Alternative pre-mRNA Splicing: Theory and Protocols

Copyright © 2012 Wiley-VCH Verlag GmbH & Co. KGaA

Alternative pre-mRNA Splicing: Theory and Protocols

Editor(s): Stefan Stamm, Christopher W. J. Smith, Reinhard Lührmann

Published Online: 2 FEB 2012

Print ISBN: 9783527326068

Online ISBN: 9783527636778

DOI: 10.1002/9783527636778

About this Book

Product Information

About The Product

This book was written for graduate and medical students, as well as clinicians and postdoctoral researchers. It describes the theory of alternative pre-mRNA splicing in
twelve introductory chapters and then introduces protocols and their theoretical background relevant for experimental research. These 43 practical chapters cover: Basic methods, Detection of splicing events, Analysis of alternative pre-mRNA splicing in vitro and in vivo, Manipulation of splicing events, and Bioinformatic analysis of alternative splicing.
A theoretical introduction and practical guide for molecular biologists, geneticists,clinicians and every researcher interested in alternative splicing.

Website: www.wiley-vch.de/home/splicing

Table of contents

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      Front Matter (pages I–XXXVII)

  2. Part One: Theory

    1. Chapter 1

      Splicing in the RNA World (pages 1–12)

      Emanuele Buratti, Maurizio Romano and Francisco E. Baralle

    2. Chapter 2

      RNPs, Small RNAs, and miRNAs (pages 13–19)

      Michaela Beitzinger and Gunter Meister

    3. Chapter 3

      RNA Elements Involved in Splicing (pages 21–31)

      William F. Mueller and Klemens J. Hertel

    4. Chapter 4

      A Structural Biology Perspective of Proteins Involved in Splicing Regulation (pages 33–48)

      Antoine Cléry and Frédéric H.-T. Allain

    5. Chapter 5

      The Spliceosome in Constitutive Splicing (pages 49–64)

      Patrizia Fabrizio and Prof. Dr. Reinhard Lührmann

    6. Chapter 6

      The Use of Saccharomyces cerevisiae to Study the Mechanism of pre-mRNA Splicing (pages 65–77)

      Brian C. Rymond

    7. Chapter 7

      Challenges in Plant Alternative Splicing (pages 79–91)

      Andrea Barta, Yamile Marquez and John W. S. Brown

    8. Chapter 8

      Alternative Splice Site Selection (pages 93–107)

      Miguel B. Coelho and Prof. Dr. Christopher W. J. Smith

    9. Chapter 9

      Integration of Splicing with Nuclear and Cellular Events (pages 109–117)

      Aparna K. Sapra and Karla Neugebauer

    10. Chapter 10

      Splicing and Disease (pages 119–128)

      Emanuele Buratti and Francisco E. Baralle

    11. Chapter 11

      From Bedside to Bench: How to Analyze a Splicing Mutation (pages 129–138)

      Marco Baralle and Diana Baralle

  3. Part Two: Basic Methods

    1. Chapter 12

      Analysis of Common Splicing Problems (pages 146–145)

      Prof. Dr. Stefan Stamm

    2. Chapter 13

      Ultracentrifugation in the Analysis and Purification of Spliceosomes Assembled In Vitro (pages 147–153)

      Klaus Hartmuth, Maria A. van Santen and Prof. Dr. Reinhard Lührmann

    3. Chapter 14

      Chemical Synthesis of RNA (pages 154–162)

      Claudia Höbartner

    4. Chapter 15

      RNA Interference (siRNA, shRNA) (pages 164–173)

      Daphne S. Cabianca and Davide Gabellini

    5. Chapter 16

      Expression and Purification of Splicing Proteins (pages 174–180)

      James Stévenin and Cyril F. Bourgeois

    6. Chapter 17

      Detection of RNA–Protein Complexes by Electrophoretic Mobility Shift Assay (pages 182–198)

      Manli Shen and Michael G. Fried

    7. Chapter 18

      Functional Analysis of Large Exonic Sequences Through Iterative In Vivo Selection (pages 200–209)

      Ravindra N. Singh and Natalia N. Singh

    8. Chapter 19

      Identification of Splicing cis-Elements Through an Ultra-Refined Antisense Microwalk (pages 210–217)

      Natalia N. Singh, Joonbae Seo and Ravindra N. Singh

    9. Chapter 20

      Genomic SELEX to Identify RNA Targets of Plant RNA-Binding Proteins (pages 218–226)

      Olga Bannikova, Maria Kalyna and Andrea Barta

  4. Part Three: Detection of Splicing Events

    1. Chapter 21

      Quantification of Alternative Splice Variants (pages 227–236)

      Miriam Llorian and Prof. Dr. Christopher W. J. Smith

    2. Chapter 22

      High-Throughput Analysis of Alternative Splicing by RT-PCR (pages 238–246)

      Roscoe Klinck, Benoit Chabot and Sherif Abou Elela

    3. Chapter 23

      Monitoring Changes in Plant Alternative Splicing Events (pages 248–259)

      Craig G. Simpson, Naeem Hasan Syed, Sujatha Manthri, John D. Fuller, Monika Maronova, Branislav Kusenda, Maria Kalyna, Andrea Barta and John W.S. Brown

    4. Chapter 24

      Array Analysis (pages 260–267)

      Pierre de la Grange

    5. Chapter 25

      The CLIP Method to Study Protein–RNA Interactions in Intact Cells and Tissues (pages 268–278)

      James Tollervey and Jernej Ule

    6. Chapter 26

      RNA–Protein Crosslinking and Immunoprecipitation (CLIP) in Schizosaccharomyces pombe (pages 280–288)

      Branislav Kusenda and Andrea Barta

    7. Chapter 27

      Identification of Proteins Bound to RNA (pages 290–297)

