Regulatory RNAs vol. 71, 2006

Table of Contents

  • Cold Spring Harbor Symposia On Quantitative Biology Volume Lxxi

    Cold Spring Harb Symp Quant Biol 2006 71: i-xxv; doi:10.1101/sqb.2006.71.067

  • Author Index

    Cold Spring Harb Symp Quant Biol 2006 71: 556-566; doi:10.1101/sqb.2006.71.069

  • Subject Index

    Cold Spring Harb Symp Quant Biol 2006 71: 567-574; doi:10.1101/sqb.2006.71.070

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
    Cold Spring Harb Symp Quant Biol 2006 71: 1-11; doi:10.1101/sqb.2006.71.016

  • Short Silencing RNA: The Dark Matter of Genetics?

    • D.C. BAULCOMBE
    Cold Spring Harb Symp Quant Biol 2006 71: 13-20; doi:10.1101/sqb.2006.71.052

  • Misexpression of the Caenorhabditis elegans miRNA let-7 Is Sufficient to Drive Developmental Programs

    • G.D. HAYES and
    • G. RUVKUN
    Cold Spring Harb Symp Quant Biol 2006 71: 21-27; doi:10.1101/sqb.2006.71.018

  • Function and Localization of MicroRNAs in Mammalian Cells

    • A.K.L. LEUNG and
    • P.A. SHARP
    Cold Spring Harb Symp Quant Biol 2006 71: 29-38; doi:10.1101/sqb.2006.71.049

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
    Cold Spring Harb Symp Quant Biol 2006 71: 39-44; doi:10.1101/sqb.2006.71.008

  • Molecular Mechanism of Target RNA Transcript Recognition by Argonaute-Guide Complexes

    • J.S. PARKER,
    • S.M. ROE,
    • and D. BARFORD
    Cold Spring Harb Symp Quant Biol 2006 71: 45-50; doi:10.1101/sqb.2006.71.029

  • Drosha in Primary MicroRNA Processing

    • Y. LEE,
    • J. HAN,
    • K.-H. YEOM,
    • H. JIN,
    • and V.N. KIM
    Cold Spring Harb Symp Quant Biol 2006 71: 51-57; doi:10.1101/sqb.2006.71.041

  • Substrate Selectivity of Exportin 5 and Dicer in the Biogenesis of MicroRNAs

    • E. LUND and
    • J.E. DAHLBERG
    Cold Spring Harb Symp Quant Biol 2006 71: 59-66; doi:10.1101/sqb.2006.71.050

  • The Argonautes

    • L. JOSHUA-TOR
    Cold Spring Harb Symp Quant Biol 2006 71: 67-72; doi:10.1101/sqb.2006.71.048

  • Structure of Dicer and Mechanistic Implications for RNAi

    • I.J. MacRAE,
    • F. LI,
    • K. ZHOU,
    • W.Z. CANDE,
    • and J.A. DOUDNA
    Cold Spring Harb Symp Quant Biol 2006 71: 73-80; doi:10.1101/sqb.2006.71.042

  • 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
    Cold Spring Harb Symp Quant Biol 2006 71: 81-93; doi:10.1101/sqb.2006.71.053

  • 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
    Cold Spring Harb Symp Quant Biol 2006 71: 95-100; doi:10.1101/sqb.2006.71.060

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
    Cold Spring Harb Symp Quant Biol 2006 71: 101-110; doi:10.1101/sqb.2006.71.068

  • 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
    Cold Spring Harb Symp Quant Biol 2006 71: 111-116; doi:10.1101/sqb.2006.71.054

  • Computational Analysis of RNAs

    • S.R. EDDY
    Cold Spring Harb Symp Quant Biol 2006 71: 117-128; doi:10.1101/sqb.2006.71.003

  • MicroRNAs in Search of a Target

    • G. STEFANI and
    • F. SLACK
    Cold Spring Harb Symp Quant Biol 2006 71: 129-134; doi:10.1101/sqb.2006.71.032

  • RNomics: Identification and Function of Small Non-Protein-coding RNAs in Model Organisms

    • A. HÜTTENHOFER
    Cold Spring Harb Symp Quant Biol 2006 71: 135-140; doi:10.1101/sqb.2006.71.007

  • Drosophila Genome-wide RNAi Screens: Are They Delivering the Promise?

