Plant Transposons and Genome Dynamics in Evolution Book

Contributors ix

Foreword xi

David Botstein

Introduction xiii

Nina V. Fedoroff

Chapter 1 The Discovery of Transposition 3

Nina V. Fedoroff

Introduction 3

Studies on Variegation 3

Mutable Genes 5

McClintock’s Studies on Chromosome Breakage 6

Recognition that Ds Transposes 8

Explaining Mutable Genes 9

Molecular Endnote 12

References 12

Chapter 2 A Field Guide to Transposable Elements 15

Alan H. Schulman and Thomas Wicker

The C-value Paradox 15

The Quantity of Transposable Elements Determines Genome Size 16

General Classification Scheme for Transposable Elements 17

Class II Elements 19

Class I: The Non-LTR and LTR Retrotransposons 20

Evolutionary Origins of Transposable Elements 25

Non-autonomous Transposable Elements 28

Transposable Element Demography and Genome Ecology 30

Conclusions: Rehabilitation of Transposable Elements 32

Acknowledgments 34

References 34

Chapter 3 The Mechanism of Ac/Ds Transposition 41

Thomas Peterson and Jianbo Zhang

Transposition of Ac/Ds Elements 41

The Enigmatic Ac Dosage Effect 42

cis and trans Effects on Ac/Ds Transposition 43

Molecular Characterization of Transposable Elements 44

The Excision and Insertion Reactions 45

Formation of Ds from Ac 48

Standard versus Alternative Transposition 48

Sister Chromatid Transposition 48

Reversed-ends Transposition 51

How Does Ds Break Chromosomes? 53

Alternative Transposition, DNA Methylation, and the Sequence of Transposition Reactions 54

Potential Applications of Alternative Transposition 55

Perspective 56

References 56

Chapter 4 McClintock and Epigenetics 61

Nina V. Fedoroff

Introduction 61

Spm-suppressible Alleles 61

Spm-dependent Alleles 64

Cryptic Spm 66

Presetting 66

Molecular Machinery of Epigenetic Regulation 67

Summary 68

References 69

Chapter 5 Molecular Mechanisms of Transposon Epigenetic Regulation 71

Robert A. Martienssen and Vicki L. Chandler

Introduction 71

Chromatin Remodeling, DNA and Histone Modification 73

RNA Interference (RNAi) and RNA-Directed DNA Methylation (RdDM) 75

Heterochromatin Reprogramming and Germ Cell Fate 79

Transgenerational Inheritance of Transposon Silencing 82

Paramutation 83

Conclusions 85

References 85

Chapter 6 Transposons in Plant Gene Regulation 93

Damon R. Lisch

Introduction 93

New Regulatory Functions 94

TE-Induced Down-Regulation 97

Deletions and Rearrangements 98

Suppressible Alleles 100

TEs and Plant Domestication 103

The Dynamic Genome 108

References 110

Chapter 7 Imprinted Gene Expression and the Contribution of Transposable Elements 117

Mary A. Gehring

Why are Genes Imprinted? 118

The Developmental Origin of Endosperm 118

Selection for Imprinted Expression 121

Principles Derived from the First Imprinted Gene 122

Gene Imprinting and Parent-of-Origin Effects on Seed Development 124

What Genes are Imprinted? 124

Epigenome Dynamics during Seed Development 127

Epigenetic Landscape in Vegetative Tissues 127

Cytological Observations of Chromatin in Seeds 129

Epigenomic Profiling in Seeds 130

Mechanisms of Gene Imprinting and the Relation to TEs 132

TEs and Allele-Specific Imprinting 136

Insights from Whole Genome Studies 137

Outstanding Questions 138

References 138

Chapter 8 Transposons and Gene Creation 143

Hugo K. Dooner and Clifford F. Weil

Introduction 143

Capture of Gene Fragments by TEs and Formation of Chimeric Genes 144

Co-Option of a TE Gene by the Host 148

Fusion of TE and Host Genes 150

Alterations of Host Gene Sequences by TE Excisions 151

Alterations of Host Coding Sequences by TE Insertions 152

Acquisition by Host Genes of New Regulatory Sequences from TEs 153

Interaction of TEs with Target Gene mRNA Splicing and Structure 155

Reshuffling of Host Sequences by Alternative Transpositions 156

Conclusion 158

References 158

Chapter 9 Transposons in Plant Speciation 165

Avraham A. Levy

Introduction 165

Genetic Models of Speciation 165

Speciation – a Gradual or a Rapid Process? 166

Speciation Through Accumulation of Mutations 166

DNA Cut-and-Paste TEs and Speciation 167

Copy-and-Paste TEs and Speciation 168

TE-Mediated Speciation – a Likely Scenario? 169

Plant Speciation Through Hybridization and Allopolyploidization 169

Induction of Transposition upon Hybridization and Polyploidization 170

Epigenetic Alteration of TEs upon Hybridization and Polyploidization 170

Transcriptional Activation of TEs upon Hybridization and Polyploidization 171

Alterations in Small RNAs upon Hybridization and Polyploidization 171

A Mechanistic Model for Responses to Genome Shock 172

Dysregulation of Gene Expression by Novel Interactions Between Regulatory Factors 173

Altered Protein Complexes 174

Why TEs Become Activated when Cellular Processes are Dysregulated 174

Conclusions 175

Acknowledgments 176

References 176

Chapter 10 Transposons, Genomic Shock, and Genome Evolution 181

Nina V. Fedoroff and Jeffrey L. Bennetzen

How Transposons Came to be Called “Selfish” DNA 181

The “Selfish DNA” Label Stuck to Transposons 182

Transposons Coevolved with Eukarotic Genomes 182

Sequence Duplication: The Real Innovation 183

The Facilitator: Epigenetic Control of Homologous Recombination 183

Epigenetic Mechanisms, Duplication and Genome Evolution 185

Plant Genome Organization: Gene Islands in a Sea of Repetitive DNA 186

Transposon Neighborhoods and Insertion Site Selection 187

Genome Evolution: Colinearity and Its Erosion 189

Genome Contraction and Divergence of Intergenic Sequences 191

Transposases Sculpt Genomes 192

Small Regulatory RNAs from Transposons 193

Genome Shocks 194

Genome Evolvability 195

References 196

Index 203

Color plate is located between pages 142 and 143.