Gene Correction: Methods and Protocols

ISBN-13: 9781627037600 / Angielski / Twarda / 2014 / 463 str.

Francesca Storici

Opis

Gene correction is a technology that gives us the tools for both repairing and mutating DNA, for discovering gene functions and for engineering new genetic variants. Gene Correction: Methods and Protocols provides a user friendly, detailed and up-to-date collection of strategies and methodologies utilized for generating specific sequence changes in the DNA of cells in the laboratory, while also tackling the major problems that the field of gene correction faces. This volume brings together many experts in the field of gene correction to disclose a wide and varied array of specific gene correction protocols for engineering mutations in DNA, for delivering correcting DNA to target cells, and for improving the accuracy and safety of the gene correction process. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls.Authoritative and easily accessible, Gene Correction: Methods and Protocols seeks to serve scientists of all backgrounds interested in the area of gene targeting/recombination/therapy.

Spis treści

Part I. Approaches for Gene Correction from Bacteria to Human Cells

 

1. RecTEPsy Mediated Recombineering in Pseudomonas syringae

            Bryan Swingle

 

2. Genome Manipulations with Bacterial Recombineering and Site-Specific Integration in Drosophila

Yi Zhang, William Schreiner, and Yikang S. Rong

 

3. Multiple Genetic Manipulations of DT40 Cell Line

Akira Motegi and Minoru Takata

 

4. Gene Targeting of Human Pluripotent Stem Cells by Homologous Recombination

Sara E. Howden and James A. Thomson

 

Part II. Gene Correction Tools Using Non-Viral or Viral Systems

 

5. Methods for the Assessment of ssODN-Mediated Gene Correction Frequencies in Muscle Cells

Carmen Bertoni

 

6. Small Fragment Homologous Replacement (SFHR): Sequence-Specific Modification of Fenomic DNA in Eukaryotic Cells by Small DNA Fragments

Andrea Luchetti, Arianna Malgieri, and Federica Sangiuolo

 

7. Preparation and Application of Triple Helix Forming Oligonucleotides and Single Strand Oligonucleotide Donors for Gene Correction

Md. Rowshon Alam, Arun Kalliat Thazhathveetil, Hong Li and Michael M Seidman

 

8. Triplex-Mediated Genome Targeting and Editing

Faisal Reza and Peter M. Glazer

 

9. Targeting piggyBac Transposon Integrations in the Human Genome

Daniel L. Galvan, Claudia S. Kettlun, and Matthew H. Wilson

 

10. Gene Targeting in Human Induced Pluripotent Stem Cells with Adenoviral Vectors

Kohnosuke Mitani

 

11. Enhanced Gene Targeting of Adult and Pluripotent Stem Cells Using Evolved Adeno-Associated Virus

Melissa A. Bartel and David V. Schaffer

 

12. Lentiviral Vectors Encoding Zinc-Finger Nucleases Specific for the Model Target Locus HPRT1

Laetitia P.L. Pelascini and Manuel A.F.V. Gonçalves

 

Part III. Breaking the DNA to Stimulate Gene Correction: Nuclease Design, in vivo Test, Efficacy, and Off-Target Effect

 

13. Designing and Testing the Activities of TAL Effector Nucleases

Yanni Lin, Thomas J. Cradick, and Gang Bao

 

14. A Bacterial One-Hybrid System to Isolate Homing Endonuclease Variants with Altered DNA Target Specificities

Rakesh Joshi and Frederick S. Gimble

 

15. Design and Analysis of Site-Specific Single-Strand Nicking Endonucleases for Gene Correction

Michael J. Metzger and Michael T. Certo

 

16. CRISPR-Cas Mediated Targeted Genome Editing in Human Cells

Luhan Yang, Prashant Mali, Caroline Kim-Kiselak, and George Church

 

17. RNA-Guided Genome Editing of Mammalian Cells

Neena K. Pyzocha, F. Ann Ran, Patrick D. Hsu, and Feng Zhang

 

18. Nuclease-Mediated Double Strand Break (DSB) Enhancement of Small Fragment Homologous Recombination (SFHR) Gene Modification in Human Induced Pluripotent Stem Cells (hiPSCs)

R Geoffrey Sargent, Shingo Suzuki, and Dieter C. Gruenert

 

19. AAV-Mediated Gene Editing via Double-Strand Break Repair

Matthew L. Hirsch and R. Jude Samulski

 

20. Genetic Modification Stimulated by the Induction of a Site-Specific Break Distant from the Locus of Correction in Haploid and Diploid Yeast Saccharomyces cerevisiae

Samantha Stuckey and Francesca Storici

 

21. A Southern Blot Protocol to Detect Chimeric Nuclease-Mediated Gene Repair

Céline J. Rocca, Hayder H. Abdul-Razak, Michael C. Holmes, Philip D. Gregory and Rafael J. Yáñez-Muñoz

 

22. High-Throughput Cellular Screening of Engineered Nuclease Activity Using the Single-Strand Annealing Assay and Luciferase Reporter

Thomas J. Cradick, Christopher J. Antico, and Gang Bao

 

23. An Unbiased Method for Detection of Genome-Wide Off Target Effects in Cell Lines Treated with Zinc Finger Nucleases

Cory R. Lindsay and David B. Roth

 

24. Identification of Off-Target Cleavage Sites of Zinc Finger Nucleases and TAL Effector Nucleases Using Predictive Models

Eli J. Fine, Thomas J. Cradick and Gang Bao

  

Part IV. Gene Correction Approaches for Specific Disease Models

 

25. Method for Retinal Gene Repair in Neonatal Mouse

Marilyn Dernigoghossian, Arthur Krigel, Francine Behar-Cohen, and Charlotte Andrieu-Soler

 

26. In utero Delivery of Oligodeoxynucleotides for Gene Correction

Lingzhi Cai, Bhanu Muni Koppanati, Carmen Bertoni, and Paula R. Clemens

 

27. Portal Vein Delivery of Viral Vectors for Gene Therapy for Hemophilia

Alexandra Sherman, Alexander Schlachterman, Mario Cooper, Elizabeth P Merricks, Robin A. Raymer, Dwight A. Bellinger, Roland W. Herzog, and Timothy C. Nichols

 

28. Gene Correction of Induced Pluripotent Stem Cells Derived from a Murine Model of X-Linked Chronic Granulomatous Disorder

Sayandip Mukherjee and Adrian J. Thrasher

 

29. Efficient Transduction of Hematopoietic Stem Cells and its Potential for Gene Correction of Hematopoietic Diseases

Dolly Deena Thomas and Gustavo Mostoslavsky