RNA and DNA Editing, Softcover reprint of the original 1st ed. 2011
Methods and Protocols
Methods in Molecular Biology Series, Vol. 718

The recent expansion in diversity of RNA and DNA editing types has stimulated the development of many unique genetic, molecular, biochemical, and computational approaches to biological issues.  In RNA and DNA Editing: Methods and Protocols, leading experts in the field introduce methods developed over the last few years to study editing substrates, mechanisms of specificity, and functions of RNA and DNA editing enzymes and complexes. Sections of the book are dedicated to state-of-the art techniques which enable investigation of uracil insertion/deletion RNA editing in mitochondrion of Trypanosoma brucei, adenosine to inosine RNA editing, cytidine to uracil RNA and DNA editing, as well as tRNA editing and RNA modifications.  Written in the highly successful Methods in Molecular Biology? series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

Part I: Uracil Insertion/Deletion RNA Editing in Mitochondrion of Trypanosoma brucei

1. Three-Dimensional Reconstruction of Trypanosoma brucei Editosomes Using Single-Particle Electron Microscopy

            H. Ulrich Göringer, Holger Stark, Cordula Böhm, Bjoern Sander, and Monika M. Golas

2. iCODA: RNAi-Based Inducible Knock-In System in Trypanosoma brucei

            Gene-Errol Ringpis, Richard H. Lathrop, and Ruslan Aphasizhev

Part II: Adenosine to Inosine RNA Editing

3. Perturbing A-to-I RNA Editing Using Genetics and Homologous Recombination

            Cynthia J. Staber, Selena Gell, James E.C. Jepson, and Robert A. Reenan

4. Laser Microdissection and Pressure Catapulting of Single Human Motor Neurons for RNA Editing Analysis

            Hui Sun, Mary A. O’Connell, Valerie Mann, Brendon Noble, and Liam P. Keegan

5. Biochemical Identification of A-to-I RNA Editing sites by the Inosine Chemical Erasing (ICE) Method

            Masayuki Sakurai and Tsutomu Suzuki

Part III: Cytidine to Uracil RNA and DNA Editing

6. Identifying mRNA Editing Deaminase Targets by RNA-Seq

            Brad R. Rosenberg, Scott Dewell, and F. Nina Papavasiliou

7. Mouse and Other Rodent Models of C to U RNA Editing

            Valerie Blanc and Nicholas O. Davidson

8. In vivo Analysis of RNA Editing in Plastids

            Stephanie Ruf and Ralph Bock

9. Identifying Specific Trans-Factors of RNA Editing in Plant Mitochondria by Multiplex Single Base Extension Typing

            Mizuki Takenaka

10. Complementation of Mutants in Plant Mitochondrial RNA Editing by Protoplast Transfection

            Mizuki Takenaka and Anja Zehrmann

11. A High Throughput Assay for DNA Deaminases

            Meng Wang, Cristina Rada, and Michael S. Neuberger

12. Biochemical Fractionation and Purification of High-Molecular-Mass APOBEC3G Complexes

            Ya-Lin Chiu

Part IV: tRNA Editing and RNA Modifications

13. Analysis of tRNA Editing in Native and Synthetic Substrates

            Jessica L. Spears, Kirk W. Gaston, and Juan D. Alfonzo

14. Post-Transcriptional Modification of RNAs by Artificial Box H/ACA and Box C/D RNPs

            Chao Huang, John Karijolich, and Yi-Tao Yu

15. Functional Analysis of Non-Coding RNAs in Trypanosomes: RNA Walk, A Novel Approach to Study RNA-RNA Interactions Between Small RNA and Its Target

            Chaim Wachtel and Shulamit Michaeli

16. A Post-Labeling Approach for the Characterization and Quantification of RNA Modifications Based on Site-Directed Cleavage by DNAzymes

            Madeleine Meusburger, Martin Hengesbach, and Mark Helm

Features cutting-edge methodologies focused on the study of this diverse field of study

Includes unique genetic, molecular, biochemical, and computational approaches

Contains expert tips and implementation advice

Includes supplementary material: sn.pub/extras