Plant Epigenetics (Annual Plant Reviews, Volume 19)

309 Pages·2005·7.59 MB·English

by  Peter Meyer

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Plant Epigenetics
Meyer:PlantEpigenetics 1405129778_1_pretoc FinalProof page 2 1.7.2005 10:41pm
Annual Plant Reviews
Aseriesforresearchersandpostgraduatesintheplantsciences.Eachvolumeinthisseries
focusesonathemeoftopicalimportance,andemphasisisplacedonrapidpublication.
EditorialBoard:
ProfessorJeremyA.Roberts(Editor-in-Chief),PlantScienceDivision,SchoolofBios-
ciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicester-
shire LE12 5RD, UK; Dr David Evans, School of Biological and Molecular Sciences,
Oxford Brookes University, Headington, Oxford OX3 0BP, UK; Professor Hidemasa
Imaseki,Obata-Minami2419,Moriyama-ku,Nagoya463,Japan;DrMichaelT.McMa-
nus, Institute of Molecular BioSciences, Massey University, Palmerston North, New
Zealand;DrJocelynK.C.Rose,DepartmentofPlantBiology,CornellUniversity,Ithaca,
NewYork14853,USA.
Recentlypublishedvolumesintheseries:
6. PlantReproduction
EditedbyS.D.O’NeillandJ.A.Roberts
7. Protein–ProteinInteractionsinPlantBiology
EditedbyM.T.McManus,W.A.LaingandA.C.Allan
8. ThePlantCellWall
EditedbyJ.K.C.Bose
9. TheGolgiApparatusandthePlantSecretoryPathway
EditedbyD.G.Robinson
10. ThePlantCytoskeletoninCellDifferentiationandDevelopment
EditedbyP.J.Hussey
11. Plant–PathogenInteractions
EditedbyN.J.Talbot
12. PolarityinPlants
EditedbyK.Lindsey
13. Plastids
EditedbyS.G.Møller
14. PlantPigmentsandtheirManipulation
EditedbyK.M.Davies
15. MembraneTransportinPlants
EditedbyM.R.Blatt
16. IntercellularCommunicationinPlants
EditedbyA.J.Fleming
17. PlantArchitectureanditsManipulation
EditedbyC.Turnbull
18. Plasmodesmata
EditedbyK.Oparka
19. PlantEpigenetics
EditedbyP.Meyer
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Plant Epigenetics
Edited by
PETER MEYER
Professor ofPlant Genetics
Centre for Plant Sciences
The University ofLeeds
UK
Meyer:PlantEpigenetics 1405129778_1_pretoc FinalProof page 4 1.7.2005 10:41pm
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Contents
Contributors xiii
Preface xvi
1 Transgene silencing 1
ANN DEPICKER, MATTHEW SANDERS and PETER MEYER
1.1 Introduction: variation oftransgene expression 1
1.2 Molecular mechanismsof transgenesilencing 2
1.2.1 Transcriptional silencing 2
1.2.1.1 Chromatinremodelling 2
1.2.1.2 DNA methylation 3
1.2.1.3 Interactions betweenDNA andhistone
methylationfunctions 4
1.2.1.4 RNA signals for transcriptional silencing 4
1.2.1.5 RNA-independent chromatinmodification 5
1.2.2 Posttranscriptional silencingwith different RNA
degradation pathways 5
1.2.2.1 Initiation 6
1.2.2.2 Sequence-specific degradation
ofsingle-stranded target RNAs 7
1.2.2.3 RNA-dependentRNA polymerases involved
insignal generation andamplification 8
1.2.2.4 Transitive silencing 9
1.2.2.5 Theroleof DNA methylationand chromatin
modification inRNA silencing 11
1.3 Systemic silencing 12
1.4 Silencing signals 13
1.4.1 Thetransgene construct 14
1.4.2 Theimpact of the transgene locus structure 15
1.4.3 RNA silencing induced by constructscarrying