    • B. MATHEY-PREVOT and
    • N. PERRIMON
    Cold Spring Harb Symp Quant Biol 2006 71: 141-148; doi:10.1101/sqb.2006.71.027

  • Deep Conservation of MicroRNA-target Relationships and 3'UTR Motifs in Vertebrates, Flies, and Nematodes

    • K. CHEN and
    • N. RAJEWSKY
    Cold Spring Harb Symp Quant Biol 2006 71: 149-156; doi:10.1101/sqb.2006.71.039

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
    Cold Spring Harb Symp Quant Biol 2006 71: 157-164; doi:10.1101/sqb.2006.71.045

  • The Function of RNAi in Plant Development

    • R.S. POETHIG,
    • A. PERAGINE,
    • M. YOSHIKAWA,
    • C. HUNTER,
    • M. WILLMANN,
    • and G. WU
    Cold Spring Harb Symp Quant Biol 2006 71: 165-170; doi:10.1101/sqb.2006.71.030

  • 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
    Cold Spring Harb Symp Quant Biol 2006 71: 171-180; doi:10.1101/sqb.2006.71.066

  • Architecture of a MicroRNA-controlled Gene Regulatory Network That Diversifies Neuronal Cell Fates

    • O. HOBERT
    Cold Spring Harb Symp Quant Biol 2006 71: 181-188; doi:10.1101/sqb.2006.71.006

  • 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
    Cold Spring Harb Symp Quant Biol 2006 71: 189-194; doi:10.1101/sqb.2006.71.035

  • MicroRNA Function and Mechanism: Insights from Zebra Fish

    • A.F. SCHIER and
    • A.J. GIRALDEZ
    Cold Spring Harb Symp Quant Biol 2006 71: 195-203; doi:10.1101/sqb.2006.71.055

  • 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
    Cold Spring Harb Symp Quant Biol 2006 71: 205-210; doi:10.1101/sqb.2006.71.014

Telomeres and Cancer

  • Expression and Suppression of Human Telomerase RNA

    • S. LI and
    • E.H. BLACKBURN
    Cold Spring Harb Symp Quant Biol 2006 71: 211-215; doi:10.1101/sqb.2006.71.009

  • RNA as a Flexible Scaffold for Proteins: Yeast Telomerase and Beyond

    • D.C. ZAPPULLA and
    • T.R. CECH
    Cold Spring Harb Symp Quant Biol 2006 71: 217-224; doi:10.1101/sqb.2006.71.011

  • Telomerase RNA Levels Limit the Telomere Length Equilibrium

    • C.W. GREIDER
    Cold Spring Harb Symp Quant Biol 2006 71: 225-229; doi:10.1101/sqb.2006.71.063

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
    Cold Spring Harb Symp Quant Biol 2006 71: 231-237; doi:10.1101/sqb.2006.71.020

  • Genetic Control by cis-Acting Regulatory RNAs in Bacillus subtilis: General Principles and Prospects for Discovery

    • IRNOV,
    • A. KERTSBURG,
    • and W.C. WINKLER
    Cold Spring Harb Symp Quant Biol 2006 71: 239-249; doi:10.1101/sqb.2006.71.021

  • A Mg2+-responding RNA That Controls the Expression of a Mg2+ Transporter

    • E.A. GROISMAN,
    • M.J. CROMIE,
    • Y. SHI,
    • and T. LATIFI
    Cold Spring Harb Symp Quant Biol 2006 71: 251-258; doi:10.1101/sqb.2006.71.005

  • Structural Studies of the Purine and SAM Binding Riboswitches

    • S.D. GILBERT,
    • R.K. MONTANGE,
    • C.D. STODDARD,
    • and R.T. BATEY
    Cold Spring Harb Symp Quant Biol 2006 71: 259-268; doi:10.1101/sqb.2006.71.015

  • Regulating Bacterial Transcription with Small RNAs

    • G. STORZ,
    • J.A. OPDYKE,
    • and K.M. WASSARMAN
    Cold Spring Harb Symp Quant Biol 2006 71: 269-273; doi:10.1101/sqb.2006.71.033

  • Turnover and Function of Noncoding RNA Polymerase II Transcripts

    • M.J. DYE,
    • N. GROMAK,
    • D. HAUSSECKER,
    • S. WEST,
    • and N.J. PROUDFOOT
    Cold Spring Harb Symp Quant Biol 2006 71: 275-284; doi:10.1101/sqb.2006.71.040

RNPs and RNA Editing

  • How Does RNA Editing Affect dsRNA-mediated Gene Silencing?

