Regulatory RNAs

Symposium Participants v Foreword xxi

Introduction

Small RNA Regulators and the Bacterial Response to Stress S. Gottesman, C.A. McCullen, M. Guillier, C.K. Vanderpool, N. Majdalani, J. Benhammou, K.M. Thompson, P.C. FitzGerald, N.A. Sowa, and D.J. FitzGerald 1 Short Silencing RNA: The Dark Matter of Genetics? D.C. Baulcombe 13 Misexpression of the Caenorhabditis elegans miRNA let-7 Is Sufficient to Drive Developmental Programs G.D. Hayes and G. Ruvkun 21 Function and Localization of MicroRNAs in Mammalian Cells A.K.L. Leung and P.A. Sharp 29

Mechanism and Biology of RNAi

The RNAi Pathway Initiated by Dicer-2 in Drosophila K. Kim, Y.S. Lee, D. Harris, K. Nakahara, and R.W. Carthew 39 Molecular Mechanism of Target RNA Transcript Recognition by Argonaute-Guide Complexes J.S. Parker, S.M. Roe, and D. Barford 45 Drosha in Primary MicroRNA Processing Y. Lee, J. Han, K.-H. Yeom, H. Jin, and V.N. Kim 51 Substrate Selectivity of Exportin 5 and Dicer in the Biogenesis of MicroRNAs E. Lund and J.E. Dahlberg 59 The Argonautes L. Joshua-Tor 67 Structure of Dicer and Mechanistic Implications for RNAi I.J. MacRae, F. Li, K. Zhou, W.Z. Cande, and J.A. Doudna 73 Structural Biology of RNA Silencing and Its Functional Implications D.J. Patel, J.-B. Ma, Y.-R. Yuan, K. Ye, Y. Pei, V. Kuryavyi, L. Malinina, G. Meister, and T. Tuschl 81 Systemic RNAi in Caenorhabditis elegans C.P. Hunter, W.M. Winston, C. Molodowitch, E.H. Feinberg, J. Shih, M. Sutherlin, A.J. Wright, and M.C. Fitzgerald 95

Genome-wide Approaches

Transcriptional Landscape of the Human and Fly Genomes: Nonlinear and Multifunctional Modular Model of Transcriptomes A.T. Willingham, S. Dike, J. Cheng, J.R. Manak, I. Bell, E. Cheung, J. Drenkow, E. Dumais, R. Duttagupta, M. Ganesh, S. Ghosh, G. Helt, D. Nix, A. Piccolboni, V. Sementchenko, H. Tammana, P. Kapranov, the ENCODE Genes and Transcripts Group, and T.R. Gingeras 101 Novel Transcribed Regions in the Human Genome J. Rozowsky, J. Wu, Z. Lian, U. Nagalakshmi, J.O. Korbel, P. Kapranov, D. Zheng, S. Dyke, P. Newburger, P. Miller, T.R. Gingeras, S. Weissman, M. Gerstein, and M. Snyder 111 Computational Analysis of RNAs S.R. Eddy 117 MicroRNAs in Search of a Target G. Stefani and F. Slack 129 RNomics: Identification and Function of Small Non-Protein-coding RNAs in Model Organisms A. Hüttenhofer 135 Drosophila Genome-wide RNAi Screens: Are They Delivering the Promise? B. Mathey-Prevot and N. Perrimon 141 Deep Conservation of MicroRNA-target Relationships and 3'UTR Motifs in Vertebrates, Flies, and Nematodes K. Chen and N. Rajewsky 149

