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The discovery of wide-spread RNA-based regulation in bacteria has led to new evaluations of the importance of bacterial regulatory RNA in every aspect of bacterial physiology. In Bacteria Regulatory RNA: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study bacterial regulatory RNA. These include methods and techniques to identify regulatory RNAs, characterizing the function and expression of regulatory RNAs in bacterial cells, RNA structure prediction, and interactions between regulatory RNAs and proteins. Written in the highly successful Methods in Molecular Biology(TM) series format, chapters include 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.
Authoritative and practical, Bacteria Regulatory RNA: Methods and Protocols seeks to aid scientists in the further study of bacterial regulatory RNA.
List of contents
Bioinformatic Discovery of Bacterial Regulatory RNAs using SIPH.-How to Identify CRISPRs in Sequencing Data.-A Strategy for Identifying Non-coding RNAs using Whole-genome Tiling Arrays.-Genetic Screens to Identify Bacterial sRNA Regulators.-Competition Assays Using Barcoded Deletion Strains to Gain Insight Into Small RNA Function.-Use of Semi-quantitative Northern Blot Analysis to Determine Relative Quantities of Bacterial CRISPR Transcripts.-RNA Visualization in Bacteria by Fluorescence in Situ Hybridization.-RNA Structure Prediction: An Overview of Methods.-Crystallization of RNA-Protein Complexes: From Synthesis and Purification of Individual Components to Crystals.-Analysis of RNA Folding and Ligand Binding by Conventional and High-Throughput Calorimetry.-Use of Aptamer Tagging to Identify in vivo Protein Binding Partners of Small Regulatory RNAs.-Gel Mobility Shift Assays to Detect Protein-RNA Interactions.-RNase Footprinting of Protein Binding Sites on an mRNA Target of Small RNAs.-Computational Identification of sRNA Targets.-Detection of sRNA-mRNA Interactions by Electrophoretic Mobility Shift Assay.-Activity of Small RNAs on the Stability of Targeted mRNAs in vivo.-Native Gel Electrophoresis to Study the Binding and Release of RNA Polymerase by 6S RNA.-Ribosome Purification Approaches for Studying Interactions of Regulatory Proteins and RNAs with the Ribosome.-Analysis of Aminoacyl- and Peptidyl-tRNAs by Gel Electrophoresis.- In vitro trans-translation Assays.
Summary
These include methods and techniques to identify regulatory RNAs, characterizing the function and expression of regulatory RNAs in bacterial cells, RNA structure prediction, and interactions between regulatory RNAs and proteins.
