RNA and DNA Editing: Methods and Protocols (Methods in Molecular Biology)

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(TM) 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.  Authoritative and cutting-edge, RNA and DNA Editing: Methods and Protocols seeks to inspire the further development of these vital and powerful techniques. Part I: Uracil Insertion/Deletion RNA E diting in M itochondrion of Trypanosoma brucei   1. Three-Dimensional Reconstruction of Trypanosoma brucei Editosomes Using Single-Particle Electron Microscopy             H. Ulrich Gringer, Holger Stark, Cordula Bhm, 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: A denosine to I nosine RNA E diting   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 E diting   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 M odifications   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