RNA and DNA editing : methods and protocols / edited by Ruslan Aphasizhev. — New York, N.Y. : Humana, c2011. – (58.17/M592/v.718)

Contents

    CONTENTS
    
    Foreword
    Preface
    Contributors
    PART I URACIL INSERTION/DELETION RNA EDITING IN MITOCHONDRION OF TRTPANOSOMA BRUCEI
    1 Three-Dimensional Reconstruction of Trypanosoma brucei Editosomes Using Single-Particle Electron Microscopy
    2 iCODA: RNAi-Based Inducible Knock-In System in Trypanosoma brucei
    PART II ADENOSINE TO INOSINE RNA EDITING
    3 Perturbing A-to-I RNA Editing Using Genetics and Homologous Recombination 41
    4 Laser Microdissection and Pressure Catapulting of Single Human Motor Neurons for RNA Editing Analysis 75
    5 Biochemical Identification of A-to-I RNA Editing Sites by the Inosine Chemical Erasing (ICE) Method
    PART III CYTIDINE TO URACIL RNA AND DNA EDITING
    6 Identifying mRNA Editing Deaminase Targets by RNA-Seq
    7 Mouse and Other Rodent Models of C to U RNA Editing
    8 In vivo Analysis of RNA Editing in Plastids
    9 Identifying Specific Trans-Factors of RNA Editing in Plant Mitochondria by Multiplex Single Base Extension Typing.
    10 Complementation of Mutants in Plant Mitochondrial RNA Editing by Protoplast Transfection
    11 A High-Throughput Assay for DNA Deaminases
    12 Biochemical Fractionation and Purification of High-Molecular-Mass APOBEC3G Complexes
    PART IV TRNA EDITING AND RNA MODIFICATIONS
    13 Analysis of tRNA Editing in Native and Synthetic Substrates 209
    14 Post-transcriptional Modification of RNAs by Artificial Box H/ACA and Box C/D RNPs 227
    15 Functional Analysis of Noncoding RNAs in Trypanosomes: RNA Walk， a Novel Approach to Study RNA-RNA Interactions Between Small RNA and Its Target 245
    16 A Post-Labeling Approach for the Characterization and Quantification of RNA Modifications Based on Site-Directed Cleavage by DNAzymes 259
    Index 271