Small RNAs in Development

Organ Polarity in Plants Is Specified through the Opposing Activity of Two Distinct Small Regulatory RNAs F.T.S. Nogueira, A.K. Sarkar, D.H. Chitwood, and M.C.P. Timmermans 157 The Function of RNAi in Plant Development R.S. Poethig, A. Peragine, M. Yoshikawa, C. Hunter, M. Willmann, and G. Wu 165 rasiRNAs, DNA Damage, and Embryonic Axis Specification W.E. Theurkauf, C. Klattenhoff, D.P. Bratu, N. McGinnis-Schultz, B.S. Koppetsch, and H.A. Cook 171 Architecture of a MicroRNA-controlled Gene Regulatory Network That Diversifies Neuronal Cell Fates O. Hobert 181 The Caenorhabditis elegans Argonautes ALG-1 and ALG-2: Almost Identical yet Different B.B.J. Tops, R.H.A. Plasterk, and R.F. Ketting 189 MicroRNA Function and Mechanism: Insights from Zebra Fish A.F. Schier and A.J. Giraldez 195 MicroRNAs and Hematopoietic Differentiation A. Fatica, A. Rosa, F. Fazi, M. Ballarino, M. Morlando, F.G. De Angelis, E. Caffarelli, C. Nervi, and I. Bozzoni 205

Telomeres and Cancer

Expression and Suppression of Human Telomerase RNA S. Li and E.H. Blackburn 211 RNA as a Flexible Scaffold for Proteins: Yeast Telomerase and Beyond D.C. Zappulla and T.R. Cech 217 Telomerase RNA Levels Limit the Telomere Length Equilibrium C.W. Greider 225

End Regulation of Transcripts

Sensing Metabolic Signals with Nascent RNA Transcripts: The T Box and S Box Riboswitches as Paradigms T.M. Henkin and F.J. Grundy 231 Genetic Control by cis-Acting Regulatory RNAs in Bacillus subtilis: General Principles and Prospects for Discovery Irnov, A. Kertsburg, and W.C. Winkler 239 A Mg2+-responding RNA That Controls the Expression of a Mg2+ Transporter E.A. Groisman, M.J. Cromie, Y. Shi, and T. Latifi 251 Structural Studies of the Purine and SAM Binding Riboswitches S.D. Gilbert, R.K. Montange, C.D. Stoddard, and R.T. Batey 259 Regulating Bacterial Transcription with Small RNAs G. Storz, J.A. Opdyke, and K.M. Wassarman 269 Turnover and Function of Noncoding RNA Polymerase II Transcripts M.J. Dye, N. Gromak, D. Haussecker, S. West, and N.J. Proudfoot 275

RNPs and RNA Editing

How Does RNA Editing Affect dsRNA-mediated Gene Silencing? B.L. Bass 285 How a Small DNA Virus Uses dsRNA but Not RNAi to Regulate Its Life Cycle R. Gu, Z. Zhang, and G.G. Carmichael 293 Regulation of Two Key Nuclear Enzymatic Activities by the 7SK Small Nuclear RNA W.-J. He, R. Chen, Z. Yang, and Q. Zhou 301 The SMN Complex: An Assembly Machine for RNPs D.J. Battle, M. Kasim, J. Yong, F. Lotti, C.-K. Lau, J. Mouaikel, Z. Zhang, K. Han, L. Wan, and G. Dreyfuss 313 Developing Global Insight into RNA Regulation R.B. Darnell 321 Regulation of Alternative Splicing by snoRNAs S. Kishore and S. Stamm 329

Biology of Short RNAs

Measuring the Rates of Transcriptional Elongation in the Female Drosophila melanogaster Germ Line by Nuclear Run-on A. Sigova, V. Vagin, and P.D. Zamore 335 Polymorphic MicroRNA–Target Interactions: A Novel Source of Phenotypic Variation M. Georges, A. Clop, F. Marcq, H. Takeda, D. Pirottin, S. Hiard, X. Tordoir, F. Caiment, F. Meish, B. Bibé, J. Bouix, J.M. Elsen, F. Eychenne, E. Laville, C. Larzul, D. Milenkovic, J. Tobin, and C. Charlier 343 Expression and Function of MicroRNAs in Viruses Great and Small C.S. Sullivan, A. Grundhoff, S. Tevethia, R. Treisman, J.M. Pipas, and D. Ganem 351 Expression and Function of MicroRNAs Encoded by Kaposi’s Sarcoma-associated Herpesvirus E. Gottwein, X. Cai, and B.R. Cullen 357 Relationship between Retroviral Replication and RNA Interference Machineries K. Moelling, A. Matskevich, and J.-S. Jung 365 Positive and Negative Modulation of Viral and Cellular mRNAs by Liver-specific MicroRNA miR-122 C.L. Jopling, K.L. Norman, and P. Sarnow 369

