Preface.- Section 1: Site-directed integration of transgenes.- 1 Transgene site-specific integration: troubles and solutions.- 1.1 Introduction.- 1.2 Random integration and clonal dominance: reality or myth.- 1.3 Principal drawbacks of gene transfer integrative systems and solutions.- 1.4 Combining long-term expression and secure integration by specific locus targeting: old solutions to new perspectives.- 1.5 Conclusion.- 2: Designing non-viral targetd integrating vectors for genome enginnering in vertebrates.- 2.1. Introduction: Ideal integrating vectors and safe insertion sites.- 2.2. Design of random integrating vectors based on DNA transposons and associated-targeting strategy.- 2. 3. Site-specific recombinase-based integrating vectors.- 2. 4. Meganuclease-based vectors.- Section 2: Integration based on homologous recombination.- 3: Gene targeting and homologous recombination in Saccharomyces cerevisiae.- 3.1 Introduction.- 3.2 Transformation with linearized plasmids: targeted integration.- 3.3 Mechanism of targeted integration: a state of the art of homologous recombination.- 3.4 Conclusions and future directions.- 4: Eucaryotic homologous recombination in mammalian cells.- 4.1. Models and products of HR.- 4.2. Molecular mechanisms of the different steps of HR.- 4.3. HR is at the heart of the genetic stability-diversity-instability equilibrium. - 4.4. The importance of sister chromatids in the cell cycle for the maintenance of genome stability.- 4.5. Deregulation of HR and tumor predisposition.- 4.6. HR in molecular evolution: concerted evolution.- 4.7. Comments/considerations regarding optimization of targeted gene replacement. - 5 Engineered Zinc Finger Nucleases for Targeted Genome Editing .- 5.1 Introduction.- 5.2 Zinc Fingers: Structure and Function.- 5.3 Zinc Finger Fusion Proteins.- 5.4 Zinc Finger Engineering Platforms.- 5.5 Modified ZFN Architectures.- 5.6 Types of ZFN-Inducible Genome Modifications.- 5.7 Cell Line and Organismic Modifications using ZFNs.- 5.8 Off-Target Effects and Cytotoxicity.- 5.9 Conclusions.- 6: Engineered meganucleases for genome engineering purposes.- 6.1. Introduction.- 6.2. Historical considerations.- 6.3. The I-SceI success story.- 6.4. The challenge of specificity toward a chosen sequence.- 6.5. Cleavage versus Nickase activity.- 6.6. Customized meganucleases for genome engineering.- 6.7. Overview on TAL Effector Nuclease (TALEN).-6.8. Conclusions.- Section3: Integration based on Site-specific recombination.- 7: Cre/loxP, Flp/FRT systems and pluripotent stem cell lines.- 7.1. A historical perspective on Cre/loxP and Flp/FRT systems.- 7.2. Mechanisms of Cre/loxP and Flp/FRT recombination.- 7.3. Mutant lox and FRT sites.- 7.4. Pluripotent stem cells, an overview.- 7.5. Basic strategies for site-specific integration of transgenes via Cre/loxP and Flp/FRT systems.- 7.6 Delivery of recombinases into PSCs.- 7.7. Applications of Cre/loxP and Flp/FRT systems in the introduction of transgenes to PSCs.- 7.8. Technological improvements and future outlook.- 8: Site-specific recombination using C31 Integrase.- 8.1 Introduction.- 8.2 C31 Integrase: Mechanism of Integration and Optimization for Heterologous Organisms.- 8.3 Use of C31 in Heterologous Organisms.- 8.4 Therapeutic Uses of C31 Integrase.- 8.5 Use of C31 in Pluripotent Stem Cells 24.- 8.6 Safety of the C31 Integrase System 28.- 8.7 The Future of C31 Integrase: Combinatorial Usage With Other Recombinases.- 9: Modified transposases used for site-directed insertion of transgenes.- 9. 1 Introduction.- 9.2 Targeted transposition in bacteria.- 9.3 Targeted transposition in insects.- 9.4 Targeted transposition in zebrafish .- 9.5 Targeted transposition in mammalian cells.- 9.6 Conclusion-Discussion.- 10: Targeted Plasmid Integration into the Human Genome by Engineered Recombinases.- 10.1 Introduction.- 10.2 Nonviral methods for transgene integration.- 10.3 Transgene integration by site-specific recombinases.- 10
