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Plant epigenetics:

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Bibliographic Details
Format:	Book
Language:	English
Published:	Oxford, UK [u.a.] Blackwell Publ. 2005
Series:	Annual plant reviews 19
Subjects:	Plantes - Régulation génétique Épigénèse Plant genetic regulation Epigenesis Gene Expression Regulation, Plant Epigenesis, Genetic Gene Silencing Pflanzen Genexpression Epigenese Aufsatzsammlung
Online Access:	Table of contents Inhaltsverzeichnis
Item Description:	Includes bibliographical references and index
Physical Description:	XV, 283 S. Ill., graph. Darst.
ISBN:	1405129778 9781405129770

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MARC


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245	1	0	\|a Plant epigenetics \|c edited by Peter Meyer
264		1	\|a Oxford, UK [u.a.] \|b Blackwell Publ. \|c 2005
300			\|a XV, 283 S. \|b Ill., graph. Darst.
336			\|b txt \|2 rdacontent
337			\|b n \|2 rdamedia
338			\|b nc \|2 rdacarrier
490	1		\|a Annual plant reviews \|v 19
500			\|a Includes bibliographical references and index
505	8		\|a Transgene silencing / Ann Depicker, Matthew Sanders, and Peter Meyer -- RNA interference: double-stranded RNAs and the processing machinery / Jan M. Kooter -- RNA-directed DNA methylation / Marjori Matzke ... [et al.] -- Heterochromatin and the control of gene silencing in plants / G. Reuter, A. Fischer, and I. Hofmann -- When alleles meet: paramutation / Marieke Louwers, Max Haring, and Maike Stam -- Genomic imprinting in plants: a predominantly maternal affair / Ueli Grossniklaus -- Nucleolar dominance and rRNA gene dosage control: a paradigm for transcriptional regulation via an epigenetic on/off switch / Nuno Neves, Wanda Viegas and Craig S. Pikaard -- Virus induced gene silencing / Tamas Dalmay -- MicroRNAs: micro-managing the plant genome / Sandra K. Floyd and John L. Bowman.
650		4	\|a Plantes - Régulation génétique
650		4	\|a Épigénèse
650		4	\|a Plant genetic regulation
650		4	\|a Epigenesis
650		4	\|a Gene Expression Regulation, Plant
650		4	\|a Epigenesis, Genetic
650		4	\|a Gene Silencing
650	0	7	\|a Pflanzen \|0 (DE-588)4045539-7 \|2 gnd \|9 rswk-swf
650	0	7	\|a Genexpression \|0 (DE-588)4020136-3 \|2 gnd \|9 rswk-swf
650	0	7	\|a Epigenese \|0 (DE-588)4152503-6 \|2 gnd \|9 rswk-swf
655		7	\|0 (DE-588)4143413-4 \|a Aufsatzsammlung \|2 gnd-content
689	0	0	\|a Pflanzen \|0 (DE-588)4045539-7 \|D s
689	0	1	\|a Epigenese \|0 (DE-588)4152503-6 \|D s
689	0	2	\|a Genexpression \|0 (DE-588)4020136-3 \|D s
689	0		\|C b \|5 DE-604
700	1		\|a Meyer, Peter \|e Sonstige \|4 oth
830		0	\|a Annual plant reviews \|v 19 \|w (DE-604)BV012859776 \|9 19
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999			\|a oai:aleph.bib-bvb.de:BVB01-014633708

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_version_	1804135117937967104
