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Method: Highly active zinc-finger nucleases by extended modular assembly
- Mital S. Bhakta,
- Isabelle M. Henry,
- David G. Ousterout,
- Kumitaa Theva Das,
- Sarah H. Lockwood,
- Joshua F. Meckler,
- Mark C. Wallen,
- Artem Zykovich,
- Yawei Yu,
- Heather Leo,
- Lifeng Xu,
- Charles A. Gersbach,
- and David J. Segal
Genome Res. March 2013 23: 530-538; Published in Advance December 5, 2012, doi:10.1101/gr.143693.112
...–280. Bhakta MS, Segal DJ. 2010. The generation of zinc finger proteins by modular assembly. Methods Mol Biol 649: 3–30. Zinc-finger nucleases by extended modular assembly Genome Research 537 www..org Bogdanove AJ, Voytas DF. 2011. TAL effectors: Customizable proteins for DNA targeting. Science 333: 1843...
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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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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
...gene-targeting approach in the monarch using zinc-finger nucleases (ZFNs), engineered nucleases that generate mutations at targeted genomic sequences. We focused our ZFN approach on targeting the type 2 vertebrate-like cryptochrome gene of the monarch (designated cry2 ), which encodes a putative...
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Methods: Targeted chromosomal deletions in human cells using zinc finger nucleases
- Hyung Joo Lee,
- Eunji Kim,
- and Jin-Soo Kim
Genome Res. January 2010 20: 81-89; Published in Advance December 1, 2009, doi:10.1101/gr.099747.109
..., Listewnik ML, Donahoe PK, Qi Y, Scherer SW, Lee C. 2004. Detection of large-scale variation in the human . Nat Genet 36: 949–951. Kim HJ, Lee HJ, Kim H, Cho SW, Kim JS. 2009. Targeted editing in human cells with zinc finger nucleases constructed via modular assembly. Genome Res 19: 1279–1288. Lupski JR...
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Method: A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs
- Christian Pflueger,
- Dennis Tan,
- Tessa Swain,
- Trung Nguyen,
- Jahnvi Pflueger,
- Christian Nefzger,
- Jose M. Polo,
- Ethan Ford,
- and Ryan Lister
Genome Res. August 2018 28: 1193-1206; Published in Advance June 15, 2018, doi:10.1101/gr.233049.117
...A modular dCas9-SunTag DNMT3A epi editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs Christian Pflueger1,2,6, Dennis Tan1,6, Tessa Swain1,2, Trung Nguyen1,2, Jahnvi Pflueger1,2, Christian Nefzger3,4,5, Jose M. Polo3,4,5, Ethan Ford1 and Ryan Lister1,2 1...
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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
...Noncoding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases Tony Gutschner 1 , 2 , Marion Baas 1 , 2 and Sven Diederichs 1 , 2 , 3 1Helmholtz-University-Group “Molecular RNA Biology...
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Method: CRISPR-based modular assembly of a UAS-cDNA/ORF plasmid library for more than 5500 Drosophila genes conserved in humans
- Ping Wei,
- Wen Xue,
- Yun Zhao,
- Guang Ning,
- and Jiwu Wang
Genome Res. January 2020 30: 95-106; Published in Advance November 13, 2019, doi:10.1101/gr.250811.119
...-throughput plasmid library editing. Theoretically, the first step of CRISPRmass manipulation, which is cleavage of shared vector sequences of library plasmids by CRISPR/Cas9, could be altered to other methods such as zinc-finger nuclease (ZFN) (Kim et al. 1996; Smith et al. 2000) and transcription activator...
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Research: Global analysis of Drosophila Cys₂-His₂ zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants
- Metewo Selase Enuameh,
- Yuna Asriyan,
- Adam Richards,
- Ryan G. Christensen,
- Victoria L. Hall,
- Majid Kazemian,
- Cong Zhu,
- Hannah Pham,
- Qiong Cheng,
- Charles Blatti,
- Jessie A. Brasefield,
- Matthew D. Basciotta,
- Jianhong Ou,
- Joseph C. McNulty,
- Lihua J. Zhu,
- Susan E. Celniker,
- Saurabh Sinha,
- Gary D. Stormo,
- Michael H. Brodsky,
- and Scot A. Wolfe
Genome Res. June 2013 23: 928-940; Published in Advance March 7, 2013, doi:10.1101/gr.151472.112
...of artificial zinc finger modules to create ZFPs with novel DNA-binding specificity. These hybrids of natural and artificial fingers can be used to create functional zinc finger nucleases for editing vertebrate genomes. Footnotes ↵ 9 Corresponding author E-mail scot...
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Method: Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins
- Sojung Kim,
- Daesik Kim,
- Seung Woo Cho,
- Jungeun Kim,
- and Jin-Soo Kim
Genome Res. June 2014 24: 1012-1019; Published in Advance April 2, 2014, doi:10.1101/gr.171322.113
...–334. Kim HJ, Lee HJ, Kim H, Cho SW, Kim JS. 2009. Targeted editing in human cells with zinc finger nucleases constructed via modular assembly. Genome Res 19: 1279–1288. Kim JS, Lee HJ, Carroll D. 2010. Genome editing with modularly assembled zinc-finger nucleases. Nat Methods 7: 91 (author reply 91...
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Perspective: Enabling functional genomics with genome engineering
- Isaac B. Hilton and
- Charles A. Gersbach
Genome Res. October 2015 25: 1442-1455; doi:10.1101/gr.190124.115
..., TALE, and Cas9-gRNA platforms for editing genomic sequence and regulatory states. Individual zinc finger domains (A) and TALE repeats (B) that recognize unique triplets or single base pairs, respectively, can be arrayed in engineered proteins to target specific genomic sequences. (C) Cas9...
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