Bacterial Regulatory RNA: Methods and Protocols

Description

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 procedures for the vital field of sRNA biology. Front Matter ....Pages i-xii Front Matter ....Pages 1-1 Workflow for a Computational Analysis of an sRNA Candidate in Bacteria (Patrick R. Wright, Jens Georg)....Pages 3-30 Guidelines for Inferring and Characterizing a Family of Bacterial trans-Acting Small Noncoding RNAs (Antonio Lagares Jr., Claudio Valverde)....Pages 31-45 Bioinformatic Approach for Prediction of CsrA/RsmA-Regulating Small RNAs in Bacteria (Carl T. Fakhry, Kourosh Zarringhalam, Rahul V. Kulkarni)....Pages 47-56 Front Matter ....Pages 57-57 Host-Pathogen Transcriptomics by Dual RNA-Seq (Alexander J. Westermann, Jörg Vogel)....Pages 59-75 Identification of New Bacterial Small RNA Targets Using MS2 Affinity Purification Coupled to RNA Sequencing (Marie-Claude Carrier, Guillaume Laliberté, Eric Massé)....Pages 77-88 Assessment of External Guide Sequences’ (EGS) Efficiency as Inducers of RNase P-Mediated Cleavage of mRNA Target Molecules (Saumya Jani, Alexis Jackson, Carol Davies-Sala, Kevin Chiem, Alfonso Soler-Bistué, Angeles Zorreguieta et al.)....Pages 89-98 Evaluating the Effect of Small RNAs and Associated Chaperones on Rho-Dependent Termination of Transcription In Vitro (Cédric Nadiras, Annie Schwartz, Mildred Delaleau, Marc Boudvillain)....Pages 99-118 Mapping Changes in Cell Surface Protein Expression Through Selective Labeling of Live Cells (Pierre Fechter)....Pages 119-127 Fluorescence-Based Methods for Characterizing RNA Interactions In Vivo (Abigail N. Leistra, Mia K. Mihailovic, Lydia M. Contreras)....Pages 129-164 Mutational Analysis of sRNA–mRNA Base Pairing by Electrophoretic Mobility Shift Assay (Eva Maria Sternkopf Lillebæk, Birgitte Haahr Kallipolitis)....Pages 165-176 An Integrated Cell-Free Assay to Study Translation Regulation by Small Bacterial Noncoding RNAs (Erich Michel, Olivier Duss, Frédéric H.-T. Allain)....Pages 177-195 Front Matter ....Pages 197-197 Quantitative Super-Resolution Imaging of Small RNAs in Bacterial Cells (Seongjin Park, Magda Bujnowska, Eric L. McLean, Jingyi Fei)....Pages 199-212 Extraction and Analysis of RNA Isolated from Pure Bacteria-Derived Outer Membrane Vesicles (Janine Habier, Patrick May, Anna Heintz-Buschart, Anubrata Ghosal, Anke K. Wienecke-Baldacchino, Esther N. M. Nolte-‘t Hoen et al.)....Pages 213-230 Absolute Regulatory Small Noncoding RNA Concentration and Decay Rates Measurements in Escherichia coli (Florent Busi, Véronique Arluison, Philippe Régnier)....Pages 231-248 Front Matter ....Pages 249-249 High-Resolution, High-Throughput Analysis of Hfq-Binding Sites Using UV Crosslinking and Analysis of cDNA (CRAC) (Brandon Sy, Julia Wong, Sander Granneman, David Tollervey, David Gally, Jai J. Tree)....Pages 251-272 Producing Hfq/Sm Proteins and sRNAs for Structural and Biophysical Studies of Ribonucleoprotein Assembly (Kimberly A. Stanek, Cameron Mura)....Pages 273-299 Single-Molecule FRET Assay to Observe the Activity of Proteins Involved in RNA/RNA Annealing (Thierry Bizebard, Véronique Arluison, Ulrich Bockelmann)....Pages 301-319 Techniques to Analyze sRNA Protein Cofactor Self-Assembly In Vitro (David Partouche, Antoine Malabirade, Thomas Bizien, Marisela Velez, Sylvain Trépout, Sergio Marco et al.)....Pages 321-340 Sequence-Specific Affinity Chromatography of Bacterial Small Regulatory RNA-Binding Proteins from Bacterial Cells (Jonathan Gans, Jonathan Osborne, Juliet Cheng, Louise Djapgne, Amanda G. Oglesby-Sherrouse)....Pages 341-350 Identification of Small RNA–Protein Partners in Plant Symbiotic Bacteria (Marta Robledo, Ana M. Matia-González, Natalia I. García-Tomsig, José I. Jiménez-Zurdo)....Pages 351-370 Front Matter ....Pages 371-371 A Modular Genetic System for High-Throughput Profiling and Engineering of Multi-Target Small RNAs (Samuel D. Stimple, Ashwin Lahiry, Joseph E. Taris, David W. Wood, Richard A. Lease)....Pages 373-391 Back Matter ....Pages 393-395