adam_text	CONTENTS CONTRIBUTORS XIII PREFACE XVI 1 TRANSGENE SILENCING 1 ANN DEPICKER, MATTHEW SANDERS AND PETER MEYER 1.1 INTRODUCTION: VARIATION OF TRANSGENE EXPRESSION 1 1.2 MOLECULAR MECHANISMS OF TRANSGENE SILENCING 2 1.2.1 TRANSCRIPTIONAL SILENCING 2 1.2.1.1 CHROMATIN REMODELLING 2 1.2.1.2 DNA METHYLATION 3 1.2.1.3 INTERACTIONS BETWEEN DNA AND HISTONE METHYLATION FUNCTIONS 4 1.2.1.4 RNA SIGNALS FOR TRANSCRIPTIONAL SILENCING 4 1.2.1.5 RNA-INDEPENDENT CHROMATIN MODIFICATION 5 1.2.2 POSTTRANSCRIPTIONAL SILENCING WITH DIFFERENT RNA DEGRADATION PATHWAYS 5 1.2.2.1 INITIATION 6 1.2.2.2 SEQUENCE-SPECIFIC DEGRADATION OF SINGLE-STRANDED TARGET RNAS 7 1.2.2.3 RNA-DEPENDENT RNA POLYMERASES INVOLVED IN SIGNAL GENERATION AND AMPLIFICATION 8 1.2.2.4 TRANSITIVE SILENCING 9 1.2.2.5 THE ROLE OF DNA METHYLATION AND CHROMATIN MODIFICATION IN RNA SILENCING 11 1.3 SYSTEMIC SILENCING 12 1.4 SILENCING SIGNALS 13 1.4.1 THE TRANSGENE CONSTRUCT 14 1.4.2 THE IMPACT OF THE TRANSGENE LOCUS STRUCTURE 15 1.4.3 RNA SILENCING INDUCED BY CONSTRUCTS CARRYING INVERTED REPEATS (SEQUENCE HOMOLOGY AND REPEATS) 17 1.5 POSITION EFFECTS 17 1.6 ENVIRONMENTAL EFFECTS 19 VI CONTENTS 2.1 INTRODUCTION 33 2.2 MECHANISM OF RNA INTERFERENCE 34 2.3 SOURCES OF DSRNA 36 2.3.1 TRANSGENE-ENCODED DSRNA 37 2.3.2 FORTUITOUS SYNTHESIS OF TRANSGENE DSRNA 37 2.3.3 REGULATED AND INDUCIBLE RNAI 40 2.3.4 VIRAL DSRNA AND VIRUS-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 IS KNOWN ABOUT PLANT DCLS? 47 2.4.2 DCL ACTIVITIES AND THE PRODUCTION OF DIFFERENT SIZE C1ASSES OF SIRNA 49 2.4.3 ARGONAUTE PROTEINS/PAZ AND PIWI DOMAIN (PPD) PROTEINS 50 2.4.3.1 THE PAZ DOMAIN 51 2.4.3.2 THE PIWI DOMAIN 51 2.4.4 MORE ABOUT PLANT ARGONAUTES 53 2.4.5 RNA-DEPENDENT RNA POLYMERASES 55 2.4.5.1 RDR1 AND RDR6: VIRUS-INDUCED RNAI AND S-PTGS 56 2.4.5.2 RDR2: A ROLE IN EPIGENETICS 57 2.4.5.3 BIOCHEMICAL PROPERTIES OF RDRS 57 2.4.5.4 RDR ACTIVITY: AMPLIFICATION AND TRANSITIVE RNAI 58 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 CONC1USIONS 2 RNA INTERFERENCE: DOUBLE-STRANDED RNAS AND THE PROCESSING MACHINERY JAN M. KOOTER 21 21 22 22 22 23 23 25 33 CONTENTS VII 3 RNA-DIRECTED DNA METHYLATION 69 MARJORI MATZKE, TATSUO KANNO, BRUNO HUETTEL, ESTELLE JALIGOT, M. FLORIAN METTE, DAVID P. KREIL, LUCIA DAXINGER, PHILIPP ROVINA, WERNER AUFSATZ AND ANTONIUS 1. M. MATZKE 3.1 INTRODUCTION 69 3.1.1 RNA INTERFERENCE 69 3.1.2 DISCOVERY AND CHARACTERISTICS OF RNA-DIRECTED DNA METHYLATION 70 3.2 RNAI-MEDIATED PATHWAYS IN THE NUCLEUS 71 3.2.1 RNAI-MEDIATED HETEROCHROMATIN FORMATION 72 3.2.2 RDDM AND RNAI-MEDIATED HETEROCHROMATIN ASSEMBLY: ONE PATHWAY OR TWO? 73 3.3 MECHANISM OF RNA-DIRECTED DNA METHYLATION: RNA AND PROTEIN REQUIREMENTS 76 3.3.1 SYSTEMS USED FOR GENETIC ANALYSES OF RDDM AND TRANSCRIPTIONAL SILENCING 76 3.3.2 STEPS IN THE RDDM PATHWAY 78 3.3.2.1 DOUBLE-STRANDED RNA SYNTHESIS AND PROCESSING 78 3.3.2.2 DNA METHYLTRANSFERASES AND HISTONE-MODIFYING ENZYMES 82 3.3.2.3 SNF2-LIKE CHROMATIN REMODELING ATPASES AND DNA METHYLATION 86 3.4 RDDM IN OTHER ORGANISMS 90 3.4.1 PATTERN OF METHYLATION 90 3.4.2 RDDM MACHINERY 91 3.4.3 RNA-DIRECTED DNA METHYLATION OF PROMOTERS IN HUMAN CELLS 92 3.5 HOW SHORT RNAS INTERACT WITH A TARGET LOCUS: RNA-DNA OR RNA-RNA? 94 3.6 FUNCTIONS OF RNA-DIRECTED DNA METHYLATION: GENOME DEFENSE, DEVELOPMENT, OTHERS? 