RNA

Recent insight into the transcripts generated from the mammalian genome (i.e. the transcriptome) has revealed that transcription is a far more complex phenomenon than previously thought. In RNA: Methods and Protocols, expert researchers provide the procedures and methods used to describe the structure of messenger RNAs and non-coding RNAs that are transcribed by RNA polymerase II as the immediate gene products in mammalian cells. Focused on the structure of the RNA products of gene X and the mapping of proteins associated with these RNAs, the volume presents appropriate information for non-specialists in RNA biology. Written in the highly successful Methods in Molecular Biology™ series format, many chapters contain 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. Comprehensive and practical, RNA: Methods and Protocols views the transcriptional landscape with an appreciation for the role that proteins play in the processing and interpretation of genetic information in an attempt to further our crucial knowledge of the many products and sophisticated regulatory networks that result from it.

Features samples for subsequent analysis by high-throughput technologies, such as deep sequencing or microarray analysis -Contains thorough, detailed methods and protocols easily implemented by novices and experts alike -Includes vital shared expert knowledge in the form of notes on avoiding potential experimental pitfalls Includes supplementary material: sn.pub/extras

Inhalt
The Transcriptional Landscape.- Working with RNA.- Synthesis of RNA by In vitro Transcription.- Efficient Poly(A)+ RNA Selection Using LNA Oligo(T) Capture.- Genome Browsers.- Web-Based Tools for Studying RNA Structure and Function.- Northern Blotting Analysis.- Rapid Amplification of cDNA Ends (RACE).- Fractionation of mRNA Based on the Length of the Poly(A) Tail.- Analysis of Mutations that Influence Pre-mRNA Splicing.- S1 Nuclease Analysis of Alternatively Spliced mRNA.- Promises and Challenges in Developing RNAi as a Research Tool and Therapy.- Inhibition of Gene Function in Mammalian Cells Using Short-Hairpin RNA (shRNA).- Validation of RNAi by Real Time PCR.- Profiling RNA Polymerase II Using the Fast Chromatin Immunoprecipitation Method.- The Post-Transcriptional Operon.- RIP-Chip Analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling.- Isolation of RNP Granules.- Electrophoretic Mobility Shift Assay for Characterizing RNA-Protein Interaction.- Polysome Analysis and RNA Purification from Sucrose Gradients.- Prediction of Targets for microRNAs.- Outsourcing of Experimental Work.- ESM1: In-Line Probing Analysis of Riboswitches.- ESM2: Analysis of the RNA Backbone: Structural Analysis of Riboswitches by In-Line Probing and Selective 2'-Hydroxyl Acylation and Primer Extension (SHAPE).