Note: Plant Epigenetics -- Contents -- Contributors -- Preface -- 1 Transgene silencing -- 1.1 Introduction: variation of transgene expression -- 1.2 Molecular mechanisms of transgene silencing -- 1.2.1 Transcriptional silencing -- 1.2.1.1 Chromatin remodelling -- 1.2.1.2 DNA methylation -- 1.2.1.3 Interactions between DNA and histone methylation functions -- 1.2.1.4 RNA signals for transcriptional silencing -- 1.2.1.5 RNA-independent chromatin modification -- 1.2.2 Posttranscriptional silencing with different RNA degradation pathways -- 1.2.2.1 Initiation -- 1.2.2.2 Sequence-specific degradation of single-stranded target RNAs -- 1.2.2.3 RNA-dependent RNA polymerases involved in signal generation and amplification -- 1.2.2.4 Transitive silencing -- 1.2.2.5 The role of DNA methylation and chromatin modification in RNA silencing -- 1.3 Systemic silencing -- 1.4 Silencing signals -- 1.4.1 The transgene construct -- 1.4.2 The impact of the transgene locus structure -- 1.4.3 RNA silencing induced by constructs carrying inverted repeats (sequence homology and repeats) -- 1.5 Position effects -- 1.6 Environmental effects -- 1.7 Strategies for the prevention of transgene silencing -- 1.7.1 Selection of single-copy transgenes with no rearrangement -- 1.7.2 Selection of favourable integration regions -- 1.7.3 Reactivation of silent transgenes -- 1.7.4 Scaffold/matrix attachment regions -- 1.7.5 The use of silencing mutants -- 1.7.6 Targeted integration of transgenes -- 1.8 Conclusions -- 2 RNA interference: double-stranded RNAs and the processing machinery -- 2.1 Introduction -- 2.2 Mechanism of RNA interference -- 2.3 Sources of dsRNA -- 2.3.1 Transgene-encoded dsRNA -- 2.3.2 Fortuitous synthesis of transgene dsRNA -- 2.3.3 Regulated and inducible RNAi -- 2.3.4 Viral dsRNA and virus-induced gene silencing -- 2.3.5 Endogenous dsRNAs. , 2.4 The protein machinery of RNAi -- 2.4.1 Double-stranded RNA-processing enzymes: the DCLs -- 2.4.1.1 What is known about plant DCLs? -- 2.4.2 DCL activities and the production of different size classes of siRNA -- 2.4.3 Argonaute proteins/PAZ and PIWI domain (PPD) proteins -- 2.4.3.1 The PAZ domain -- 2.4.3.2 The PIWI domain -- 2.4.4 More about plant Argonautes -- 2.4.5 RNA-dependent RNA polymerases -- 2.4.5.1 RDR1 and RDR6: virus-induced RNAi and S-PTGS -- 2.4.5.2 RDR2: a role in epigenetics -- 2.4.5.3 Biochemical properties of RDRs -- 2.4.5.4 RDR activity: amplification and transitive RNAi -- 3 RNA-directed DNA methylation -- 3.1 Introduction -- 3.1.1 RNA interference -- 3.1.2 Discovery and characteristics of RNA-directed DNA methylation -- 3.2 RNAi-mediated pathways in the nucleus -- 3.2.1 RNAi-mediated heterochromatin formation -- 3.2.2 RdDM and RNAi-mediated heterochromatin assembly: one pathway or two? -- 3.3 Mechanism of RNA-directed DNA methylation: RNA and protein requirements -- 3.3.1 Systems used for genetic analyses of RdDM and transcriptional silencing -- 3.3.2 Steps in the RdDM pathway -- 3.3.2.1 Double-stranded RNA synthesis and processing -- 3.3.2.2 DNA methyltransferases and histone-modifying enzymes -- 3.3.2.3 SNF2-like chromatin remodeling ATPases and DNA methylation -- 3.4 RdDM in other organisms -- 3.4.1 Pattern of methylation -- 3.4.2 RdDM machinery -- 3.4.3 RNA-directed DNA methylation of promoters in human cells -- 3.5 How short RNAs interact with a target locus: RNA-DNA or RNA-RNA? -- 3.6 Functions of RNA-directed DNA methylation: genome defense, development, others? -- 3.7 Concluding remarks -- 4 Heterochromatin and the control of gene silencing in plants -- 4.1 Introduction -- 4.2 Cytological, molecular and genetic characteristics of heterochromatin in plants. , 4.2.1 Discovery of heterochromatin and defining its cytological characteristics -- 4.2.2 Sequence content, chromosomal and genomic organisation of heterochromatin -- 4.2.3 Heterochromatin and genetic recombination -- 4.2.4 Heterochromatin and gene silencing in position effect variegation -- 4.2.5 Transcriptional gene silencing by heterochromatisation -- 4.3 DNA and histone modification in plant heterochromatin -- 4.3.1 SUVH proteins and the control of heterochromatic chromatin domains -- 4.3.2 DNA methylation and the epigenetic control of heterochromatic domains -- 4.3.3 Interdependence of heterochromatic DNA and histone methylation -- 4.4 Epigenetic inheritance in plants and heterochromatin -- 5 When alleles meet: paramutation -- 5.1 Introduction -- 5.2 Paramutation across kingdoms -- 5.2.1 Paramutation in plants -- 5.2.1.1 Paramutation