RNA Interference, Editing and Modification Methods and Protocols

About this book

This is a comprehensive collection of cutting-edge methods for elucidating the function of new genes and altering gene expression. These readily reproducible techniques can be used either in transient and stable gene splicing applied to worms, flies, trypanosomes, mammals, and plants, or in studying RNA editing mechanisms in a wide range of organisms, including systems that involve the conversion of one base to another and insertion/deletion editing. Topics of interest include stable and transient RNA interference, gene silencing, RNA editing, bioinformatics, small noncoding RNAs, and RNomics. Special attention is given to methods for the identification and characterization of small RNAs involved in RNA interference or modification.

Contents

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, Gerard Keith, and Louis Droogmans Functional Characterization of 2'-O-Methylation and Pseudouridylation Guide RNAs Tamas Kiss and Beata E. Jady Experimental RNomics: A Global Approach to Identifying Small Nuclear RNAs and Their Targets in Different Model Organisms Alexander Huttenhofer, Jerome Cavaille, and Jean-Pierre Bachellerie Index

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