Exon Skipping Methods and Protocols

“Next generation” sequencing techniques allow for more detailed analysis of exons and introns in multiple genes at the same time. This will reveal many mutations that potentially lead to exon skipping. To functionally test these a lot can be achieved with a limited set of protocols, while for the intentional induction of exon skipping different tools and target genes are involved and the translational path from in vitro splicing to in vivo tests in animal models requiring a more extensive set of protocols. Exon Skipping: Methods and Protocols provides scientist with a comprehensive guide to many of the methods and techniques used for exon skipping, such as methods on how to discriminate “real polymorphisms” from mutations that affect splicing. 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 key tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical Exon Skipping: Methods and Protocols seeks to aid scientists in the continuing study of exon skipping.

Part I: Mutations

1.   DNA Diagnostics and Exon Skipping

Umasuthan Srirangalingam and Shern L. Chew

2. Bioinformatics and Mutations Leading to Exon Skipping

F.O. Desmet and C. Béroud

3. Minigenes to Confirm Exon Skipping Mutations

Lourdes R. Desviat, Belén Pérez & Magdalena Ugarte

4.Analysis and Interpretation of RNA Splicing Alterations in Genes Involved in Genetic Disorders

Maaike P.G. Vreeswijk and Heleen M. van der Klift

5. Exon Skipping Mutations in Neurofibromatosis

Emanuele Buratti and Diana Baralle

Part II: Tools to Induce Exon Skipping

6. Overview on Applications of Antisense-mediated Exon Skipping

Willeke van Roon-Mom and Annemieke Aartsma-Rus

7. Overview on DMD Exon Skipping

Annemieke Aartsma-Rus

8. Overview on AON Design

Annemieke Aartsma-Rus

9. Optimizing RNA/ENA Chimeric Antisense Oligonucleotides Using in vitro Splicing

Yasuhiro Takeshima, Mariko Yagi, Masafumi Matsuo

10. Optimizing Antisense Oligonucleotides using Phosphorodiamidate Morpholino Oligomers

Linda J Popplewell, Alberto Malerba, and George Dickson

11. Optimizing Splice Switching Oligomer Sequences using 2’-O-methyl Phosphorothioate Chemistry

Carl Adkin, Sue Fletcher and Steve D Wilton

12. Exon Skipping Quantification by Real Time PCR

Alessandra Ferlini and Paola Rimessi

13. Antisense-mediated Exon Skipping to Shift Alternative Splicing to Treat Cancer

Jing Wan

14. Antisense-mediated Exon Skipping to Generate Soluble Receptors

A. Seda Yilmaz-Elis and J. Sjef Verbeek

15. Antisense-mediated Exon Skipping to Reframe Transcripts

Sandrina Turczynski, Matthias Titeux, Nathalie Pironon^, and Alain Hovnanian

16. U1 snRNA as an Effective Vector for Stable Expression of Antisense Molecules andfor the Inhibition of the Splicing Reaction

Martone Julie, De Angelis Fernanda Gabriella and Bozzoni Irene

17. Engineering U7snRNA Gene to Reframe Transcripts

Aurélie Goyenvalle

18. Dynamic Fluorescent and Luminescent Reporters for Cell Based Splicing Screens

Claude C. Warzecha, Ruben Hovhannisyan, and Russ P. Carstens

19. Antisense-mediated Exon Skipping to Induce Gene Knockdown

Petra Disterer and Bernard Khoo

20. Antisense-mediated Exon Inclusion

Yimin Hua and Adrian R. Krainer

21. Antisense Genes to Induce Exon Inclusion

22. Using Mini-genes to Identify Factors that Modulate Alternative Splicing

Robert Morse, Adrian G. Todd and Philip J. Young

Part III: Delivery

23. Overview of Alternative Oligonucleotide Chemistries for Exon Skipping

Amer F. Saleh, Andrey A. Arzumanov and Michael J. Gait

24. Identification of Peptides for Tissue Specific Delivery

Hans Heemskerk

^{25. Systemic Delivery of Antisense Oligomer in Animal Models and its Implications for Treating DMD}

^{Qi Long Lu and Bo Wu}

26. Cell-penetrating Peptides Enhance Systemic Delivery of Antisense Morpholino Oligomers

Hong M Moulton

27. Optimizing Tissue-specific Antisense Oligonucleotide-peptide Conjugates

Corinne A Betts, Suzan M Hammond, Hai-fang Yin, and Matthew JA Wood