Regulation of Transcription in Plants (Annual Plant Reviews, Volume 29)

Regulation of Transcription in Plants......Page 1
Contents......Page 7
Contributors......Page 15
Preface......Page 17
1.2 Origins of the eukaryotic promoter......Page 21
1.3 Organization of the eukaryotic promoter......Page 24
1.4 Transcription factor IID......Page 28
1.5 Role of TFIID in development......Page 29
1.6 Mediator......Page 31
1.6.1 Tail module......Page 32
1.6.2 Middle complex......Page 35
1.6.4 CDK8/Srb8-11 module......Page 36
1.6.5 Mediator subunits unique to metazoans and plants......Page 37
1.7 Transcription factor IIB......Page 38
1.8 Summary......Page 39
References......Page 41
2.1 Introduction......Page 48
2.2.1 General considerations for genome-wide analyses......Page 49
2.2.2 Arabidopsis transcription factors......Page 50
2.2.3 Rice transcription factors: a comparison to Arabidopsis......Page 55
2.2.4 Gene duplications, functional redundancy, and the transcription factor phenome......Page 58
2.3 Plant promoters......Page 60
References......Page 63
3.1 Introduction......Page 74
3.2.1 Structure and expression......Page 75
3.2.2 DNA and chromatin interactions......Page 77
3.3.1 Structure and expression......Page 79
3.3.2 DNA and chromatin interactions......Page 84
3.4 Dynamic interaction of histone H1 and HMG proteins with chromatin......Page 86
3.5 HMGA and HMGB proteins as architectural assistant factors......Page 87
References......Page 92
4.1 Introduction......Page 99
4.2 Histone acetylation and transcriptional activation......Page 103
4.2.1 Plant histone acetyltransferases......Page 105
4.2.1.1 GNAT/MYST family......Page 106
4.2.1.3 P300/CBP family......Page 107
4.2.2 Bromodomain proteins......Page 108
4.2.2.1 Bromodomain extra-terminal proteins......Page 109
4.2.3.1 RPD3/HDA1 family......Page 110
4.2.3.3 SIR2 family......Page 112
4.3 Histone methylation......Page 113
4.3.1 Plant SET-domain proteins......Page 115
4.3.1.1 E(Z)- and Trithorax-type HMTases......Page 116
4.3.1.2 Su(var)3-9-type HMTases......Page 117
4.3.2 Histone demethylase......Page 119
4.4 Interplay between histone acetylation and methylation in transcriptional regulation......Page 120
4.5 Conclusions......Page 122
References......Page 123
5.1 Introduction......Page 132
5.2 ATP-dependent chromatin remodeling......Page 133
5.2.1 SWI/SNF-like complexes in plants......Page 135
5.2.2 Other ATPases of the SNF2 family that control plant development......Page 139
5.3 Chromatin remodeling and DNA methylation......Page 140
5.3.2 The model of DDM1 action......Page 141
5.3.3 DDM1 and methylation of histone H3......Page 143
5.3.5 DRD1 – another SNF2 family protein involved in control of DNA methylation......Page 144
5.4.1 Occurrence and functional role of core histone variants......Page 145
5.4.2 Role of H1 histone in chromatin and significance of nonallelic H1 variants......Page 148
References......Page 150
6.1 Introduction......Page 156
6.3 Position effects......Page 157
6.4.1 Post-transcriptional gene silencing......Page 158
6.4.2 Transcriptional gene silencing......Page 159
6.5 Matrix attachment regions......Page 160
6.6.1 MARs reduce gene silencing......Page 162
6.6.2 MARs have a dual effect......Page 168
6.6.3 Hypotheses to explain MAR effects......Page 169
6.7 MAR effects in Arabidopsis......Page 171
6.7.2 How might MARs decrease net transgene expression?......Page 172
References......Page 173
7.2 Organization of rRNA genes......Page 182
7.3 Ribosomal RNA transcription and the nucleolus......Page 183
7.4 rRNA gene promoters and transcription factors......Page 186
7.5 RNA pol I holoenzymes: evidence and controversies......Page 189
7.6 Coupling rDNA transcription and processing of pre-rRNA......Page 191
7.7 Growth and hormonal control of RNA pol I transcription......Page 192
7.8 Nucleolar dominance......Page 193
Acknowledgements......Page 196
References......Page 197
8.1 Introduction......Page 204