    • B.L. BASS
    Cold Spring Harb Symp Quant Biol 2006 71: 285-292; doi:10.1101/sqb.2006.71.037

  • How a Small DNA Virus Uses dsRNA but Not RNAi to Regulate Its Life Cycle

    • R. GU,
    • Z. ZHANG,
    • and G.G. CARMICHAEL
    Cold Spring Harb Symp Quant Biol 2006 71: 293-299; doi:10.1101/sqb.2006.71.017

  • Regulation of Two Key Nuclear Enzymatic Activities by the 7SK Small Nuclear RNA

    • W.-J. HE,
    • R. CHEN,
    • Z. YANG,
    • and Q. ZHOU
    Cold Spring Harb Symp Quant Biol 2006 71: 301-311; doi:10.1101/sqb.2006.71.019

  • 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
    Cold Spring Harb Symp Quant Biol 2006 71: 313-320; doi:10.1101/sqb.2006.71.001

  • Developing Global Insight into RNA Regulation

    • R.B. DARNELL
    Cold Spring Harb Symp Quant Biol 2006 71: 321-327; doi:10.1101/sqb.2006.71.002

  • Regulation of Alternative Splicing by snoRNAs

    • S. KISHORE and
    • S. STAMM
    Cold Spring Harb Symp Quant Biol 2006 71: 329-334; doi:10.1101/sqb.2006.71.024

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
    Cold Spring Harb Symp Quant Biol 2006 71: 335-341; doi:10.1101/sqb.2006.71.031

  • Polymorphic 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 AND C. CHARLIER
    Cold Spring Harb Symp Quant Biol 2006 71: 343-350; doi:10.1101/sqb.2006.71.056

  • 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
    Cold Spring Harb Symp Quant Biol 2006 71: 351-356; doi:10.1101/sqb.2006.71.065

  • Expression and Function of MicroRNAs Encoded by Kaposi's Sarcoma-associated Herpesvirus

    • E. GOTTWEIN,
    • X. CAI,
    • and B.R. CULLEN
    Cold Spring Harb Symp Quant Biol 2006 71: 357-364; doi:10.1101/sqb.2006.71.004

  • Relationship between Retroviral Replication and RNA Interference Machineries

    • K. MOELLING,
    • A. MATSKEVICH,
    • and J.-S. JUNG
    Cold Spring Harb Symp Quant Biol 2006 71: 365-368; doi:10.1101/sqb.2006.71.010

  • Positive and Negative Modulation of Viral and Cellular mRNAs by Liver-specific MicroRNA miR-122

    • C.L. JOPLING,
    • K.L. NORMAN,
    • and P. SARNOW
    Cold Spring Harb Symp Quant Biol 2006 71: 369-376; doi:10.1101/sqb.2006.71.022

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
    Cold Spring Harb Symp Quant Biol 2006 71: 377-384; doi:10.1101/sqb.2006.71.057

  • 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
    Cold Spring Harb Symp Quant Biol 2006 71: 385-394; doi:10.1101/sqb.2006.71.026

  • Noncoding RNAs of the H/ACA Family

    • M. TERNS and
    • R. TERNS
    Cold Spring Harb Symp Quant Biol 2006 71: 395-405; doi:10.1101/sqb.2006.71.034

  • 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
    Cold Spring Harb Symp Quant Biol 2006 71: 407-417; doi:10.1101/sqb.2006.71.025

  • RNA and Protein Actors in X-Chromosome Inactivation

    • O. MASUI and
    • E. HEARD
    Cold Spring Harb Symp Quant Biol 2006 71: 419-428; doi:10.1101/sqb.2006.71.058

  • X-Chromosome Kiss and Tell: How the Xs Go Their Separate Ways

    • M.C. ANGUERA,
    • B.K. SUN,
    • N. XU,
    • and J.T. LEE
    Cold Spring Harb Symp Quant Biol 2006 71: 429-437; doi:10.1101/sqb.2006.71.012

