidization: evolutionary reduction in genetic redundancy -- 1.4.1 Resolution of meiosis by karyotype rearrangement -- 1.4.2 Evolutionary divergence of duplicated sequences -- 1.4.3 Bias and dominance during rediploidization -- 1.4.4 Incomplete and lineage-specific rediploidizations -- 1.5 Functions and evolution of duplicated genes -- 1.5.1 Redundancy and subfunctionalization -- 1.5.2 Neofunctionalization and evolutionary innovations -- 1.5.3 Gene repertoire bias -- 1.5.4 Regulatory blocks and splitting of regulatory regions -- 1.6 Whole-genome duplications and evolutionary diversification -- 1.6.1 Association with geological crises -- 1.6.2 Evolutionary speciations and radiations -- 1.7 Perspectives and conclusions -- 1.8 References -- Chapter 2 Segmental Duplications and CNVs: Adaptive Potential of Structural Polymorphism 47 Patricia BALARESQUE and Franklin DELEHELLE -- 2.1 The multiple facets of genetic polymorphism -- 2.2 From Segmental Duplications to Copy Number Variants: terminology -- 2.3 SDs: a general overview -- 2.3.1 Background -- 2.3.2 SDs: more than a category of sequences, superstructures -- 2.3.3 SD and CNV: study biases related to the attractiveness of subjects as well as to the technological developments of the moment -- 2.3.4 SD: characteristics in human and non-human primates -- 2.4 Methodologies for detecting structural variation in genomes -- 2.4.1 In vitro methods -- 2.4.2 Methods on reads -- 2.4.3 Post-assembly methods -- 2.5 The molecular mechanisms at the origin of structural variation -- 2.5.1 Homologous recombination mechanisms -- 2.5.2 Non-homologous recombination mechanisms -- 2.6 Regions rich in SDs/LCRs favor the creation of CNVs: insertions/duplications, deletions and inversions -- 2.6.1 Insertions/duplications and deletions -- 2.6.2 Inversions -- 2.7 From SDs to CNVs in humans and primates -- 2.7.1 General overview -- 2.7.2 Delineating regions of interest -- 2.7.3 Heterogeneity in the distribution of intra- and interchromosomal SDs -- 2.7.4 Intrachromosomal and interchromosomal SDs: what do they teach us about the evolutionary history and origin of SDs? -- 2.7.5 Intra- and interchromosomal SDs: the specific case of sex chromosomes -- 2.7.6 SDs: an association with specific sequences? -- 2.8 SDs in little-studied species: general genomic profiles -- 2.8.1 Twelve genomes under study -- 2.8.2 Distribution and characteristics of SDs in genomes -- 2.9 SD content: impact of a duplicated environment on sequences that make up the SDs -- 2.9.1 SDs and non-coding sequences: the case of microsatellites -- 2.9.2 SDs and coding genes: the fate of genes in SDs -- 2.10 SDs and epigenetic modifications -- 2.11 The adaptive potential of SDs: between the benefit of innovation and the cost of pathology -- 2.11.1 The organism's defense: immune system -- 2.11.2 Nutrient/food assimilation -- 2.11.3 Sensory perception of the environment -- 2.11.4 Neurological processes -- 2.11.5 Reproduction and the X and Y chromosomes: true SD concentrates -- 2.12 SDs and associated CNVs: their roles in species adaptation to changes in environments -- 2.12.1 SDs: a link between genomic architecture, adaptive potential and environmental changes? -- 2.12.2 Adaptation to global environmental stress -- 2.12.3 Adaptation to nutrient-poor surroundings -- 2.12.4 Adaptation to low and high temperatures -- 2.12.5 Heavy-metal adaptation -- 2.12.6 Antibiotics and drugs -- 2.12.7 Pesticide resistance -- 2.12.8 Domestication and post-domestication of plant and animal species -- 2.12.9 Competition and evolutionary success: invasive species and hybridization -- 2.13 Conclusion -- 2.14 Glossary of terms -- 2.15 References -- Chapter 3 Transposable Elements: Parasites that Shape Genome Evolution 117 Amandine BONNET, Karine CASIER, Clement CARRE, Laure TEYSSET and Pascale LESAGE -- 3.1 Transposable elements in eukaryotic genomes -- 3.1.1 TEs: essential components of eukaryotic genomes -- 3.1.2 Acquisition of new TEs by horizontal transfer -- 3.2 Classification of TEs and transposition mechanisms -- 3.2.1 Class I retrotransposons -- 3.2.2 Class II DNA transposons -- 3.3 TE self-regulation -- 3.3.1 Spatio-temporal regulation of TE expression -- 3.3.2 Self-regulation of transposition efficiency -- 3.3.3 Selective integration to better protect the genome -- 3.4 TE restriction by the host -- 3.4.1 Transcriptional repression of genomic copies -- 3.4.2 TE transcripts: choice targets for multiple restrictions -- 3.4.3 The Swiss knives of TE restriction: piRNAs -- 3.4.4 Reverse transcription of retroelements: a key step to inhibit -- 3.5 The impact of transposition events on genomes -- 3.5.1 The structural and functional consequences of TE