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RNA-protein complexes and interactions : methods and protocols / edited by Ren-Jang Lin. -- Second edition. -- New York, NY : Humana Press, 2023. – (58.17/M592/v.2666) |
Contents
Dedication
Preface
Contributors
1 A Simple Method for the Detection of Wybutosine-Modified tRNApheGAA as a Readout of Retrograde tRNA Nuclear Import and Re-export: HCl/Aniline Cleavage and Nonradioactive Northern Hybridization
2 Analysis of Gene Expression Patterns and RNA Localization by Fluorescence in Situ Hybridization in Whole Mount Drosophila Testes
3 Electrophoretic Mobility Shift Assay (EMSA) and Microscale Thermophoresis (MST) Methods to Measure Interactions Between tRNAs and Their Modifying Enzymes
4 Mapping of RNase P Ribozyme Regions in Proximity with a Human RNase P Subunit Protein Using Fe(II)-EDTA Cleavage and Nuclease Footprint Analyses
5 SHAPE to Probe RNA Structure and RNA-Protein Interactions In Vitro
6 Chemical Probing of RNA Structure In Vivo Using SHAPE-MaP and DMS-MaP
7 .analysis of RNA-Protein Interaction Networks Using RNP-MaP
8 Native RNA Immunoprecipitation (RIP) for Precise Detection and Quantification of Protein-Interacting RNA
9 In Vivo Cross-Linking and Co-Immunoprecipitation Procedure to Analyze Nuclear tRNA Export Complexes in Yeast Cells
10 Identify MicroRNA Targets Using AGO2-CLASH (Cross-linking, Ligation, and Sequencing of Hybrids) and AGO2-CLIP(Cross-Linking and Immuno-Precipitation) in Cells with or Without the MicroRNA of Interest Depleted
11 Ribosomal Profiling by Gradient Fractionation of Cell Lysates
12 Global Assessment of Protein Translation in Mammalian Cells Using Polysome Fractionation
13 Fluorescent In Situ Detection of RNA-Protein Interactions in Intact Cells by RNA-PLA
14 In Vitro Reconstitution of Pseudouridylation Catalyzed by Human Box H/ACA Ribonucleoprotein Particles
15 Arresting Spliceosome Intermediates at Various Stages of the Splicing Pathway
16 Streamlined Purification of RNA-Protein Complexes Using UV Cross-Linking and RNA Antisense Purification
17 MS2-MBP-Based Affinity Purification of Nucleus- or Cytoplasm-Localized lncRNA-Protein Complexes Formed In Vivo.
18 RNA and Protein Interactomes of an RNA-Binding Protein Tagged with FLAG Epitopes Using Combinatory Approaches of Genome Engineering and Stable Transfection
19 Detecting R-Loop Formation Using a Plasmid-Based In Vitro Transcription Assay
20 Methods to Study RNA-Chromatin Interactions
21 Challenges for Studying and Isolating Extracellular Vesicles from Cell-Conditioned Media
22 Evolution of Cell-Type-Specific RNA Aptamers via Live Cell-Based SELEX
Index
