EVOLUTIONARY AND GENETIC BIOLOGY OF PRIMATES
1 A Glance at Evolution through the Genomic Window 1 Abstract 1 Introduction 2 Towards the Understanding of “The Mechanisms That Bring about Evolutionary Changes” 2 Genome Structures and New Concepts of Evolution 14 How Could Transposable Elements Contribute to Evolution? 21 Concluding Remarks: What about Genes That Make Us Humans? 25 2 Complex Genome Comparisons: Problems and Approaches 31 Abstract 31 Introduction: Complex Genomes—The Ocean of Cryptic Information 31 Classification of Comparative Techniques 32 Information Content and Resolution Power of Different Methods for Complex Genome Comparisons 34 Random Displays: From Fingerprinting to Flowthrough-Based Assays 35 Display Methods Targeted at the Flanks of Interspersed Repetitive Elements 38 DNA Microarrays As a New Tool to Display Genomic Differences 40 Genomic Subtractive Hybridization 42 Conclusion 45 3 A Brief Introduction to Primate Evolution 51 Abstract 51 Introduction 51 The Problem of Primate Definition 52 Linking Primates to Other Eutherian Orders 53 The Major Groups of Primates 56 Evolution of Anatomically Modern Humans 64 Concluding Remarks 65 4 How Different Is the Human Genome from the Genomes of the Great Apes? 68 Abstract 68 Introduction 68 First Human—Chimpanzee Molecular Comparisons: Changes in Regulatory Systems Are Most Important for Speciation 71 General Characteristics of Interspecies Divergence and Intraspecies Polymorphisms in Hominoids 72 Differences between Particular Elements of the Hominoid Genomes 78 Conclusion: A Supercomplex Disease—To Be a Human 84 5 Retroviruses, Their Domesticated Relatives and Other Retroinvaders: Potential Genetic and Epigenetic Mediators of Phenotypic Variation 93 Abstract 93 Introduction: Continuum of The Retroworld 93 Retroviral Particles 94 Retroviral RNA Genome 95 Retroviral Life Cycle 97 Taxonomy of Retroviruses 98 Endogenization of Exogenous Retroviruses 98 Army of Retroelements in the Human Genome 99 Some Traditionally Discussed Functional Potentials of Retroelements 100 Stochastic Drivers of Organismal Epigenetic Mosaicism All of Us Are Probably Complex Epigenetic Mosaics, and What? 101 Concluding Remarks 102 6 Genomic Distributions of Human Retroelements 104 Abstract 104 Introduction 104 Types of Human Retroelements 104 Effects of Transposable Elements on Genomes 106 Integration Patterns of Exogenous Retroviruses 106 Impact of Genetic Drift and Selection 107 Insights from Other Species 107 Experimental Determinations of Distributions 109 Large Scale Analysis of Retroelement Distributions 110 Retroelement Distributions Relative to Genes 113 Retroelements and the Y Chromosome 116 Genomic Clearance of Retroelements 118 Concluding Remarks 118 7 Influence of Human Endogenous Retroviruses on Cellular Gene Expression 123 Abstract 123 Introduction 123 Variations in LTR Structure and Activity of Different HERV Families 123 Endogenous and Exogenous Factors Influencing HERV Expression 129 Modulation of Cellular Gene Expression 130 Concluding Remarks 139 8 Genome-Wide Search for Human Specific Retroelements 144 Abstract 144 Introduction: Hypotheses Are Indispensable on the Way towards Understanding the Genetic Basis of Humankind Evolution 144 Retroelement Families and Subfamilies in the Homo Sapiens Genome 145 What Makes REs Possible Candidates for Evolutionary Pacemakers? 146 Strategies and Approaches to the Genome-Wide Identification of Human-Specific RE Integrations 148 Concluding Remarks 156 9 Genome-Wide Analysis of Human Gene Expression: Application to the Expression of Human Endogenous Retroviruses 162 Abstract 162 Introduction: What Is the Function of a Genomic Constituent? 162 Detection of Gene Expression and Comparative Analysis of the Expression Using Cross-Hybridization of the Samples Under Comparison 163 Methods of Detection and Comparison of Transcripts Avoiding Denaturation-Renaturation Steps 171 Concluding Remarks 182 10 Phylogeny of Human Endogenous and Exogenous Retroviruses 186 Abstract 186 Introduction 186 Identification and Phylogenetic Reconstruction of Endogenous Retroviruses in the Human Genome 188 HERV Lineages within Retroviral Phylogeny 189 Characterization of New Families 194 Further Characterization of Previously Reported Families 196 Relationships between HERVs and Exogenous Retroviruses 196 Ancient and Modern HERV Families 198 Concluding Remarks: Prospects for HERV Phylogenetics 200 11 Evolutionary Aspects of Human Endogenous Retroviral Sequences (HERVs) and Disease 204 Abstract 204 Introduction 204 Animal ERVs and Disease 205 Events following Endogenization of a Retrovirus 206 Active HERVs, Expressed As Particles or As Proteins 209 Diseases Where a Connection with HERVs Has Been Implicated 215 What Can Be Done to Demonstrate a HERV-Disease Connection? 228 Conclusions 229