CiNii 図書 - The eukaryotic RNA exosome : methods and protocols

This volume provides a cross-section of RNA exosome research protocols, 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 protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, The Eukaryotic RNA Exosome: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Part I: Introduction to the RNA Exosome in Biomedicine 1. The RNA Exosome and Human Disease Milo B. Fasken, Derrick J. Morton, Emily G. Kuiper, Stephanie K. Jones, Sara W. Leung, and Anita H. Corbett Part II: Prokaryotic RNases and Exosomes 2. The Bacterial Counterparts of the Eukaryotic Exosome: An Evolutionary Perspective Sandra C. Viegas , Rute G. Matos, and Cecilia M. Arraiano 3. In vitro Characterization of the Prokaryotic Counterparts of the Exosome Complex Rute G. Matos, Sandra C. Viegas, and Cecilia M. Arraiano 4. Enzymatic Analysis of Reconstituted Archaeal Exosomes Elena Evguenieva-Hackenberg, A. Susann Gauernack, Linlin Hou, and Gabriele Klug Part III: Analyzing Exosome Substrates 5. Protocols for Northern Analysis of Exosome Substrates and Other Non-coding RNAs Cristina Cruz and Jonathan Houseley 6. Mapping Exosome-substrate Interactions in vivo by UV-crosslinking Clementine Delan-Forino and David Tollervey 7. Global Identification of Human Exosome Substrates using RNA Interference and RNA-sequencing Marta Lloret-Llinares and Torben Heick Jensen 8. High-resolution Mapping of 3' Extremities of RNA Exosome Substrates by 3' RACE-seq Helene Scheer, Caroline De Almeida, Natalia Sikorska, Sandrine Koechler, Dominique Gagliardi, and Helene Zuber 9. Determining mRNA Stability by Metabolic RNA Labeling and Chemical Nucleoside Conversion Veronika A. Herzog, Nina Fasching, and Stefan L. Ameres 10. 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, Jeffrey Bashin, Christian Riml, Thomas Amort, and Ronald Micura Part IV: Exosomes and their Supramolecular Functional Interactions 11. RNA Exosomes and their Co-factors Cornelia Kilchert 12. Purification of Endogenous Tagged TRAMP4/5 and Exosome Complexes from Yeast and in vitro Polyadenylation-Exosome Activation Assays Dagmar Zigackova, Veronika Rajecka, and Stepanka Vanacova 13. Comparative poly(A)+ RNA Interactome Capture of RNA Surveillance Mutants Cornelia Kilchert, Svenja Hester, Alfredo Castello, Shabaz Mohammed, and Lidia Vasiljeva 14. Purification and in vitro Analysis of the Exosome Cofactors Nrd1-Nab3 and Trf4-Air2 Odil Porrua 15. Affinity Proteomic Analysis of the Human Exosome and its Cofactor Complexes Kinga Winczura, Michal Domanski, and John LaCava 16. In vitro Characterization of the Activity of the Mammalian RNA exosome on mRNAs in Ribosomal Translation Complexes Alexandra Zinoviev, Christopher U.T. Hellen, and Tatyana V. Pestova Part V: Recombinant Expression Strategies and Structural Characterization of Exosomes 17. Native Mass Spectrometry Analysis of Affinity-captured Endogenous Yeast RNA Exosome Complexes Paul Dominic B. Olinares and Brian T. Chait 18. Chemical Cross-Linking and Mass Spectrometric Analysis of the Endogenous Yeast Exosome Complexes Yufei Xiang, Zhuolun Shen, and Yi Shi 19. Cryo-Electron Microscopy of Endogenous Yeast Exosomes Jun-Jie Liu and Hong-Wei Wang 20. Strategies for Generating RNA Exosome Complexes from Recombinant Expression Hosts Eva-Maria Weick, John C. Zinder, and Christopher D. Lima 21. Reconstitution of S. cerevisiae RNA Exosome Complexes Using Recombinantly Expressed Proteins John C. Zinder and Christopher D. Lima 22. Reconstitution of the Schizosaccharomyces pombe RNA Exosome Kurt Januszyk and Christopher D. Lima 23. Reconstitution of the Human Nuclear RNA Exosome Kurt Januszyk, Eva-Maria Weick, and Christopher D. Lima 24. Purification and Reconstitution of the S. cerevisiae TRAMP and Ski Complexes for Biochemical and Structural Studies Achim Keidel, Elena Conti, and Sebastian Falk

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The eukaryotic RNA exosome : methods and protocols

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