mRNA processing : methods and protocols

Description

This detailed volume assembles a number of the most commonly used and state-of-the-art methodologies in the revolutionary field of mRNA processing in order to aid researchers in choosing the best method for their specific problems. Given that the vast majority of alternative mRNA processing events has yet to be explored, these techniques promise to breathe new life into the myriad new ideas currently underway. 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. Practical and easy to use, mRNA Processing: Methods and Protocols seeks to aid scientists venturing into what’s certain to be another explosive period of growth in this dynamic field of study. Read more... Abstract: This detailed volume assembles a number of the most commonly used and state-of-the-art methodologies in the revolutionary field of mRNA processing in order to aid researchers in choosing the best method for their specific problems. Read more... Front Matter ....Pages i-xi Detection and Identification of Uncapped RNA by Ligation-Mediated Reverse Transcription Polymerase Chain Reaction (C. Kiong Ho)....Pages 1-9 Preparation of Splicing Competent Nuclear Extract from Mammalian Cells and In Vitro Pre-mRNA Splicing Assay (Maliheh Movassat, Hossein Shenasa, Klemens J. Hertel)....Pages 11-26 Single-Molecule Analysis of Pre-mRNA Splicing with Colocalization Single-Molecule Spectroscopy (CoSMoS) (Joerg E. Braun, Victor Serebrov)....Pages 27-37 In Vitro Modulation of Endogenous Alternative Splicing Using Splice-Switching Antisense Oligonucleotides (Jeong Eun Park, Luca Cartegni)....Pages 39-52 Purification of mRNA Processing Complexes Using an RNA Affinity Approach (Xiuye Wang, Yongsheng Shi)....Pages 53-63 Polyadenylation Site-Based Analysis of Transcript Expression by 3′READS+ (Dinghai Zheng, Bin Tian)....Pages 65-77 Comprehensive Identification of mRNA Polyadenylation Sites by PAPERCLIP (Hun-Way Hwang, Robert B. Darnell)....Pages 79-93 Microinjection and Fluorescence In Situ Hybridization Assay for Studying mRNA Export in Mammalian Cells (Ke Wang, Min Shi, Hong Cheng)....Pages 95-102 Methods for the Detection of Adenosine-to-Inosine Editing Events in Cellular RNA (Eimile Oakes, Pranathi Vadlamani, Heather A. Hundley)....Pages 103-127 Using RNA-Seq to Discover Genetic Polymorphisms That Produce Hidden Splice Variants (Shayna Stein, Emad Bahrami-Samani, Yi Xing)....Pages 129-142 Inducible Expression of Eukaryotic Circular RNAs from Plasmids (Deirdre C. Tatomer, Dongming Liang, Jeremy E. Wilusz)....Pages 143-154 Methods for Extraction of RNA, Proteins, or Protein Complexes from Subcellular Compartments of Eukaryotic Cells (Kyu-Hyeon Yeom, Andrey Damianov)....Pages 155-167 Isolation of Newly Transcribed RNA Using the Metabolic Label 4-Thiouridine (Angela Garibaldi, Francisco Carranza, Klemens J. Hertel)....Pages 169-176 Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP) (Eric L. Van Nostrand, Thai B. Nguyen, Chelsea Gelboin-Burkhart, Ruth Wang, Steven M. Blue, Gabriel A. Pratt et al.)....Pages 177-200 Purification of Transcript-Specific mRNP Complexes Formed In Vivo from Saccharomyces cerevisiae (Jenna E. Smith, Kristian E. Baker)....Pages 201-220 A Cell-Based High-Throughput Method for Identifying Modulators of Alternative Splicing (Sika Zheng)....Pages 221-233 Genome-Wide RNAi Screens for RNA Processing Events in Drosophila melanogaster S2 Cells (Natoya Peart, Eric J. Wagner)....Pages 235-245 Assaying RNA Structure Inside Living Cells with SHAPE (Chao Feng, Dalen Chan, Robert C. Spitale)....Pages 247-256 Back Matter ....Pages 257-258