Bacterial Regulatory RNA

Part I- Identification of Regulatory RNAs 1. Bioinformatic Discovery of Bacterial Regulatory RNAs using SIPH Jonathan Livny 2. How to Identify CRISPRs in Sequencing Data Christine Drevet and Christine Pourcel 3. A Strategy for Identifying Non-coding RNAs using Whole-genome Tiling Arrays Stephen G. Landt and Eduardo Abeliuk 4. Genetic Screens to Identify Bacterial sRNA Regulators Pierre Mandin Part II - Function and Expression of Regulatory RNAs 5. Competition Assays Using Barcoded Deletion Strains to Gain Insight Into Small RNA Function Errett C. Hobbs and Gisela Storz 6. Use of Semi-quantitative Northern Blot Analysis to Determine Relative Quantities of Bacterial CRISPR Transcripts Ksenia Pougach and Konstantin Severinov 7. RNA Visualization in Bacteria by Fluorescence in Situ Hybridization Jay H. Russell and Kenneth C. Keiler Part III - RNA Structure and Biophysical Measurements 8. RNA Structure Prediction: An Overview of MethodsMatthew G. Seetin and David H. Mathews 9. Crystallization of RNA-Protein Complexes: From Synthesis and Purification of Individual Components to Crystals Anna Perederina and Andrey S. Krasilnikov 10. Analysis of RNA Folding and Ligand Binding by Conventional and High-Throughput Calorimetry Joshua E. Sokoloski and Philip C. Bevilacqua Part IV - RNA-Protein Interactions 11. Use of Aptamer Tagging to Identify in vivo Protein Binding Partners of Small Regulatory RNAs Colin P. Corcoran, Renate Rieder, Dimitri Podkaminski, Benjamin Hofmann, and Jörg Vogel 12. Gel Mobility Shift Assays to Detect Protein-RNA Interactions Alexander V. Yakhnin, Helen Yakhnin and Paul Babitzke 13. RNase Footprinting of Protein Binding Sites on an mRNA Target of Small RNAs Peng Yi, Soper, Toby J., and Woodson Sarah A Part V - RNA-RNA Interactions 14.Computational Identification of sRNA Targets Brian Tjaden 15. Detection of sRNA-mRNA Interactions by Electrophoretic Mobility Shift AssayTeppei Morita , Kimika Maki, and Hiroji Aiba 16. Activity of Small RNAs on the Stability of Targeted mRNAs in vivo Guillaume Desnoyers and Eric Massé Part VI -Interactions of Regulatory RNA with RNA Polymerase and the Ribosome 17. Native Gel Electrophoresis to Study the Binding and Release of RNA Polymerase by 6S RNA Karen M. Wassarman 18. Ribosome Purification Approaches for Studying Interactions of Regulatory Proteins and RNAs with the Ribosome Preeti Mehta, Perry Woo, Krithika Venkataraman, and A. Wali Karzai 19. Analysis of Aminoacyl- and Peptidyl-tRNAs by Gel Electrophoresis Brian D. Jansse, Elie J. Diner, and Christopher S. Hayes 20. In vitro trans-translation Assays Daisuke Kurit, Akira Muto, and Hyouta Himeno... Mehr