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Method: Targeted chromosomal duplications and inversions in the human genome using zinc finger nucleases
- Hyung Joo Lee,
- Jiyeon Kweon,
- Eunji Kim,
- Seokjoong Kim,
- and Jin-Soo Kim
Genome Res. March 2012 22: 539-548; Published in Advance December 19, 2011, doi:10.1101/gr.129635.111
...Targeted chromosomal duplications and inversions in the human genome using zinc finger nucleases Hyung Joo Lee 1 , 2 , Jiyeon Kweon 1 , Eunji Kim , Seokjoong Kim 3 and Jin-Soo Kim 4 National Creative Research Initiatives...
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Research: ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters
- Nina L. Haring,
- Elisabeth J. van Bree,
- Whitney S. Jordaan,
- Judith R.E. Roels,
- Gonzalo Congrains Sotomayor,
- Tiziana M. Hey,
- Fred T.G. White,
- Marc D. Galland,
- Marten P. Smidt,
- and Frank M.J. Jacobs
Genome Res. April 2021 31: 551-563; Published in Advance March 15, 2021, doi:10.1101/gr.265348.120
...silenced by KRAB zinc finger (KZNF) proteins recruiting corepressor proteins that establish a repressive chromatin state. A number of KZNFs have been reported to bind SVAs, but their individual contribution to repressing SVAs and their roles in suppressing SVA-mediated gene-regulatory effects remains...
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Method: Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases
- Christine Merlin,
- Lauren E. Beaver,
- Orley R. Taylor,
- Scot A. Wolfe,
- and Steven M. Reppert
Genome Res. January 2013 23: 159-168; Published in Advance September 25, 2012, doi:10.1101/gr.145599.112
...nucleases. Proc Natl Acad Sci 105: 19821–19826. Bibikova M, Golic M, Golic KG, Carroll D. 2002. Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 161: 1169–1175. Brower LP. 1996. Monarch butterfly orientation: Missing pieces of a magnificent puzzle. J Exp Biol...
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Method: Targeted chromosomal deletions and inversions in zebrafish
- Ankit Gupta,
- Victoria L. Hall,
- Fatma O. Kok,
- Masahiro Shin,
- Joseph C. McNulty,
- Nathan D. Lawson,
- and Scot A. Wolfe
Genome Res. June 2013 23: 1008-1017; Published in Advance March 11, 2013, doi:10.1101/gr.154070.112
.... Genome Res 19: 1279–1288. Kim E, Kim S, Kim DH, Choi BS, Choi IY, Kim JS. 2012. Precision engineering with programmable DNA-nicking enzymes.Genome Res 22: 1327–1333. LeeHJ, KimE, Kim JS. 2010. Targeted chromosomal deletions in human cells using zinc finger nucleases. Genome Res 20: 81–89. Lee HJ, Kweon J...
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Method: Cancer translocations in human cells induced by zinc finger and TALE nucleases
- Marion Piganeau,
- Hind Ghezraoui,
- Anne De Cian,
- Lionel Guittat,
- Mark Tomishima,
- Loic Perrouault,
- Oliver René,
- George E. Katibah,
- Lei Zhang,
- Michael C. Holmes,
- Yannick Doyon,
- Jean-Paul Concordet,
- Carine Giovannangeli,
- Maria Jasin,
- and Erika Brunet
Genome Res. July 2013 23: 1182-1193; Published in Advance April 8, 2013, doi:10.1101/gr.147314.112
...rearrangements, including chromosomal translocations (Richardson and Jasin 2000; Mani and Chinnaiyan 2010). With the development of tailored endonucleases like zinc finger nucleases (ZFNs) (Urnov et al. 2010; Carroll 2011) and more recently transcription activator-like effector nucleases (TALENs) (Doyon et al...
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Methods: Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly
- Hye Joo Kim,
- Hyung Joo Lee,
- Hyojin Kim,
- Seung Woo Cho,
- and Jin-Soo Kim
Genome Res. July 2009 19: 1279-1288; Published in Advance May 21, 2009, doi:10.1101/gr.089417.108
...of deletions, insertions, and complex mutations for each ZFN pair (as shown in C for Z836) were counted, and the percentages of these incidents were plotted. Targeted editing with zinc finger nucleases Genome Research 1281 www..org We chose for further study eight representative ZFN pairs, each of which...
