Plant Transposons and Genome Dynamics in Evolution

Nina V. Fedoroff is Distinguished Professor of Biosciences, King Abdullah University of Science and Technology, and Evan Pugh Professor, Huck Institutes of Life Sciences, Penn State University.

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.