Plant genes, genomes, and genetics / Erich Grotewold, Joseph Chappell, Elizabeth A. Kellogg

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Acknowledgements.. Introduction.. About the Companion Website.. Part I: Plant Genomes and Genes.. Chapter 1 Plant genetic material.. 1.1 DNA is the genetic material of all living organisms, including plants.. 1.2 The plant cell contains three independent genomes.. 1.3 A gene is a complete set of instructions for building an RNA molecule.. 1.4 Genes include coding sequences and regulatory sequences.. 1.5 Nuclear genome size in plants is variable but the numbers of protein-coding, non-transposable element genes are roughly the same.. 1.6 Genomic DNA is packaged in chromosomes.. 1.7 Summary.. 1.8 Problems.. References.. Chapter 2 The shifting genomic landscape.. 2.1 The genomes of individual plants can differ in many ways.. 2.2 Differences in sequences between plants provide clues about gene function.. 2.3 SNPs and lengthmutations in simple sequence repeats are useful tools for genome mapping and marker assisted selection.. 2.4 Genome size and chromosome number are variable.. 2.5 Segments of DNA are often duplicated and can recombine.. 2.6 Some genes are copied nearby in the genome.. 2.7 Whole genome duplications are common in plants.. 2.8 Whole genome duplication has many effects on the genome and on gene function.. 2.9 Summary.. 2.10 Problems.. Further reading.. References.. Chapter 3 Transposable elements.. 3.1 Transposable elements are common in genomes of all organisms.. 3.2 Retrotransposons are mainly responsible for increases in genome size.. 3.3 DNA transposons create small mutations when they insert and excise.. 3.4 Transposable elements move genes and change their regulation.. 3.5 How are transposable elements controlled?.. 3.6 Summary.. 3.7 Problems.. References.. Chapter 4 Chromatin, centromeres and telomeres.. 4.1 Chromosomes are made up of chromatin, a complex of DNA and protein.. 4.2 Telomeres make up the ends of chromosomes.. 4.3 The chromosome middles-centromeres.. 4.4 Summary.. 4.5 Problems.. Further reading.. References

Chapter 5 Genomes of organelles.. 5.1 Plastids and mitochondria are descendants of free-living bacteria.. 5.2 Organellar genes have been transferred to the nuclear genome.. 5.3 Organellar genes sometimes include introns.. 5.4 Organellar mRNA is often edited.. 5.5 Mitochondrial genomes contain fewer genes than chloroplasts.. 5.6 Plant mitochondrial genomes are large and undergo frequent recombination.. 5.7 All plastid genomes in a cell are identical.. 5.8 Plastid genomes are similar among land plants but contain some structural rearrangements.. 5.9 Summary.. 5.10 Problems.. Further reading.. References.. Part II: Transcribing Plant Genes.. Chapter 6 RNA.. 6.1 RNA links components of the Central Dogma.. 6.2 Structure provides RNA with unique properties.. 6.3 RNA has multiple regulatory activities.. 6.4 Summary.. 6.5 Problems.. References.. Chapter 7 The plant RNA polymerases.. 7.1 Transcription makes RNA from DNA.. 7.2 Varying numbers of RNA polymerases in the different kingdoms.. 7.3 RNA polymerase I transcribes rRNAs.. 7.4 RNA polymerase III recruitment to upstream and internal promoters.. 7.5 Plant-specific RNP-IV and RNP-V participate in transcriptional gene silencing.. 7.6 Organelles have their own set of RNA polymerases.. 7.7 Summary.. 7.8 Problems.. References.. Chapter 8 Making mRNAs - Control of transcription by RNA polymerase II.. 8.1 RNA polymerase II transcribes protein-coding genes.. 8.2 The structure of RNA polymerase II reveals how it functions.. 8.3 The core promoter.. 8.4 Initiation of transcription.. 8.5 The mediator complex.. 8.6 Transcription elongation: the role of RNP-II phosphorylation.. 8.7 RNP-II pausing and termination.. 8.8 Transcription re-initiation.. 8.9 Summary.. 8.10 Problems.. References.. Chapter 9 Transcription factors interpret cis-regulatory information.. 9.1 Information on when, where and how much a gene is expressed is codified by the gene's regulatory regions