Control of Gene Expression by Noncoding RNAs

The Challenge of Viral snRNPs N.K. Conrad, V. Fok, D. Cazalla, S. Borah, and J.A. Steitz 377 MSL Complex Associates with Clusters of Actively Transcribed Genes along the Drosophila Male X Chromosome E. Larschan, A.A. Alekseyenko, W.R. Lai, P.J. Park, and M.I. Kuroda 385 Noncoding RNAs of the H/ACA Family M. Terns and R. Terns 395 Biogenesis and Intranuclear Trafficking of Human Box C/D and H/ACA RNPs T. Kiss, E. Fayet, B.E. Jády, P. Richard, and M. Weber 407 RNA and Protein Actors in X-Chromosome Inactivation O. Masui and E. Heard 419 X-Chromosome Kiss and Tell: How the Xs Go Their Separate Ways M.C. Anguera, B.K. Sun, N. Xu, and J.T. Lee 429

Heterochromatin

Genetic Analyses of DNA Methyltransferases in Arabidopsis thaliana X. Zhang and S.E. Jacobsen 439 RNA-directed DNA Methylation and Pol IVb in Arabidopsis M. Matzke, T. Kanno, B. Huettel, L. Daxinger, and A.J.M. Matzke 449 Studies on the Mechanism of RNAi-dependent Heterochromatin Assembly D. Moazed, M. Bühler, S.M. Buker, S.U. Colmenares, E.L. Gerace, S.A. Gerber, E.-J.E. Hong, M.R. Motamedi, A. Verdel, J. Villén, and S.P. Gygi 461 Cell Biology of the Arabidopsis Nuclear siRNA Pathway for RNA-directed Chromatin Modification C.S. Pikaard 473 A Paragenetic Perspective on Integration of RNA Silencing into the Epigenome and Its Role in the Biology of Higher Plants R.A. Jorgensen, N. Doetsch, A. Müller, Q. Que, K. Gendler, and C.A. Napoli 481 RNAi-mediated Heterochromatin Assembly in Fission Yeast M. Zofall and S.I.S. Grewal 487 Slicing and Spreading of Heterochromatic Silencing by RNA Interference S.M. Locke and R.A. Martienssen 497

Quality Control, Messenger RNA Turnover, and Translational Control

Molecular Chaperones and Quality Control in Noncoding RNA Biogenesis S.L. Wolin and E.J. Wurtmann 505 Stress-induced Reversal of MicroRNA Repression and mRNA P-body Localization in Human Cells S.N. Bhattacharyya, R. Habermacher, U. Martine, E.I. Closs, and W. Filipowicz 513 MicroRNAs Silence Gene Expression by Repressing Protein Expression and/or by Promoting mRNA Decay I. Behm-Ansmant, J. Rehwinkel, and E. Izaurralde 523 MicroRNAs, mRNAs, and Translation P.A. Maroney, Y. Yu, and T.W. Nilsen 531 Regulation of Poly(A)-binding Protein through PABP-interacting Proteins M.C. Derry, A. Yanagiya, Y. Martineau, and N. Sonenberg 537 Two Distinct Conformations of the Conserved RNA-rich Decoding Center of the Small Ribosomal Subunit Are Recognized by tRNAs and Release Factors E.M. Youngman, L. Cochella, J.L. Brunelle, S. He, and R. Green 545 Summary: The Expanding Universe of Noncoding RNAs G.J. Hannon, F.V. Rivas, E.P. Murchison, and J.A. Steitz 551 Author Index 565 Subject Index 567