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The study of RNA interference, editing, and modification has led to major shifts in our understanding of how genes are expressed and regulated. In RNA Interference, Editing, and Modification: Methods and Protocols, hands-on experimentalists describe in detail the protocols and assays they have developed to study these processes in most of the major biological systems in which they are known to occur-a wide range of organisms that includes worms, flies, trypanosomes, mammals, and plants. A historical overview of each subject is provided to put related chapters into a larger context. RNA interference (RNAi) has also emerged in recent years as an important and promising tool for gene discovery and reverse genetic engineering. Application of this cutting-edge technique is described for a range of experimental systems. Topics of interest include stable and transient RNA interference, RNA editing, gene silencing, bioinformatics, small noncoding RNAs, and RNomics. Special attention is given to methods for the identification and characterization of small RNAs, many of which are involved in RNA interference or modification. In addition, techniques used to study RNA editing mechanisms are elaborated for both systems that involve the conversion of one base to another and insertion-deletion editing. To promote the adaptation of their assays and approaches for use in other biological systems, the authors have included a range of methods representative of the major experimental systems in a given field. All protocols presented follow the successful Methods in Molecular Biology(TM) series format, each one offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.
State-of-the-art and highly practical, RNA Interference, Editing, and Modification: Methods and Protocols offers not only geneticists, molecular biologists, and bioinformaticists a comprehensive collection of readily reproducible techniques for the elucidation of gene function and the alteration of gene expression, but also describes how best they may be productively used to address outstanding mechanistic questions and adapted to novel biological systems.

RNA Interference, Editing, and Modification: Methods and Protocols

Part I. RNA Interference and Gene Silencing

RNA Interference: Historical Overview and Significance
Mary K. Montgomery

Delivery of Double-Stranded RNA into Caenorhabditis elegans
Dawn Hull and Lisa Timmons

Induction and Biochemical Purification of RNA-Induced Silencing Complex From Drosophila S2 Cells
Amy A. Caudy and Gregory J. Hannon

Analysis of Gene Function in Trypanosoma brucei Using RNA Interference
Appolinaire Djikeng, Shuiyuan Shen, Christian Tschudi, and Elisabetta Ullu

Short Hairpin Activated Gene Silencing in Mammalian Cells
Patrick J. Paddison, Amy A. Caudy, Ravi Sachidanandam, and Gregory J. Hannon

Geminivirus Vectors for Transient Gene Silencing in Plants
Nooduan Muangsan and Dominique Robertson

Posttranscriptional Gene Silencing in Plants
Susan Varsha Wesley, Chris Helliwell, Ming-Bo Wang, and Peter Waterhouse

Identification of microRNAs and Other Tiny Noncoding RNAs by cDNA Cloning
Victor Ambros and Rosalind C. Lee

Part II. RNA Editing and Modification

A Historical Perspective on RNA Editing: How the Peculiar and Bizarre Became Mainstream
Donna J. Koslowsky

Identification of Substrates for Adenosine Deaminases That Act on RNA
Daniel P. Morse

Purification and Assay of Recombinant ADAR Proteins Expressed in the Yeast Pichia pastoris or in Escherichia coli
Gillian M. Ring, Mary A. O'Connell, and Liam P. Keegan

Isolation of an mRNA-Binding Protein Involved in C-to-U Editing
Carri A. Gerber, Anne Relich, and Donna M. Driscoll

In Vitro Assays for Kinetoplastid U Insertion-Deletion Editing and Associated Activities
Kenneth Stuart, Reza Salavati, Robert P. Igo, Jr., Nancy Lewis Ernst, Setareh S. Palazzo, and Bingbing Wang

Identification and Characterization of Trypanosome RNA-Editing Complex Components
Kenneth Stuart, Aswini K.Panigrahi, and Achim Schnaufer

Chimeric Templates and Assays Used to Study Physarum Cotranscriptional Insertional Editing In Vitro
Elaine M. Byrne

Methods for Analysis of Mitochondrial tRNA Editing in Acanthamoeba castellanii
Amanda J. Lohan and Michael W. Gray

In Vitro RNA Editing Systems From Higher Plant Chloroplasts
Tetsuro Hirose, Tetsuya Miyamoto, Junichi Obokata, and Masahiro Sugiura

Studying RNA Editing in Transgenic Chloroplasts of Higher Plants
Ralph Bock

Detection and Quantification of Modified Nucleotides in RNA Using Thin-Layer Chromatography
Henri Grosjean, Gérard Keith, and Louis Droogmans

Functional Characterization of 2'-O-Methylation and Pseudouridylation Guide RNAs
Tamás Kiss and Beáta E. Jády

Experimental RNomics: A Global Approach to Identifying Small Nuclear RNAs and Their Targets in Different Model Organisms
Alexander Hüttenhofer, Jérome Cavaillé, and Jean-Pierre Bachellerie

Index