The eukaryotic RNA exosome : methods and protocols [electronic resource]

  • LaCava, John , Vaňáčová, Štěpánka
  • Humana Press
  • 2020
The eukaryotic RNA exosome : methods and protocols [electronic resource]


This volume provides a cross-section of RNA exosome research prools, applied to a diversity of model organisms. Chapters guide readers through methods that e.g. delineate eukaryotic exosomes’ origins in prokaryotes, probe its RNA substrates, adapter complexes and macromolecular interaction of networks, and establish critical structural-function relationships. 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 prools, and tips on troubleshooting and avoiding known pitfalls.


Introduction to the RNA Exosome in Biomedicine
The RNA Exosome and Human Disease / Milo B. Fasken, Derrick J. Morton, Emily G. Kuiper, Stephanie K. Jones, Sara W. Leung, Anita H. Corbett

Prokaryotic RNases and Exosomes
The Bacterial Counterparts of the Eukaryotic Exosome: An Evolutionary Perspective / Sandra C. Viegas, Rute G. Matos, Cecília M. Arraiano
In Vitro Characterization of the Prokaryotic Counterparts of the Exosome Complex / Rute G. Matos, Sandra C. Viegas, Cecília M. Arraiano
Enzymatic Analysis of Reconstituted Archaeal Exosomes / Elena Evguenieva-Hackenberg, A. Susann Gauernack, Linlin Hou, Gabriele Klug

Analyzing Exosome Substrates
Protocols for Northern Analysis of Exosome Substrates and Other Noncoding RNAs / Cristina Cruz, Jonathan Houseley
Mapping Exosome–Substrate Interactions In Vivo by UV Cross-Linking / Clémentine Delan-Forino, David Tollervey
Global Identification of Human Exosome Substrates Using RNA Interference and RNA Sequencing / Marta Lloret-Llinares, Torben Heick Jensen
High-Resolution Mapping of 3’ Extremities of RNA Exosome Substrates by 3’ RACE-Seq / Hélène Scheer, Caroline De Almeida, Natalia Sikorska, Sandrine Koechler, Dominique Gagliardi, Hélène Zuber
Determining mRNA Stability by Metabolic RNA Labeling and Chemical Nucleoside Conversion / Veronika A. Herzog, Nina Fasching, Stefan L. Ameres
Thiouridine-to-Cytidine Conversion Sequencing (TUC-Seq) to Measure mRNA Transcription and Degradation Rates / Alexandra Lusser, Catherina Gasser, Lukas Trixl, Paolo Piatti, Isabel Delazer, Dietmar Rieder et al.

Exosomes and Their Supramolecular Functional Interactions
RNA Exosomes and Their Cofactors / Cornelia Kilchert
Purification of Endogenous Tagged TRAMP4/5 and Exosome Complexes from Yeast and In Vitro Polyadenylation-Exosome Activation Assays / Dagmar Zigáčková, Veronika Rájecká, Štěpánka Vaňáčová
Comparative Poly(A)+ RNA Interactome Capture of RNA Surveillance Mutants / Cornelia Kilchert, Svenja Hester, Alfredo Castello, Shabaz Mohammed, Lidia Vasiljeva
Purification and In Vitro Analysis of the Exosome Cofactors Nrd1-Nab3 and Trf4-Air2 / Odil Porrua
Affinity Proteomic Analysis of the Human Exosome and Its Cofactor Complexes / Kinga Winczura, Michal Domanski, John LaCava
In Vitro Characterization of the Activity of the Mammalian RNA Exosome on mRNAs in Ribosomal Translation Complexes / Alexandra Zinoviev, Christopher U. T. Hellen, Tatyana V. Pestova

Recombinant Expression Strategies and Structural Characterization of Exosomes
Native Mass Spectrometry Analysis of Affinity-Captured Endogenous Yeast RNA Exosome Complexes / Paul Dominic B. Olinares, Brian T. Chait
Chemical Cross-Linking and Mass Spectrometric Analysis of the Endogenous Yeast Exosome Complexes / Yufei Xiang, Zhuolun Shen, Yi Shi
Cryo-Electron Microscopy of Endogenous Yeast Exosomes / Jun-Jie Liu, Hong-Wei Wang
Strategies for Generating RNA Exosome Complexes from Recombinant Expression Hosts / Eva-Maria Weick, John C. Zinder, Christopher D. Lima
Reconstitution of S. cerevisiae RNA Exosome Complexes Using Recombinantly Expressed Proteins / John C. Zinder, Christopher D. Lima
Reconstitution of the Schizosaccharomyces pombe RNA Exosome / Kurt Januszyk, Christopher D. Lima
Reconstitution of the Human Nuclear RNA Exosome / Kurt Januszyk, Eva-Maria Weick, Christopher D. Lima
Purification and Reconstitution of the S. cerevisiae TRAMP and Ski Complexes for Biochemical and Structural Studies / Achim Keidel, Elena Conti, Sebastian Falk