1;Contents;5 2;Contributors;7 3;RNA Interference in Mammalian Cell Systems;9 3.1;1 Introduction;9 3.2;2 The RNAi Pathway in Mammals;10 3.3;3 Triggers of RNAi in Mammals;15 3.4;4 Genome-Wide Approaches Using RNAi;17 3.5;5 Off-Target Effects;19 3.6;6 RNAi in the Clinic?;20 3.7;7 Concluding Remarks;21 3.8;References;21 4;RNAi Pathway in C. elegans: The Argonautes and Collaborators;28 4.1;1 A Tiny Worm Shed Light on New Gene Regulation Mechanisms;28 4.2;2 The Argonautes: The Heroes of RNAi Pathways;30 4.3;3 The Argonautes Are Not Alone;36 4.4;4 RNAi Important to Maintain Genome Integrity: A Primitive Immune System in C. elegans?;39 4.5;5 Closing Remarks;40 4.6;References;40 5;Genetics and Biochemistry of RNAi in Drosophila;44 5.1;1 Dicer: RNAi Initiation;46 5.2;2 siRNA: Structure and Its Impact on RNAi;48 5.3;3 Argonaute Proteins: Structure and Function;49 5.4;4 Drosophila AGO Proteins: Unique Features and Crucial Role in RNAi;50 5.5;5 RISC Assembly;52 5.6;6 RISC Assembly Pathway and Target mRNA Cleavage;53 5.7;7 Kinetics of RISC: Consolidating the Structural and Biochemical Data;56 5.8;8 Transcriptional Gene Silencing in Relation to the Polycomb Complex and RNAi;57 5.9;9 RNAi and Transposable Element Expression;59 5.10;10 Cosuppression and I Factor Repression;60 5.11;11 Heterochromatin and P Element Control;61 5.12;12 Hybrid Dysgenesis in D. virilis;62 5.13;13 siRNAs Homologous to Transposable Elements and Viruses;63 5.14;14 Germinal Versus Somatic Silencing;64 5.15;15 Length Maintenance of the Telomeres;66 5.16;16 Transposons Regulate Neighboring Genes by RNAi;67 5.17;17 RNAi Interactions with Heterochromatin, RNA Editing, and DNA Repair;67 5.18;18 Role of RNAi Genes with Chromatin Insulators;72 5.19;19 Stability of the Nucleolus;72 5.20;20 Silencing Interactions with the MSL Complex;72 5.21;21 Concluding Remarks;74 5.22;References;74 6;Role of Dicer in Posttranscriptional RNA Silencing;83 6.1;1 Introduction;83 6.2;2 RNase III Family;84 6.3;3 Dicer Proteins in Different Organisms;86 6.4;4 Proteins Interacting with Dicer;87 6.5;5 Mechanism of dsRNA and Pre-miRNA Processing by Dicer;92 6.6;6 Function of Dicer in the Assembly of Effector Complexes;94 6.7;7 Role of Dicer In Vivo;97 6.8;References;97 7;The Mechanism of RNase III Action: How Dicer Dices;104 7.1;1 Introduction;105 7.2;2 Domain Structure and Function of RNase III Proteins;107 7.3;3 Minimal Functional Core of RNase III Proteins;115 7.4;4 Conclusions;118 7.5;References;119 8;MicroRNA Metabolism in Plants;122 8.1;1 MicroRNA Discovery in Plants;123 8.2;2 MicroRNA Genes in Plants: Organization, Conservation, and Origin;125 8.3;3 MicroRNA Biogenesis in Arabidopsis;126 8.4;4 Regulation of MicroRNA Biogenesis;133 8.5;5 Mode of Action of Plant MicroRNAs;134 8.6;6 Outstanding Questions;135 8.7;References;137 9;Structure-Function Relationships Among RNA-Dependent RNA Polymerases;142 9.1;1 Introduction;143 9.2;2 RdRP Structures;143 9.3;3 Structures of RdRP Complexes;147 9.4;4 Phosphodiester Bond Formation;151 9.5;5 Fidelity;153 9.6;6 RdRPs of RNAi;156 9.7;7 Concluding Remarks;156 9.8;References;157 10;RNAi-Mediated Chromatin Silencing in Fission Yeast;162 10.1;1 Overview;163 10.2;2 The Organisation of Fission Yeast Centromeres;164 10.3;3 Methylated Histone H3 Binds Swi6 to Form Heterochromatin;166 10.4;4 The Role of Heterochromatin at Specific Chromosomal Loci;168 10.5;5 RNAi Components Are Required for Heterochromatin Integrity;170 10.6;6 RNAi Is Dispensable at the Mating-Type Locus and Telomeres;180 10.7;7 Perspectives;182 10.8;References;183 11;A Role for RNAi in Heterochromatin Formation in Drosophila;189 11.1;1 Definition of Heterochromatin;190 11.2;2 Biochemistry of RNAi;194 11.3;3 Links Between RNAi and Heterochromatin;198 11.4;4 Experiments Testing an RNAi Connection in Drosophila;202 11.5;5 Outlook;207 11.6;References;208 12;RNA-Mediated Transcriptional Gene Silencing in Human Cells;214 12.1;1 Introduction;215 12.2;2 Conclusion;224 12.3;References;225 13;RNA Silencing in M