Plant Epigenetics (Annual Plant Reviews, Volume 19)

Cover\r......Page 1
Plant Epigenetics......Page 2
Contents......Page 6
Contributors......Page 14
Preface......Page 17
1.1 Introduction: variation of transgene expression......Page 18
1.2.1.1 Chromatin remodelling......Page 19
1.2.1.2 DNA methylation......Page 20
1.2.1.4 RNA signals for transcriptional silencing......Page 21
1.2.2 Posttranscriptional silencing with different RNA\rdegradation pathways......Page 22
1.2.2.1 Initiation......Page 23
1.2.2.2 Sequence-specific degradation\rof single-stranded target RNAs......Page 24
1.2.2.3 RNA-dependent RNA polymerases involved\rin signal generation and amplification......Page 25
1.2.2.4 Transitive silencing......Page 26
1.2.2.5 The role of DNA methylation and chromatin\rmodification in RNA silencing......Page 28
1.3 Systemic silencing......Page 29
1.4 Silencing signals......Page 30
1.4.1 The transgene construct......Page 31
1.4.2 The impact of the transgene locus structure......Page 32
1.5 Position effects......Page 34
1.6 Environmental effects......Page 36
1.7.1 Selection of single-copy transgenes\rwith no rearrangement......Page 38
1.7.4 Scaffold/matrix attachment regions......Page 39
1.7.6 Targeted integration of transgenes......Page 40
1.8 Conclusions......Page 42
2.1 Introduction......Page 50
2.2 Mechanism of RNA interference......Page 51
2.3 Sources of dsRNA......Page 53
2.3.2 Fortuitous synthesis of transgene dsRNA......Page 54
2.3.3 Regulated and inducible RNAi......Page 57
2.3.4 Viral dsRNA and virus-induced gene silencing......Page 58
2.3.5 Endogenous dsRNAs......Page 60
2.4.1 Double-stranded RNA-processing enzymes:\rthe DCLs......Page 61
2.4.1.1 What is known about plant DCLs?......Page 64
2.4.2 DCL activities and the production of different\rsize classes of siRNA......Page 66
2.4.3 Argonaute proteins/PAZ and PIWI domain (PPD)\rproteins......Page 67
2.4.3.2 The PIWI domain......Page 68
2.4.4 More about plant Argonautes......Page 70
2.4.5 RNA-dependent RNA polymerases......Page 72
2.4.5.1 RDR1 and RDR6: virus-induced RNAi\rand S-PTGS......Page 73
2.4.5.3 Biochemical properties of RDRs......Page 74
2.4.5.4 RDR activity: amplification and transitive\rRNAi......Page 75
3.1.1 RNA interference......Page 86
3.1.2 Discovery and characteristics of RNA-directed DNA\rmethylation......Page 87
3.2 RNAi-mediated pathways in the nucleus......Page 88
3.2.1 RNAi-mediated heterochromatin formation......Page 89
3.2.2 RdDM and RNAi-mediated heterochromatin assembly:\rone pathway or two?......Page 90
3.3.1 Systems used for genetic analyses of RdDM and\rtranscriptional silencing......Page 93
3.3.2.1 Double-stranded RNA synthesis and processing......Page 95
3.3.2.2 DNA methyltransferases and\rhistone-modifying enzymes......Page 99
3.3.2.3 SNF2-like chromatin remodeling ATPases\rand DNA methylation......Page 103
3.4.1 Pattern of methylation......Page 107
3.4.2 RdDM machinery......Page 108
3.4.3 RNA-directed DNA methylation of promoters\rin human cells......Page 109
3.5 How short RNAs interact with a target locus: RNA–DNA\ror RNA–RNA?......Page 111
3.6 Functions of RNA-directed DNA methylation: genome\rdefense, development, others?......Page 112
3.7 Concluding remarks......Page 113
4.1 Introduction......Page 123
4.2.1 Discovery of heterochromatin and defining\rits cytological characteristics......Page 124
4.2.2 Sequence content, chromosomal and genomic\rorganisation of heterochromatin......Page 127
4.2.3 Heterochromatin and genetic recombination......Page 129
4.2.5 Transcriptional gene silencing\rby heterochromatisation......Page 130
4.3.1 SUVH proteins and the control of heterochromatic\rchromatin domains......Page 134
4.3.2 DNA methylation and the epigenetic control\rof heterochromatic domains......Page 137
4.3.3 Interdependence of heterochromatic DNA\rand histone methylation......Page 139
4.4 Epigenetic inheritance in plants and heterochromatin......Page 141