95 3.7 CONCLUDING REMARKS 96 4 HETEROCHROMATIN AND THE CONTROL OF GENE SILENCING IN PLANTS 106 G. REUTER, A. FISCHER AND I. HOFMANN 4.1 INTRODUCTION 106 4.2 CYTOLOGICAL, MOLECULAR AND GENETIC CHARACTERISTICS OF HETEROCHROMATIN IN PLANTS 107 4.2.1 DISCOVERY OF HETEROCHROMATIN AND DEFINING ITS CYTOLOGICAL CHARACTERISTICS 107 VIII CONTENTS 4.2.2 SEQUENCE CONTENT, CHROMOSOMAL AND GENOMIC ORGANISATION OF HETEROCHROMATIN 110 4.2.3 HETEROCHROMATIN AND GENETIC RECOMBINATION 112 4.2.4 HETEROCHROMATIN AND GENE SILENCING IN POSITION EFFECT VARIEGATION 113 4.2.5 TRANSCRIPTIONAL GENE SILENCING BY HETEROCHROMATISATION 113 4.3 DNA AND HISTONE MODIFICATION IN PLANT HETEROCHROMATIN 117 4.3.1 SUVH PROTEINS AND THE CONTROL OF HETEROCHROMATIC CHROMATIN DOMAINS 117 4.3.2 DNA METHYLATION AND THE EPIGENETIC CONTROL OF HETEROCHROMATIC DOMAINS 120 4.3.3 INTERDEPENDENCE OF HETEROCHROMATIC DNA AND HISTONE METHYLATION 122 4.4 EPIGENETIC INHERITANCE IN PLANTS AND HETEROCHROMATIN 124 5 WHEN ALLELES MEET: PARAMUTATION 134 MARIEKE LOUWERS, MAX HARING AND MAIKE STAM 5.1 INTRODUCTION 134 5.2 PARAMUTATION ACROSS KING DOMS 137 5.2.1 PARAMUTATION IN PLANTS 137 5.2.1.1 PARAMUTATION AT THE BL LOCUS IN MAIZE 137 5.2.1.2 PARAMUTATION AT THE PL L LOCUS IN MAIZE 138 5.2.1.3 PARAMUTATION AT THE SULFUREA LOCUS IN TOMATO 139 5.2.1.4 PARAMUTATION AT THE TRANSGENIC AL LOCUS IN PETUNIA 140 5.2.1.5 TRANS- INACTIVATION AT THE PAI LOCI IN ARABIDOPSIS 141 5.2.2 PARAMUTATION IN MAMMALS AND FUNGI 142 5.2.2.1 LOXP TRANS-SILENCING IN MICE 142 5.2.2.2 TRANS-NUCLEAR INACTIVATION OF THE INFL GENE IN PHYTOPHTHORA INFESTANS 143 5.2.2.3 INTERCHROMOSOMAL DNA METHYLATION TRANSFER IN ASEOBOLUS IMMERSES 143 5.3 PARAMUTATION MODELS 144 5.3.1 RNA-BASED MODEL 144 5.3.1.1 SILENCING BY DSRNA AND SIRNAS 145 5.3.1.2 SILENCING BY LANG RNAS 145 5.3.1.3 RNA INVOLVEMENT IN PARAMUTATION 145 5.3.2 PAIRING-BASED MODEL 146 5.3.3 COMBINED MODEL 148 CONTENTS IX 5.4 COMMON FEATURES OF PARAMUTATION PHENOMENA 148 5.4.1 INVOLVEMENT OF REPEATS 148 5.4.1.1 PARAMUTATION INDUCED BY REPEATS 149 5.4.1.2 PARAMUTATION INDUCED BY SINGLE-COPY SEQUENCES 151 5.4.2 SEQUENCE REQUIREMENTS FOR PARAMUTATION 151 5.4.3 INVOLVEMENT OF DNA METHYLATION AND CHROMATIN STRUCTURE 152 5.4.4 SECONDARY PARAMUTATION 153 5.4.5 STABILITY OF THE 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 ARABIDOPSIS MUTATIONS AFFECTING TRANS-INACTIVATION 162 5.6 THE POSSIBLE ROLES AND IMPLICATIONS OF PARAMUTATION 163 5.7 CONCLUDING REMARKS AND FUTURE DIRECTIONS 164 6 GENOMIC IMPRINTING IN PLANTS: A PREDOMINANTLY MATERNAL AFFAIR 174 UELI GROSSNIKLAUS 6.1 INTRODUCTION 174 6.2 PLANT REPRODUCTION 174 6.2.1 GAMETOGENESIS AND DOUBLE FERTILIZATION 175 6.2.2 SEED DEVELOPMENT 175 6.3 THE NATURE OF GENOMIC IMPRINTING 177 6.3.1 PARENTAL EFFECTS AND THE DISCOVERY OF GENOMIC IMPRINTING 177 6.3.2 GENOMIC IMPRINTING AND GENE DOSAGE EFFECTS 178 6.3.3 GENOMIC IMPRINTING AND ASYMMETRY OF PARENTAL GENE ACTIVITY 180 6.4 IMPRINTED GENES IN ZEA MAYS AND ARABIDOPSIS THALIANA 182 6.4.1 IMPRINTED GENES AND POTENTIALLY IMPRINTED GENES IN MAIZE 182 6.4.2 THE FIS CLASS OF GENES IN ARABIDOPSIS 183 6.4.3 THE MEA-FIE POLYCOMB GROUP COMPLEX 184 6.4.4 IMPRINTED GENES AND POTENTIALLY IMPRINTED GENES IN ARABIDOPSIS 185 6.4.5 GENOMIC IMPRINTING