9.2 Identifying regulatory regions requires the use of reporter genes.. 9.3 Gene regulatory regions have a modular structure.. 9.4 Enhancers: Cis-regulatory elements or modules that function at a distance.. 9.5 Transcription factors interpret the gene regulatory code.. 9.6 Transcription factors can be classified in families.. 9.7 How transcription factors bind DNA.. 9.8 Modular structure of transcription factors.. 9.9 Organization of transcription factors into gene regulatory grids and networks.. 9.10 Summary.. 9.11 Problems.. More challenging problems.. References.. Chapter 10 Control of transcription factor activity.. 10.1 Transcription factor phosphorylation.. 10.2 Protein-protein interactions.. 10.3 Preventing transcription factors from access to the nucleus.. 10.4 Movement of transcription factors between cells.. 10.5 Summary.. 10.6 Problems.. References.. Chapter 11 Small RNAs.. 11.1 The phenomenon of cosuppression or gene silencing.. 11.2 Discovery of small RNAs.. 11.3 Pathways for miRNA formation and function.. 11.4 Plant siRNAs originate from different types of double-stranded RNAs.. 11.5 Intercellular and systemic movement of small RNAs.. 11.6 Role of miRNAs in plant physiology and development.. 11.7 Summary.. 11.8 Problems.. References .. Chapter 12 Chromatin and gene expression.. 12.1 Packing long DNA molecules in a small space: the function of chromatin.. 12.2 Heterochromatin and euchromatin.. 12.3 Histone modifications.. 12.4 Histone modifications affect gene expression.. 12.5 Introducing and removing histone marks: writers and erasers.. 12.6 'Readers' recognize histone modifications.. 12.7 Nucleosome positioning.. 12.8 DNA methylation.. 12.9 RNA-directed DNA methylation.. 12.10 Control of flowering by histone modifications.. 12.11 Summary.. 12.12 Problems.. References.. Part III: From RNA to Proteins.. Chapter 13 RNA processing and transport.. 13.1 RNA processing can be thought of as steps

13.2 RNA capping provides a distinctive 5' end to mRNAs.. 13.3 Transcription termination consists of mRNA 3'-end formation and polyadenylation.. 13.4 RNA splicing is another major source of genetic variation.. 13.5 Export of mRNA from the nucleus is a gateway for regulating which mRNAs actually get translated.. 13.6 Summary.. 13.7 Problems.. References.. Chapter 14 Fate of RNA.. 14.1 Regulation of RNA continues upon export from nucleus.. 14.2 Mechanisms for RNA turnover.. 14.3 RNA surveillance mechanisms.. 14.4 RNA sorting.. 14.5 RNA movement.. 14.6 Summary.. 14.7 Problems.. Further reading.. References.. Chapter 15 Translation of RNA.. 15.1 Translation: a key aspect of gene expression.. 15.2 Initiation.. 15.3 Elongation.. 15.4 Termination.. 15.5 Tools for studying the regulation of translation.. 15.6 Specific translational control mechanisms.. 15.7 Summary.. 15.8 Problems.. Further reading.. References.. Chapter 16 Protein folding and transport.. 16.1 The pathway to a protein's function is a complicated matter.. 16.2 Protein folding and assembly.. 16.3 Protein targeting.. 16.4 Co-translational targeting.. 16.5 Post-translational targeting.. 16.6 Post-translational modifications regulating function.. 16.7 Summary.. 16.8 Problems.. Further reading.. References.. Chapter 17 Protein degradation.. 17.1 Two sides of gene expression-synthesis and degradation.. 17.2 Autophagy, senescence and programmed cell death.. 17.3 Protein-tagging mechanisms.. 17.4 The ubiquitin proteasome system rivals gene transcription.. 17.5 Summary.. 17.6 Problems.. Further reading.. Reference.. Index

Plant Genes, Genomes and Genetics provides a comprehensive treatment of all aspects of plant gene expression. Unique in explaining the subject from a plant perspective, it highlights the importance of key processes, many first discovered in plants, that impact how plants develop and interact with the environment. This text covers topics ranging from plant genome structure and the key control points in how genes are expressed, to the mechanisms by which proteins are generated and how their activities are controlled and altered by posttranslational modifications. Written by a highly respected team of specialists in plant biology with extensive experience in teaching at undergraduate and graduate level, this textbook will be invaluable for students and instructors alike. Plant Genes, Genomes and Genetics also includes: • specific examples that highlight when and how plants operate differently from other organisms; • special sections that provide in-depth discussions of particular issues; • end-of-chapter problems to help students recapitulate the main concepts; • rich, full-colour illustrations and diagrams clearly showing important processes in plant gene expression; • a companion website with PowerPoint slides, downloadable figures, and answers to the questions posed in the book. Aimed at upper level undergraduates and graduate students in plant biology, this text is equally suited for advanced agronomy and crop science students inclined to understand molecular aspects of organismal phenomena. It is also an invaluable starting point for professionals entering the field of plant biology. eng