THE ENZYMES. Department of Microbiology, Immunology, and Molecular Genetics, Molecular Biology Institute University of California

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1 VOLUME THIRTY TWO THE ENZYMES Eukaryotic RNases and their Partners in RNA Degradation and Biogenesis, Part B Edited by FENG GUO Department of Biological Chemistry, David Geffen School of Medicine, Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA FUYUHIKO TAMANOI Department of Microbiology, Immunology, and Molecular Genetics, Molecular Biology Institute University of California Los Angeles, CA 90095, USA ELSEVIER AMSTERDAM BOSTON HEIDELBERG LONDON NEW YORK OXFORD PARIS SAN DIEGO SAN FRANCISCO SINGAPORE SYDNEY TOKYO Academu Press is an imprint of Elsevier

2 CONTENTS Preface ix 1. Dicer Proteins and Their Role in Gene Silencing Pathways 1 Michael Doyle, Lukasz Jaskiewicz, and Witold Filipowicz 1. Introduction 2 2. Dicers: RNase III Family Members with a Role in Gene Silencing 3 3. Mechanism of Processing and the Role of the Catalytic RNase III Domains 5 4. Role of Other Domains in Dicer Function Domain Arrangement in Metazoan Dicers Inside-Out Processing Mechanism by the Yeast Dicer Function of Dicer in the Nucleus Proteins Interacting with Dicer and the Assembly of RISC Effector Complexes Future Perspectives 27 Acknowledgments 28 References Loquacious, a Dicer Partner Protein, Functions in Both the MicroRNA and sirna Pathways 37 Ryuya Fukunaga and Phillip D. Zamore 1. Introduction mirna and sirna Pathways in the Fruit Fly Drosophila Melanogaster Drosophila Dicer-1 and Dicer-2: Similar but Distinct Domain Structures Conserved Partnerships Between Dicer and Dicer-Binding Partner dsrbd Proteins Loqs Encodes Four Alternatively Spliced Isoforms Loqs-PA and Loqs-PB Bind to Dicer-1, While Loqs-PD and R2D2 Bind to Dicer Partner Protein Mutant Phenotypes in Flies and Mammals Loqs-PA and Loqs-PB Function in the mirna Pathway Loqs-PD Functions in the sirna Pathway Loqs-PB Is Required to Maintain Ovarian Germline Stem Cells For Some mirnas, Loqs-PB Tunes Mature mirna Length Future Directions 60

3 vi Contents 13. Concluding Remarks 62 Acknowledgments 63 References Translin:TRAX Complex (C3PO), a Novel Ribonuclease for the Degradation of Small RNAs 69 Hong Zhang and Qinghua Liu 1. Introduction: Earlier Studies of Translin and TRAX Discovery of C3PO as a Novel Endoribonuclease Involved in the Activation of RNA-lnduced Silencing Complex C3PO Ribonuclease in trna Processing Structure of C3PO: An Unusual Asymmetrical Hetero-Octamer Oligomeric States of C3PO and Implications for Substrate Binding and Activation Enzymatic Properties of C3PO Concluding Remarks 79 Acknowledgments 80 References Structure and Mechanism of Argonaute Proteins 83 Nicole T. Schirle and Ian J. MacRae 1. Introduction Basic Argonaute Architecture Recognition of the Guide 5'-end by the MID Domain Preorganization of the Seed Facilitates Target Recognition 88 5., Recognition of the Guide RNA 3'-end by the PAZ Domain 90 6.' The Two-State Model of Target Binding The Rubber Band Model of RISC Loading The Slicer Active Site Resides in the PIWI Domain Recruitment of Silencing Factors 95 Acknowledgments 97 References Drosha and DGCR8 in MicroRNA Biogenesis 101 Feng Guo 1. Introduction Drosha DGCR8 as the RNA-Binding Partner of Drosha 105

4 Contents vii 4. DGCR8 as a Heme Protein DGCR8 in DiGeorge Syndrome How do DGCR8 and Drosha Structurally Recognize Pri-miRNAs? How Is Pri-miRNA Processing Regulated? Drosha and DGCR8 Bind RNAs Other Than Pri-miRNAs Future Perspectives 117 Acknowledgments 118 References Control of Drosha-Mediated MicroRNA Maturation by Smad Proteins 123 Hara Kang and Akiko Hata 1. mirna Biogenesis Drosha and DGCR Modulators of the Drosha Microprocessor Complex Smad Proteins mirna Regulation by Smads Closing Remark 133 Acknowledgments 133 References PIWI Proteins and Their Slicer Activity in pirna Biogenesis and Transposon Silencing 137 Kaoru Sato and Haruhiko Siomi 1. Introduction Drosophila PIWI Proteins pirna Biogenesis Outstanding Questions 154 References Control of MicroRNA Maturation by p53 Tumor Suppressor and MCPIP1 Ribonuclease 163 Hiroshi I. Suzuki and Kohei Miyazono 1. Introduction Two-Step Endoribonuclease Reactions in mirna Maturation Control of mirna Biosynthesis by p Negative Regulation of mirna Processing by MCPIP Autoregulation of mirna Processing Processes 176

5 viii Contents 6. Alteration of mirna Biogenesis in Human Cancer Conclusion 178 Acknowledgments 178 References Nanoparticle-Based Delivery of sirna and mirna for Cancer Therapy 185 Rolando E. Yanes, Jie Lu, and Fuyuhiko Tamanoi 1. Introduction Potential Use of sirnas and mirnas for Cancer Therapy Nanoparticle-Based Delivery Summary and Future Prospects 199 Acknowledgment 200 References 200 Author Index Subject Index