| Acknowledgements |
|
xi | |
| Introduction |
|
xiii | |
| About the Companion Website |
|
xix | |
|
PART I PLANT GENOMES AND GENES |
|
|
|
Chapter 1 Plant genetic material |
|
|
3 | (14) |
|
1.1 DNA is the genetic material of all living organisms, including plants |
|
|
3 | (5) |
|
1.2 The plant cell contains three independent genomes |
|
|
8 | (2) |
|
1.3 A gene is a complete set of instructions for building an RNA molecule |
|
|
10 | (1) |
|
1.4 Genes include coding sequences and regulatory sequences |
|
|
11 | (1) |
|
1.5 Nuclear genome size in plants is variable but the numbers of protein-coding, non-transposable element genes are roughly the same |
|
|
12 | (3) |
|
1.6 Genomic DNA is packaged in chromosomes |
|
|
15 | (1) |
|
|
|
15 | (1) |
|
|
|
15 | (2) |
|
|
|
16 | (1) |
|
Chapter 2 The shifting genomic landscape |
|
|
17 | (28) |
|
2.1 The genomes of individual plants can differ in many ways |
|
|
17 | (3) |
|
2.2 Differences in sequences between plants provide clues about gene function |
|
|
20 | (2) |
|
2.3 SNPs and length mutations in simple sequence repeats are useful tools for genome mapping and marker assisted selection |
|
|
22 | (6) |
|
2.4 Genome size and chromosome number are variable |
|
|
28 | (2) |
|
2.5 Segments of DNA are often duplicated and can recombine |
|
|
30 | (1) |
|
2.6 Some genes are copied nearby In the genome |
|
|
31 | (3) |
|
2.7 Whole genome duplications are common in plants |
|
|
34 | (3) |
|
2.8 Whole genome duplication has many effects on the genome and on gene function |
|
|
37 | (4) |
|
|
|
41 | (1) |
|
|
|
42 | (3) |
|
|
|
42 | (1) |
|
|
|
42 | (3) |
|
Chapter 3 Transposable elements |
|
|
45 | (18) |
|
3.1 Transposable elements are common in genomes of all organisms |
|
|
45 | (1) |
|
3.2 Retrotransposons are mainly responsible for increases in genome size |
|
|
46 | (6) |
|
3.3 DNA transposons create small mutations when they insert and excise |
|
|
52 | (5) |
|
3.4 Transposable elements move genes and change their regulation |
|
|
57 | (3) |
|
3.5 How are transposable elements controlled? |
|
|
60 | (1) |
|
|
|
60 | (1) |
|
|
|
61 | (2) |
|
|
|
61 | (2) |
|
Chapter 4 Chromatin, centromeres and telomeres |
|
|
63 | (16) |
|
4.1 Chromosomes are made up of chromatin, a complex of DNA and protein |
|
|
63 | (3) |
|
4.2 Telomeres make up the ends of chromosomes |
|
|
66 | (5) |
|
4.3 The chromosome middles -- centromeres |
|
|
71 | (6) |
|
|
|
77 | (1) |
|
|
|
77 | (2) |
|
|
|
77 | (1) |
|
|
|
77 | (2) |
|
Chapter 5 Genomes of organelles |
|
|
79 | (20) |
|
5.1 Plastids and mitochondria are descendants of free-living bacteria |
|
|
79 | (1) |
|
5.2 Organellar genes have been transferred to the nuclear genome |
|
|
80 | (2) |
|
5.3 Organellar genes sometimes include introns |
|
|
82 | (1) |
|
5.4 Organellar mRNA is often edited |
|
|
82 | (2) |
|
5.5 Mitochondrial genomes contain fewer genes than chloroplasts |
|
|
84 | (3) |
|
5.6 Plant mitochondrial genomes are large and undergo frequent recombination |
|
|
87 | (4) |
|
5.7 All plastid genomes in a cell are identical |
|
|
91 | (2) |
|
5.8 Plastid genomes are similar among land plants but contain some structural rearrangements |
|