IN EMBRYO AND ENDOSPERM 186 6.5 MOLECULAR MECHANISMS OF GENOMIC IMPRINTING 188 6.5.1 TRANS-ACTING FACTORS AFFECTING IMPRINTING 188 X CONTENTS 6.5.2 CIS-ACTING ELEMENTS INVOLVED IN IMPRINTING 6.6 ROLE OF IMPRINTING IN PLANT DEVELOPMENT AND EVOLUTION 191 192 7 NUCLEOLAR DOMINANCE AND RRNA GENE DOSAGE CONTROI: A PARADIGM FOR TRANSCRIPTIONAL REGULATION VIA AN EPIGENETIC ON/OFF SWITCH 201 NUNO NEVES, WANDA VIEGAS AND CRAIG S. PIKAARD 7.1 INTRODUCTION 201 7.2 RIBOSOMAL RNA GENE DOSAGE CONTRAL 203 7.3 NUCLEOLAR DOMINANCE 205 7.4 DNA METHYLATION AND RRNA GENE REGULATION 206 7.5 HISTONE MODIFICATIONS AND RRNA GENE REGULATION 208 7.5.1 HISTONE ACETYLATION 208 7.5.2 HISTONE METHYLATION 209 7.6 CONCERTED CHANGES IN DNA AND HISTONE METHYLATION COMPRISE AN ON/OFF SWITCH 211 7.7 FUTURE STUDIES: IDENTIFYING GENES REQUIRED FOR THE EPIGENETIC ON/OFF SWITCH 213 8 VIRUS-INDUCED GENE SILENCING 223 TAMAS DALMAY 8.1 INTRODUCTION 223 8.1.1 TRANSGENE-TRIGGERED GENE SILENCING TARGETS VIRUSES 223 8.1.2 VIRUSES TRIGGER PTGS 224 8.1.3 SYSTEMIC SILENCING 225 8.2 VIRUS-INDUCED GENE SILENCING 227 8.2.1 MECHANISM OF VIRUS-INDUCED GENE SILENCING 227 8.2.2 VIRUS VECTORS FOR GENE SILENCING 229 8.2.3 TRANSGENIE VIRUS-INDUCED GENE SILENCING 230 8.2.4 APPLICATION OF VIRUS-INDUCED GENE SILENCING 231 8.2.4.1 IDENTIFICATION OF GENE FUNCTION 231 8.2.4.2 ANALYSING THE FUNCTION OF DISEASE RESISTANCE GENES 231 8.3 VIRAL SUPPRESSORS OF GENE SILENCING 234 8.3.1 CHARACTERISATION OF P19 AND HCPRA 235 8.3.2 SUPPRESSORS BREAK PATHOGEN-DERIVED RESISTANCE 236 8.3.3 APPLICATION OF VIRAL SUPPRESSORS OF GENE SILENCING 236 8.3.3.1 ANALYSING THE SILENCING MACHINERY 237 8.3.3.2 OVEREXPRESSION OF PROTEINS 237 CONTENTS XI 9 MICRORNAS: MICRO-MANAGING THE PLANT GENOME 244 SANDRA K. FLOYD AND JOHN L. BOWMAN 9.1 ABSTRACT 244 9.2 DISCOVERY OF MIRNAS 244 9.3 MIRNAS VERSUS SIRNAS 245 9.4 BIOGENESIS OF MIRNAS: PRI-MIRNA, PRE-MIRNA, MATURE MIRNAS 246 9.5 MIRNA NOMENCLATURE 248 9.6 MODES OF GENE REGULATION BY MIRNAS: TRANSLATION VERSUS MRNA CLEAVAGE VERSUS CHROMATIN 248 9.7 MIRNAS AND THEIR TARGETS 251 9.8 FUNCTIONAL CHARACTERIZATION OF MIRNAS - CASE STUDIES 255 9.8.1 MIR165/166 AND CLASS III HD-ZIP GENES 255 9.8.2 MIR319/JAWAND TCP GENES 258 9.8.3 MIR159 AND MYB GENES 259 9.8.4 MIR164 AND CUC-LIKE NAC GENES 259 9.8.5 MIR172 AND AP2 AND RELATED GENES 260 9.8.6 MIR170/171 AND HAM-LIKE GRAS GENES 261 9.8.7 MIR168 AND ARGONAUTEI AND MIR162 AND DICER-LIKEI 262 9.8.8 SUMMARY 263 9.9 EVOLUTION OF MIRNA-MEDIATED GENE REGULATION 264 9.9.1 WITHIN THE PLANT KINGDOM 264 9.9.2 MIRNAS IN PLANTS VERSUS METAZOANS 266 INDEX 279
adam_txt	CONTENTS CONTRIBUTORS XIII PREFACE XVI 1 TRANSGENE SILENCING 1 ANN DEPICKER, MATTHEW SANDERS AND PETER MEYER 1.1 INTRODUCTION: VARIATION OF TRANSGENE EXPRESSION 1 1.2 MOLECULAR MECHANISMS OF TRANSGENE SILENCING 2 1.2.1 TRANSCRIPTIONAL SILENCING 2 1.2.1.1 CHROMATIN REMODELLING 2 1.2.1.2 DNA METHYLATION 3 1.2.1.3 INTERACTIONS BETWEEN DNA AND HISTONE METHYLATION FUNCTIONS 4 1.2.1.4 RNA SIGNALS FOR TRANSCRIPTIONAL SILENCING 4 1.2.1.5 RNA-INDEPENDENT CHROMATIN MODIFICATION 5 1.2.2 POSTTRANSCRIPTIONAL SILENCING WITH DIFFERENT RNA DEGRADATION PATHWAYS 