Plant genes, genomes and genetics
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 th...
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| Main Authors | , , |
|---|---|
| Format | eBook Book |
| Language | English |
| Published |
Chichester
WILEY
2015
John Wiley & Sons Wiley John Wiley & Sons, Incorporated Wiley-Blackwell |
| Edition | 1 |
| Subjects | |
| Online Access | Get full text |
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Table of Contents:
- Plant genes, genomes and genetics -- Contents -- Acknowledgements -- Introduction -- About the Companion Website -- Part I: Plant Genomes and Genes -- Chapter 1: Plant genetic material -- Chapter 2: The shifting genomic landscape -- Chapter 3: Transposable elements -- Chapter 4: Chromatin, centromeres and telomeres -- Chapter 5: Genomes of organelles -- Part II: Transcribing Plant Genes -- Chapter 6: RNA -- Chapter 7: The plant RNA polymerases -- Chapter 8: Making mRNAs-Control of transcription by RNA polymerase II -- Chapter 9: Transcription factors interpret cis-regulatory information -- Chapter 10: Control of transcription factor activity -- Chapter 11: Small RNAs -- Chapter 12: Chromatin and gene expression -- Part III: From RNA to Proteins -- Chapter 13: RNA processing and transport -- Chapter 14: Fate of RNA -- Chapter 15: Translation of RNA -- Chapter 16: Protein folding and transport -- Chapter 17: Protein degradation -- Index -- EULA
- 3.3 DNA transposons create small mutations when they insert and excise -- 3.3.1 hAT elements -- 3.3.2 Mutator-like elements -- 3.3.3 CACTA elements -- 3.3.4 MITES -- 3.4 Transposable elements move genes and change their regulation -- 3.4.1 Disruption of genes and regulatory regions -- 3.4.2 Movement of genes or gene fragments -- 3.4.3 Modification of gene expression -- 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 -- 4.3.1 Centromere nucleosomes contain a centromere-specific histone -- 4.3.2 Centromeric DNA generally contains repeated sequences and few genes -- 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
- 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 -- 12.5.1 Histone acetylation -- 12.5.2 Histone methylation -- 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 -- 13.3.1 Alternative polyadenylation creates additional mRNA diversity -- 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 -- EULA
- Cover -- Title Page -- Copyright -- Contents -- 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 length mutations 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 -- 2.6.1 Tandem duplications-genes for ribosomal RNA -- 2.6.2 Tandem duplications-genes encoding proteins for defense, receptor-like kinases, seed storage proteins -- 2.6.3 Segmental duplications -- 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 -- 3.2.1 LTR retrotransposons -- 3.2.2 Non-LTR retrotransposons
- 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 -- 8.4.1 TFIID -- 8.4.2 TFIIA -- 8.4.3 TFIIB -- 8.4.4 TFIIF -- 8.4.5 TFIIE -- 8.4.6 TFIIH -- 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