Part I: Introductory Chapters

1. The Pre-mRNA Splicing Reaction

Somsakul Wongpalee and Shalini Sharma

2. Diversity and Evolution of Spliceosomal Systems

Scott William Roy and Manuel Irimia

3. Mechanisms of Spliceosomal Assembly

Ni-ting Chiou and Kristen W. Lynch

4. Alternative Pre-mRNA Splicing

Stacey D. Wagner and J. Andrew Berglund

5. Regulation of Alternative Pre-mRNA Splicing

Miguel B. Coelho and Christopher W.J. Smith

6. Introduction to Co-Transcriptional RNA Splicing

Evan C. Merkhofer, Peter Hu, and Tracy L. Johnson

7. Chromatin and Splicing

Nazmul Haque and Shalini Oberdoerffer

Part II: Methods Chapters

8. Preparation of Splicing Competent Nuclear Extracts

Chiu-Ho T. Webb and Klemens J. Hertel

9. Preparation of Yeast Whole Cell Splicing Extract

Elizabeth A. Dunn and Stephen D. Rader

10. Efficient Splinted Ligation of Synthetic RNA Using RNA Ligase

Martha R. Stark and Stephen D. Rader

11. In Vitro Assay of Pre-mRNA Splicing in Mammalian Nuclear Extract

Maliheh Movassat, William F. Mueller, and Klemens J. Hertel

12. Kinetic Analysis of In Vitro Pre-mRNA Splicing in HeLa Nuclear Extract

William F. Mueller and Klemens J. Hertel

13. In Vitro Systems for Coupling RNAP II Transcription to Splicing and Polyadenylation

Eric G. Folco and Robin Reed

14. Isolation and Accumulation of Spliceosomal Assembly Intermediates

Janine O. Ilagan and Melissa S. Jurica

15. Complementation of U4 snRNA in S. cerevisiae Splicing Extracts for Biochemical Studies of snRNP Assembly and Function

Martha R. Stark and Stephen D. Rader

16. Expression and Purification of Splicing Proteins from Mammalian Cells

Eric Allemand and Michelle L. Hastings

17. Single Molecule Approaches for Studying Spliceosome Assembly and Catalysis

Eric G. Anderson and Aaron A. Hoskins

18. Cell-Based Splicing of Minigenes

Sarah A. Smith and Kristen W. Lynch

19. Quantifying the Ratio of Spliceosome Components Assembled on Pre-mRNA

Noa Neufeld, Yehuda Brody, and Yaron Shav-Tal

20. Antisense Methods to Modulate Pre-mRNA Splicing

Joonbae Seo, Eric W. Ottesen, and Ravindra N. Singh

21. Using Yeast Genetics to Study Splicing Mechanisms

Munshi Azad Hossain and Tracy L. Johnson

22. Medium Throughput Analysis of Alternative Splicing by Fluorescently Labeled RT-PCR

Ryan Percifield, Daniel Murphy, and Peter Stoilov

23. Chromatin Immunoprecipitation Approaches to Determine Co-Transcriptional Nature of Splicing

Nicole I. Bieberstein, Korinna Straube, and Karla M. Neugebauer

24. Computational Approaches to Mine Publicly Available Databases

Rodger B. Voelker, William A. Cresko, and J. Andrew Berglund

25. Approaches to Link RNA Secondary Structures with Splicing Regulation

Mireya Plass and Eduardo Eyras

26. Methods to Study Splicing from High-Throughput RNA Sequencing Data

Gael P. Alamancos, Eneritz Agirre, and Eduardo Eyras

27. Global Protein-RNA Interaction Mapping at Single Nucleotide Resolution by iCLIP-Seq

Chengguo Yao, Lingjie Weng, and Yongsheng Shi

28. Predicting Alternative Splicing

Yoseph Barash and Jorge Vaquero Garcia