Preface
Contents
List of Contributors
Chapter 1: Drosophila Satellite Repeats at the Intersection of Chromatin, Gene Regulation and Evolution
1.1 Introduction
1.2 Seeing the Dark Matter of the Genome
1.3 Biophysical Properties of Satellites
1.4 How Do Satellites Expand, Move and Change?
1.5 Evolution of Satellite Repeats Is Rapid and Driven
1.6 Satellites, Silencing, and Organization of Chromatin
1.7 Tandem Repeats in Euchromatin Modulate Nearby Genes
1.8 Chromosome Identification During Dosage Compensation
1.9 Satellites and Centromeres
1.10 Satellites Are the Ammunition of Genomic Conflicts
1.11 Satellite Repeats Mediate Conflict Between Species
References
Chapter 2: Structure, Organization, and Evolution of Satellite DNAs: Insights from the Drosophila repleta and D. virilis Speci...
2.1 Introduction
2.2 Contrasting Patterns in the repleta and virilis Groups
2.3 Testing Concerted Evolution
2.4 SatDNAs as Major (but Likely Not Exclusive) Components of Centromeres
2.5 Common Structural Features Among Centromeric satDNAs
2.6 Not Just Homogeneous Arrays
2.7 TE-Tandem Repeat Associations
2.8 Ξ²-Heterochromatin: Origin of New Tandem Repeats and the Chromatin Sink Hypothesis
2.9 Alternative Scenarios for Tandem Repeat Origin from TEs
2.10 Euchromatic satDNAs: It Depends
2.11 The Special Case of 154 TR: A Transitional satDNA?
References
Chapter 3: Exploring Satellite DNAs: Specificities of Bivalve Mollusks Genomes
3.1 Introduction
3.2 Chronology of Key Advancements in satDNA Research
3.2.1 Detection and Characterization of satDNAs in the Pre-genomic Era
3.2.2 SatDNA Studies in the Genomic Era
3.2.3 SatDNAs and the Third-Generation Sequencing
3.3 SatDNA Outside of the Heterochromatin and Their Association to Mobile Elements
3.4 The Importance of Bivalve Mollusks in Genome Research
3.5 Satellite DNAs and Heterochromatin in Bivalve Mollusks
3.5.1 Heterochromatin in Bivalves
3.5.2 Genome Sequencing and Repetitive DNA Characterization in Bivalve Mollusks
3.5.3 Extremely Long Ancestry of Bivalve satDNAs
3.5.4 Close Connection of Bivalve satDNAs to Mobile Elements
3.5.5 Conserved Boxes in satDNA Monomers of Bivalve Species
3.5.6 Low Abundance and a Large Palette of satDNAs in Bivalve Genomes Questioning the satDNA Library Concept
3.5.7 Methylation Patterns of satDNA Repeats
3.6 Future Perspectives
References
Chapter 4: Satellite DNA Is an Inseparable Fellow Traveler of B Chromosomes
4.1 Introduction
4.2 SatDNA Is the Prevalent Repetitive DNA on B Chromosomes in Some Species
4.3 SatDNA as Marker of B Chromosome Origin
4.4 Function of satDNA for B Chromosomes
4.5 Future Directions
References
Chapter 5: The Genomics of Plant Satellite DNA
5.1 Plant Satellite DNA
5.2 satDNA Origin and Evolution
5.3 satDNA Location, Organization, and Function
5.3.1 Centromeres and Pericentromeric Heterochromatin
5.3.2 Subtelomeric Heterochromatin
5.3.3 Interstitial Heterochromatin
5.3.4 Monomers
5.3.5 Monomer Signatures
5.3.6 satDNA Function
5.4 What Has Genomics Contributed to the Study of satDNAs?
5.4.1 On the Satellitome
5.4.2 On the Origin of satDNAs
5.4.3 On satDNA Function
5.5 Concluding Remarks and Perspectives
References
Chapter 6: Satellite DNA-Mediated Gene Expression Regulation: Physiological and Evolutionary Implication
6.1 Introduction
6.2 Proliferation and Dispersion of Satellite DNA Within Euchromatin
6.3 Satellite DNA Transcription: Heat Stress Activation
6.4 Satellite RNA and Euchromatic Satellite Repeats in Gene Expression Regulation
6.5 ``Macroheterochromatin´´ in Gene Expression Regulation
6.6 Satellite DNA Role in Stress Response and Environmental Adaptation
6.7 Satellite DNA in Pathological Transformation and Development
References
Chapter 7: Centromeres Transcription and Transcripts for Better and for Worse
7.1 Satellite DNA Underlies (Peri)centromeric Chromosomal Regions
7.1.1 Examples of Centromere Organization Across Species
7.2 Transcription of Centromeric Repeats and Their Transcripts
7.2.1 Regulation of Centromere Transcription/Transcripts Levels
7.2.2 Mechanisms of Transcriptional Regulation
7.2.2.1 Transcriptional Machinery at Centromeric Repeats
7.2.2.2 Transcription Factors
7.2.2.3 Histone Marks and DNA Methylation
7.3 Functional Relevance of Centromeric Transcripts/Transcription
7.3.1 Centromeres Transcription and Chromatin Remodeling Processes
7.3.2 Functional Relevance of Centromeric Transcripts themselves
7.3.3 Regulation of the Levels of (Peri)centromeric Transcripts Themselves
7.4 Centromeric Transcripts: Cause or Consequence of Disease?
7.4.1 Accumulation of Satellite Transcripts in Various Types of Cellular Stress
7.4.2 Deregulation of Satellite Transcription/Transcripts in Cancer
7.4.3 Deregulation of Satellite Transcripts in the ICF Syndrome
7.5 Conclusion
References
Chapter 8: Global Repeat Map (GRM): Advantageous Method for Discovery of Largest Higher-Order Repeats (HORs) in Neuroblastoma ...
8.1 Introduction
8.2 HORs and GRM
8.2.1 Higher-Order Repeats (HORs)
8.2.2 HOR-Searching and Monomer-Searching Methods
8.2.3 GRM Algorithm: A Robust Tool for Identification of Large Repeats and Higher-Order Repeats in a Given Genomic Sequence
8.3 Human-Specific NBPF HORs in Human Chromosome 1
8.3.1 The NBPF Gene Family with ~1.6 kb Primary Repeat
8.3.2 NBPF HORs in Human Chromosome 1 (Build 36.3 Human Genome Assembly) Determined Using HOR-Searching GRM Method
8.3.3 NBPF HORs in Human Chromosome 1 (hg38 Human Genome Assembly) Using HOR-Searching GRM Method
8.3.4 NBPF HORs in Neanderthal Genome and Evolution
8.3.5 NBPF HORs in Chimpanzee Genome and Cognitive Evolution
8.3.6 HOR-Searching Method Versus DUF1220-Monomer-Searching Method for NBPF Repeats
8.4 Unique Hornerine Quartic HOR Array Embedded Within One Hornerin Exon
8.5 33mer Alpha Satellite HOR in Human Chromosome 21: the Longest HOR Repeat Unit in Human Chromosomes
8.5.1 GRM Diagrams for 33mer, 23mer, 22mer, two 20mers, 16mer, 11mer, and 8mer in Human Chromosome 21
8.5.2 Dot-Matrix Analysis of HORs in Chromosome 21 Identified Using GRM Diagrams
8.5.3 Four Human Chromosomes, 21, 13, 22, and 14 Share the Same 33mer HOR in hg38 Assembly
8.5.4 Novel GRM Tandem Repeat Database
References