Assaying RNA structure inside living cells with SHAPE / Chao Feng, Dalen Chan, and Robert C. Spitale. Preparation of splicing competent nuclear extract from mammalian cells and in vitro pre-mRNA splicing assay / Maliheh Movassat, Hossein Shenasa, and Klemens J. Hertel -- Single-molecule analysis of pre-mRNA splicing with colocalization single-molecule spectroscopy (CoSMoS) / Joerg E. Braun and Victor Serebrov -- In vitro modulation of endogenous alternative splicing using splice-switching antisense oligonucleotides / Jeong Eun Park and Luca Cartegni -- Purification of mRNA processing complexes using an RNA affinity approach / Xiuye Wang and Yongsheng Shi -- Polyadenylation site-based analysis of transcript expression by 3'READS+ / Dinghai Zheng and Bin Tian -- Comprehensive identification of mRNA polyadenylation sites by PAPERCLIP / Hun-Way Hwang and Robert B. Darnell -- Microinjection and fluorescence in situ hybridization assay for studying mRNA export in mammalian cells / Ke Wang, Min Shi, and Hong Cheng -- Methods for the detection of adenosine-to-inosine editing events in cellular RNA / Eimile Oakes, Pranathi Vadlamani, and Heather A. Hundley -- Using RNA-Seq to discover genetic polymorphisms that produce hidden splice variants / Shayna Stein, Emad Bahrami-Samani, and Yi Xing -- Inducible expression of eukaryotic circular RNAs from plasmids / Deirdre C. Tatomer, Dongming Liang, and Jeremy E. Wilusz -- Methods for extraction of RNA, proteins, or protein complexes from subcellular compartments of eukaryotic cells / Kyu-Hyeon Yeom and Andrey Damianov -- Isolation of newly transcribed RNA using the metabolic label 4-thiouridine / Angela Garibaldi, Francisco Carranza, and Klemens J. Hertel -- 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, Ashley L. Louie, and Gene W. Yeo -- Purification of transcript-specific mRNP complexes formed in vivo from Saccharomyces cerevisiae / Jenna E. Smith and Kristian E. Baker -- Cell-based high-throughput method for identifying modulators of alternative splicing / Sika Zheng -- Genome-wide RNAi screens for RNA processing events in Drosophila melanogaster S2 cells / Natoya Peart and Eric J. Wagner -- Assaying RNA structure inside living cells with SHAPE / Chao Feng, Dalen Chan, and Robert C. Spitale.
Summary:
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.
Series:
Methods in molecular biology, 1064-3745 ; 1648 Springer protocols, 1949-2448
This resource is supported by the Institute of Museum and Library Services under the provisions of the Library Services and Technology Act as administered by State Library of Iowa.