8.2 RNA polymerases......Page 205
8.2.1 NEP: Nuclear-encoded RNA polymerase......Page 207
8.2.2 PEP: Plastid-encoded RNA polymerase......Page 208
8.3.1 PEP promoters......Page 209
8.3.2 NEP promoters......Page 210
8.4 Regulation......Page 212
8.4.1 Role of diverse and multiple promoters in developmental regulation of gene expression......Page 213
8.4.2.1 Nuclear-encoded plastidial e-factors......Page 216
8.4.2.2 Role of e-factor diversity in transcriptional regulation......Page 218
8.4.2.3 NEP transcription factors......Page 223
8.4.3 Effects of environmental factors and crosstalk between plastids and nucleus......Page 224
References......Page 229
9.2 Regulation of FLC expression through the ‘autonomous pathway’......Page 245
9.3 Chromatin-related pleiotropic regulators of FLC......Page 249
9.4 Vernalization-associated repression of FLC......Page 252
9.5 Transcriptional repression of flowering by FLC......Page 255
9.6 Transcriptional regulation in the photoperiodic induction of flowering......Page 256
9.7 Activation of SOC1 by CO......Page 257
9.8 Chromatin-related mechanisms of photoperiod pathway regulation......Page 258
9.9 Transcriptional activation of AP1 by FT and FD......Page 260
9.10 Transcriptional mechanisms in the promotion of flowering by GAs......Page 262
9.11 PcG-mediated repression of floral homeotic genes......Page 263
References......Page 264
10.2 ABC: early genetic models of floral organ identity......Page 273
10.3 From the ABC to the ABCDE model......Page 276
10.4 Elective affinities of homeotic proteins: the floral quartet model......Page 277
10.5 Beyond the floral quartets sensu stricto: multimeric complexes of other MIKC-type proteins......Page 280
10.6 Outlook: the devil is always in the details – what we still don’t know about floral quartets......Page 281
References......Page 283
11.1 Introduction......Page 286
11.2 Defense transcriptome......Page 287
11.3 Regulatory sequences mediating defense gene expression......Page 288
11.4 Transcription factors involved in defense gene regulation......Page 290
11.5 Transcriptional networks......Page 295
11.7 Summary and outlook......Page 297
References......Page 299
12.1.2 Heat stress sensing and signaling......Page 305
12.1.3 Heat stress transcription factors: structure and function......Page 306
12.1.4 Class A HSF: immediate early regulators of the heat-shock response......Page 308
12.1.5 Second-level regulation......Page 309
12.1.6 Heat stress target genes......Page 310
12.1.7 Common stress-response genes and pathways......Page 311
12.2.2 Low-temperature sensing and signaling......Page 312
12.2.3 Transcription factors in ABA-independent pathways......Page 316
12.2.5 Cold stress target genes......Page 318
12.3 Perspectives for plant biotechnology......Page 320
References......Page 322
13.2 Conditional expression of transgenes......Page 329
13.2.2 Generic mechanisms......Page 330
13.2.3 Physical stimuli for activation......Page 332
13.2.4 Chemical activators related to plant metabolism......Page 334
13.2.5 Chemical activators unrelated to plant metabolism......Page 336
13.2.6 The conditional expression tool kit and its further development......Page 339
13.3 Applications to plant functional genomics......Page 340
13.3.2 Conditional knockout/knockdown......Page 341
13.4 Potential applications to plant biotechnology......Page 342
References......Page 344
14.1 Introduction......Page 349
14.2 Genes, regulatory factors, regulatory pathways, regulatory nodes, and regulatory networks......Page 350
14.3 Functional characterization of transcription factor genes......Page 351
14.4 Reverse engineering of transcription regulatory network......Page 353
14.5 Transcription network in crop plants......Page 357
14.6 Transcription factors as gene switches for genetic engineering......Page 359
14.7 Perspectives......Page 360
References......Page 362
Index......Page 367
The colour plate section appears after Page 142......Page 371