RNA Interference (eBook)

Contents 5
Contributors 7
RNA Interference in Mammalian Cell Systems 9
1 Introduction 9
2 The RNAi Pathway in Mammals 10
3 Triggers of RNAi in Mammals 15
4 Genome-Wide Approaches Using RNAi 17
5 Off-Target Effects 19
6 RNAi in the Clinic? 20
7 Concluding Remarks 21
References 21
RNAi Pathway in C. elegans: The Argonautes and Collaborators 28
1 A Tiny Worm Shed Light on New Gene Regulation Mechanisms 28
2 The Argonautes: The Heroes of RNAi Pathways 30
3 The Argonautes Are Not Alone 36
4 RNAi Important to Maintain Genome Integrity: A Primitive Immune System in C. elegans? 39
5 Closing Remarks 40
References 40
Genetics and Biochemistry of RNAi in Drosophila 44
1 Dicer: RNAi Initiation 46
2 siRNA: Structure and Its Impact on RNAi 48
3 Argonaute Proteins: Structure and Function 49
4 Drosophila AGO Proteins: Unique Features and Crucial Role in RNAi 50
5 RISC Assembly 52
6 RISC Assembly Pathway and Target mRNA Cleavage 53
7 Kinetics of RISC: Consolidating the Structural and Biochemical Data 56
8 Transcriptional Gene Silencing in Relation to the Polycomb Complex and RNAi 57
9 RNAi and Transposable Element Expression 59
10 Cosuppression and I Factor Repression 60
11 Heterochromatin and P Element Control 61
12 Hybrid Dysgenesis in D. virilis 62
13 siRNAs Homologous to Transposable Elements and Viruses 63
14 Germinal Versus Somatic Silencing 64
15 Length Maintenance of the Telomeres 66
16 Transposons Regulate Neighboring Genes by RNAi 67
17 RNAi Interactions with Heterochromatin, RNA Editing, and DNA Repair 67
18 Role of RNAi Genes with Chromatin Insulators 72
19 Stability of the Nucleolus 72
20 Silencing Interactions with the MSL Complex 72
21 Concluding Remarks 74
References 74
Role of Dicer in Posttranscriptional RNA Silencing 83
1 Introduction 83
2 RNase III Family 84
3 Dicer Proteins in Different Organisms 86
4 Proteins Interacting with Dicer 87
5 Mechanism of dsRNA and Pre-miRNA Processing by Dicer 92
6 Function of Dicer in the Assembly of Effector Complexes 94
7 Role of Dicer In Vivo 97
References 97
The Mechanism of RNase III Action: How Dicer Dices 104
1 Introduction 105
2 Domain Structure and Function of RNase III Proteins 107
3 Minimal Functional Core of RNase III Proteins 115
4 Conclusions 118
References 119
MicroRNA Metabolism in Plants 122
1 MicroRNA Discovery in Plants 123
2 MicroRNA Genes in Plants: Organization, Conservation, and Origin 125
3 MicroRNA Biogenesis in Arabidopsis 126
4 Regulation of MicroRNA Biogenesis 133
5 Mode of Action of Plant MicroRNAs 134
6 Outstanding Questions 135
References 137
Structure-Function Relationships Among RNA-Dependent RNA Polymerases 142
1 Introduction 143
2 RdRP Structures 143
3 Structures of RdRP Complexes 147
4 Phosphodiester Bond Formation 151
5 Fidelity 153
6 RdRPs of RNAi 156
7 Concluding Remarks 156
References 157
RNAi-Mediated Chromatin Silencing in Fission Yeast 162
1 Overview 163
2 The Organisation of Fission Yeast Centromeres 164
3 Methylated Histone H3 Binds Swi6 to Form Heterochromatin 166
4 The Role of Heterochromatin at Specific Chromosomal Loci 168
5 RNAi Components Are Required for Heterochromatin Integrity 170
6 RNAi Is Dispensable at the Mating-Type Locus and Telomeres 180
7 Perspectives 182
References 183
A Role for RNAi in Heterochromatin Formation in Drosophila 189
1 Definition of Heterochromatin 190
2 Biochemistry of RNAi 194
3 Links Between RNAi and Heterochromatin 198
4 Experiments Testing an RNAi Connection in Drosophila 202
5 Outlook 207
References 208
RNA-Mediated Transcriptional Gene Silencing in Human Cells 214
1 Introduction 215
2 Conclusion 224
References 225
RNA Silencing in Mammalian Oocytes and Early Embryos 228
1 Introduction 229
2 Mechanisms of RNA Silencing 230
3 Other dsRNA-Responding Pathways 232
4 RNA Silencing in Mouse Oocytes and Early Embryos 238
5 Experimental Use of RNA Silencing in Mouse Oocytes and Early Embryos 245
6 Conclusions 250
References 250
Identifying Human MicroRNAs 260
1 Introduction 260
2 Bioinformatic MicroRNA Prediction: Principles and Challenges 262
3 A Novel, ‘Integrated’ Approach to MicroRNA Identification 264
4 On-going Trends in MicroRNA Discovery 268
References 270
Index 273