      Emanuele Buratti

    8. Chapter 28

      Single-Cell Detection of Splicing Events with Fluorescent Splicing Reporters (pages 298–309)

      Hidehito Kuroyanagi, Akihide Takeuchi, Takayuki Nojima and Masatoshi Hagiwara

  5. Part Four: Analysis of Splicing In Vitro

    1. Chapter 29

      The Preparation of HeLa Cell Nuclear Extracts (pages 311–319)

      Klaus Hartmuth, Maria A. van Santen, Tanja Rösel, Berthold Kastner and Prof. Dr. Reinhard Lührmann

    2. Chapter 30

      In Vitro Splicing Assays (pages 320–329)

      Akila Mayeda and Adrian R. Krainer

    3. Chapter 31

      Assembly and Isolation of Spliceosomal Complexes In Vitro (pages 330–340)

      Klaus Hartmuth, Maria A. van Santen, Peter Odenwälder and Prof. Dr. Reinhard Lührmann

    4. Chapter 32

      Analysis of Site-Specific RNA–Protein Interactions (pages 342–356)

      Nathalie Marmier-Gourrier, Audrey Vautrin, Christiane Branlant and Isabelle Behm-Ansmant

    5. Chapter 33

      Immunoprecipitation and Pull-Down of Nuclear Proteins (pages 358–364)

      Natalya Benderska, Chiranthani Sumanasekera and Prof. Dr. Stefan Stamm

    6. Chapter 34

      Analysis of Protein (-RNA) Complexes by (Quantitative) Mass Spectrometric Analysis (pages 366–379)

      Carla Schmidt and Henning Urlaub

  6. Part Five: Analysis of Splicing In Vivo

    1. Chapter 35

      Fast Cloning of Splicing Reporter Minigenes (pages 381–391)

      Zhaiyi Zhang, Amit Khanna and Prof. Dr. Stefan Stamm

    2. Chapter 36

      In Vivo Analysis of Splicing Assays (pages 392–399)

      Isabel C. López-Mejía and Jamal Tazi

    3. Chapter 37

      Coupled Promoter Splicing Systems (pages 400–407)

      Manuel J. Mu∼noz, Manuel de la Mata and Alberto R. Kornblihtt

    4. Chapter 38

      Stable Cell Lines with Splicing Reporters (pages 408–414)

      Christian Kroun Damgaard, Søren Lykke-Andersen and Jørgen Kjems

    5. Chapter 39

      Splicing Factor ChIP and ChRIP: Detection of Splicing and Splicing Factors at Genes by Chromatin Immunoprecipitation (pages 416–427)

      Aparna K. Sapra, Fernando Carrillo Oesterreich, Marta Pabis, Imke Listerman, Nicole Bardehle and Karla M. Neugebauer

    6. Chapter 40

      Yeast Genetics to Investigate the Function of Core Pre-mRNA Splicing Factors (pages 428–436)

      Raymond T. O. Keefe and Jean D. Beggs

    7. Chapter 41

      Analysis of HIV-1 RNA Splicing (pages 438–448)

      Simon Duffy and Alan Cochrane

    8. Chapter 42

      In Vivo Analysis of Plant Intron Splicing (pages 450–462)

      Craig G. Simpson, Michele Liney, Diane Davidson, Dominika Lewandowska, Maria Kalyna, Sean Chapman, Andrea Barta and John W. S. Brown

    9. Chapter 43

      Modification State-Specific Antibodies (pages 464–473)

      Jordan B. Fishman, Olga Kelemen and Eric A. Berg

    10. Chapter 44

      Analysis of Alternative Splicing in Drosophila Genetic Mosaics (pages 474–479)

      Shihuang Su, Diana O'Day, Shanzhi Wang and William Mattox

    11. Chapter 45

      Antisense Derivatives of U7 Small Nuclear RNA as Modulators of Pre-mRNA Splicing (pages 481–494)

      Kathrin Meyer and Daniel Schümperli

    12. Chapter 46

      Screening for Alternative Splicing Modulators (pages 496–508)

      Peter Stoilov

    13. Chapter 47

      Use of Oligonucleotides to Change Splicing (pages 510–520)

      Annemieke Aartsma-Rus and Judith C. T. van Deutekom

    14. Chapter 48

      Changing Signals to the Spliceosome (pages 522–534)

      Denise R. Cooper and Niketa A. Patel

    15. Chapter 49

      Overview of Splicing Relevant Databases (pages 535–543)

      Pierre de la Grange

    16. Chapter 50

      Analysis of RNA Transcripts by High-Throughput RNA Sequencing (pages 544–554)

      Paolo Ribeca, Vincent Lacroix, Michael Sammeth and Roderic Guigó

    17. Chapter 51

      Identification of Splicing Factor Target Genes by High-Throughput Sequencing (pages 556–564)

      Chaolin Zhang and Michael Q. Zhang

    18. Chapter 52

      Bioinformatic Analysis of Splicing Events (pages 566–573)

      Zhaiyi Zhang and Prof. Dr. Stefan Stamm

    19. Chapter 53

      Analysis of Pre-mRNA Secondary Structures and Alternative Splicing (pages 574–580)

      Michael Hiller

    20. Chapter 54

      Structure Prediction for Alternatively Spliced Proteins (pages 582–591)

      Lukasz Kozlowski, Jerzy Orlowski and Janusz M. Bujnicki

    21. Chapter 55

      Comparative Genomics Methods for the Prediction of Small RNA-Binding Sites (pages 592–601)

      Rym Kachouri-Lafond and Mihaela Zavolan

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      Appendix A1: Yeast Nomenclature Systematic Open Reading Frame (ORF) and Other Genetic Designations (pages 603–607)

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      Appendix A2: Glossary (pages 609–613)

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      Index (pages 615–622)

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