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 ixForeword xiDavid BotsteinIntroduction xiiiNina V. FedoroffChapter 1 The Discovery of Transposition 3Nina V. FedoroffIntroduction 3Studies on Variegation 3Mutable Genes 5McClintock’s Studies on Chromosome Breakage 6Recognition that Ds Transposes 8Explaining Mutable Genes 9Molecular Endnote 12References 12Chapter 2 A Field Guide to Transposable Elements 15Alan H. Schulman and Thomas WickerThe C-value Paradox 15The Quantity of Transposable Elements Determines Genome Size 16General Classification Scheme for Transposable Elements 17Class II Elements 19Class I: The Non-LTR and LTR Retrotransposons 20Evolutionary Origins of Transposable Elements 25Non-autonomous Transposable Elements 28Transposable Element Demography and Genome Ecology 30Conclusions: Rehabilitation of Transposable Elements 32Acknowledgments 34References 34Chapter 3 The Mechanism of Ac/Ds Transposition 41Thomas Peterson and Jianbo ZhangTransposition of Ac/Ds Elements 41The Enigmatic Ac Dosage Effect 42cis and trans Effects on Ac/Ds Transposition 43Molecular Characterization of Transposable Elements 44The Excision and Insertion Reactions 45Formation of Ds from Ac 48Standard versus Alternative Transposition 48Sister Chromatid Transposition 48Reversed-ends Transposition 51How Does Ds Break Chromosomes? 53Alternative Transposition, DNA Methylation, and the Sequence of Transposition Reactions 54Potential Applications of Alternative Transposition 55Perspective 56References 56Chapter 4 McClintock and Epigenetics 61Nina V. FedoroffIntroduction 61Spm-suppressible Alleles 61Spm-dependent Alleles 64Cryptic Spm 66Presetting 66Molecular Machinery of Epigenetic Regulation 67Summary 68References 69Chapter 5 Molecular Mechanisms of Transposon Epigenetic Regulation 71Robert A. Martienssen and Vicki L. ChandlerIntroduction 71Chromatin Remodeling, DNA and Histone Modification 73RNA Interference (RNAi) and RNA-Directed DNA Methylation (RdDM) 75Heterochromatin Reprogramming and Germ Cell Fate 79Transgenerational Inheritance of Transposon Silencing 82Paramutation 83Conclusions 85References 85Chapter 6 Transposons in Plant Gene Regulation 93Damon R. LischIntroduction 93New Regulatory Functions 94TE-Induced Down-Regulation 97Deletions and Rearrangements 98Suppressible Alleles 100TEs and Plant Domestication 103The Dynamic Genome 108References 110Chapter 7 Imprinted Gene Expression and the Contribution of Transposable Elements 117Mary A. GehringWhy are Genes Imprinted? 118The Developmental Origin of Endosperm 118Selection for Imprinted Expression 121Principles Derived from the First Imprinted Gene 122Gene Imprinting and Parent-of-Origin Effects on Seed Development 124What Genes are Imprinted? 124Epigenome Dynamics during Seed Development 127Epigenetic Landscape in Vegetative Tissues 127Cytological Observations of Chromatin in Seeds 129Epigenomic Profiling in Seeds 130Mechanisms of Gene Imprinting and the Relation to TEs 132TEs and Allele-Specific Imprinting 136Insights from Whole Genome Studies 137Outstanding Questions 138References 138Chapter 8 Transposons and Gene Creation 143Hugo K. Dooner and Clifford F. WeilIntroduction 143Capture of Gene Fragments by TEs and Formation of Chimeric Genes 144Co-Option of a TE Gene by the Host 148Fusion of TE and Host Genes 150Alterations of Host Gene Sequences by TE Excisions 151Alterations of Host Coding Sequences by TE Insertions 152Acquisition by Host Genes of New Regulatory Sequences from TEs 153Interaction of TEs with Target Gene mRNA Splicing and Structure 155Reshuffling of Host Sequences by Alternative Transpositions 156Conclusion 158References 158Chapter 9 Transposons in Plant Speciation 165Avraham A. LevyIntroduction 165Genetic Models of Speciation 165Speciation – a Gradual or a Rapid Process? 166Speciation Through Accumulation of Mutations 166DNA Cut-and-Paste TEs and Speciation 167Copy-and-Paste TEs and Speciation 168TE-Mediated Speciation – a Likely Scenario? 169Plant Speciation Through Hybridization and Allopolyploidization 169Induction of Transposition upon Hybridization and Polyploidization 170Epigenetic Alteration of TEs upon Hybridization and Polyploidization 170Transcriptional Activation of TEs upon Hybridization and Polyploidization 171Alterations in Small RNAs upon Hybridization and Polyploidization 171A Mechanistic Model for Responses to Genome Shock 172Dysregulation of Gene Expression by Novel Interactions Between Regulatory Factors 173Altered Protein Complexes 174Why TEs Become Activated when Cellular Processes are Dysregulated 174Conclusions 175Acknowledgments 176References 176Chapter 10 Transposons, Genomic Shock, and Genome Evolution 181Nina V. Fedoroff and Jeffrey L. BennetzenHow Transposons Came to be Called “Selfish” DNA 181The “Selfish DNA” Label Stuck to Transposons 182Transposons Coevolved with Eukarotic Genomes 182Sequence Duplication: The Real Innovation 183The Facilitator: Epigenetic Control of Homologous Recombination 183Epigenetic Mechanisms, Duplication and Genome Evolution 185Plant Genome Organization: Gene Islands in a Sea of Repetitive DNA 186Transposon Neighborhoods and Insertion Site Selection 187Genome Evolution: Colinearity and Its Erosion 189Genome Contraction and Divergence of Intergenic Sequences 191Transposases Sculpt Genomes 192Small Regulatory RNAs from Transposons 193Genome Shocks 194Genome Evolvability 195References 196Index 203

“I do love books where the text points toward the future as well as distilling the past and present.  This volume does both.”  (The Quarterly Review of Biology, 1 December 2014)