Table of Contents Preface Contributors
1. Bioinformatics Approaches for Studying Untranslated Regions of mRNAs Paramjeet S. Bagga 2. Identification of mRNA Polyadenylation Sites in genomes Using cDNA Sequences, Expressed Sequence Tags and Trace Ju Youn Lee, Ji Yeon Park and Bin Tian 3. Bioinformatic Tools for Studying Post-Transcriptional Gene Regulation: The UAlbany TUTR (Training UTR) Collection and other Informatic Resources Francis Doyle, Christopher Zaleski, Alish D. George, Eric Stenson, Adele Ricciardi and Scott A. Tenenbaum
4. In-Line Probing Analysis of Riboswitches Elizabeth E. Regulski and Ronald R. Breaker 5. Ribotrap: Targeted Purification of RNA-Specific RNPs from Cell Lysates via Immunoaffinity Precipitation to Identify Regulatory Proteins and RNAs Dale L. Beach and Jack D. Keene 6. Advances in RIP-Chip Analysis: RNA-Binding Protein Immunoprecipitation- Microarray (Chip) Profiling Timothy E. Baroni, Sridar V. Chittur, Ajish D. George and Scott A. Tenenbaum 7. Biosensors for RNA Aptamer-Protein Interaction Sara Tombelli, Maria Minunni and Marco Mascini 8. A Tethering Approach to Study Proteins that Activate mRNA Turnover in Human Cells Sandra L. Clement and Jens Lykke-Andersen 9. RNA Analysis by Biosynthetic Tagging (RABT) Using 4-Thiouracil and Uracil Phosphoribosyltransferase Gusti M. Zeiner, Michael D. Cleary, Ashley E. Fotus, Christopher D. Meiring, Edward S. Mocarski and John C. Boothroyd 10. Efficient 5' Cap Dependent RNA Purification: Use in Identifying and Studying Subsets of RNA Edyta Z. Bajak and Curt H. Hagedorn 11. Enrichment of Alternatively Spliced Isoforms (EASI) Julian P. Venables 12. In Vivo Methods to Assess Polyadenylation Efficiency Lisa K. Hague, Tyra Hall-Pogarand Carol S. Lutz 13. Monitoring the Temporal and Spatial Distribution of RNA in Living Yeast Cells Roy M. Long and Carl R. Urbinati 14. Analysis of mRNA Partitioning Between the Cytosol and Endoplasmic Reticulum Compartments of Mammalian Cells Samuel B. Stephens, Rebecca D. Dodd, Rachel S. Lerner, Brook M. Pyhtila and Christopher V. Nicchitta 15. In Vivo and In Vitro Analysis of Poly(A) Length Effects on mRNA Translation Jing Peng, Elizabeth L. Murray and Daniel R. Schoenberg........................... 16. A Ribosomal Density Mapping (RDM) Procedure to Explore Ribosome Positions Along Translating mRNAs Naama Eldad and Yoav Arava 17. Identification of Changes in Gene Expression by Quantitation of mRNA Levels Wendy M. Olivas 18. Application of the InvaderR RNA Assay to the Polarity of Vertebrate mRNA Decay Elizabeth L. Murray and Daniel R. Schoenberg 19. Development of an In Vitro mRNA Decay System in Insect Cells Kevin Sokoloski, John R. Andersen and Jeffrey Wilusz 20. Using Synthetic Precursor and Inhibitor miRNAs to Understand miRNA Function Lance P. Ford and Angie Cheng 21. A Step-By-Step Procedure to Analyze the Efficacy of siRNA Using Real-Time PCR Angie Cheng, Charles L. Johnson and Lance P. Ford