5 1.2.2.1 INITIATION 6 1.2.2.2 SEQUENCE-SPECIFIC DEGRADATION OF SINGLE-STRANDED TARGET RNAS 7 1.2.2.3 RNA-DEPENDENT RNA POLYMERASES INVOLVED IN SIGNAL GENERATION AND AMPLIFICATION 8 1.2.2.4 TRANSITIVE SILENCING 9 1.2.2.5 THE ROLE OF DNA METHYLATION AND CHROMATIN MODIFICATION IN RNA SILENCING 11 1.3 SYSTEMIC SILENCING 12 1.4 SILENCING SIGNALS 13 1.4.1 THE TRANSGENE CONSTRUCT 14 1.4.2 THE IMPACT OF THE TRANSGENE LOCUS STRUCTURE 15 1.4.3 RNA SILENCING INDUCED BY CONSTRUCTS CARRYING INVERTED REPEATS (SEQUENCE HOMOLOGY AND REPEATS) 17 1.5 POSITION EFFECTS 17 1.6 ENVIRONMENTAL EFFECTS 19 VI CONTENTS 2.1 INTRODUCTION 33 2.2 MECHANISM OF RNA INTERFERENCE 34 2.3 SOURCES OF DSRNA 36 2.3.1 TRANSGENE-ENCODED DSRNA 37 2.3.2 FORTUITOUS SYNTHESIS OF TRANSGENE DSRNA 37 2.3.3 REGULATED AND INDUCIBLE RNAI 40 2.3.4 VIRAL DSRNA AND VIRUS-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 IS KNOWN ABOUT PLANT DCLS? 47 2.4.2 DCL ACTIVITIES AND THE PRODUCTION OF DIFFERENT SIZE C1ASSES OF SIRNA 49 2.4.3 ARGONAUTE PROTEINS/PAZ AND PIWI DOMAIN (PPD) PROTEINS 50 2.4.3.1 THE PAZ DOMAIN 51 2.4.3.2 THE PIWI DOMAIN 51 2.4.4 MORE ABOUT PLANT ARGONAUTES 53 2.4.5 RNA-DEPENDENT RNA POLYMERASES 55 2.4.5.1 RDR1 AND RDR6: VIRUS-INDUCED RNAI AND S-PTGS 56 2.4.5.2 RDR2: A ROLE IN EPIGENETICS 57 2.4.5.3 BIOCHEMICAL PROPERTIES OF RDRS 57 2.4.5.4 RDR ACTIVITY: AMPLIFICATION AND TRANSITIVE RNAI 58 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 CONC1USIONS 2 RNA INTERFERENCE: DOUBLE-STRANDED RNAS AND THE PROCESSING MACHINERY JAN M. KOOTER 21 21 22 22 22 23 23 25 33 CONTENTS VII 3 RNA-DIRECTED DNA METHYLATION 69 MARJORI MATZKE, TATSUO KANNO, BRUNO HUETTEL, ESTELLE JALIGOT, M. FLORIAN METTE, DAVID P. KREIL, LUCIA DAXINGER, PHILIPP ROVINA, WERNER AUFSATZ AND ANTONIUS 1. M. MATZKE 3.1 INTRODUCTION 69 3.1.1 RNA INTERFERENCE 69 3.1.2 DISCOVERY AND CHARACTERISTICS OF RNA-DIRECTED DNA METHYLATION 70 3.2 RNAI-MEDIATED PATHWAYS IN THE NUCLEUS 71 3.2.1 RNAI-MEDIATED HETEROCHROMATIN FORMATION 72 3.2.2 RDDM AND RNAI-MEDIATED HETEROCHROMATIN ASSEMBLY: ONE PATHWAY OR TWO? 73 3.3 MECHANISM OF RNA-DIRECTED DNA METHYLATION: RNA AND PROTEIN REQUIREMENTS 76 3.3.1 SYSTEMS USED FOR GENETIC ANALYSES OF RDDM AND TRANSCRIPTIONAL SILENCING 76 3.3.2 STEPS IN THE RDDM PATHWAY 78 3.3.2.1 DOUBLE-STRANDED RNA SYNTHESIS AND PROCESSING 78 3.3.2.2 DNA METHYLTRANSFERASES AND HISTONE-MODIFYING ENZYMES 82 3.3.2.3 SNF2-LIKE CHROMATIN REMODELING ATPASES AND DNA METHYLATION 86 3.4 RDDM IN OTHER ORGANISMS 90 3.4.1 PATTERN OF METHYLATION 90 3.4.2 RDDM MACHINERY 91 3.4.3 RNA-DIRECTED DNA METHYLATION OF PROMOTERS IN HUMAN CELLS 92 3.5 HOW SHORT RNAS INTERACT WITH A TARGET LOCUS: RNA-DNA OR RNA-RNA? 94 3.6 FUNCTIONS OF RNA-DIRECTED DNA METHYLATION: GENOME DEFENSE, DEVELOPMENT, OTHERS? 