Bacterial Regulatory RNA: Methods and Protocols

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