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  • 1
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    Precise genome modification in the crop species Zea mays using zinc-finger nucleases (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-05-01
    Description: Agricultural biotechnology is limited by the inefficiencies of conventional random mutagenesis and transgenesis. Because targeted genome modification in plants has been intractable, plant trait engineering remains a laborious, time-consuming and unpredictable undertaking. Here we report a broadly applicable, versatile solution to this problem: the use of designed zinc-finger nucleases (ZFNs) that induce a double-stranded break at their target locus. We describe the use of ZFNs to modify endogenous loci in plants of the crop species Zea mays. We show that simultaneous expression of ZFNs and delivery of a simple heterologous donor molecule leads to precise targeted addition of an herbicide-tolerance gene at the intended locus in a significant number of isolated events. ZFN-modified maize plants faithfully transmit these genetic changes to the next generation. Insertional disruption of one target locus, IPK1, results in both herbicide tolerance and the expected alteration of the inositol phosphate profile in developing seeds. ZFNs can be used in any plant species amenable to DNA delivery; our results therefore establish a new strategy for plant genetic manipulation in basic science and agricultural applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shukla, Vipula K -- Doyon, Yannick -- Miller, Jeffrey C -- DeKelver, Russell C -- Moehle, Erica A -- Worden, Sarah E -- Mitchell, Jon C -- Arnold, Nicole L -- Gopalan, Sunita -- Meng, Xiangdong -- Choi, Vivian M -- Rock, Jeremy M -- Wu, Ying-Ying -- Katibah, George E -- Zhifang, Gao -- McCaskill, David -- Simpson, Matthew A -- Blakeslee, Beth -- Greenwalt, Scott A -- Butler, Holly J -- Hinkley, Sarah J -- Zhang, Lei -- Rebar, Edward J -- Gregory, Philip D -- Urnov, Fyodor D -- England -- Nature. 2009 May 21;459(7245):437-41. doi: 10.1038/nature07992. Epub 2009 Apr 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Dow AgroSciences, 9330 Zionsville Road, Indianapolis, Indiana 46268, USA. vkshukla@dow.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19404259" target="_blank"〉PubMed〈/a〉
    Keywords: Biotechnology/*methods ; Deoxyribonucleases/*chemistry/genetics/*metabolism ; Food, Genetically Modified ; Gene Targeting/*methods ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Herbicide Resistance/genetics ; Herbicides/pharmacology ; Heredity ; Inositol Phosphates/metabolism ; Mutagenesis, Site-Directed/methods ; Plants, Genetically Modified ; Recombination, Genetic/genetics ; Reproducibility of Results ; Zea mays/*genetics ; *Zinc Fingers
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Knockout rats via embryo microinjection of zinc-finger nucleases (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-07-25
    Description: The toolbox of rat genetics currently lacks the ability to introduce site-directed, heritable mutations into the genome to create knockout animals. By using engineered zinc-finger nucleases (ZFNs) designed to target an integrated reporter and two endogenous rat genes, Immunoglobulin M (IgM) and Rab38, we demonstrate that a single injection of DNA or messenger RNA encoding ZFNs into the one-cell rat embryo leads to a high frequency of animals carrying 25 to 100% disruption at the target locus. These mutations are faithfully and efficiently transmitted through the germline. Our data demonstrate the feasibility of targeted gene disruption in multiple rat strains within 4 months time, paving the way to a humanized monoclonal antibody platform and additional human disease models.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2831805/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2831805/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Geurts, Aron M -- Cost, Gregory J -- Freyvert, Yevgeniy -- Zeitler, Bryan -- Miller, Jeffrey C -- Choi, Vivian M -- Jenkins, Shirin S -- Wood, Adam -- Cui, Xiaoxia -- Meng, Xiangdong -- Vincent, Anna -- Lam, Stephen -- Michalkiewicz, Mieczyslaw -- Schilling, Rebecca -- Foeckler, Jamie -- Kalloway, Shawn -- Weiler, Hartmut -- Menoret, Severine -- Anegon, Ignacio -- Davis, Gregory D -- Zhang, Lei -- Rebar, Edward J -- Gregory, Philip D -- Urnov, Fyodor D -- Jacob, Howard J -- Buelow, Roland -- 5P01HL082798-03/HL/NHLBI NIH HHS/ -- 5U01HL066579-08/HL/NHLBI NIH HHS/ -- P01 HL082798/HL/NHLBI NIH HHS/ -- P01 HL082798-03/HL/NHLBI NIH HHS/ -- U01 HL066579/HL/NHLBI NIH HHS/ -- U01 HL066579-08/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2009 Jul 24;325(5939):433. doi: 10.1126/science.1172447.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 52336, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19628861" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Dna ; Embryo, Mammalian ; Endodeoxyribonucleases/genetics/*metabolism ; Feasibility Studies ; Female ; *Gene Knockout Techniques ; Green Fluorescent Proteins ; Immunoglobulin M/*genetics ; Male ; *Microinjections ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; RNA, Messenger ; Rats ; *Zinc Fingers/genetics ; rab GTP-Binding Proteins/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Translating dosage compensation to trisomy 21 (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-07-19