at the b1 locus in maize -- 5.2.1.2 Paramutation at the pl1 locus in maize -- 5.2.1.3 Paramutation at the sulfurea locus in tomato -- 5.2.1.4 Paramutation at the transgenic A1 locus in petunia -- 5.2.1.5 Trans-inactivation at the PAI loci in Arabidopsis -- 5.2.2 Paramutation in mammals and fungi -- 5.2.2.1 LoxP trans-silencing in mice -- 5.2.2.2 Trans-nuclear inactivation of the inf1 gene in Phytophthora infestans -- 5.2.2.3 Interchromosomal DNA methylation transfer in Ascobolus immerses -- 5.3 Paramutation models -- 5.3.1 RNA-based model -- 5.3.1.1 Silencing by dsRNA and siRNAs -- 5.3.1.2 Silencing by long RNAs -- 5.3.1.3 RNA involvement in paramutation -- 5.3.2 Pairing-based model -- 5.3.3 Combined model -- 5.4 Common features of paramutation phenomena -- 5.4.1 Involvement of repeats -- 5.4.1.1 Paramutation induced by repeats -- 5.4.1.2 Paramutation induced by single-copy sequences -- 5.4.2 Sequence requirements for paramutation -- 5.4.3 Involvement of DNA methylation and chromatin structure. , 5.4.4 Secondary paramutation -- 5.4.5 Stability of the epigenetic state -- 5.4.6 Timing of paramutation -- 5.5 Trans-acting mutations affecting paramutation -- 5.5.1 Maize mutations affecting paramutation -- 5.5.2 Arabidopsis mutations affecting trans-inactivation -- 5.6 The possible roles and implications of paramutation -- 5.7 Concluding remarks and future directions -- 6 Genomic imprinting in plants: a predominantly maternal affair -- 6.1 Introduction -- 6.2 Plant reproduction -- 6.2.1 Gametogenesis and double fertilization -- 6.2.2 Seed development -- 6.3 The nature of genomic imprinting -- 6.3.1 Parental effects and the discovery of genomic imprinting -- 6.3.2 Genomic imprinting and gene dosage effects -- 6.3.3 Genomic imprinting and asymmetry of parental gene activity -- 6.4 Imprinted genes in Zea mays and Arabidopsis thaliana -- 6.4.1 Imprinted genes and potentially imprinted genes in maize -- 6.4.2 The FIS class of genes in Arabidopsis -- 6.4.3 The MEA-FIE Polycomb group complex -- 6.4.4 Imprinted genes and potentially imprinted genes in Arabidopsis -- 6.4.5 Genomic imprinting in embryo and endosperm -- 6.5 Molecular mechanisms of genomic imprinting -- 6.5.1 Trans-acting factors affecting imprinting -- 6.5.2 Cis-acting elements involved in imprinting -- 6.6 Role of imprinting in plant development and evolution -- 7 Nucleolar dominance and rRNA gene dosage control: a paradigm for transcriptional regulation via an epigenetic on/off switch -- 7.1 Introduction -- 7.2 Ribosomal RNA gene dosage control -- 7.3 Nucleolar dominance -- 7.4 DNA methylation and rRNA gene regulation -- 7.5 Histone modifications and rRNA gene regulation -- 7.5.1 Histone acetylation -- 7.5.2 Histone methylation -- 7.6 Concerted changes in DNA and histone methylation comprise an on/off switch -- 7.7 Future studies: identifying genes required for the epigenetic on/off switch. , 8 Virus-induced gene silencing -- 8.1 Introduction -- 8.1.1 Transgene-triggered gene silencing targets viruses -- 8.1.2 Viruses trigger PTGS -- 8.1.3 Systemic silencing -- 8.2 Virus-induced gene silencing -- 8.2.1 Mechanism of virus-induced gene silencing -- 8.2.2 Virus vectors for gene silencing -- 8.2.3 Transgenic virus-induced gene silencing -- 8.2.4 Application of virus-induced gene silencing -- 8.2.4.1 Identification of gene function -- 8.2.4.2 Analysing the function of disease resistance genes -- 8.3 Viral suppressors of gene silencing -- 8.3.1 Characterisation of P19 and HcPro -- 8.3.2 Suppressors break pathogen-derived resistance -- 8.3.3 Application of viral suppressors of gene silencing -- 8.3.3.1 Analysing the silencing machinery -- 8.3.3.2 Overexpression of proteins -- 9 MicroRNAs: micro-managing the plant genome -- 9.1 Abstract -- 9.2 Discovery of miRNAs -- 9.3 miRNAs versus siRNAs -- 9.4 Biogenesis of miRNAs: pri-miRNA, pre-miRNA, mature miRNAs -- 9.5 miRNA nomenclature -- 9.6 Modes of gene regulation by miRNAs: translation versus mRNA cleavage versus chromatin -- 9.7 miRNAs and their targets -- 9.8 Functional characterization of miRNAs - case studies -- 9.8.1 miR165/166 and Class III HD-Zip genes -- 9.8.2 miR319/JAW and TCP genes -- 9.8.3 miR159 and MYB genes -- 9.8.4 miR164 and CUC-like NAC genes -- 9.8.5 miR172 and AP2 and related genes -- 9.8.6 miR170/171 and HAM-like GRAS genes -- 9.8.7 miR168 and ARGONAUTE1 and miR162 and DICER-LIKE1 -- 9.8.8 Summary -- 9.9 Evolution of miRNA-mediated gene regulation -- 9.9.1 Within the plant kingdom -- 9.9.2 miRNAs in plants versus metazoans -- Index.