RNA

1. Front Matter

   Pages i-xv

   PDF

2. RNA Methods

   1. Front Matter

      Pages 1-1

      PDF

   2. The Transcriptional Landscape

      • Henrik Nielsen

      Pages 3-14

   3. Working with RNA

      • Henrik Nielsen

      Pages 15-28

   4. Synthesis of RNA by In Vitro Transcription

      • Bertrand Beckert, Benoît Masquida

      Pages 29-41

   5. Efficient Poly(A)+ RNA Selection Using LNA Oligo(T) Capture

      • Nana Jacobsen, Jens Eriksen, Peter Stein Nielsen

      Pages 43-51

   6. Genome Browsers

      • Elfar Torarinsson

      Pages 53-65

   7. Web-Based Tools for Studying RNA Structure and Function

      • Ajish D. George, Scott A. Tenenbaum

      Pages 67-86

   8. Northern Blotting Analysis

      • Knud Josefsen, Henrik Nielsen

      Pages 87-105

   9. Rapid Amplification of cDNA Ends (RACE)

      • Oladapo Yeku, Michael A. Frohman

      Pages 107-122

   10. Fractionation of mRNA Based on the Length of the Poly(A) Tail

       • Hedda A. Meijer, Cornelia H. de Moor

       Pages 123-135

   11. Analysis of Mutations that Influence Pre-mRNA Splicing

       • Zhaiyi Zhang, Stefan Stamm

       Pages 137-160

   12. S1 Nuclease Analysis of Alternatively Spliced mRNA

       • Martin Lützelberger, Jørgen Kjems

       Pages 161-171

   13. Promises and Challenges in Developing RNAi as a Research Tool and Therapy

       • Mouldy Sioud

       Pages 173-187

   14. Inhibition of Gene Function in Mammalian Cells Using Short-Hairpin RNA (shRNA)

       • Jørn Remi Henriksen, Jochen Buechner, Cecilie Løkke, Trond Flægstad, Christer Einvik

       Pages 189-204

   15. Validation of RNAi by Real Time PCR

       • Knud Josefsen, Ying C. Lee

       Pages 205-217

   16. Profiling RNA Polymerase II Using the Fast Chromatin Immunoprecipitation Method

       • Joel Nelson, Oleg Denisenko, Karol Bomsztyk

       Pages 219-234

3. RNP Methods

   1. Front Matter

      Pages 235-235

      PDF

   2. The Post-transcriptional Operon

      • Scott A. Tenenbaum, Jan Christiansen, Henrik Nielsen

      Pages 237-245

   3. 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 et al.

      Pages 247-263

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.

• Bioinformatics
• Mammalian genome
• Messenger RNAs
• Microarray analysis
• Non-coding RNAs
• Protein mapping
• RNA polymerase II
• RNP methods
• Transcriptional landscape
• Transcriptome
• miRNA profiling
• gene expression

• The Panum Institute, Dept. of Cellular & Molecular Medicine, University of Copenhagen, Copenhagen, Denmark

  Henrik Nielsen

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