    Description: Down's syndrome is a common disorder with enormous medical and social costs, caused by trisomy for chromosome 21. We tested the concept that gene imbalance across an extra chromosome can be de facto corrected by manipulating a single gene, XIST (the X-inactivation gene). Using genome editing with zinc finger nucleases, we inserted a large, inducible XIST transgene into the DYRK1A locus on chromosome 21, in Down's syndrome pluripotent stem cells. The XIST non-coding RNA coats chromosome 21 and triggers stable heterochromatin modifications, chromosome-wide transcriptional silencing and DNA methylation to form a 'chromosome 21 Barr body'. This provides a model to study human chromosome inactivation and creates a system to investigate genomic expression changes and cellular pathologies of trisomy 21, free from genetic and epigenetic noise. Notably, deficits in proliferation and neural rosette formation are rapidly reversed upon silencing one chromosome 21. Successful trisomy silencing in vitro also surmounts the major first step towards potential development of 'chromosome therapy'.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848249/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848249/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiang, Jun -- Jing, Yuanchun -- Cost, Gregory J -- Chiang, Jen-Chieh -- Kolpa, Heather J -- Cotton, Allison M -- Carone, Dawn M -- Carone, Benjamin R -- Shivak, David A -- Guschin, Dmitry Y -- Pearl, Jocelynn R -- Rebar, Edward J -- Byron, Meg -- Gregory, Philip D -- Brown, Carolyn J -- Urnov, Fyodor D -- Hall, Lisa L -- Lawrence, Jeanne B -- 1F32CA154086/CA/NCI NIH HHS/ -- 2T32HD007439/HD/NICHD NIH HHS/ -- F32 CA154086/CA/NCI NIH HHS/ -- GM053234/GM/NIGMS NIH HHS/ -- GM085548/GM/NIGMS NIH HHS/ -- GM096400 RC4/GM/NIGMS NIH HHS/ -- MOP-13680/Canadian Institutes of Health Research/Canada -- R01 GM053234/GM/NIGMS NIH HHS/ -- R01 GM085548/GM/NIGMS NIH HHS/ -- RC4 GM096400/GM/NIGMS NIH HHS/ -- T32 HD007439/HD/NICHD NIH HHS/ -- England -- Nature. 2013 Aug 15;500(7462):296-300. doi: 10.1038/nature12394. Epub 2013 Jul 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23863942" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cell Proliferation ; Chromosomes, Human, Pair 21/*genetics ; DNA Methylation ; *Dosage Compensation, Genetic ; Down Syndrome/*genetics/therapy ; Gene Silencing ; Humans ; Induced Pluripotent Stem Cells ; Male ; Mice ; Mutagenesis, Insertional ; Neurogenesis ; RNA, Long Noncoding/genetics/*metabolism ; Sex Chromatin/genetics ; X Chromosome Inactivation/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    In vivo genome editing restores haemostasis in a mouse model of haemophilia (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-06-28
    Description: Editing of the human genome to correct disease-causing mutations is a promising approach for the treatment of genetic disorders. Genome editing improves on simple gene-replacement strategies by effecting in situ correction of a mutant gene, thus restoring normal gene function under the control of endogenous regulatory elements and reducing risks associated with random insertion into the genome. Gene-specific targeting has historically been limited to mouse embryonic stem cells. The development of zinc finger nucleases (ZFNs) has permitted efficient genome editing in transformed and primary cells that were previously thought to be intractable to such genetic manipulation. In vitro, ZFNs have been shown to promote efficient genome editing via homology-directed repair by inducing a site-specific double-strand break (DSB) at a target locus, but it is unclear whether ZFNs can induce DSBs and stimulate genome editing at a clinically meaningful level in vivo. Here we show that ZFNs are able to induce DSBs efficiently when delivered directly to mouse liver and that, when co-delivered with an appropriately designed gene-targeting vector, they can stimulate gene replacement through both homology-directed and homology-independent targeted gene insertion at the ZFN-specified locus. The level of gene targeting achieved was sufficient to correct the prolonged clotting times in a mouse model of haemophilia B, and remained persistent after induced liver regeneration. Thus, ZFN-driven gene correction can be achieved in vivo, raising the possibility of genome editing as a viable strategy for the treatment of genetic disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152293/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3152293/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Hojun -- Haurigot, Virginia -- Doyon, Yannick -- Li, Tianjian -- Wong, Sunnie Y -- Bhagwat, Anand S -- Malani, Nirav -- Anguela, Xavier M -- Sharma, Rajiv -- Ivanciu, Lacramiora -- Murphy, Samuel L -- Finn, Jonathan D -- Khazi, Fayaz R -- Zhou, Shangzhen -- Paschon, David E -- Rebar, Edward J -- Bushman, Frederic D -- Gregory, Philip D -- Holmes, Michael C -- High, Katherine A -- P01 HL064190/HL/NHLBI NIH HHS/ -- P01 HL064190-11A1/HL/NHLBI NIH HHS/ -- T32 HL007150/HL/NHLBI NIH HHS/ -- T32 HL007150-35/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Jun 26;475(7355):217-21. doi: 10.1038/nature10177.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Hematology, CTRB 5000, Children's Hospital of Philadelphia, 3501 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21706032" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Cell Line, Tumor ; DNA Breaks, Double-Stranded ; DNA Repair/*genetics ; *Disease Models, Animal ; Endonucleases/chemistry/genetics/metabolism ; Exons/genetics ; Factor IX/analysis/genetics ; Gene Targeting/*methods ; Genetic Therapy/*methods ; Genetic Vectors/genetics ; Genome/*genetics ; HEK293 Cells ; Hemophilia B/*genetics/physiopathology ; *Hemostasis ; Humans ; Introns/genetics ; Liver/metabolism ; Liver Regeneration ; Mice ; Mice, Inbred C57BL ; Mutation/genetics ; Phenotype ; Sequence Homology ; Zinc Fingers