Heterochromatin

  • Genetic Analyses of DNA Methyltransferases in Arabidopsis thaliana

    • X. ZHANG and
    • S.E. JACOBSEN
    Cold Spring Harb Symp Quant Biol 2006 71: 439-447; doi:10.1101/sqb.2006.71.047

  • RNA-directed DNA Methylation and Pol IVb in Arabidopsis

    • M. MATZKE,
    • T. KANNO,
    • B. HUETTEL,
    • L. DAXINGER,
    • and A.J.M. MATZKE
    Cold Spring Harb Symp Quant Biol 2006 71: 449-459; doi:10.1101/sqb.2006.71.028

  • 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
    Cold Spring Harb Symp Quant Biol 2006 71: 461-471; doi:10.1101/sqb.2006.71.044

  • Cell Biology of the Arabidopsis Nuclear siRNA Pathway for RNA-directed Chromatin Modification

    • C.S. PIKAARD
    Cold Spring Harb Symp Quant Biol 2006 71: 473-480; doi:10.1101/sqb.2006.71.046

  • 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
    Cold Spring Harb Symp Quant Biol 2006 71: 481-485; doi:10.1101/sqb.2006.71.023

  • RNAi-mediated Heterochromatin Assembly in Fission Yeast

    • M. ZOFALL and
    • S.I.S. GREWAL
    Cold Spring Harb Symp Quant Biol 2006 71: 487-496; doi:10.1101/sqb.2006.71.059

  • Slicing and Spreading of Heterochromatic Silencing by RNA Interference

    • S.M. LOCKE and
    • R.A. MARTIENSSEN
    Cold Spring Harb Symp Quant Biol 2006 71: 497-503; doi:10.1101/sqb.2006.71.062

Quality Control, Messenger RNA Turnover, and Translational Control

  • Molecular Chaperones and Quality Control in Noncoding RNA Biogenesis

    • S.L. WOLIN and
    • E.J. WURTMANN
    Cold Spring Harb Symp Quant Biol 2006 71: 505-511; doi:10.1101/sqb.2006.71.051

  • 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
    Cold Spring Harb Symp Quant Biol 2006 71: 513-521; doi:10.1101/sqb.2006.71.038

  • MicroRNAs Silence Gene Expression by Repressing Protein Expression and/or by Promoting mRNA Decay

    • I. BEHM-ANSMANT,
    • J. REHWINKEL,
    • and E. IZAURRALDE
    Cold Spring Harb Symp Quant Biol 2006 71: 523-530; doi:10.1101/sqb.2006.71.013

  • MicroRNAs, mRNAs, and Translation

    • P.A. MARONEY,
    • Y. YU,
    • and T.W. NILSEN
    Cold Spring Harb Symp Quant Biol 2006 71: 531-535; doi:10.1101/sqb.2006.71.043

  • Regulation of Poly(A)-binding Protein through PABP-interacting Proteins

    • M.C. DERRY,
    • A. YANAGIYA,
    • Y. MARTINEAU,
    • and N. SONENBERG
    Cold Spring Harb Symp Quant Biol 2006 71: 537-543; doi:10.1101/sqb.2006.71.061

  • 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
    Cold Spring Harb Symp Quant Biol 2006 71: 545-549; doi:10.1101/sqb.2006.71.036

  • The Expanding Universe of Noncoding RNAs

    • G.J. HANNON,
    • F.V. RIVAS,
    • E.P. MURCHISON,
    • and J.A. STEITZ
    Cold Spring Harb Symp Quant Biol 2006 71: 551-564; doi:10.1101/sqb.2006.71.064
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This Volume

Regulatory RNAs vol. 71, 2006
Cover
  1. Introduction
  2. Mechanism and Biology of RNAi
  3. Genome-wide Approaches
  4. Small RNAs in Development
  5. Telomeres and Cancer
  6. End Regulation of Transcripts
  7. RNPs and RNA Editing
  8. Biology of Short RNAs
  9. Control of Gene Expression by Noncoding RNAs
  10. Heterochromatin
  11. Quality Control, Messenger RNA Turnover, and Translational Control

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