95 3.7 CONCLUDING REMARKS 96 4 HETEROCHROMATIN AND THE CONTROL OF GENE SILENCING IN PLANTS 106 G. REUTER, A. FISCHER AND I. HOFMANN 4.1 INTRODUCTION 106 4.2 CYTOLOGICAL, MOLECULAR AND GENETIC CHARACTERISTICS OF HETEROCHROMATIN IN PLANTS 107 4.2.1 DISCOVERY OF HETEROCHROMATIN AND DEFINING ITS CYTOLOGICAL CHARACTERISTICS 107 VIII CONTENTS 4.2.2 SEQUENCE CONTENT, CHROMOSOMAL AND GENOMIC ORGANISATION OF HETEROCHROMATIN 110 4.2.3 HETEROCHROMATIN AND GENETIC RECOMBINATION 112 4.2.4 HETEROCHROMATIN AND GENE SILENCING IN POSITION EFFECT VARIEGATION 113 4.2.5 TRANSCRIPTIONAL GENE SILENCING BY HETEROCHROMATISATION 113 4.3 DNA AND HISTONE MODIFICATION IN PLANT HETEROCHROMATIN 117 4.3.1 SUVH PROTEINS AND THE CONTROL OF HETEROCHROMATIC CHROMATIN DOMAINS 117 4.3.2 DNA METHYLATION AND THE EPIGENETIC CONTROL OF HETEROCHROMATIC DOMAINS 120 4.3.3 INTERDEPENDENCE OF HETEROCHROMATIC DNA AND HISTONE METHYLATION 122 4.4 EPIGENETIC INHERITANCE IN PLANTS AND HETEROCHROMATIN 124 5 WHEN ALLELES MEET: PARAMUTATION 134 MARIEKE LOUWERS, MAX HARING AND MAIKE STAM 5.1 INTRODUCTION 134 5.2 PARAMUTATION ACROSS KING DOMS 137 5.2.1 PARAMUTATION IN PLANTS 137 5.2.1.1 PARAMUTATION AT THE BL LOCUS IN MAIZE 137 5.2.1.2 PARAMUTATION AT THE PL L LOCUS IN MAIZE 138 5.2.1.3 PARAMUTATION AT THE SULFUREA LOCUS IN TOMATO 139 5.2.1.4 PARAMUTATION AT THE TRANSGENIC AL LOCUS IN PETUNIA 140 5.2.1.5 TRANS- INACTIVATION AT THE PAI LOCI IN ARABIDOPSIS 141 5.2.2 PARAMUTATION IN MAMMALS AND FUNGI 142 5.2.2.1 LOXP TRANS-SILENCING IN MICE 142 5.2.2.2 TRANS-NUCLEAR INACTIVATION OF THE INFL GENE IN PHYTOPHTHORA INFESTANS 143 5.2.2.3 INTERCHROMOSOMAL DNA METHYLATION TRANSFER IN ASEOBOLUS IMMERSES 143 5.3 PARAMUTATION MODELS 144 5.3.1 RNA-BASED MODEL 144 5.3.1.1 SILENCING BY DSRNA AND SIRNAS 145 5.3.1.2 SILENCING BY LANG RNAS 145 5.3.1.3 RNA INVOLVEMENT IN PARAMUTATION 145 5.3.2 PAIRING-BASED MODEL 146 5.3.3 COMBINED MODEL 148 CONTENTS IX 5.4 COMMON FEATURES OF PARAMUTATION PHENOMENA 148 5.4.1 INVOLVEMENT OF REPEATS 148 5.4.1.1 PARAMUTATION INDUCED BY REPEATS 149 5.4.1.2 PARAMUTATION INDUCED BY SINGLE-COPY SEQUENCES 151 5.4.2 SEQUENCE REQUIREMENTS FOR PARAMUTATION 151 5.4.3 INVOLVEMENT OF DNA METHYLATION AND CHROMATIN STRUCTURE 152 5.4.4 SECONDARY PARAMUTATION 153 5.4.5 STABILITY OF THE 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 ARABIDOPSIS MUTATIONS AFFECTING TRANS-INACTIVATION 162 5.6 THE POSSIBLE ROLES AND IMPLICATIONS OF PARAMUTATION 163 5.7 CONCLUDING REMARKS AND FUTURE DIRECTIONS 164 6 GENOMIC IMPRINTING IN PLANTS: A PREDOMINANTLY MATERNAL AFFAIR 174 UELI GROSSNIKLAUS 6.1 INTRODUCTION 174 6.2 PLANT REPRODUCTION 174 6.2.1 GAMETOGENESIS AND DOUBLE FERTILIZATION 175 6.2.2 SEED DEVELOPMENT 175 6.3 THE NATURE OF GENOMIC IMPRINTING 177 6.3.1 PARENTAL EFFECTS AND THE DISCOVERY OF GENOMIC IMPRINTING 177 6.3.2 GENOMIC IMPRINTING AND GENE DOSAGE EFFECTS 178 6.3.3 GENOMIC IMPRINTING AND ASYMMETRY OF PARENTAL GENE ACTIVITY 180 6.4 IMPRINTED GENES IN ZEA MAYS AND ARABIDOPSIS THALIANA 182 6.4.1 IMPRINTED GENES AND POTENTIALLY IMPRINTED GENES IN MAIZE 182 6.4.2 THE FIS CLASS OF GENES IN ARABIDOPSIS 183 6.4.3 THE MEA-FIE POLYCOMB GROUP COMPLEX 184 6.4.4 IMPRINTED GENES AND POTENTIALLY IMPRINTED GENES IN ARABIDOPSIS 185 6.4.5 GENOMIC IMPRINTING IN EMBRYO AND ENDOSPERM 186 6.5 MOLECULAR MECHANISMS OF GENOMIC IMPRINTING 188 6.5.1 TRANS-ACTING FACTORS AFFECTING IMPRINTING 188 X CONTENTS 6.5.2 CIS-ACTING ELEMENTS INVOLVED IN IMPRINTING 6.6 ROLE OF IMPRINTING IN PLANT DEVELOPMENT AND EVOLUTION 191 192 7 NUCLEOLAR DOMINANCE AND RRNA GENE