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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. Book + Online Access

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 Jorgen 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)
Jorn Remi Henriksen, Jochen Buechner, Cecilie Lokke, Trond Flagstad, 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 Jonson, 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
Tomás Masek, Leos Valásek, and Martin Pospísek

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