Preface

Abbreviations

A Glance at Evolution through the Genomic Window

(30)

Eugene D. Sverdlov

Abstract

(1)

Introduction

(1)

Towards the Understanding of ``The Mechanisms That Bring about Evolutionary Changes''

(12)

Genome Structures and New Concepts of Evolution

(7)

How Could Transposable Elements Contribute to Evolution?

(4)

Concluding Remarks: What about Genes That Make Us Humans?

(6)

Complex Genome Comparisons: Problems and Approaches

(20)

Natalia E. Broude

Eugene D. Sverdlov

Abstract

(1)

Introduction: Complex Genomes---The Ocean of Cryptic Information

(1)

Classification of Comparative Techniques

(2)

Information Content and Resolution Power of Different Methods for Complex Genome Comparisons

(1)

Random Displays: From Fingerprinting to Flowthrough-Based Assays

(3)

Display Methods Targeted at the Flanks of Interspersed Repetitive Elements

(2)

DNA Microarrays As a New Tool to Display Genomic Differences

(2)

Genomic Subtractive Hybridization

(3)

Conclusion

(6)

A Brief Introduction to Primate Evolution

(17)

Hans Zischler

Christian Roos

Gerhard Hunsmann

Abstract

(1)

Introduction

(1)

The Problem of Primate Definition

(1)

Linking Primates to Other Eutherian Orders

(3)

The Major Groups of Primates

(8)

Evolution of Anatomically Modern Humans

(1)

Concluding Remarks

(3)

How Different Is the Human Genome from the Genomes of the Great Apes?

(25)

Eugene V. Nadezhdin

Eugene D. Sverdlov

Abstract

(1)

Introduction

(3)

First Human---Chimpanzee Molecular Comparisons: Changes in Regulatory Systems Are Most Important for Speciation

(1)

General Characteristics of Interspecies Divergence and Intraspecies Polymorphisms in Hominoids

(6)

Differences between Particular Elements of the Hominoid Genomes

(6)

Conclusion: A Supercomplex Disease---To Be a Human

(9)

Retroviruses, Their Domesticated Relatives and Other Retroinvaders: Potential Genetic and Epigenetic Mediators of Phenotypic Variation

(11)

Eugene D. Sverdlov

Abstract

(1)

Introduction: Continuum of The Retroworld

(1)

Retroviral Particles

(1)

Retroviral RNA Genome

(2)

Retroviral Life Cycle

(1)

Taxonomy of Retroviruses

(1)

Endogenization of Exogenous Retroviruses

(1)

Army of Retroelements in the Human Genome

(1)

Some Traditionally Discussed Functional Potentials of Retroelements

100

(1)

Stochastic Drivers of Organismal Epigenetic Mosaicism. All of Us Are Probably Complex Epigenetic Mosaics, and What?

101

(1)

Concluding Remarks

102

(2)

Genomic Distributions of Human Retroelements

104

(19)

Dixie L. Mager

Louie N. van de Lagemaat

Patrik Medstrand

Abstract

104

(1)

Introduction

104

(1)

Types of Human Retroelements

104

(2)

Effects of Transposable Elements on Genomes

106

(1)

Integration Patterns of Exogenous Retroviruses

106

(1)

Impact of Genetic Drift and Selection

107

(1)

Insights from Other Species

107

(2)

Experimental Determinations of Distributions

109

(1)

Large Scale Analysis of Retroelement Distributions

110

(3)

Retroelement Distributions Relative to Genes

113

(3)

Retroelements and the Y Chromosome

116

(2)

Genomic Clearance of Retroelements

118

(1)

Concluding Remarks

118

(5)

Influence of Human Endogenous Retroviruses on Cellular Gene Expression

123

(21)

Christine Leib-Mosch

Wolfgang Seifarth

Ulrike Schon

Abstract

123

(1)

Introduction

123

(1)

Variations in LTR Structure and Activity of Different HERV Families

123

(6)

Endogenous and Exogenous Factors Influencing HERV Expression

129

(1)

Modulation of Cellular Gene Expression

130

(9)

Concluding Remarks

139

(5)

Genome-Wide Search for Human Specific Retroelements

144

(18)

Yuri B. Lebedev

Abstract

144

(1)

Introduction: Hypotheses Are Indispensable on the Way towards Understanding the Genetic Basis of Humankind Evolution

144

(1)

Retroelement Families and Subfamilies in the Homo Sapiens Genome

145

(1)

What Makes REs Possible Candidates for Evolutionary Pacemakers?

146

(2)

Strategies and Approaches to the Genome-Wide Identification of Human-Specific RE Integrations

148

(8)

Concluding Remarks

156

(6)

Genome-Wide Analysis of Human Gene Expression: Application to the Expression of Human Endogenous Retroviruses

162

(24)

Tatyana V. Vinogradova

Abstract

162

(1)

Introduction: What Is the Function of a Genomic Constituent?

162

(1)

Detection of Gene Expression and Comparative Analysis of the Expression Using Cross-Hybridization of the Samples Under Comparison

163

(8)

Methods of Detection and Comparison of Transcripts Avoiding Denaturation-Renaturation Steps

171

(11)

Concluding Remarks

182

(4)

Phylogeny of Human Endogenous and Exogenous Retroviruses

186

(18)

Aris Katzourakis

Michael Tristem

Abstract

186

(1)

Introduction

186

(2)

Identification and Phylogenetic Reconstruction of Endogenous Retroviruses in the Human Genome

188

(1)

HERV Lineages within Retroviral Phylogeny

189

(5)

Characterization of New Families

194

(2)

Further Characterization of Previously Reported Families

196

(1)

Relationships between HERVs and Exogenous Retroviruses

196

(2)

Ancient and Modern HERV Families

198

(2)

Concluding Remarks: Prospects for HERV Phylogenetics

200

(4)

Evolutionary Aspects of Human Endogenous Retroviral Sequences (HERVs) and Disease

204

(35)

Jonas Blomberg

Dmitrijs Ushameckis

Patric Jern

Abstract

204

(1)

Introduction

204

(1)

Animal ERVs and Disease

205

(1)

Events following Endogenization of a Retrovirus

206

(3)

Active HERVs, Expressed As Particles or As Proteins

209

(6)

Diseases Where a Connection with HERVs Has Been Implicated

215

(13)

What Can Be Done to Demonstrate a HERV-Disease Connection?

228

(1)

Conclusions

229

(10)

Index

239

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Retroviruses And Primate Genome Evolution

9781587062131

1587062135

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