Alternative pre-mRNA Splicing. Theory and Protocols. Edition No. 1

Table of Contents

Baralle)
RNPs, small RNAs, miRNAs (Michaela Beitzinger and Gunter Meister)
RNA Elements Involved in Splicing (William F. Mueller and Klemens J. Hertel)
A Structural Biology Perspective of Proteins Involved in Splicing Regulation (Antoine Cléry and Frederic Allain)
The Spliceosome in Constitutive Splicing (Patrizia Fabrizio and Reinhard Lührmann)
The Use of Saccharomyces cerevisiae to Study the Mechanism of pre-mRNA Splicing (Brian C. Rymond)
Challenges in Plant Alternative Splicing (Andrea Barta, Yamile Marquez and John WS Brown)
Alternative Splice Site Selection (Miguel B. Coelho and Christopher WJ Smith)
Integration of Splicing with Nuclear and Cellular Events (Aparna K. Sapra and Carla Neugebauer)
Splicing and Disease (Emanuele Buratti and Francisco E. Baralle)
From Bedside to Bench: How to Analyze a Splicing Mutation (Marco Baralle and Diana Baralle)
Analysis of Splicing Problems (Stefan Stamm)
BASIC METHODS
Ultracentrifugation in the Analysis and Purification by of Spliceosomes Assembled in Vitro
(Klaus Hartmuth, Maria A. van Santen and Reinhard Lührmann)
Chemical Synthesis of RNA (Claudia Höbartner)
RNA Interference (siRNA, ShRNA) (Daphne S. Cabianca and Davide Gabellini)
Expression and Purification of Splicing Proteins (James Stévenin and Cyril F. Bourgeois)
Detection of RNA-Protein Complexes By Electrophoretic Mobility Shift Assay (Manli Shen and Michael G. Fried)
Functional Analysis of large Exonic Sequences through Iterative in Vivo Selection (Natalia N. Singh, Joonbae Seo and Ravindra N. Singh)
Identification of Splicing cis-Elements through an Ultra-Refined Antisense Microwalk (Ravindra N. Singh and Natalia N. Singh)
Genomic SELEX to Identify RNA Targets of Plant RNA Binding Proteins (Olga Bannikova and Andrea Barta)
DETECTION OF SPLICING EVENTS
Quantification of Alternative Splice Variants (Miriam LLorian and Christopher WJ Smith)
High-Throughput Analysis of Alternative Splicing by RT-PCR (Roscoe Klinck, Benoit Chabot and Sherif Abou Elela)
Monitoring Changes in Plant Alternative Splicing Events (Craig G. Simpson, Naeem Hasan Syed, Sujatha Manthri, John D. Fuller, Monika Maronova, Branislav Kusenda, Maria Kalyna, Andrea Barta and John WS Brown)
Array Analysis (Pierre de la Grange)
The CLIP Method to Study Protein-RNA Interactions in Intact Cells and Tissues (James Tollervey and Jernej Ule)
RNA: Protein Crosslinking and Immunoprecipitation in Yeast (CLIP) (Branislav Kusenda and Andrea Barta)
Identification of Proteins Bound to RNA (Emanuele Buratti)
Single Cell Detection of Splicing Events with Fluorescent Splicing Reporters (Hidehito Kuroyanagi, Akihide Takeuchi, Takayuki Nojima and Masatoshi Hagiwara)
ANALYSIS OF SPLICING IN VITRO
The Preparation of HeLa Cell Nuclear Extracts (Klaus Hartmuth, Maria A. van Santen, Tanja Rösel, Berthold Kastner and Reinhard Lührmann)
In Vitro Splicing Assays (Akila Mayeda and Adrian R. Krainer)
Assembly of Spliceosomes in Vitro(Klaus Hartmuth, Maria A. van Santen, Peter Odenwälder and Reinhard Lührmann)
Analysis of Site-Specific RNA-Protein Interactions (Nathalie Marmier-Gourrier, Audrey Vautrin, Christiane Branlant and Isabelle Behm-Ansmant)
Immunoprecipitation and Pull-Down of Nuclear Proteins
(Natalya Benderska, Chiranthani Sumanasekera and Stefan Stamm)
Analysis of Protein (RNA) Complexes by (Quantitative) Mass Spec Analysis (Carla Schmidt and Henning Urlaub)
ANALYSIS OF SPLICING IN VIVO
Fast cloning of splicing reporter minigenes (Zhaiyi Zhang, Amit Khanna and Stefan Stamm)
In Vivo Splicing Assays (Isabel Cristina López Mejía and Jamal Tazi)
Coupled Promoter Splicing Systems (Manuel J. Muñoz, Manuel de la Mata and Alberto R. Kornblihtt)
Stable Cell Lines With Splicing Reporters (Christian Kroun Damgaard, Søren Lykke-Andersen and Jørgen Kjems)
Splicing Factor ChIP and ChRIP: Detection of Splicing and Splicing Factors at Genes by Chromatin Immunoprecipitation (Aparna K. Sapra, Fernando Carrillo Oesterreich, Marta Pabis, Imke Listerman, Nicole Bardehle and Karla M. Neugebauer)
Yeast Genetics to Investigate the Function of Core Pre-mRNA Splicing Factors (Raymond T. O?Keefe and Jean D. Beggs)
Analysis of HIV-1 RNA Splicing (Simon Duffy and Alan Cochrane)
In Vivo Analysis of Plant Intron Splicing (Craig G. Simpson, Michele Liney, Diane Davidson, Dominika Lewandowska, Maria Kalyna, Sean Chapman, Andrea Barta and John WS Brown)
Modificaton State-Specific Antibodies (Jordan B. Fishman, Olga Kelemen and Eric A. Berg)
Analysis of Alternative Splicing in Drosophila Genetic Mosaics (Shihuang Su, Diana O?Day, Shanzhi Wang and William Mattox)
MANIPULATION OF SPLICING EVENTS
Antisense Derivatives of U7 Small Nuclear RNA as Modulators of Pre-mRNA Splicing (Kathrin Meyer and Daniel Schümperli)
Screening for Alternative Splicing Modulators (Peter Stoilov)
Use of Oligonucleotides to Change Splicing (Annemieke Aartsma-Rus and Judith C.T. van Deutekom)
Changing Signals to the Spliceosome (Denise R. Cooper and Niketa A. Patel)
BIOINFORMATIC ANALYSIS OF SPLICING
Overview of Splicing Relevant Databases (Pierre de la Grange)
High Throughput Sequencing (Paolo Ribeca, Vincent Lacroix, Michael Sammeth and Roderic Guigó)
Identification of Splicing Factor Target Genes by High Throughput Sequencing
(Chaolin Zhang and Michael Q. Zhang)
Bioinformatic Analysis of Splicing Events (Zhaiyi Zhang and Stefan Stamm)
Analysis of Pre-mRNA Secondary Structures and Alternative Splicing (Michael Hiller)
Structure Prediction for Alternatively Spliced Proteins
(Lukasz Kozlowski, Jerzy Orlowski and Janusz M. Bujnicki)
Comparative Genomics Methods for the Prediction of Small RNA Binding Sites (Rym Kachouri-Lafond and Mihaela Zavolan)

Authors

Stefan Stamm University of Kentucky, Lexington, USA. Chris Smith University of Cambridge, UK. Reinhard Lührmann MPI for Biophysical Chemistry, Göttingen, Ge.