DOSAGE CONTROI: A PARADIGM FOR TRANSCRIPTIONAL REGULATION VIA AN EPIGENETIC ON/OFF SWITCH 201 NUNO NEVES, WANDA VIEGAS AND CRAIG S. PIKAARD 7.1 INTRODUCTION 201 7.2 RIBOSOMAL RNA GENE DOSAGE CONTRAL 203 7.3 NUCLEOLAR DOMINANCE 205 7.4 DNA METHYLATION AND RRNA GENE REGULATION 206 7.5 HISTONE MODIFICATIONS AND RRNA GENE REGULATION 208 7.5.1 HISTONE ACETYLATION 208 7.5.2 HISTONE METHYLATION 209 7.6 CONCERTED CHANGES IN DNA AND HISTONE METHYLATION COMPRISE AN ON/OFF SWITCH 211 7.7 FUTURE STUDIES: IDENTIFYING GENES REQUIRED FOR THE EPIGENETIC ON/OFF SWITCH 213 8 VIRUS-INDUCED GENE SILENCING 223 TAMAS DALMAY 8.1 INTRODUCTION 223 8.1.1 TRANSGENE-TRIGGERED GENE SILENCING TARGETS VIRUSES 223 8.1.2 VIRUSES TRIGGER PTGS 224 8.1.3 SYSTEMIC SILENCING 225 8.2 VIRUS-INDUCED GENE SILENCING 227 8.2.1 MECHANISM OF VIRUS-INDUCED GENE SILENCING 227 8.2.2 VIRUS VECTORS FOR GENE SILENCING 229 8.2.3 TRANSGENIE VIRUS-INDUCED GENE SILENCING 230 8.2.4 APPLICATION OF VIRUS-INDUCED GENE SILENCING 231 8.2.4.1 IDENTIFICATION OF GENE FUNCTION 231 8.2.4.2 ANALYSING THE FUNCTION OF DISEASE RESISTANCE GENES 231 8.3 VIRAL SUPPRESSORS OF GENE SILENCING 234 8.3.1 CHARACTERISATION OF P19 AND HCPRA 235 8.3.2 SUPPRESSORS BREAK PATHOGEN-DERIVED RESISTANCE 236 8.3.3 APPLICATION OF VIRAL SUPPRESSORS OF GENE SILENCING 236 8.3.3.1 ANALYSING THE SILENCING MACHINERY 237 8.3.3.2 OVEREXPRESSION OF PROTEINS 237 CONTENTS XI 9 MICRORNAS: MICRO-MANAGING THE PLANT GENOME 244 SANDRA K. FLOYD AND JOHN L. BOWMAN 9.1 ABSTRACT 244 9.2 DISCOVERY OF MIRNAS 244 9.3 MIRNAS VERSUS SIRNAS 245 9.4 BIOGENESIS OF MIRNAS: PRI-MIRNA, PRE-MIRNA, MATURE MIRNAS 246 9.5 MIRNA NOMENCLATURE 248 9.6 MODES OF GENE REGULATION BY MIRNAS: TRANSLATION VERSUS MRNA CLEAVAGE VERSUS CHROMATIN 248 9.7 MIRNAS AND THEIR TARGETS 251 9.8 FUNCTIONAL CHARACTERIZATION OF MIRNAS - CASE STUDIES 255 9.8.1 MIR165/166 AND CLASS III HD-ZIP GENES 255 9.8.2 MIR319/JAWAND TCP GENES 258 9.8.3 MIR159 AND MYB GENES 259 9.8.4 MIR164 AND CUC-LIKE NAC GENES 259 9.8.5 MIR172 AND AP2 AND RELATED GENES 260 9.8.6 MIR170/171 AND HAM-LIKE GRAS GENES 261 9.8.7 MIR168 AND ARGONAUTEI AND MIR162 AND DICER-LIKEI 262 9.8.8 SUMMARY 263 9.9 EVOLUTION OF MIRNA-MEDIATED GENE REGULATION 264 9.9.1 WITHIN THE PLANT KINGDOM 264 9.9.2 MIRNAS IN PLANTS VERSUS METAZOANS 266 INDEX 279
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contents	Transgene silencing / Ann Depicker, Matthew Sanders, and Peter Meyer -- RNA interference: double-stranded RNAs and the processing machinery / Jan M. Kooter -- RNA-directed DNA methylation / Marjori Matzke ... [et al.] -- Heterochromatin and the control of gene silencing in plants / G. Reuter, A. Fischer, and I. Hofmann -- When alleles meet: paramutation / Marieke Louwers, Max Haring, and Maike Stam -- Genomic imprinting in plants: a predominantly maternal affair / Ueli Grossniklaus -- Nucleolar dominance and rRNA gene dosage control: a paradigm for transcriptional regulation via an epigenetic on/off switch / Nuno Neves, Wanda Viegas and Craig S. Pikaard -- Virus induced gene silencing / Tamas Dalmay -- MicroRNAs: micro-managing the plant genome / Sandra K. Floyd and John L. Bowman.