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    Zinc finger phage: affinity selection of fingers with new DNA-binding specificities (1994)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1994-02-04
    Description: A phage display system was developed and used to select zinc finger proteins with altered DNA-binding specificities. The three zinc fingers of the Zif268 protein were expressed on the surface of filamentous phage, and a library of variants was prepared by randomizing critical amino acids in the first zinc finger. Affinity selections, using DNA sites with base changes in the region recognized by the first finger, yielded Zif268 variants that bound tightly and specifically to the new sites. This phage system provides a tool for the study of protein-DNA interactions and may offer a general method for selecting zinc finger proteins that recognize desired target sites on double-stranded DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rebar, E J -- Pabo, C O -- New York, N.Y. -- Science. 1994 Feb 4;263(5147):671-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8303274" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacteriophages/genetics ; Base Sequence ; Cloning, Molecular ; DNA/*metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Genetic Variation ; Genetic Vectors ; Molecular Sequence Data ; Protein Binding ; Transcription Factors/chemistry/genetics/*metabolism ; Zinc Fingers/genetics/*physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Targeted genome editing across species using ZFNs and TALENs (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-06-28
    Description: Evolutionary studies necessary to dissect diverse biological processes have been limited by the lack of reverse genetic approaches in most organisms with sequenced genomes. We established a broadly applicable strategy using zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) for targeted disruption of endogenous genes and cis-acting regulatory elements in diverged nematode species.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489282/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489282/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wood, Andrew J -- Lo, Te-Wen -- Zeitler, Bryan -- Pickle, Catherine S -- Ralston, Edward J -- Lee, Andrew H -- Amora, Rainier -- Miller, Jeffrey C -- Leung, Elo -- Meng, Xiangdong -- Zhang, Lei -- Rebar, Edward J -- Gregory, Philip D -- Urnov, Fyodor D -- Meyer, Barbara J -- GM30702/GM/NIGMS NIH HHS/ -- R01 GM030702/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Jul 15;333(6040):307. doi: 10.1126/science.1207773. Epub 2011 Jun 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute (HHMI), Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3204, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21700836" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Caenorhabditis/*genetics ; Caenorhabditis elegans/*genetics ; Deoxyribonucleases, Type II Site-Specific/genetics/*metabolism ; Gene Targeting ; Genes, Helminth ; *Genetic Techniques ; *Genome, Helminth ; INDEL Mutation ; Mutagenesis ; Regulatory Elements, Transcriptional/*genetics ; Transcription Factors/chemistry ; Transgenes ; *Zinc Fingers
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Targeted gene knockout in mammalian cells by using engineered zinc-finger nucleases (2008)
    National Academy of Sciences
    Details
    Publication Date: 2008-03-21
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 8
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    Efficient targeted gene disruption in the soma and germ line of the frog Xenopus tropicalis using engineered zinc-finger nucleases (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-04-06
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 9
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    Efficient targeted gene disruption in the soma and germ line of the frog Xenopus tropicalis using engineered zinc-finger nucleases [Developmental Biology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-04-27
    Description: The frog Xenopus, an important research organism in cell and developmental biology, currently lacks tools for targeted mutagenesis. Here, we address this problem by genome editing with zinc-finger nucleases (ZFNs). ZFNs directed against an eGFP transgene in Xenopus tropicalis induced mutations consistent with nonhomologous end joining at the target site, resulting in mosaic loss of the fluorescence phenotype at high frequencies. ZFNs directed against the noggin gene produced tadpoles and adult animals carrying up to 47% disrupted alleles, and founder animals yielded progeny carrying insertions and deletions in the noggin gene with no indication of off-target effects. Furthermore, functional tests demonstrated an allelic series of activity between three germ-line mutant alleles. Because ZFNs can be designed against any locus, our data provide a generally applicable protocol for gene disruption in Xenopus.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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