Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
Includes supplementary material: sn.pub/extras
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.
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
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.
RecTEPsy Mediated Recombineering in Pseudomonas syringae.- Genome Manipulations with Bacterial Recombineering and Site-Specific Integration in Drosophila.- Multiple Genetic Manipulations of DT40 Cell Line.- Gene Targeting of Human Pluripotent Stem Cells by Homologous Recombination.- Methods for the Assessment of ssODN-Mediated Gene Correction Frequencies in Muscle Cells.- Small Fragment Homologous Replacement (SFHR): Sequence-Specific Modification of Fenomic DNA in Eukaryotic Cells by Small DNA Fragments.- Preparation and Application of Triple Helix Forming Oligonucleotides and Single Strand Oligonucleotide Donors for Gene Correction.- Triplex-Mediated Genome Targeting and Editing.- Targeting piggyBac Transposon Integrations in the Human Genome.- Gene Targeting in Human Induced Pluripotent Stem Cells with Adenoviral Vectors.- Enhanced Gene Targeting of Adult and Pluripotent Stem Cells Using Evolved Adeno-Associated Virus.- Lentiviral Vectors Encoding Zinc-Finger Nucleases Specific for the Model Target Locus HPRT1.- Designing and Testing the Activities of TAL Effector Nucleases.- A Bacterial One-Hybrid System to Isolate Homing Endonuclease Variants with Altered DNA Target Specificities.- Design and Analysis of Site-Specific Single-Strand Nicking Endonucleases for Gene Correction.- CRISPR-Cas Mediated Targeted Genome Editing in Human Cells.- RNA-Guided Genome Editing of Mammalian Cells.- Nuclease-Mediated Double Strand Break (DSB) Enhancement of Small Fragment Homologous Recombination (SFHR) Gene Modification in Human Induced Pluripotent Stem Cells (hiPSCs).- AAV-Mediated Gene Editing via Double-Strand Break Repair.- Genetic Modification Stimulated by the Induction of a Site-Specific Break Distant from the Locus of Correction in Haploid and Diploid Yeast Saccharomyces cerevisiae.- A Southern Blot Protocol to Detect Chimeric Nuclease-Mediated Gene Repair.- High-Throughput Cellular Screening of Engineered Nuclease Activity Using the Single-Strand Annealing Assay and Luciferase Reporter.- An Unbiased Method for Detection of Genome-Wide Off Target Effects in Cell Lines Treated with Zinc Finger Nucleases.- Identification of Off-Target Cleavage Sites of Zinc Finger Nucleases and TAL Effector Nucleases Using Predictive Models.- Method for Retinal Gene Repair in Neonatal Mouse.- In utero Delivery of Oligodeoxynucleotides for Gene Correction.- Portal Vein Delivery of Viral Vectors for Gene Therapy for Hemophilia.- Gene Correction of Induced Pluripotent Stem Cells Derived from a Murine Model of X-Linked Chronic Granulomatous Disorder.- Efficient Transduction of Hematopoietic Stem Cells and its Potential for Gene Correction of Hematopoietic Diseases.
Inhaltsverzeichnis
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
Klappentext
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.nAuthoritative and easily accessible, Gene Correction: Methods and Protocols seeks to serve scientists of all backgrounds interested in the area of gene targeting/recombination/therapy.
Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
Includes supplementary material: sn.pub/extras
