Read more
This volume details the most important methods used for studying prokaryotic non-coding RNAs and their protein accomplices. Chapters present methods in sections covering different aspects of the biology of that field: identification of ncRNAs, their differential expression, characterization of their structure, abundance, intracellular location and function, their interaction with RNA binding proteins, and plausible applications of ncRNA elements in the rapidly emerging field of synthetic biology. 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 serves as a guidebook for scientists working toward the development of new tools and proceduresfor the vital field of sRNA biology.
List of contents
Workflow for a Computational Analysis of an sRNA Candidate in Bacteria.- Molecular Phylogenomics for the Identification and Characterization of trans-encoded Small Non-coding RNA Families.- Bioinformatic Approach for Prediction of CsrA/RsmA-regulating small RNAs in Bacteria.- Host-pathogen Transcriptomics by Dual RNA-seq.- Identification of New Bacterial Small RNA Targets using MS2 Affinity Purification Coupled to RNA Sequencing.- Assessment of External Guide Sequences' (EGS) Efficiency as Inducers of RNase P-mediated Cleavage of mRNA Target Molecules.- Evaluating the Effect of Small RNAs and Associated Chaperones on Rho-dependent Termination of Transcription in vitro.- A Method to Map Changes in Bacterial Surface Composition Induced by Regulatory RNAs.- Fluorescence-based Methods for Characterizing RNA interactions in vivo.- Mutational Analysis of sRNA-mRNA Base Pairing by Electrophoretic Mobility Shift Assay.- An Integrated Cell-free Assay to Study TranslationRegulation by Small Bacterial Non-coding RNAs.- Quantitative Super-resolution Imaging of Small RNAs in Bacterial Cells.- Extraction and Analysis of RNA Isolated from Pure Bacteria-Derived outer Membrane Vesicles.- Absolute Regulatory Small Noncoding RNA Concentration and Decay Rates Measurements in Escherichia coli.- High-resolution, High-throughput Analysis of Hfq Binding Sites using UV-crosslinking and Analysis of cDNA (CRAC).- Producing Hfq/Sm Proteins and sRNAs for Structural and Biophysical Studies of Ribonucleoprotein Assembly.- Single Molecule FRET Assay to Observe the Activity of Proteins Involved in RNA/RNA Annealing.- Techniques to Analyse sRNA-protein Cofactor Self-assembly in vitro.- Sequence-specific Affinity Chromatography of RNA-binding Proteins from Bacterial Cells.- Identification of Small RNA-protein Partners in Plant Symbiotic Bacteria.- A Modular Genetic System for High-throughput Profiling and Engineering of Multi-target Small RNAs.
Summary
This volume details the most important methods used for studying prokaryotic non-coding RNAs and their protein accomplices. Chapters present methods in sections covering different aspects of the biology of that field: identification of ncRNAs, their differential expression, characterization of their structure, abundance, intracellular location and function, their interaction with RNA binding proteins, and plausible applications of ncRNA elements in the rapidly emerging field of synthetic biology. 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 serves as a guidebook for scientists working toward the development of new tools and proceduresfor the vital field of sRNA biology.
