RNA WorldsFrom Life's Origins to Diversity

in Gene Regulation

EDITED BY

John F. Atkins Raymond F. GestelandUniversity of Utah University of Utah

University College Cork

Trinity College Dublin

Thomas R. CechHoward Hughes Medical Institute

University of Colorado

www.cshperspectives.org

COLD SPRING HARBOR LABORATORY PRESSCold Spring Harbor, New York • www.cshlpress.com

Contents

Preface, vii

Foreword to the First Edition of The RNA World, ixFrancis Crick

Prologue to the First Edition of The RNA World, xi

James D. Watson

The RNA Worlds in Context, 1

Thomas R. Cech

THE EARLY RNA WORLD

Setting the Stage: The History, Chemistry, and Geobiologybehind RNA, 7

Steven A. Benner, Hyo-Joong Kim, and Zunyi Yang

The Origins of the RNA World, 21

Michael P. Robertson and Gerald F. Joyce

Getting Past the RNA World: The Initial DarwinianAncestor, 43Michael Yams

The Origins of Cellular Life, 51Jason R Schrum, Ting F. Zhu, and Jack W. Szostak

WHAT RNA CAN DO BY ITSELF

Riboswitches and the RNA World, 63Ronald R. Breaker

Riboswitches: Structures and Mechanisms, 79Andrew D. Garst, Andrea L. Edwards, and Robert T. Batey

Small Self-cleaving Ribozymes, 93Adrian R. Ferre-D'Amare and William G. Scott

Group II Introns: Mobile Ribozymes that Invade DNA, 103Alan M. Lambowitz and Steven Zimmerly

EXIT THE RNA WORLD: PROTEIN SYNTHESISON RIBOSOMES

The Roles of RNA in the Synthesis of Protein, 123Peter B. Moore and Thomas A. Steitz

Evolution of Protein Synthesis from an RNA World, 141Harry F. Noller

The Ribosome: Some Hard Facts about Its Structureand Hot Air about Its Evolution, 155V. Ramakrishnan

RNP-ZYMES: WHAT RNA CAN DO INCOLLABORATION WITH PROTEIN

Noncoding RNPs of Viral Origin, 165Joan Steitz, Sumit Borah, Demian Cazalla, Victor Fok, Robin Lytle,

Rachel Mitton-Fry, Kasandra Riley, and Tasleem Samji

Spliceosome Structure and Function, 181

Cindy L. Will and Reinhard Luhrmann

Telomerase: An RNP Enzyme Synthesizes DNA, 205Elizabeth H. Blackburn and Kathleen Collins

RNA REGULATED GENE EXPRESSION

Bacterial Small RNA Regulators: Versatile Roles and RapidlyEvolving Variations, 215Susan Gottesman and Gisela Storz

RNA in Defense: CRISPRs Protect Prokaryotes againstMobile Genetic Elements, 231

Matthijs M. Jore, Stan J.J. Brouns, and John van der Oost

Ancestral Roles of Small RNAs: An Ago-CentricPerspective, 243

Leemor Joshua-Tor and Gregory J. Hannon

RNA Interference and Heterochromatin Assembly, 255Tom Volpe and Robert A. Martienssen

The X as Model for RNA's Niche in EpigenomicRegulation, 267Jeannie T. Lee

The Long Arm of Long Noncoding RNAs: Roles as SensorsRegulating Gene Transcriptional Programs, 279Xiangting Wang, Xiaoyuan Song, Christopher K. Glass, andMichael G. Rosenfeld

Contents

TOOLS FOR RNA SCIENCE Aptamers and the RNA World, Past and Present, 333

Folding and Finding RNA Secondary Structure, 293 ^ ^ Gold' N e b o ) s a JanJk> nale Jarvts' Dan Schnetder>David H. Mathews, Walter N. Moss, and Douglas H. Turner ] e ^ l Walker> Shen * Wlkox' and Dom Zkhi

n ,. .. , . . , ,. „... . ... . -.„„ In Vivo RNAi: Today and Tomorrow, 343Predicting and Modeling RNA Architecture, 309 '„ . , . . , , „ « , , ., , „ , . T . Norbert Perrimon, Jian-Quan Ni, and Lizabeth PerkinsEric Westhof, Benoit Masquida, and Fabnce Jossinet

RNA Reactions One Molecule at a Time, 321 Index, 355

Ignacio Tinoco, Gang Chen, and Xiaohui Qu

VI