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Method: Noncoding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases
- Tony Gutschner,
- Marion Baas,
- and Sven Diederichs
Genome Res. November 2011 21: 1944-1954; Published in Advance August 15, 2011, doi:10.1101/gr.122358.111
...–3093. Bibikova M, Golic M, Golic KG, Carroll D. 2002. Targeted chromosomal cleavage and mutagenesis in Drosophila using zinc-finger nucleases. Genetics 161: 1169–1175. Caley DP, Pink RC, Trujillano D, Carter DR. 2010. Long noncoding RNAs, chromatin, and development. TheScientificWorldJOURNAL 10: 90–102. Carninci...
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Method: Efficient gene targeting by homology-directed repair in rat zygotes using TALE nucleases
- Séverine Remy,
- Laurent Tesson,
- Séverine Menoret,
- Claire Usal,
- Anne De Cian,
- Virginie Thepenier,
- Reynald Thinard,
- Daniel Baron,
- Marine Charpentier,
- Jean-Baptiste Renaud,
- Roland Buelow,
- Gregory J. Cost,
- Carine Giovannangeli,
- Alexandre Fraichard,
- Jean-Paul Concordet,
- and Ignacio Anegon
Genome Res. August 2014 24: 1371-1383; Published in Advance July 2, 2014, doi:10.1101/gr.171538.113
...andmore cost-effective strategy compared to the use of ES cells.We and others have shown that zinc finger nucleases (ZFNs) (Geurts et al. 2009; Mashimo et al. 2010), transcription activator-like effector (TALE) nucleases (Tesson et al. 2011; Tong et al. 2012; Mashimo et al. 2013), meganucleases (Menoret...
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Method: Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome
- Russell C. DeKelver,
- Vivian M. Choi,
- Erica A. Moehle,
- David E. Paschon,
- Dirk Hockemeyer,
- Sebastiaan H. Meijsing,
- Yasemin Sancak,
- Xiaoxia Cui,
- Eveline J. Steine,
- Jeffrey C. Miller,
- Phillip Tam,
- Victor V. Bartsevich,
- Xiangdong Meng,
- Igor Rupniewski,
- Sunita M. Gopalan,
- Helena C. Sun,
- Kathleen J. Pitz,
- Jeremy M. Rock,
- Lei Zhang,
- Gregory D. Davis,
- Edward J. Rebar,
- Iain M. Cheeseman,
- Keith R. Yamamoto,
- David M. Sabatini,
- Rudolf Jaenisch,
- Philip D. Gregory,
- and Fyodor D. Urnov
Genome Res. August 2010 20: 1133-1142; Published in Advance May 27, 2010, doi:10.1101/gr.106773.110
...zinc finger nucleases (ZFNs) for efficient transgenesis without drug selection into the PPP1R12C gene, a “safe harbor” locus known as AAVS1 . ZFNs enable targeted transgenesis at a frequency of up to 15% following transient transfection of both transformed and primary human cells, including...
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Method: Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzyme
- Jianbin Wang,
- Geoffrey Friedman,
- Yannick Doyon,
- Nathaniel S. Wang,
- Carrie Jiaxin Li,
- Jeffrey C. Miller,
- Kevin L. Hua,
- Jenny Jiacheng Yan,
- Joshua E. Babiarz,
- Philip D. Gregory,
- and Michael C. Holmes
Genome Res. July 2012 22: 1316-1326; Published in Advance March 20, 2012, doi:10.1101/gr.122879.111
...and deletions (indels) characteristic of repair via NHEJ. Gene addition by these CCR5-targeted zinc finger nickases (ZFNickases) occurs in both transformed and primary human cells at efficiencies of up to ~1%–8%. Interestingly, ZFNickases targeting the AAVS1 ‘‘safe harbor’’ locus revealed similar in vitro...

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