RNA Interference Technology: From Basic Science to Drug Development

by Edited by Krishnarao Appasani , Foreword by Andrew Fire , Marshall Nirenberg

• ISBN13: 9780521836777
• ISBN10: 0521836778
• Edition: 1st
• Format: Hardcover
• Copyright: 2005-01-17
• Publisher: Cambridge University Press

Summary

RNA Interference (RNAi) technology has rapidly become one of the key methods used in functional genomics. RNAi is used to block the expression of genes and create phenotypes that can potentially yield clues about the function of these genes. In the postgenomic era, the elucidation of the physiological function of genes has become the rate-limiting step in the quest to develop 'gene-based drugs' and RNAi could potentially play a pivotal role in the validation of such novel drugs. In this cutting-edge overview, the basic concepts of RNAi biology are discussed, as well as the current and potential applications. Leading experts from both academia and industry have contributed to this invaluable reference for graduate students, post-docs and researchers from academia wanting to initiate RNAi research in their own labs, as well as for those working in research and development in biotech and pharmaceutical companies who need to understand this emerging technology.

Table of Contents

Foreword	xi
Andrew Fire
Foreword	xiii
Marshall Nirenberg
List of Contributors	xv
Introduction	1	(16)
Krishnarao Appasani
Section one. Basic RNAi, siRNA, microRNAs and gene-silencing mechanisms
RNAi beginnings. Overview of the pathway in C. elegans	17	(12)
Alla Grishok
Dicer in RNAi: Its roles in vivo and utility in vitro	29	(26)
Jason W. Myers
James E. Ferrell, Jr.
Genes required for RNA interference	55	(14)
Nathaniel R. Dudley
Ahmad Z. Amin
Bob Goldstein
MicroRNAs: A small contribution from worms	69	(15)
Amy E. Pasquinelli
miRNAs in the brain and the application of RNAi to neurons	84	(19)
Anna M. Krichevsky
Shih-Chu Kao
Li-Huei Tsai
Kenneth S. Kosik
Section two. Design, synthesis of siRNAs
Design and synthesis of small interfering RNA (siRNA)	103	(15)
Queta Boese
William S. Marshall
Anastasia Khvorova
Automated design and high throughput chemical synthesis of siRNA	118	(11)
Yerramilli V. B. K. Subrahmanyam
Eric Lader
Rational design of siRNAs with the Sfold software	129	(10)
Ye Ding
Charles E. Lawrence
Enzymatic production of small interfering RNAs	139	(8)
Muhammad Sohail
Graeme Doran
Section three. Vector development and in vivo, in vitro and in ovo delivery methods
Six methods of inducing RNAi in mammalian cells	147	(14)
Kathy Latham
Vince Pallotta
Lance Ford
Mike Byrom
Mehd Banan
Po-Tsan Ku
David Brown
Viral delivery of shRNA	161	(13)
Ying Mao
Chris Mello
Laurence Lamarcq
Brad Scherer
Thomas Quinn
Patty Wong
Andrew Farmer
siRNA delivery by lentiviral vectors: Design and applications	174	(12)
Oded Singer
Gustavo Tiscornia
Inder Verma
Liposomal delivery of siRNAs in mice	186	(8)
Mouldy Sioud
Dag R. Sorensen
Chemical modifications to achieve increased stability and sensitive detection of siRNA	194	(13)
Philipp Hadwiger
Hans-Peter Vornlocher
RNA interference in postimplantation mouse embryos	207	(13)
Frank Buchholz
Federico Calegari
Ralf Kittler
Wieland B. Huttner
In ovo RNAi opens new possibilities for functional genomics in vertebrates	220	(15)
Dimitris Bourikas
Thomas Baeriswyl
Rejina Sadhu
Esther T. Stoeckli
Section four. Gene silencing in model organisms
Practical applications of RNAi in C. elegans	235	(12)
Karen E. Stephens
Olivier Zugasti
Nigel J. O'Neil
Patricia E. Kuwabara
Inducible RNAi as a forward genetic tool in Trypanosoma brucei	247	(10)
Mark E. Drew
Shawn A. Motyka
James C. Morris
Zefeng Wang
Paul T. Englund
RNA-mediated gene silencing in fission yeast	257	(13)
Greg M. Arndt
RNA silencing in filamentous fungi: Mucor ciccinelloides as a model organism	270	(10)
Rosa M. Ruiz-Vazque
RNAi and gene silencing phenomena mediated by viral suppressors in plants	280	(23)
Ramachandran Vanitharani
Padmanabhan Chellappan
Claude M. Fauquet
Section five. Drug target validation
Delivering siRNA in vivo for functional genomics and novel therapeutics	303	(15)
Patrick Y. Lu
Martin C. Woodle
The role of RNA interference in drug target validation: Application to Hepatitis C	318	(13)
Antje Ostareck-Lederer
Sandra Clauder-Munster
Rolf Thermann
Maria Polycarpou-Schwarz
Marc Gentzel
Matthias Wilm
Joe D. Lewis
RNAi in the drug discovery process	331	(16)
Steven A. Haney
Peter Lapan
Jeff Aalfs
Chris Childs
Paul Yaworsky
Chris Miller
RNA interference technology in the discovery and validation of druggable targets	347	(16)
Neil J. Clarke
John E. Bisi
Caretha L. Creasy
Michael K. Dush
Kris J. Fisher
John M. Johnson III
Christopher J. A. Ring
Mark R. Edbrooke
Section six. Therapeutic and drug development
RNAi-mediated silencing of viral gene expression and replication	363	(21)
Derek M. Dykxhoorn
RNAi in drug development: Practical considerations	384	(12)
Dmitry Samarsky
Margaret Taylor
Mark A. Kay
Anton P. McCaffrey
RNA interference studies in liver failure	396	(10)
Lars Zender
Michael P. Manns
Stefan Kubicka
RNAi applications in living animal systems	406	(13)
Lisa Scherer
John J. Rossi
Section seven. High-throughput genome-wide RNAi analysis
High-throughput RNAi by soaking in Caenorhabtis elegans	419	(14)
Asako Sugimoto
Tools for integrative genomics: Genome-wide RNAi and expression profiling in Drosophila	433	(14)
Michael Boutros
Marc Hild
Microarray analysis and RNA silencing to determine genes functionally important in mesothelioma	447	(23)
Maria E. Ramos-Nino
Brooke T. Mossman
High-throughput RNA interference	470	(10)
Howard Y. Chang
Nancy N. Wang
Jen-Tsan Chi
Generation of highly specific vector-based shRNAi libraries directed against the entire human genome	480	(17)
Makoto Miyagishi
Sahohime Matsumoto
Takashi Futami
Hideo Akashi
Krishnarao Appasani
Yasuomi Takagi
Shizuyo Sutou
Takashi Kadowaki
Ryozo Nagai
Kazunari Taira
Index	497