inverted repeats (sequence homology and repeats) 17
1.5 Position effects 17
1.6 Environmental effects 19
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vi CONTENTS
1.7 Strategiesfor the prevention oftransgene silencing 21
1.7.1 Selection ofsingle-copy transgenes
with no rearrangement 21
1.7.2 Selection offavourable integration regions 22
1.7.3 Reactivationof silent transgenes 22
1.7.4 Scaffold/matrix attachment regions 22
1.7.5 Theuseofsilencingmutants 23
1.7.6 Targeted integration oftransgenes 23
1.8 Conclusions 25
2 RNA interference: double-stranded RNAs
and theprocessing machinery 33
JAN M. KOOTER
2.1 Introduction 33
2.2 Mechanism ofRNA interference 34
2.3 Sources ofdsRNA 36
2.3.1 Transgene-encoded dsRNA 37
2.3.2 Fortuitous synthesisof transgene dsRNA 37
2.3.3 Regulatedand inducibleRNAi 40
2.3.4 Viral dsRNA andvirus-induced gene silencing 41
2.3.5 Endogenous dsRNAs 43
2.4 The protein machinery of RNAi 44
2.4.1 Double-stranded RNA-processing enzymes:
the DCLs 44
2.4.1.1 What isknown about plantDCLs? 47
2.4.2 DCLactivities and the production ofdifferent
sizeclasses ofsiRNA 49
2.4.3 Argonaute proteins/PAZ andPIWI domain (PPD)
proteins 50
2.4.3.1 The PAZdomain 51
2.4.3.2 The PIWI domain 51
2.4.4 More about plantArgonautes 53
2.4.5 RNA-dependentRNA polymerases 55
2.4.5.1 RDR1 andRDR6:virus-induced RNAi
andS-PTGS 56
2.4.5.2 RDR2: a role inepigenetics 57
2.4.5.3 Biochemicalproperties of RDRs 57
2.4.5.4 RDR activity:amplification and transitive
RNAi 58
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CONTENTS vii
3 RNA-directed DNA methylation 69
MARJORI MATZKE, TATSUO KANNO, BRUNOHUETTEL,
ESTELLEJALIGOT, M.FLORIAN METTE, DAVID P. KREIL,
LUCIA DAXINGER, PHILIPP ROVINA, WERNER AUFSATZ
and ANTONIUS J. M. MATZKE
3.1 Introduction 69
3.1.1 RNA interference 69
3.1.2 Discovery andcharacteristicsofRNA-directed DNA
methylation 70
3.2 RNAi-mediated pathways inthe nucleus 71
3.2.1 RNAi-mediated heterochromatinformation 72
3.2.2 RdDM and RNAi-mediated heterochromatinassembly:
onepathway ortwo? 73
3.3 Mechanism ofRNA-directed DNA methylation: RNA and
protein requirements 76
3.3.1 Systems used for genetic analyses ofRdDM and
transcriptional silencing 76
3.3.2 Steps inthe RdDM pathway 78
3.3.2.1 Double-stranded RNA synthesisand processing 78
3.3.2.2 DNA methyltransferases and
histone-modifyingenzymes 82
3.3.2.3 SNF2-like chromatinremodeling ATPases
andDNA methylation 86
3.4 RdDM inotherorganisms 90
3.4.1 Pattern ofmethylation 90
3.4.2 RdDM machinery 91
3.4.3 RNA-directed DNA methylationof promoters
inhuman cells 92
3.5 Howshort RNAsinteract with a target locus:RNA–DNA
orRNA–RNA? 94
3.6 Functions of RNA-directed DNA methylation:genome
defense, development, others? 95
3.7 Concludingremarks 96
4 Heterochromatin and the controlofgene silencing in plants 106
G. REUTER, A.FISCHER andI. HOFMANN
4.1 Introduction 106
4.2 Cytological, molecularand genetic characteristics
ofheterochromatininplants 107
4.2.1 Discovery ofheterochromatinand defining
itscytological characteristics 107
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viii CONTENTS
