Bacterial Regulatory RNA

Methods and Protocols
2012
ISBN: 978-1-61779-948-8
Verlag: Humana Press

Buch, Englisch, Band 905, 333 Seiten, Format (B × H): 183 mm x 260 mm, Gewicht: 852 g

Reihe: Methods in Molecular Biology

The discovery of wide-spread RNA-based regulation in bacteria has led to new evaluations of the importance of bacterial regulatory RNA in every aspect of bacterial physiology. In Bacteria Regulatory RNA: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study bacterial regulatory RNA. These include methods and techniques to identify regulatory RNAs, characterizing the function and expression of regulatory RNAs in bacterial cells, RNA structure prediction, and interactions between regulatory RNAs and proteins. 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 key tips on troubleshooting and avoiding known pitfalls.

 

 Authoritative and practical, Bacteria Regulatory RNA: Methods and Protocols seeks to aid scientists in the further study of bacterial regulatory RNA.

Zielgruppe

Professional/practitioner

Autoren/Hrsg.

Keiler, Kenneth C.

Fachgebiete

• Naturwissenschaften Biowissenschaften Bakteriologie
• Naturwissenschaften Biowissenschaften Proteinforschung
• Naturwissenschaften Biowissenschaften Biowissenschaften Genetik und Genomik (nichtmedizinisch)
• Medizin | Veterinärmedizin Medizin | Public Health | Pharmazie | Zahnmedizin Vorklinische Medizin: Grundlagenfächer Humangenetik
• Medizin | Veterinärmedizin Medizin | Public Health | Pharmazie | Zahnmedizin Medizinische Fachgebiete Medizinische Mikrobiologie & Virologie

Inhaltsverzeichnis

Part I- Identification of Regulatory RNAs
 
1. Bioinformatic Discovery of Bacterial Regulatory RNAs using SIPH
Jonathan Livny
 
2. How to Identify CRISPRs in Sequencing Data
Christine Drevet and Christine Pourcel
 
3. A Strategy for Identifying Non-coding RNAs using Whole-genome Tiling Arrays
Stephen G. Landt and Eduardo Abeliuk
 
4. Genetic Screens to Identify Bacterial sRNA Regulators
Pierre Mandin
 
 
Part II - Function and Expression of Regulatory RNAs
 
5. Competition Assays Using Barcoded Deletion Strains to Gain Insight Into Small RNA Function
Errett C. Hobbs and Gisela Storz
 
6. Use of Semi-quantitative Northern Blot Analysis to Determine Relative Quantities of Bacterial CRISPR Transcripts
Ksenia Pougach and Konstantin Severinov
 
7. RNA Visualization in Bacteria by Fluorescence in Situ Hybridization
Jay H. Russell and Kenneth C. Keiler
 
 
Part III - RNA Structure and Biophysical Measurements
 8. RNA Structure Prediction: An Overview of MethodsMatthew G. Seetin and David H. Mathews 
9. Crystallization of RNA-Protein Complexes: From Synthesis and Purification of Individual Components to Crystals
Anna Perederina and Andrey S. Krasilnikov
 
10. Analysis of RNA Folding and Ligand Binding by Conventional and High-Throughput Calorimetry
Joshua E. Sokoloski and Philip C. Bevilacqua
 
Part IV – RNA-Protein Interactions
11. Use of Aptamer Tagging to Identify in vivo Protein Binding Partners of Small Regulatory RNAs
Colin P. Corcoran,  Renate Rieder, Dimitri Podkaminski, Benjamin Hofmann, and Jörg Vogel
12. Gel Mobility Shift Assays to Detect Protein-RNA Interactions
Alexander V. Yakhnin, Helen Yakhnin and Paul Babitzke
 
13. RNase Footprinting of Protein Binding Sites on an mRNA Target of Small RNAs
Peng Yi, Soper, Toby J., and Woodson Sarah A
 
Part V – RNA-RNA Interactions
14.Computational Identification of sRNA TargetsBrian Tjaden
 15. Detection of sRNA-mRNA Interactions by Electrophoretic Mobility Shift AssayTeppei Morita, Kimika Maki, and Hiroji Aiba 
16. Activity of Small RNAs on the Stability of Targeted mRNAs in vivo
Guillaume Desnoyers and Eric Massé
 
Part VI –Interactions of Regulatory RNA with RNA Polymerase and the Ribosome
17. Native Gel Electrophoresis to Study the Binding and Release of RNA Polymerase by 6S RNA
Karen M. Wassarman
 
18. Ribosome Purification Approaches for Studying Interactions of Regulatory Proteins and RNAs with the Ribosome
Preeti Mehta, Perry Woo, Krithika Venkataraman, and A. Wali Karzai
 
19. Analysis of Aminoacyl- and Peptidyl-tRNAs by Gel Electrophoresis
Brian D. Jansse, Elie J. Diner, and Christopher S. Hayes 
20. In vitro trans-translation Assays
Daisuke Kurit, Akira Muto, and Hyouta Himeno

 
16. Activity of Small RNAs on the Stability of Targeted mRNAs in vivo
Guillaume Desnoyers and Eric Massé
 
Part VI –Interactions of Regulatory RNA with RNA Polymerase and the Ribosome
17. Native Gel Electrophoresis to Study the Binding and Release of RNA Polymerase by 6S RNA
Karen M. Wassarman
 
18. Ribosome Purification Approaches for Studying Interactions of Regulatory Proteins and RNAs with the Ribosome
Preeti Mehta, Perry Woo, Krithika Venkataraman, and A. Wali Karzai
 
19. Analysis of Aminoacyl- and Peptidyl-tRNAs by Gel Electrophoresis
Brian D. Jansse, Elie J. Diner, and Christopher S. Hayes 
20. In vitro trans-translation Assays
Daisuke Kurit, Akira Muto, and Hyouta Himeno

 
20. In vitro trans-translation Assays
Daisuke Kurit, Akira Muto, and Hyouta Himeno
 
16. Activity of Small RNAs on the Stability of Targeted mRNAs in vivo
Guillaume Desnoyers and Eric Massé
 
Part VI –Interactions of Regulatory RNA with RNA Polymerase and the Ribosome
17. Native Gel Electrophoresis to Study the Binding and Release of RNA Polymerase by 6S RNA
Karen M. Wassarman
 
18. Ribosome Purification Approaches for Studying Interactions of Regulatory Proteins and RNAs with the Ribosome
Preeti Mehta, Perry Woo, Krithika Venk