RNA-Protein Complexes and Interactions

In vivo cross-linking and co-immunoprecipitation procedure to analyze nuclear tRNA export complexes in yeast cells.- Analysis of Gene Expression Patterns and RNA Localization by Fluorescence in situ Hybridization in Whole Mount Drosophila Testes.- Electrophoretic mobility shift assay (EMSA) and microscale thermophoresis (MST) methods to measure interactions between tRNAs and their modifying enzymes.- Mapping of RNase P ribozyme regions in proximity with a human RNase P subunit protein using Fe(II)-EDTA cleavage and nuclease footprint analyses.- SHAPE to probe RNA structure and RNA-protein interactions in vitro.- Chemical probing of RNA structure in vivo using SHAPE-MaP and DMS-MaP.- Analysis of RNA-protein interaction networks using RNP-MaP.- Native RNA immunoprecipitation (RIP) for precise detection and quantification of protein-interacting RNA.- In vivo cross-linking and co-immunoprecipitation procedure to analyze nuclear tRNA export complexes in yeast cells.- 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.- Ribosomal Profiling by Gradient Fractionation of Cell Lysates.- Global assessment of protein translation in mammalian cells using polysome fractionation.- Fluorescent in situ detection of RNA-Protein interactions in intact cells by RNA-PLA.- Arresting Spliceosome Intermediates at Various Stages of the Splicing Pathway.- Streamlined purification of RNA-protein complexes using UV crosslinking and RNA antisense purification.- MS2-MBP based affinity purification of nucleus- or cytoplasm-localized lncRNA-protein complexes formed in vivo.- RNA and protein interactomes of an RNA-binding protein tagged with FLAG epitopes using combinatory approaches of genome engineering and stable transfection.- Detecting R-loop formation using a plasmid-based in vitro transcription assayMethods to Study RNA-Chromatin Interactions.- Challenges for Studying and Isolating Extracellular Vesicles from Cell-conditioned Media.- Evolution of Cell-Type-Specific RNA Aptamers Via Live Cell-Based SELEX.