|
93 | (2) |
|
|
|
95 | (1) |
|
|
|
95 | (4) |
|
|
|
95 | (1) |
|
|
|
95 | (4) |
|
PART II TRANSCRIBING PLANT GENES |
|
|
|
|
|
99 | (12) |
|
6.1 RNA links components of the Central Dogma |
|
|
99 | (3) |
|
6.2 Structure provides RNA with unique properties |
|
|
102 | (3) |
|
6.3 RNA has multiple regulatory activities |
|
|
105 | (3) |
|
|
|
108 | (1) |
|
|
|
108 | (3) |
|
|
|
109 | (2) |
|
Chapter 7 The plant RNA polymerases |
|
|
111 | (10) |
|
7.1 Transcription makes RNA from DNA |
|
|
111 | (1) |
|
7.2 Varying numbers of RNA polymerases in the different kingdoms |
|
|
112 | (2) |
|
7.3 RNA polymerase I transcribes rRNAs |
|
|
114 | (2) |
|
7.4 RNA polymerase III recruitment to upstream and internal promoters |
|
|
116 | (1) |
|
7.5 Plant-specific RNP-IV and RNP-V participate in transcriptional gene silencing |
|
|
117 | (1) |
|
7.6 Organelles have their own set of RNA polymerases |
|
|
117 | (1) |
|
|
|
118 | (1) |
|
|
|
118 | (3) |
|
|
|
118 | (3) |
|
Chapter 8 Making mRNAs - Control of transcription by RNA polymerase II |
|
|
121 | (12) |
|
8.1 RNA polymerase II transcribes protein-coding genes |
|
|
121 | (1) |
|
8.2 The structure of RNA polymerase II reveals how it functions |
|
|
121 | (2) |
|
|
|
123 | (1) |
|
8.4 Initiation of transcription |
|
|
123 | (4) |
|
|
|
127 | (1) |
|
8.6 Transcription elongation: the role of RNP-II phosphorylation |
|
|
128 | (1) |
|
8.7 RNP-II pausing and termination |
|
|
129 | (1) |
|
8.8 Transcription re-initiation |
|
|
130 | (1) |
|
|
|
130 | (1) |
|
|
|
130 | (3) |
|
|
|
130 | (3) |
|
Chapter 9 Transcription factors interpret cis-regulatory information |
|
|
133 | (16) |
|
9.1 Information on when, where and how much a gene is expressed is codified by the gene's regulatory regions |
|
|
133 | (1) |
|
9.2 Identifying regulatory regions requires the use of reporter genes |
|
|
134 | (1) |
|
9.3 Gene regulatory regions have a modular structure |
|
|
135 | (2) |
|
9.4 Enhancers: Cis-regulatory elements or modules that function at a distance |
|
|
137 | (1) |
|
9.5 Transcription factors interpret the gene regulatory code |
|
|
138 | (1) |
|
9.6 Transcription factors can be classified In families |
|
|
138 | (1) |
|
9.7 How transcription factors bind DNA |
|
|
139 | (4) |
|
9.8 Modular structure of transcription factors |
|
|
143 | (3) |
|
9.9 Organization of transcription factors into gene regulatory grids and networks |
|
|
146 | (1) |
|
|
|
146 | (1) |
|
|
|
146 | (3) |
|
More challenging problems |
|
|
147 | (1) |
|
|
|
147 | (2) |
|
Chapter 10 Control of transcription factor activity |
|
|
149 | (12) |
|
10.1 Transcription factor phosphorylation |
|
|
149 | (2) |
|
10.2 Protein-protein interactions |
|
|
151 | (4) |
|
10.3 Preventing transcription factors from access to the nucleus |
|
|
155 | (1) |
|
10.4 Movement of transcription factors between cells |
|
|
156 | (2) |
|
|
|
158 | (1) |
|
|
|
158 | (3) |
|
|
|
58 | (103) |
|
|
|
161 | (12) |
|
11.1 The phenomenon of cosuppression or gene silencing |
|
|
161 | (1) |
|
11.2 Discovery of small RNAs |
|
|
162 | (1) |
|
11.3 Pathways for miRNA formation and function |
|
|
163 | (3) |
|
11.4 Plant siRNAs originate from different types of double-stranded RNAs |
