RNA Mapping

1. Front Matter

   Pages i-xi

   PDF

2. Structural RNA Mapping

   1. Front Matter

      Pages 1-1

      PDF

   2. Full-Length Characterization of Transcribed Genomic Regions

      • Marc R. Reboll, M. Lucrecia Alvarez, Mahtab Nourbakhsh

      Pages 3-18

   3. Rapid Mapping of RNA 3′ and 5′ Ends

      • Victoria Zismann, Mahtab Nourbakhsh

      Pages 19-25

   4. Single Nucleotide Mapping of RNA 5′ and 3′ Ends

      • Mahtab Nourbakhsh

      Pages 27-34

   5. Analysis of RNA Secondary Structure

      • Mahtab Nourbakhsh

      Pages 35-42

   6. Tertiary Structure Mapping of the Pri-miRNA miR-17~92

      • Steven G. Chaulk, Richard P. Fahlman

      Pages 43-55

   7. In Situ Hybridization Detection of miRNA Using LNA™ Oligonucleotides

      • Stefania Cotta Doné, Olga Beltcheva

      Pages 57-71

   8. Quantification of miRNAs by a Simple and Specific qPCR Method

      • Susanna Cirera, Peter K. Busk

      Pages 73-81

   9. RNA Isolation for Small RNA Next-Generation Sequencing from Acellular Biofluids

      • Kasandra L. Burgos, Kendall Van Keuren-Jensen

      Pages 83-92

   10. Sequencing Small RNA: Introduction and Data Analysis Fundamentals

       • Jai Prakash Mehta

       Pages 93-103

   11. Measuring Expression Levels of Small Regulatory RNA Molecules from Body Fluids and Formalin-Fixed, Paraffin-Embedded Samples

       • Adrienn Gyongyosi, Otto Docs, Zsolt Czimmerer, Laszlo Orosz, Attila Horvath, Olga Török et al.

       Pages 105-119

   12. MicroRNA Profiling in Plasma or Serum Using Quantitative RT-PCR

       • Marina C. Costa, Ana Lúcia Leitão, Francisco J. Enguita

       Pages 121-129

   13. MicroRNA Profiling of Exosomes Isolated from Biofluids and Conditioned Media

       • Sweta Rani

       Pages 131-144

   14. Isolation of Urinary Exosomes for RNA Biomarker Discovery Using a Simple, Fast, and Highly Scalable Method

       • M. Lucrecia Alvarez

       Pages 145-170

3. Functional RNA Mapping

   1. Front Matter

      Pages 171-171

      PDF

   2. Identification of Actively Translated mRNAs

      • Marc R. Reboll, Mahtab Nourbakhsh

      Pages 173-178

   3. Mapping of Internal Ribosome Entry Sites (IRES)

      • Sarah Mehrtens, Marc R. Reboll

      Pages 179-185

   4. Mapping of Protein Binding RNA Elements

      • Marc R. Reboll

      Pages 187-194

   5. Purification of RNA-Binding Proteins

      • Birgit Ritter, Marc R. Reboll

      Pages 195-201

In RNA Mapping- Methods and Protocols expert researchers in the field detail many of the methods which are now commonly used to study RNA. These include protocols for the consequence of the emerging interest in the characterization of cellular RNAs urged by their potential use as diagnostic biomarkers or therapeutic targets. In particular, the biological relevance of microRNAs in human physiology and disease development is highlighted in the 16 chapters focused on methods for their physical and functional mapping. 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, RNA Mapping- Methods and Protocols provides instruction and inspiration for scientists who are facing the challenges of the discovery and/or functional characterization of RNA molecules for a wide variety of applications ranging from novel biomedical diagnostics to therapeutics and biomaterials.

• RNA boundaries
• RNA identification
• RNA profiling
• cellular RNAs
• diagnostic biomarkers
• mapping of internal ribosome
• microRNA targets prediction
• novel RNA functions
• quantitative real-time PCR
• regulatory mRNA elements
• target RNAs
• tertiary RNA
• therapeutic targets

• Diabetes, Cardiovascular, and Metabolic Diseases, Translational Genomics Research Institute, Phoenix, USA

  M. Lucrecia Alvarez

• Department of Plastic Surgery, University Hospital of the RWTH Aachen, Germany

  Mahtab Nourbakhsh

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