5.1 Introduction......Page 151
5.2.1.1 Paramutation at the b1 locus in maize......Page 154
5.2.1.2 Paramutation at the pl1 locus in maize......Page 155
5.2.1.3 Paramutation at the sulfurea locus in tomato......Page 156
5.2.1.4 Paramutation at the transgenic A1 locus\rin petunia......Page 157
5.2.1.5 Trans-inactivation at the PAI loci\rin Arabidopsis......Page 158
5.2.2.1 LoxP trans-silencing in mice......Page 159
5.2.2.3 Interchromosomal DNA methylation transfer\rin Ascobolus immerses......Page 160
5.3.1 RNA-based model......Page 161
5.3.1.3 RNA involvement in paramutation......Page 162
5.3.2 Pairing-based model......Page 163
5.4.1 Involvement of repeats......Page 165
5.4.1.1 Paramutation induced by repeats......Page 166
5.4.2 Sequence requirements for paramutation......Page 168
5.4.3 Involvement of DNA methylation and chromatin\rstructure......Page 169
5.4.5 Stability of the epigenetic state......Page 170
5.4.6 Timing of paramutation......Page 172
5.5.1 Maize mutations affecting paramutation......Page 174
5.5.2 Arabidopsis mutations affecting trans-inactivation......Page 179
5.6 The possible roles and implications of paramutation......Page 180
5.7 Concluding remarks and future directions......Page 181
6.2 Plant reproduction......Page 191
6.2.2 Seed development......Page 192
6.3.1 Parental effects and the discovery of genomic\rimprinting......Page 194
6.3.2 Genomic imprinting and gene dosage effects......Page 195
6.3.3 Genomic imprinting and asymmetry of parental gene activity......Page 197
6.4.1 Imprinted genes and potentially imprinted genes in maize......Page 199
6.4.2 The FIS class of genes in Arabidopsis......Page 200
6.4.3 The MEA–FIE Polycomb group complex......Page 201
6.4.4 Imprinted genes and potentially imprinted genes in Arabidopsis......Page 202
6.4.5 Genomic imprinting in embryo and endosperm......Page 203
6.5.1 Trans-acting factors affecting imprinting......Page 205
6.5.2 Cis-acting elements involved in imprinting......Page 208
6.6 Role of imprinting in plant development and evolution......Page 209
7.1 Introduction......Page 218
7.2 Ribosomal RNA gene dosage control......Page 220
7.3 Nucleolar dominance......Page 222
7.4 DNA methylation and rRNA gene regulation......Page 223
7.5.1 Histone acetylation......Page 225
7.5.2 Histone methylation......Page 226
7.6 Concerted changes in DNA and histone methylation comprise an on/off switch......Page 228
7.7 Future studies: identifying genes required for the epigenetic on/off switch......Page 230
8.1.1 Transgene-triggered gene silencing targets viruses......Page 240
8.1.2 Viruses trigger PTGS......Page 241
8.1.3 Systemic silencing......Page 242
8.2.1 Mechanism of virus-induced gene silencing......Page 244
8.2.2 Virus vectors for gene silencing......Page 246
8.2.3 Transgenic virus-induced gene silencing......Page 247
8.2.4.2 Analysing the function of disease resistance genes......Page 248
8.3 Viral suppressors of gene silencing......Page 251
8.3.1 Characterisation of P19 and HcPro......Page 252
8.3.3 Application of viral suppressors of gene silencing......Page 253
8.3.3.2 Overexpression of proteins......Page 254
9.2 Discovery of miRNAs......Page 261
9.3 miRNAs versus siRNAs......Page 262
9.4 Biogenesis of miRNAs: pri-miRNA, pre-miRNA, mature miRNAs......Page 263
9.6 Modes of gene regulation by miRNAs: translation versus mRNA cleavage versus chromatin......Page 265
9.7 miRNAs and their targets......Page 268
9.8.1 miR165/166 and Class III HD-Zip genes......Page 272
9.8.2 miR319/JAW and TCP genes......Page 275
9.8.4 miR164 and CUC-like NAC genes......Page 276
9.8.5 miR172 and AP2 and related genes......Page 277
9.8.6 miR170/171 and HAM-like GRAS genes......Page 278
9.8.7 miR168 and ARGONAUTE1 and miR162 and DICER-LIKE1......Page 279
9.8.8 Summary......Page 280
9.9.1 Within the plant kingdom......Page 281
9.9.2 miRNAs in plants versus metazoans......Page 283
Index......Page 296