activity on the genome -- 3.5.2 Pathologies associated with TE activity -- 3.5.3 The impact of TEs on the evolution of the host -- 3.6 Conclusion -- 3.7 References -- Chapter 4 Insights Into the Evolutionary Diversity of Centromeres 181 Nuria CORTES-SILVA, Aruni P SENARATNE and Ines A DRINNENBERG -- 4.1 The centromere -- 4.1.1 Definition and historical background -- 4.1.2 Two main types of centromeric architectures -- 4.2 Monocentromeres -- 4.2.1 The diversity of monocentric architectures across fungi -- 4.2.2 Animal and plant models contain long repetitive regional centromeres -- 4.3 Holocentromeres -- 4.3.1 Nematodes -- 4.3.2 Plants -- 4.3.3 Insects -- 4.4 Open questions -- 4.5 Acknowledgments -- 4.6 References -- Chapter 5 Evolution and Functions of Telomeres 207 Arturo LONDONO-VALLEJO -- 5.1 Primary structure of telomeres -- 5.1.1 Origin and evolution of telomeres -- 5.1.2 Nucleoprotein structure of telomeres -- 5.2 A telomere specific higher order structure: the T-loop -- 5.2.1 Telomere replication, a fundamental mechanism for telomere maintenance -- 5.3 Telomere lengthening mechanisms -- 5.4 Telomere length homeostasis -- 5.5 Telomeres and genome organization and function -- 5.6 Cell senescence, aging and disease -- 5.7 Conclusion -- 5.8 Acknowledgments -- 5.9 References -- Chapter 6 G-quadruplexes: Structure, Detection and Functions 239 Emilia Puig LOMBARDI -- 6.1 From guanine-guanine base-pairing to a secondary structure -- 6.1.1 G-quartets -- 6.1.2 Folding into a G-quadruplex structure -- 6.2 The G4 structure: variations on a theme -- 6.2.1 RNA G-quadruplexes (rG4) -- 6.2.2 Exceptions to the rule(s): non-canonical G-quadruplexes -- 6.3 Finding G-quadruplexes in a genome -- 6.3.1 Experimental methods for G-quadruplex detection -- 6.3.2 Computational methods -- 6.4 Biological roles of G-quadruplexes -- 6.4.1 First role attributed to quadruplexes: their formation -- telomeres -- 6.4.2 Predictions based on bioinformatic analyses -- 6.5 Perspective: G-quadruplexes as anticancer therapeutic targets -- 6.6 References -- Chapter 7 Satellite DNA, Microsatellites and Minisatellites 273 Wilhelm VAYSSE-ZINKHOFER and Guy-Franck RICHARD -- 7.1 Satellite DNAs, origin and definition -- 7.1.1 Minisatellites -- 7.1.2 Microsatellites -- 7.2 From semantics to biology -- 7.2.1 Distribution of satellite DNAs in genomes -- 7.2.2 Polymorphic genetic markers -- 7.2.3 Trinucleotide repeat expansions -- 7.2.4 Microsatellites regulate gene expression -- 7.2.5 Minisatellites are important in cell adhesion -- 7.2.6 Function of megasatellites -- 7.2.7 Centromeric satellite DNA, complexity of structure-function studies -- 7.3 The evolutionary mechanisms of tandem repeats -- 7.3.1 Historical model of slippage during replication -- 7.3.2 Slippage during DNA repair -- 7.3.3 Repeat expansions and contractions during homologous recombination -- 7.4 Microsatellites in human diseases -- 7.4.1
Triplet repeat expansion disorders -- 7.4.2 Colorectal cancers and the mismatch repair system -- 7.4.3 Fragile sites -- 7.5 De novo fo.
rmation and evolution of tandem repeats -- 7.5.1 Birth and death of microsatellites -- 7.5.2 Formation of minisatellites -- 7.6 Perspectives -- 7.6.1 Inadequacy of software tools -- 7.6.2 The importance of definitions in biology -- 7.7 Acknowledgments -- 7.8 References -- Chapter 8 CRISPR-Cas: An Adaptive Immune System 319 Marie TOUCHON -- 8.1 A brief history of the discovery of CRISPR-Cas systems -- 8.2 General characteristics of CRISPR-Cas systems -- 8.2.1 Diversity of repeats -- 8.2.2 Diversity and origin of spacers -- 8.2.3 Diversity and evolutionary classification of cas genes -- 8.2.4 Origin of CRISPR-Cas systems -- 8.3 Evolution of CRISPR-Cas systems -- 8.3.1 Scattered distribution of CRISPR-Cas systems -- 8.3.2 Massive transfer of CRISPR-Cas systems -- 8.3.3 Commonly lost systems -- 8.3.4 Evolutionary dynamics of CRISPR arrays -- 8.4 An adaptive immune system -- 8.4.1 A three-stage immune response -- 8.4.2 Diversity of CRISPR-Cas molecular mechanisms -- 8.4.3 Self- and none self-discrimination: avoiding self-targeting by CRISPR -- 8.5 Phage escape mechanisms -- 8.5.1 Genomic modifications -- 8.5.2 Anti-CRISPR proteins -- 8.6 Biological cost of CRISPR-Cas systems -- 8.6.1 Cost of expression -- 8.6.2 Cost of autoimmunity -- 8.6.3 The genetic background of the host -- 8.6.4 Limiting horizontal gene transfer -- 8.6.5 Naive and primed adaptation -- 8.7 Importance in nature: impact of ecological factors -- 8.7.1 Phage diversity - mutation rate -- 8.7.2 Phage diversity - population size -- 8.7.3 Infectious risk - alternative strategies -- 8.8 Conclusions and perspectives -- 8.9 References -- List of Authors -- Index.