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.

Includes cutting-edge methods and protocols

Part I-Structural RNA Mapping1.      Full-Length Characterization Of Transcribed Genomic Regions Marc René Reboll, M. Lucrecia Alvarez, and Mahtab Nourbakhsh 2.      Rapid Mapping Of RNA 3¿and 5¿Ends Victoria Zismann and Mahtab Nourbakhsh 3.      Single Nucleotide Mapping Of RNA 5¿and 3¿EndsMahtab Nourbakhsh 4.      RNA Secondary Structure Analysis Mahtab  Nourbakhsh 5.      Tertiary Structure Mapping Of Pri-Mirna17~92Steven G. Chaulk and Richard P. Fahlman  6.      In Situ Hybridization Detection Of Micrornas Using LNA OligonucleotidesOlga Beltcheva and Stefania Cotta Done  7.      Quantification Of Micrornas By A Simple And Specific Qpcr MethodPeter Busk and Susanna Cirera 8.      RNA Isolation For Small RNA Next Generation Sequencing From Acellular BiofluidsKasandra L. Burgos and Kendall Van Keuren-Jensen 9.      Sequencing Small RNA: Introduction and Data Analysis FundamentalsJai Prakash Mehta 10.  Measuring Expression Levels Of Small Regulatory RNA Molecules From Formalin-Fixed, Paraffin-Embedded Samples and Body FluidsAdrienn Gyongyosi, Otto Docs, Zsolt Czimmerer, Laszlo Orosz, Attila Horvath, Olga Török, Gabor Mehes, Laszlo Nagy, and Balint L Balint 11.  Microrna Profiling In Plasma Or Serum Using Quantitative RT-QpcrMarina C. Costa, Ana Lúcia Leitão, and Francisco J. Enguita 12.  Microrna Profiling Of Exosomes Isolated From Biofluids And Conditioned MediaSweta Rani  13.  Isolation Of Urinary Exosomes For RNA Biomarker Discovery Using A Simple, Fast, And Highly Scalable Method M. Lucrecia AlvarezPart II- Functional RNA Mapping14.  Identification Of Actively Translated Mrnas Marc René Reboll and Mahtab Nourbakhsh 15.  Mapping Of Internal Ribosome Entry Sites (IRES) Sarah Mehrtens and Marc René Reboll 16.  Mapping Of Protein Binding RNA Elements Marc René Reboll 17.  Purification Of RNA Binding Proteins Birgit Ritter and Marc René Reboll 18.  De Novo Approach To Classify Protein-Coding And Non-Coding Transcripts By Utilizing Sequence Intrinsic CompositionHaitao Luo, Dechao Bu, Liang Sun, and Yi Zhao 19.  Computational Methods To Predict Long Non-Coding RNA Functions Based On Co-Expression Network Yi Zhao, Haitao Luo, Xiaowei Chen, Yi Xiao, and Runsheng Chen 20.  Microrna Biogenesis - Dicing AssayCarlos A. Melo and Sonia A. Melo 21.  Faster Experimental Validation Of Microrna Targets Using Cold Fusion Cloning And A Dual Firefly-Renilla Luciferase Reporter AssayM. Lucrecia Alvarez 22.  Experimental Validation Of Predicted Mammalian Micrornas Of Mirtron OriginAnita Schamberger and Tamás I. Orbán 23.  A Guide For Microrna Target Prediction And Analysis Using Web-Based ApplicationsAna Lúcia Leitão, Marina C. Costa, and Francisco J. Enguita 24.  Tapping Microrna Regulation Networks Through Integrated Analysis Of Microrna-Mrna High-Throughput ProfilesAnthony D. Saleh and Hui Cheng 25.  Mirwalk Database For Microrna-Target Interactions Harsh Dweep, Norbert Gretz And Carsten Sticht26.  A Schematic Workflow For Collecting The Interaction Information Between Copy Number Variants And Micrornas Using Existing ResourcesHarsh Dweep, Norbert Gretz,  and Kyriakos Felekkis 27.  SYBR Green and Taqman PCR Arrays: Expression Profile Of Genes Relevant To A Pathway Or Disease State M. Lucrecia Alvarez And Stefania Cotta Done 28.  Comprehensive Meta-Analysis Of Microrna Expression Using A Robust Rank Aggregation Approach Urmo Võsa, Raivo Kolde, Jaak Vilo, Andres Metspalu, and Tarmo Annilo