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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(TM) 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.

RNA: Methods and Protocols

Part I: RNA Methods1. The Transcriptional LandscapeHenrik Nielsen2. Working with RNAHenrik Nielsen3. Synthesis of RNA by In vitro TranscriptionBertrand Beckert and Benoit Masquida4. Efficient Poly(A)+ RNA Selection Using LNA Oligo(T) CaptureNana Jacobsen, Jens Eriksen, and Peter Stein Nielsen5. Genome BrowsersElfar Torarinsson6. Web-Based Tools for Studying RNA Structure and FunctionAjish D. George and Scott A. Tenenbaum7. Northern Blotting AnalysisKnud Josefsen and Henrik Nielsen8. Rapid Amplification of cDNA Ends (RACE)Oladapo Yeku and Michael A. Frohman9. Fractionation of mRNA Based on the Length of the Poly(A) TailHedda A. Meijer and Cornelia H. de Moor10. Analysis of Mutations that Influence Pre-mRNA SplicingZhaiyi Zhang and Stefan Stamm11. S1 Nuclease Analysis of Alternatively Spliced mRNAMartin Lützelberger and Jorgen Kjems12. Promises and Challenges in Developing RNAi as a Research Tool and TherapyMouldy Sioud13. Inhibition of Gene Function in Mammalian Cells Using Short-Hairpin RNA (shRNA)Jorn Remi Henriksen, Jochen Buechner, Cecilie Lokke, Trond Flagstad, and Christer Einvik14. Validation of RNAi by Real Time PCRKnud Josefsen and Ying C. Lee15. Profiling RNA Polymerase II Using the Fast Chromatin Immunoprecipitation MethodJoel Nelson, Oleg Denisenko, and Karol BomsztykPart II: RNP Methods16. The Post-Transcriptional OperonScott A. Tenenbaum, Jan Christiansen, and Henrik Nielsen17. RIP-Chip Analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) ProfilingRitu Jain, Tiffany Devine, Ajish D. George, Sridar V. Chittur, Timothy E. Baroni, Luiz O. Penalva, and Scott A. Tenenbaum18. Isolation of RNP GranulesLars Jonson, Finn Cilius Nielsen, and Jan Christiansen19. Electrophoretic Mobility Shift Assay for Characterizing RNA-Protein InteractionKeith T. Gagnon and E. Stuart Maxwell20. Polysome Analysis and RNA Purification from Sucrose GradientsTomás Masek, Leos Valásek, and Martin Pospísek21. Prediction of Targets for microRNAsMorten Lindow22. Outsourcing of Experimental WorkHenrik NielsenAlso features electronic supplemental chapters:ESM1: In-Line Probing Analysis of RiboswitchesElizabeth E. Regulski and Ronald R. BreakerESM2: 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