4.2.2 Sequencecontent, chromosomal andgenomic
organisationof heterochromatin 110
4.2.3 Heterochromatin and genetic recombination 112
4.2.4 Heterochromatin and gene silencinginposition
effect variegation 113
4.2.5 Transcriptional gene silencing
byheterochromatisation 113
4.3 DNA and histone modification in plantheterochromatin 117
4.3.1 SUVH proteinsand the control ofheterochromatic
chromatindomains 117
4.3.2 DNA methylationand the epigenetic control
ofheterochromatic domains 120
4.3.3 Interdependence ofheterochromatic DNA
andhistone methylation 122
4.4 Epigenetic inheritance in plants and heterochromatin 124
5 When alleles meet: paramutation 134
MARIEKE LOUWERS,MAXHARINGand MAIKE STAM
5.1 Introduction 134
5.2 Paramutationacrosskingdoms 137
5.2.1 Paramutationinplants 137
5.2.1.1 Paramutationat the b1 locusinmaize 137
5.2.1.2 Paramutationat the pl1 locus inmaize 138
5.2.1.3 Paramutationat the sulfurea locus intomato 139
5.2.1.4 Paramutationat the transgenic A1 locus
inpetunia 140
5.2.1.5 Trans-inactivationat the PAIloci
inArabidopsis 141
5.2.2 Paramutationinmammals andfungi 142
5.2.2.1 LoxP trans-silencing inmice 142
5.2.2.2 Trans-nuclearinactivationofthe inf1
gene inPhytophthorainfestans 143
5.2.2.3 Interchromosomal DNA methylationtransfer
inAscobolusimmerses 143
5.3 Paramutationmodels 144
5.3.1 RNA-basedmodel 144
5.3.1.1 Silencing by dsRNA and siRNAs 145
5.3.1.2 Silencing by long RNAs 145
5.3.1.3 RNA involvement inparamutation 145
5.3.2 Pairing-based model 146
5.3.3 Combined model 148
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CONTENTS ix
5.4 Common featuresofparamutation phenomena 148
5.4.1 Involvement of repeats 148
5.4.1.1 Paramutationinducedby repeats 149
5.4.1.2 Paramutationinducedby single-copy
sequences 151
5.4.2 Sequence requirements for paramutation 151
5.4.3 Involvement of DNA methylationand chromatin
structure 152
5.4.4 Secondary paramutation 153
5.4.5 Stability ofthe epigenetic state 153
5.4.6 Timing of paramutation 155
5.5 Trans-acting mutations affecting paramutation 157
5.5.1 Maize mutations affecting paramutation 157
5.5.2 Arabidopsismutations affecting trans-inactivation 162
5.6 Thepossible roles andimplications ofparamutation 163
5.7 Concludingremarksand future directions 164
6 Genomic imprintingin plants: apredominantly
maternal affair 174
UELI GROSSNIKLAUS
6.1 Introduction 174
6.2 Plantreproduction 174
6.2.1 Gametogenesis anddouble fertilization 175
6.2.2 Seed development 175
6.3 Thenatureof genomic imprinting 177
6.3.1 Parental effects and the discoveryof genomic
imprinting 177
6.3.2 Genomic imprintingand gene dosage effects 178
6.3.3 Genomic imprintingand asymmetry of parental
gene activity 180
6.4 Imprintedgenes inZea mays andArabidopsis thaliana 182
6.4.1 Imprinted genes andpotentially imprinted genes
inmaize 182
6.4.2 TheFIS class ofgenes in Arabidopsis 183
6.4.3 TheMEA–FIE Polycomb group complex 184
6.4.4 Imprinted genes andpotentially imprinted genes
inArabidopsis 185
6.4.5 Genomic imprintinginembryoand endosperm 186
6.5 Molecular mechanismsof genomic imprinting 188
6.5.1 Trans-acting factors affectingimprinting 188