|
|
166 | (2) |
|
11.5 Intercellular and systemic movement of small RNAs |
|
|
168 | (2) |
|
11.6 Role of miRNAs in plant physiology and development |
|
|
170 | (1) |
|
|
|
171 | (1) |
|
|
|
171 | (2) |
|
|
|
172 | (1) |
|
Chapter 12 Chromatin and gene expression |
|
|
173 | (12) |
|
12.1 Packing long DNA molecules in a small space: the function of chromatin |
|
|
173 | (1) |
|
12.2 Heterochromatin and euchromatin |
|
|
173 | (1) |
|
12.3 Histone modifications |
|
|
174 | (1) |
|
12.4 Histone modifications affect gene expression |
|
|
175 | (1) |
|
12.3 Introducing and removing histone marks: writers and erasers |
|
|
175 | (2) |
|
12.6 `Readers' recognize histone modifications |
|
|
177 | (1) |
|
12.7 Nucleosome positioning |
|
|
177 | (1) |
|
|
|
178 | (1) |
|
12.9 RNA-directed DNA methylation |
|
|
179 | (1) |
|
12.10 Control of flowering by histone modifications |
|
|
180 | (1) |
|
|
|
181 | (1) |
|
|
|
181 | (4) |
|
|
|
181 | (4) |
|
PART III FROM RNA TO PROTEINS |
|
|
|
Chapter 13 RNA processing and transport |
|
|
185 | (14) |
|
13.1 RNA processing can be thought of as steps |
|
|
185 | (1) |
|
13.2 RNA capping provides a distinctive 5' end to mRNAs |
|
|
185 | (4) |
|
13.3 Transcription termination consists of mRNA 3'-end formation and polyadenylation |
|
|
189 | (3) |
|
13.4 RNA splicing is another major source of genetic variation |
|
|
192 | (2) |
|
13.5 Export of mRNA from the nucleus is a gateway for regulating which mRNAs actually get translated |
|
|
194 | (2) |
|
|
|
196 | (1) |
|
|
|
196 | (3) |
|
|
|
196 | (3) |
|
|
|
199 | (8) |
|
14.1 Regulation of RNA continues upon export from nucleus |
|
|
199 | (1) |
|
14.2 Mechanisms for RNA turnover |
|
|
199 | (2) |
|
14.3 RNA surveillance mechanisms |
|
|
201 | (1) |
|
|
|
202 | (1) |
|
|
|
203 | (1) |
|
|
|
204 | (1) |
|
|
|
204 | (3) |
|
|
|
205 | (1) |
|
|
|
205 | (2) |
|
Chapter 15 Translation of RNA |
|
|
207 | (8) |
|
15.1 Translation: a key aspect of gene expression |
|
|
207 | (2) |
|
|
|
209 | (1) |
|
|
|
209 | (1) |
|
|
|
210 | (1) |
|
15.5 Tools for studying the regulation of translation |
|
|
211 | (1) |
|
15.6 Specific translational control mechanisms |
|
|
211 | (2) |
|
|
|
213 | (1) |
|
|
|
214 | (1) |
|
|
|
21 | (193) |
|
|
|
214 | (1) |
|
Chapter 16 Protein folding and transport |
|
|
215 | (10) |
|
16.1 The pathway to a protein's function is a complicated matter |
|
|
215 | (1) |
|
16.2 Protein folding and assembly |
|
|
215 | (3) |
|
|
|
218 | (1) |
|
16.4 Co-translational targeting |
|
|
218 | (1) |
|
16.5 Post-translational targeting |
|
|
219 | (1) |
|
16.6 Post-translational modifications regulating function |
|
|
220 | (2) |
|
|
|
222 | (1) |
|
|
|
223 | (2) |
|
|
|
223 | (1) |
|
|
|
224 | (1) |
|
Chapter 17 Protein degradation |
|
|
225 | (8) |
|
17.1 Two sides of gene expression--synthesis and degradation |
|
|
225 | (1) |
|
17.2 Autophagy, senescence and programmed cell death |
|
|
225 | (1) |
|
17.3 Protein-tagging mechanisms |
|
|
226 | (2) |
|
17.4 The ubiquitin proteasome system rivals gene transcription |
|
|
228 | (3) |
|
|
|
231 | (1) |
|
|
|
231 | (2) |
|
|
|
231 | (1) |
|
|
|
231 | (2) |
| Index |
|
233 | |