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Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus

Inés G. Muñoz, Jesús Prieto, Sunita Subramanian, Javier Coloma, Pilar Redondo, Maider Villate, Nekane Merino, Marco Marenchino, Marco D'Abramo, Francesco L. Gervasio, Sylvestre Grizot, Fayza Daboussi (+9 others)
2010 Nucleic Acids Research  
This is the first time that an engineered meganuclease variant targets the human RAG1 locus by stimulating homologous recombination in human cell lines up to 265 bp away from the cleavage site.  ...  We have modified the homodimeric I-CreI endonuclease through protein engineering to target a specific DNA sequence within the human RAG1 gene.  ...  ACKNOWLEDGEMENTS The authors would like to thank the beamline staff at the ESRF and SLS for helpful advice during data collection.  ... 
doi:10.1093/nar/gkq801 pmid:20846960 pmcid:PMC3025557 fatcat:yspb3htegvbifc4xbggebvtu7y

Meganucleases and Other Tools for Targeted Genome Engineering: Perspectives and Challenges for Gene Therapy

George Silva, Laurent Poirot, Roman Galetto, Julianne Smith, Guillermo Montoya, Philippe Duchateau, Frederic Paques
2011 Current Gene Therapy  
While a new generation of viral vectors is in the process of replacing the classical gamma-retrovirus-based approach, a number of strategies have emerged based on non-viral vectorization and/or targeted  ...  Nuclease-based approaches, wherein an endonuclease is used to trigger site-specific genome editing, can significantly increase the percentage of targeted cells.  ...  Re-engineering meganuclease specificity: example of a custom meganuclease targeting a sequence from the human XPC gene. (a) Comparison of the starting and final targets.  ... 
doi:10.2174/156652311794520111 pmid:21182466 pmcid:PMC3267165 fatcat:xpcdrq73cragthw7kbnpttmgam

Identification of Genes Regulating Gene Targeting by a High-Throughput Screening Approach

Fabien Delacôte, Christophe Perez, Valérie Guyot, Catherine Mikonio, Pierrick Potrel, Jean-Pierre Cabaniols, Christophe Delenda, Frédéric Pâques, Philippe Duchateau
2011 Journal of Nucleic Acids  
We used this assay to explore a collection of siRNAs targeting 19,121 human genes. At the end of secondary screening, we had identified 64 genes for which knockdown affected nuclease-induced HGT.  ...  Homologous gene targeting (HGT) is a precise but inefficient process for genome engineering.  ...  For validation of the ability of the ATF7IP and EP300 siRNAs to increase HGT frequency at an endogenous locus in human cells, we used a meganuclease cleaving the human RAG1 locus described in a previous  ... 
doi:10.4061/2011/947212 pmid:21716659 pmcid:PMC3118287 fatcat:4nejp555kzernpapk5zb23bs3q

Meganucleases can restore the reading frame of a mutated dystrophin

P Chapdelaine, C Pichavant, J Rousseau, F Pâques, J P Tremblay
2010 Gene Therapy  
These experiments are thus a proof of principle that MGNs that are adequately engineered to target appropriate sequences in the human dystrophin gene should be able to restore the normal reading frame  ...  Meganucleases (MGNs) can be engineered to induce double-strand breaks (DSBs) at specific DNA sequences.  ...  Conflict of interest Dr Pâques is the scientific director of Cellectis Inc. Thus, his salary is obtained from that company and he has shares in that company.  ... 
doi:10.1038/gt.2010.26 pmid:20393509 fatcat:o7enqz3dmjgb5iskpcv7nft4tm

Comparison of the Feasibility, Efficiency, and Safety of Genome Editing Technologies

Nicolás González González Castro, Jan Bjelic, Gunya Malhotra, Cong Huang, Salman Hasan Alsaffar
2021 International Journal of Molecular Sciences  
Currently, no technology can be regarded as ideal or even applicable to every case as the context dictates the best approach for genetic modification within a target organism.  ...  In this review, we implement a four-pillar framework (context, feasibility, efficiency, and safety) to assess the main genome editing platforms, as a basis for rational decision-making by an expanding  ...  of RAG1 in 5.3% of transfected cells Plasmid in human 293H cells RAG1 MN (single- chain I-CreI variant) [25] Gene insertion for repairing RAG1 in up to 6% of transfected cells RAG1 MN (single  ... 
doi:10.3390/ijms221910355 pmid:34638696 fatcat:nvrlxxkbqbhbrhmhkdrrsxmjoi

