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RNA Interference, Editing, and Modification
Methods and Protocols
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Main description:

Two of the more fascinating biological phenomena that have been d- covered in recent years are RNA editing and RNA interference. Each of these processes has been found in a cross-section of biological systems, including mammals, viruses, plants, and a range of model organisms (C. elegans,Dro- phila, and various lower eukaryotes). RNA editing, which results in an RNA product different from that predicted by the genome, occurs through a variety of mechanisms. Alterations can occur at either the base level, in which one base is changed to another (substitutional editing/base modification), or via the addition and/or deletion of nucleotides relative to the original template (insertion/deletion editing). RNA interference (RNAi) involves the specific degradation of targeted mRNAs. Although RNA interference, editing, and modification use different enzymes and mechanisms, the targets of each of these reactions are often specified by RNA molecules.
Indeed, the discovery of guide RNAs (gRNAs) that direct nucleotide insertion and deletion in trypa- some mitochondria set the precedent for subsequent discoveries of the small nuclear RNAs (snoRNAs) that target pseudouridylylation and methylation of stable RNAs and the small double-stranded RNA fragments (siRNAs) that mediate RNAi. Other small RNAs are known to mediate translational regu- tion during development (small temporal RNAs [stRNAs]) and mRNA stab- ity (microRNAs [miRNAs]), and the recent identification of more than a hundred small "noncoding" RNAs has led to the realization that they may represent only the proverbial "tip of the iceberg.


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


PRODUCT DETAILS

ISBN-13: 9781617374456
Publisher: Springer (Humana Press Inc.)
Publication date: November, 2010
Pages: 450
Weight: 660g
Availability: Available
Subcategories: Biochemistry
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