RNA: Methods and Protocols

ISBN-13: 9781588299130 / Angielski / Twarda / 2010 / 329 str.

Henrik Nielsen

Opis

Recent insight into the transcripts generated from the mammalian genome (i.e. the transcriptome) has revealed that transcription is a far more complex phenomenon than previously thought. In RNA: Methods and Protocols, expert researchers provide the procedures and methods used to describe the structure of messenger RNAs and non-coding RNAs that are transcribed by RNA polymerase II as the immediate gene products in mammalian cells. Focused on the structure of the RNA products of "gene X" and the mapping of proteins associated with these RNAs, the volume presents appropriate information for non-specialists in RNA biology. Written in the highly successful Methods in Molecular Biology series format, many chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Comprehensive and practical, RNA: Methods and Protocols views the transcriptional landscape with an appreciation for the role that proteins play in the processing and interpretation of genetic information in an attempt to further our crucial knowledge of the many products and sophisticated regulatory networks that result from it.

Spis treści

Part I: RNA Methods 1. The Transcriptional Landscape Henrik Nielsen 2. Working with RNA Henrik Nielsen 3. Synthesis of RNA by In vitro Transcription Bertrand Beckert and Benoit Masquida 4. Efficient Poly(A)+ RNA Selection Using LNA Oligo(T) Capture Nana Jacobsen, Jens Eriksen, and Peter Stein Nielsen 5. Genome Browsers Elfar Torarinsson 6. Web-Based Tools for Studying RNA Structure and Function Ajish D. George and Scott A. Tenenbaum 7. Northern Blotting Analysis Knud Josefsen and Henrik Nielsen 8. Rapid Amplification of cDNA Ends (RACE) Oladapo Yeku and Michael A. Frohman 9. Fractionation of mRNA Based on the Length of the Poly(A) Tail Hedda A. Meijer and Cornelia H. de Moor 10. Analysis of Mutations that Influence Pre-mRNA Splicing Zhaiyi Zhang and Stefan Stamm 11. S1 Nuclease Analysis of Alternatively Spliced mRNA Martin Lützelberger and Jørgen Kjems 12. Promises and Challenges in Developing RNAi as a Research Tool and Therapy Mouldy Sioud 13. Inhibition of Gene Function in Mammalian Cells Using Short-Hairpin RNA (shRNA) Jørn Remi Henriksen, Jochen Buechner, Cecilie Løkke, Trond Flægstad, and Christer Einvik 14. Validation of RNAi by Real Time PCR Knud Josefsen and Ying C. Lee 15. Profiling RNA Polymerase II Using the Fast Chromatin Immunoprecipitation Method Joel Nelson, Oleg Denisenko, and Karol Bomsztyk Part II: RNP Methods 16. The Post-Transcriptional Operon Scott A. Tenenbaum, Jan Christiansen, and Henrik Nielsen 17. RIP-Chip Analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling Ritu Jain, Tiffany Devine, Ajish D. George, Sridar V. Chittur, Timothy E. Baroni, Luiz O. Penalva, and Scott A. Tenenbaum 18. Isolation of RNP Granules Lars Jønson, Finn Cilius Nielsen, and Jan Christiansen 19. Electrophoretic Mobility Shift Assay for Characterizing RNA-Protein Interaction Keith T. Gagnon and E. Stuart Maxwell 20. Polysome Analysis and RNA Purification from Sucrose Gradients Tomáš Mašek, Leoš Valášek, and Martin Pospíšek 21. Prediction of Targets for microRNAs Morten Lindow 22. Outsourcing of Experimental Work Henrik Nielsen Also features electronic supplemental chapters: ESM1: In-Line Probing Analysis of Riboswitches Elizabeth E. Regulski and Ronald R. Breaker ESM2: Analysis of the RNA Backbone: Structural Analysis of Riboswitches by In-Line Probing and Selective 2'-Hydroxyl Acylation and Primer Extension (SHAPE) Catherine A. Wakeman1 and Wade C. Winkler