Mrna Processing: Methods and Protocols

ISBN-13: 9781493984152 / Angielski / Miękka / 2018 / 258 str.

Yongsheng Shi

Spis treści

1. Detection and Identification of Uncapped RNA by Ligation-Mediated Reverse Transcription Polymerase Chain Reaction

            C. Kiong Ho

 

2. Preparation of Splicing Competent Nuclear Extract from Mammalian Cells and In Vitro Pre-mRNA Splicing Assay

            Maliheh Movassat, Hossein Shenasa, and Klemens J. Hertel

 

3. Single-Molecule Analysis of Pre-mRNA Splicing with Colocalization Single-Molecule Spectroscopy (CoSMoS)

            Joerg E. Braun and Victor Serebrov

 

4. In Vitro Modulation of Endogenous Alternative Splicing Using Splice-Switching Antisense Oligonucleotides

            Jeong Eun Park and Luca Cartegni

 

5. Purification of mRNA Processing Complexes Using an RNA Affinity Approach

            Xiuye Wang and Yongsheng Shi

 

6. Polyadenylation Site-Based Analysis of Transcript Expression by 3’READS+

            Dinghai Zheng and Bin Tian

 

7. Comprehensive Identification of mRNA Polyadenylation Sites by PAPERCLIP

            Hun-Way Hwang and Robert B. Darnell

 

8. Microinjection and Fluorescence In Situ Hybridization Assay for Studying mRNA Export in Mammalian Cells

            Ke Wang, Min Shi, and Hong Cheng

 

9. Methods for the Detection of Adenosine-to-Inosine Editing Events in Cellular RNA

            Eimile Oakes, Pranathi Vadlamani, and Heather A. Hundley

 

10. Using RNA-Seq to Discover Genetic Polymorphisms that Produce Hidden Splice Variants

            Shayna Stein, Emad Bahrami-Samani, and Yi Xing

 

11. Inducible Expression of Eukaryotic Circular RNAs from Plasmids

            Deirdre C. Tatomer, Dongming Liang, and Jeremy E. Wilusz

 

12. Methods for Extraction of RNA, Proteins, or Protein Complexes from Subcellular Compartments of Eukaryotic Cells

            Kyu-hyeon Yeom and Andrey Damianov

 

13. Isolation of Newly Transcribed RNA Using the Metabolic Label 4-Thiouridine

            Angela Garibaldi, Francisco Carranza, and Klemens J. Hertel

 

14. Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-End 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

 

15. Purification of Transcript-Specific mRNP Complexes Formed In Vivo from Saccharomyces cerevisiae

            Jenna E. Smith and Kristian E. Baker

 

16. A Cell-Based High-Throuput Method for Identifying Modulators of Alternative Splicing

            Sika Zheng

 

17. Genome-Wide RNAi Screens for RNA Processing Events in Drosophila Melanogaster S2 Cells

            Natoya J. Peart and Eric J. Wagner

 

18. Assaying RNA Structure Inside Living Cells with SHAPE

            Chao Feng, Dalen Chan, and Robert C. Spitale

Blurb

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.