Bacterial Regulatory RNA Methods and Protocols

This second edition details new and updated methods used for studying prokaryotic non-coding RNAs and their protein accomplices. Chapters detail discovery of ncRNAs, characterization of their structure, functions, and their interactomes. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

 

Authoritative and cutting-edge, Bacterial Regulatory RNA: Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

RNA extraction from Gram-positive bacteria membrane vesicles using a polymer-based precipitation method.- Extraction and purification of outer membrane vesicles and their associated RNAs.- Analysis of phage regulatory RNAs: sequencing library construction from the fraction of small prokaryotic RNAs less than 50 nucleotides in length.- Discovering Novel Bacterial Small RNA by RNA-seq Analysis Toolkit ANNOgesic.- Ribosome profiling methods adapted to the study of RNA-dependent translation regulation in Staphylococcus aureus.- CRISPR interference-based functional small RNA genomics.- Investigation of sRNA-mRNA interactions in Bacillus subtilis in vivo.- In vitro methods for the investigation of sRNA-mRNA interactions in Bacillus subtilis.- RNA double helix hybridization measured by fluorescence correlation spectroscopy.- New perspectives on cross talks between bacterial regulatory RNAs from outer membrane vesicles and eukaryotic cells.- Experimental validation of RNA-RNA interactions by Electrophoretic Mobility Shift Assay.- Dynamics and function of sRNA/mRNAs under the scrutiny of computational simulation methods.-Analysis of sRNAs and their mRNA targets in Sinorhizobium meliloti: focus on half-live determinationEvaluation of 5'-end phosphorylation for small RNA stability and target regulation in vivo.- In-gel cyanoethylation for pseudouridines mass spectrometry detection of bacterial regulatory RNA.- Directed screening for sRNA targets in E. coli using a plasmid library.- Defining Bacterial RNA-RNA Interactomes Using CLASH.- Global identification of RNA-binding proteins in bacteria.- An integrated affinity chromatography-based approach to unravel the sRNA interactome in nitrogen-fixing rhizobia.- sRNA structural modeling based on NMR data.- Circular and linear dichroism for the analysis of small noncoding RNA properties.