RNA and DNA Editing: Methods and Protocols (Hardcover) (ISBN-13: 9781617790171)

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 Ginger, Holger Stark, Cordula Bm, 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