Reviews
Description
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
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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
Reviews