Engineering altered protein–DNA recognition specificity

Adam J Bogdanove, Andrew Bohm, Jeffrey C Miller, Richard D Morgan, Barry L Stoddard
2018 Nucleic Acids Research  
The ease of re-engineering each system is related both to the modularity of the protein and the extent to which the proteins have evolved to be capable of readily modifying their recognition specificities  ...  Nevertheless, progress has been made in the redesign of protein-DNA specificity, much of it driven by the development of engineered enzymes for genome modification.  ...  the basis for the results of the engineering study described above.  ... 
doi:10.1093/nar/gky289 pmid:29718463 pmcid:PMC6007267 fatcat:zazdrfgoanagfby6yqvhydhzia

Gene Editing in Pluripotent Stem Cells and Their Derived Organoids

Hang Zhou, Yun Wang, Li-Ping Liu, Yu-Mei Li, Yun-Wen Zheng, Antonio C. Campos de Carvalho
2021 Stem Cells International  
Are the tools for rewriting the code of life a boon to humanity or a Pandora's box? These technologies raise concerns regarding ethical issues, unexpected mutations, viral infection, etc.  ...  The development of regenerative medicine technologies, regardless of whether it is PSCs or gene editing, is consistently met with controversy.  ...  Acknowledgments This research was supported partly by the National Natural Science Foundation of China (82070638 and 81770621), JSPS KAKENHI (18H02866), and the Natural Science Foundation of Jiangsu Province  ... 
doi:10.1155/2021/8130828 pmid:34887928 pmcid:PMC8651378 fatcat:g7kj3nfrwrfltd4qxmyalw7iny

Advances in Genome Editing and Application to the Generation of Genetically Modified Rat Models

Vanessa Chenouard, Séverine Remy, Laurent Tesson, Séverine Ménoret, Laure-Hélène Ouisse, Yacine Cherifi, Ignacio Anegon
2021 Frontiers in Genetics  
The objective of this review is to provide a comprehensive description of the advantages and potential of rat models for addressing specific scientific questions and to characterize the best genome-engineering  ...  Many genetically engineered rat models have emerged in the last two decades, and the advent of gene-specific nucleases has accelerated their generation in recent years.  ...  AUTHOR CONTRIBUTIONS All authors performed the bibliographic research and participated in writing the manuscript. IA planned the review and secured the funding.  ... 
doi:10.3389/fgene.2021.615491 pmid:33959146 pmcid:PMC8093876 fatcat:6rygmc2dq5gorfeyyjiugg4wgq

Recent Advances and Improvements in the Biosafety of Gene Therapy [chapter]

Jaichandran Sivalingam, Oi Lian
2011 Gene Therapy - Developments and Future Perspectives  
Thus far two engineered meganucleases cleaving unique genomic loci in the human XPC (Arnould et al., 2007) and Rag1 genes (Grizot et al., 2009 ) have been reported.  ...  However, they have been used to bind vector sequences bearing their recognition elements and, fused with other endogenous DBPs, can be engineered to recognise elements in the human genome (Ivics et al  ...  The aim of this book is to cover key aspects of existing problems in the field of development and future perspectives in gene therapy.  ... 
doi:10.5772/21733 fatcat:utqxetzf6vbphkgke3iyreqcd4

Cut and Paste - Using CRISPR/Cas9 to model RAG1 deficiency

Lisa Ott De Bruin, Luigi Notarangelo
2018 Zenodo  
The main aim of this thesis was to generate novel in vitro and in vivo models of RAG1 deficiency to study the mechanisms underlying the different RAG phenotypes.  ...  However, phenotypic variability remains even between patients with mutations that affect the same region of RAG1, showing the same residual RAG1 activity using in vitro models.  ...  Acknowledgments The authors thank K. Musunuru for his guidance in designing the gRNA to generate the Rag1-mutant mice and W. Yang and M.  ... 
doi:10.5281/zenodo.2625487 fatcat:4auhvifpincedcatl3ndxqdary

