The Eukaryotic RNA Exosome

The RNA Exosome and Human Disease.- The Bacterial Counterparts of the Eukaryotic Exosome: An Evolutionary Perspective.- In vitro Characterization of the Prokaryotic Counterparts of the Exosome Complex.- Enzymatic Analysis of Reconstituted Archaeal Exosomes.- Protocols for Northern Analysis of Exosome Substrates and Other Non-coding RNAs.- Mapping Exosome-substrate Interactions in vivo by UV-crosslinking.- Global Identification of Human Exosome Substrates using RNA Interference and RNA-sequencing.- High-resolution Mapping of 3’ Extremities of RNA Exosome Substrates by 3’ RACE-seq.- Determining mRNA Stability by Metabolic RNA Labeling and Chemical Nucleoside Conversion.-Thiouridine-to-Cytidine Conversion Sequencing (TUC-seq) to Measure mRNA Transcription and Degradation Rates.- RNA Exosomes and their Co-factors.- Purification of Endogenous Tagged TRAMP4/5 and Exosome Complexes from Yeast and in vitro Polyadenylation-Exosome Activation Assays.- Comparative poly(A)+ RNA Interactome Capture of RNA Surveillance Mutants.- Purification and in vitro Analysis of the Exosome Cofactors Nrd1-Nab3 and Trf4-Air2.- Affinity Proteomic Analysis of the Human Exosome and its Cofactor Complexes.- In vitro Characterization of the Activity of the Mammalian RNA exosome on mRNAs in Ribosomal Translation Complexes.- Native Mass Spectrometry Analysis of Affinity-captured Endogenous Yeast RNA Exosome Complexes.- Chemical Cross-Linking and Mass Spectrometric Analysis of the Endogenous Yeast Exosome Complexes.- Cryo-Electron Microscopy of Endogenous Yeast Exosomes.- Strategies for Generating RNA Exosome Complexes from Recombinant Expression Hosts.- Reconstitution of S. cerevisiae RNA Exosome Complexes Using Recombinantly Expressed Proteins.- Reconstitution of the Schizosaccharomyces pombe RNA Exosome.- Reconstitution of the Human Nuclear RNA Exosome.- Purification and Reconstitution of the S. cerevisiae TRAMP and Ski Complexes for Biochemical and Structural Studies.