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spelling	Plant epigenetics edited by Peter Meyer Oxford, UK [u.a.] Blackwell Publ. 2005 XV, 283 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Annual plant reviews 19 Includes bibliographical references and index Transgene silencing / Ann Depicker, Matthew Sanders, and Peter Meyer -- RNA interference: double-stranded RNAs and the processing machinery / Jan M. Kooter -- RNA-directed DNA methylation / Marjori Matzke ... [et al.] -- Heterochromatin and the control of gene silencing in plants / G. Reuter, A. Fischer, and I. Hofmann -- When alleles meet: paramutation / Marieke Louwers, Max Haring, and Maike Stam -- Genomic imprinting in plants: a predominantly maternal affair / Ueli Grossniklaus -- Nucleolar dominance and rRNA gene dosage control: a paradigm for transcriptional regulation via an epigenetic on/off switch / Nuno Neves, Wanda Viegas and Craig S. Pikaard -- Virus induced gene silencing / Tamas Dalmay -- MicroRNAs: micro-managing the plant genome / Sandra K. Floyd and John L. Bowman. Plantes - Régulation génétique Épigénèse Plant genetic regulation Epigenesis Gene Expression Regulation, Plant Epigenesis, Genetic Gene Silencing Pflanzen (DE-588)4045539-7 gnd rswk-swf Genexpression (DE-588)4020136-3 gnd rswk-swf Epigenese (DE-588)4152503-6 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Pflanzen (DE-588)4045539-7 s Epigenese (DE-588)4152503-6 s Genexpression (DE-588)4020136-3 s b DE-604 Meyer, Peter Sonstige oth Annual plant reviews 19 (DE-604)BV012859776 19 http://www.loc.gov/catdir/toc/ecip058/2005005883.html Table of contents OEBV Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014633708&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis
spellingShingle	Plant epigenetics Annual plant reviews Transgene silencing / Ann Depicker, Matthew Sanders, and Peter Meyer -- RNA interference: double-stranded RNAs and the processing machinery / Jan M. Kooter -- RNA-directed DNA methylation / Marjori Matzke ... [et al.] -- Heterochromatin and the control of gene silencing in plants / G. Reuter, A. Fischer, and I. Hofmann -- When alleles meet: paramutation / Marieke Louwers, Max Haring, and Maike Stam -- Genomic imprinting in plants: a predominantly maternal affair / Ueli Grossniklaus -- Nucleolar dominance and rRNA gene dosage control: a paradigm for transcriptional regulation via an epigenetic on/off switch / Nuno Neves, Wanda Viegas and Craig S. Pikaard -- Virus induced gene silencing / Tamas Dalmay -- MicroRNAs: micro-managing the plant genome / Sandra K. Floyd and John L. Bowman. Plantes - Régulation génétique Épigénèse Plant genetic regulation Epigenesis Gene Expression Regulation, Plant Epigenesis, Genetic Gene Silencing Pflanzen (DE-588)4045539-7 gnd Genexpression (DE-588)4020136-3 gnd Epigenese (DE-588)4152503-6 gnd
subject_GND	(DE-588)4045539-7 (DE-588)4020136-3 (DE-588)4152503-6 (DE-588)4143413-4
title	Plant epigenetics
title_auth	Plant epigenetics
title_exact_search	Plant epigenetics
title_exact_search_txtP	Plant epigenetics
title_full	Plant epigenetics edited by Peter Meyer
title_fullStr	Plant epigenetics edited by Peter Meyer
title_full_unstemmed	Plant epigenetics edited by Peter Meyer
title_short	Plant epigenetics
title_sort	plant epigenetics
topic	Plantes - Régulation génétique Épigénèse Plant genetic regulation Epigenesis Gene Expression Regulation, Plant Epigenesis, Genetic Gene Silencing Pflanzen (DE-588)4045539-7 gnd Genexpression (DE-588)4020136-3 gnd Epigenese (DE-588)4152503-6 gnd
topic_facet	Plantes - Régulation génétique Épigénèse Plant genetic regulation Epigenesis Gene Expression Regulation, Plant Epigenesis, Genetic Gene Silencing Pflanzen Genexpression Epigenese Aufsatzsammlung
url	http://www.loc.gov/catdir/toc/ecip058/2005005883.html http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014633708&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
volume_link	(DE-604)BV012859776
work_keys_str_mv	AT meyerpeter plantepigenetics

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