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|a Front Matter -- Theory. Splicing in the RNA World / Emanuele Buratti, Maurizio Romano, Francisco E Baralle -- RNPs, Small RNAs, and miRNAs / Michaela Beitzinger, Gunter Meister -- RNA Elements Involved in Splicing / William F Mueller, Klemens J Hertel -- A Structural Biology Perspective of Proteins Involved in Splicing Regulation / Antoine Cľry, Fřďric H-T Allain -- The Spliceosome in Constitutive Splicing / Patrizia Fabrizio, Reinhard Luhrmann -- The Use of to Study the Mechanism of pre-mRNA Splicing / Brian C Rymond -- Challenges in Plant Alternative Splicing / Andrea Barta, Yamile Marquez, John W S Brown -- Alternative Splice Site Selection / Miguel B Coelho, Christopher W J Smith -- Integration of Splicing with Nuclear and Cellular Events / Aparna K Sapra, Karla Neugebauer -- Splicing and Disease / Emanuele Buratti, Francisco E Baralle -- From Bedside to Bench: How to Analyze a Splicing Mutation / Marco Baralle, Diana Baralle -- Basic Methods. Analysis of Common Splicing Problems / Stefan Stamm -- Ultracentrifugation in the Analysis and Purification of Spliceosomes Assembled / Klaus Hartmuth, Maria A van Santen, Reinhard Luhrmann -- Chemical Synthesis of RNA / Claudia H̲bartner -- RNA Interference (siRNA, shRNA) / Daphne S Cabianca, Davide Gabellini -- Expression and Purification of Splicing Proteins / James Sťvenin, Cyril F Bourgeois -- Detection of RNA-Protein Complexes by Electrophoretic Mobility Shift Assay / Manli Shen, Michael G Fried -- Functional Analysis of Large Exonic Sequences Through Iterative Selection / Ravindra N Singh, Natalia N Singh -- Identification of Splicing cis-Elements Through an Ultra-Refined Antisense Microwalk / Natalia N Singh, Joonbae Seo, Ravindra N Singh -- Genomic SELEX to Identify RNA Targets of Plant RNA-Binding Proteins / Olga Bannikova, Maria Kalyna, Andrea Barta -- Detection of Splicing Events. Quantification of Alternative Splice Variants / Miriam Llorian, Christopher W J Smith -- High-Throughput Analysis of Alternative Splicing by RT-PCR / Roscoe Klinck, Benoit Chabot, 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, John WS Brown -- Array Analysis / Pierre de la Grange -- The CLIP Method to Study Protein-RNA Interactions in Intact Cells and Tissues / James Tollervey, Jernej Ule -- RNA₆Protein Crosslinking and Immunoprecipitation (CLIP) in / Branislav Kusenda, 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, Masatoshi Hagiwara -- Analysis of Splicing . The Preparation of HeLa Cell Nuclear Extracts / Klaus Hartmuth, Maria A van Santen, Tanja R̲sel, Berthold Kastner, Reinhard Luhrmann -- Splicing Assays / Akila Mayeda, Adrian R Krainer -- Assembly and Isolation of Spliceosomal Complexes / Klaus Hartmuth, Maria A van Santen, Peter Odenw̃lder, Reinhard Luhrmann -- Analysis of Site-Specific RNA-Protein Interactions / Nathalie Marmier-Gourrier, Audrey Vautrin, Christiane Branlant, Isabelle Behm-Ansmant -- Immunoprecipitation and Pull-Down of Nuclear Proteins / Natalya Benderska, Chiranthani Sumanasekera, Stefan Stamm -- Analysis of Protein ( -RNA) Complexes by (Quantitative) Mass Spectrometric Analysis / Carla Schmidt, Henning Urlaub -- Fast Cloning of Splicing Reporter Minigenes / Zhaiyi Zhang, Amit Khanna, Stefan Stamm -- Analysis of Splicing Assays / Isabel C L̤pez-Mej̕a, Jamal Tazi -- Coupled Promoter Splicing Systems / Manuel J Munoz, Manuel de la Mata, Alberto R Kornblihtt -- Stable Cell Lines with Splicing Reporters / Christian Kroun Damgaard, Soren Lykke-Andersen, J̜rgen 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, Karla M Neugebauer -- Yeast Genetics to Investigate the Function of Core Pre-mRNA Splicing Factors / Raymond T O Keefe, Jean D Beggs -- Analysis of HIV-1 RNA Splicing / Simon Duffy, Alan Cochrane -- Analysis of Plant Intron Splicing / Craig G Simpson, Michele Liney, Diane Davidson, Dominika Lewandowska, Maria Kalyna, Sean Chapman, Andrea Barta, John W S Brown -- Modification State-Specific Antibodies / Jordan B Fishman, Olga Kelemen, Eric A Berg -- Analysis of Alternative Splicing in Genetic Mosaics / Shihuang Su, Diana O'Day, Shanzhi Wang, William Mattox -- Manipulation of Splicing Events. Antisense Derivatives of U7 Small Nuclear RNA as Modulators of Pre-mRNA Splicing / Kathrin Meyer, Daniel Schumperli -- Screening for Alternative Splicing Modulators / Peter Stoilov -- Use of Oligonucleotides to Change Splicing / Annemieke Aartsma-Rus, Judith C T van Deutekom -- Changing Signals to the Spliceosome / Denise R Cooper, Niketa A Patel -- Bioinformatic Analysis of Splicing. Overview of Splicing Relevant Databases / Pierre de la Grange -- Analysis of RNA Transcripts by High-Throughput RNA Sequencing / Paolo Ribeca, Vincent Lacroix, Michael Sammeth, Roderic Guig̤ -- Identification of Splicing Factor Target Genes by High-Throughput Sequencing / Chaolin Zhang, Michael Q Zhang -- Bioinformatic Analysis of Splicing Events / Zhaiyi Zhang, Stefan Stamm -- Analysis of Pre-mRNA Secondary Structures and Alternative Splicing / Michael Hiller -- Structure Prediction for Alternatively Spliced Proteins / Lukasz Kozlowski, Jerzy Orlowski, Janusz M Bujnicki -- Comparative Genomics Methods for the Prediction of Small RNA-Binding Sites / Rym Kachouri-Lafond, Mihaela Zavolan -- Appendix A1: Yeast Nomenclature Systematic Open Reading Frame (ORF) and Other Genetic Designations -- Appendix A2: Glossary -- Index.
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