Plant Transposons and Genome Dynamics in Evolution

Herausgegeben von Fedoroff, Nina V.

• Gebundenes Buch

Produktbeschreibung

The transposable genetic elements, or transposons, as they are now known, have had a tumultuous history. Discovered in the mid-20th century by Barbara McClintock, they were initially received with puzzlement. When their genomic abundance began to be apparent, they were categorized as "junk DNA" and acquired the label of parasites. Expanding understanding of gene and genome organization has revealed the profound extent of their impact on both.

Plant Transposons and Genome Dynamics in Evolution captures and distills the voluminous research literature on plant transposable elements and seeks to assemble the big picture of how transposons shape gene structure and regulation, as well as how they sculpt genomes in evolution. Individual chapters provide concise overviews of the many flavors of plant transposons and of their roles in gene creation, gene regulation, development, genome evolution, and organismal speciation, as well as of their epigenetic regulation.

This volume is essential reading for anyone working in plant genetics, epigenetics, or evolutionary biology.

Produktdetails

• Verlag: Wiley & Sons
• 1. Auflage
• Seitenzahl: 232
• Erscheinungstermin: 15. April 2013
• Englisch
• Abmessung: 246mm x 175mm x 15mm
• Gewicht: 590g
• ISBN-13: 9780470959947
• ISBN-10: 0470959940
• Artikelnr.: 36839999

Autorenporträt

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.

Inhaltsangabe

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.