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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 elucidati...

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Bibliographic Details
Other Authors: Richard, Guy-Franck (Editor)
Format: eBook
Language:English
Published: London, UK : Hoboken, NJ : ISTE, Ltd. ; John Wiley & Sons, Inc., 2023.
Series:Biology. Genetics, epigenetics
Subjects:
Nucleotide sequence.
Online Access:Connect to the full text of this electronic book
Table of Contents:
  • 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.