Bacterial Regulatory RNA Methods and Protocols [Hardcover]

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.

Part I: Identification of sRNA

1. Workflow for a Computational Analysis of an sRNA Candidate in Bacteria

Patrick R. Wright and Jens Georg

2. Molecular Phylogenomics for the Identification and Characterization of trans-encoded Small Non-coding RNA Families

Antonio Lagares (Jr) and Claudio Valverde

3. Bioinformatic Approach for Prediction of CsrA/RsmA-regulating small RNAs in Bacteria

Carl T. Fakhry, Kourosh Zarringhalam, and Rahul V. Kulkarni

Part II: Function and Differential Expression of sRNA

4. Host-pathogen Transcriptomics by Dual RNA-seq

Alexander J. Westermann and J?rg Vogel

5. Identification of New Bacterial Small RNA Targets using MS2 Affinity PurificationlÓ{