RNA and DNA Editing: Methods and Protocols

ISBN-13: 9781493958214 / Angielski / Miękka / 2016 / 275 str.

Ruslan Aphasizhev

Opis

Covering many state-of-the-art techniques, this book features leading experts in the field who introduce methods developed in recent years to study editing substrates, mechanisms of specificity, and the functions of RNA- and DNA-editing enzymes and complexes.

Recenzje

From the reviews:

"This book on RNA and DNA Editing, Methods and Protocols provides methods to study editing substrates, mechanisms of specificity and functions of RNA and DNA editing enzymes and complexes ... . The apparent audience is molecular biologists interested in RNA and DNA editing." (Omer Iqbal, Doody's Book Reviews, March, 2012)

"It is quite timely that a Methods book dedicated at experimental approaches to investigate RNA editing mechanisms should find its rightful place in the series. To achieve this aim, the editor ... has successfully united many leading experts in this field to write several Chapters dedicated at explaining state-of-the-art techniques ... . this is an invaluable store of information that can potentially save weeks or months spent simply in learning what-to-do and what-not-to-do when setting up a particular procedure in their own lab." (Emanuele Buratti, Molecular Biotechnology, September, 2011)

Spis treści

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

Blurb

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.

 

Authoritative and cutting-edge, RNA and DNA Editing: Methods and Protocols seeks to inspire the further development of these vital and powerful techniques.