CRISPR to fix bad blood: a new tool in basic and clinical hematology

Elisa González-Romero, Cristina Martínez-Valiente, Cristian García-Ruiz, Rafael P. Vázquez-Manrique, José Cervera, Alejandra Sanjuan-Pla
2019 Haematologica  
Advances in genome engineering in the last decade, particularly in the development of programmable nucleases, have made it possible to edit the genomes of most cell types precisely and efficiently.  ...  We provide an overview of the applications of gene editing in experimental, preclinical and clinical hematology including interrogation of gene function, target identification and drug discovery and chimeric  ...  Thus, researchers keen to perform gene editing require only a basic knowledge of molecular biology to design a targeting system against a locus of choice.  ... 
doi:10.3324/haematol.2018.211359 pmid:30923099 pmcid:PMC6518885 fatcat:unq36nyb7vb4lnkshxoeyoofxq

Concerted nicking of donor and chromosomal acceptor DNA promotes homology-directed gene targeting in human cells

Manuel A. F. V. Gonçalves, Gijsbert P. van Nierop, Maarten Holkers, Antoine A. F. de Vries
2011 Nucleic Acids Research  
of the targeting vector.  ...  Here, to investigate the role of nicked DNA molecules as HR-initiating substrates in human somatic cells, we devised a homology-directed gene targeting system based on exogenous donor and chromosomal target  ...  ACKNOWLEDGEMENTS The authors thank Martijn Everts for PCR amplification and cloning of the p5 element.  ... 
doi:10.1093/nar/gkr1234 pmid:22189101 pmcid:PMC3333848 fatcat:emwm53oacfbhvlrwnkipmlemn4

Activation-Induced Cytidine Deaminase in Antibody Diversification and Chromosome Translocation [chapter]

Anna Gazumyan, Anne Bothmer, Isaac A. Klein, Michel C. Nussenzweig, Kevin M. McBride
2012 Advances in Cancer Research  
DNA damage, rearrangement and mutation of the human genome are the basis of carcinogenesis and thought to be avoided at all costs.  ...  Here we review the molecular basis of AID regulation, targeting, and initiation of CSR and SHM, as well as AID's role in generating chromosome translocations that contribute to lymphomagenesis.  ...  The two groups that simultaneously developed this method both engineered I-SceI meganuclease sites at the IgH or the c-myc locus.  ... 
doi:10.1016/b978-0-12-394280-7.00005-1 pmid:22429855 pmcid:PMC4353630 fatcat:f4hyre5wc5a3jcnnqyqnan5thq

Homing endonucleases from mobile group I introns: discovery to genome engineering

Barry L Stoddard
2014 Mobile DNA  
This combination of molecular functions is mutually advantageous: the endonuclease activity allows surrounding introns and inteins to act as invasive DNA elements, while the splicing activity allows the  ...  Several homing endonucleases have been completely redesigned and used for a variety of genome engineering applications.  ...  Acknowledgments The work conducted in the authors laboratory, and the preparation of this review, were supported by a research grant from the NIH (R01 GM49857).  ... 
doi:10.1186/1759-8753-5-7 pmid:24589358 pmcid:PMC3943268 fatcat:guvzcedoozglpngb3bsqb4vehe

Humanization of Immunodeficient Animals for the Modeling of Transplantation, Graft Versus Host Disease and Regenerative Medicine

George Adigbli, Séverine Ménoret, Amy R. Cross, Joanna Hester, Fadi Issa, Ignacio Anegon
2020 Transplantation  
The humanization of animals is a powerful tool for the exploration of human disease pathogenesis in biomedical research, as well as for the development of therapeutic interventions with enhanced translational  ...  These advances, together with ongoing developments in the incorporation of human transgenes and additional mutations in humanized mouse models, have expanded our opportunities to replicate aspects of human  ...  [64] [65] [66] This is supported by a recent study in which expression of full-length human BAFF from cDNA in the endogenous mouse locus did not improve maturation of human B cells in HIS mice. 67  ... 
doi:10.1097/tp.0000000000003177 pmid:32068660 pmcid:PMC7590965 fatcat:ddvzbordwrhjdi7sw2jzbmsxyy
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