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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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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
...Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly Hye Joo Kim 1 , 2 , 3 , Hyung Joo Lee 1 , 3 , Hyojin Kim 1 , Seung Woo Cho 1 and Jin-Soo Kim 1 , 2 , 4 1 Department...
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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: 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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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
...-binding domains, including zinc fingers, transcription activator-like effectors (TALEs), and deactivated Cas9 domains (dCas9) to induce targeted deposition of DNA methylation (Rivenbark et al. 2012; Siddique et al. 2013; Nunna et al. 2014; Bernstein et al. 2015; Stolzenburg et al. 2015; Amabile et al. 2016; Liu...
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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
...cleave genomic DNA that matches the protospacer (i.e., the noncomplementary strand) and genomic DNA with complementarity to the protospacer (i.e., the complementary strand), respectively (indicated by black triangles). (D) Zinc fingers and TALEs fused to nuclease domains or Cas9 in complex with a g...
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Method: System-wide analyses of the fission yeast poly(A)⁺ RNA interactome reveal insights into organization and function of RNA–protein complexes
- Cornelia Kilchert,
- Tea Kecman,
- Emily Priest,
- Svenja Hester,
- Ebru Aydin,
- Krzysztof Kus,
- Oliver Rossbach,
- Alfredo Castello,
- Shabaz Mohammed,
- and Lidia Vasiljeva
Genome Res. July 2020 30: 1012-1026; Published in Advance June 18, 2020, doi:10.1101/gr.257006.119
...with the zinc finger domains 2 and 3 of CPSF30, as well as the WD40 domain and the N-terminal region of WDR33 (Schönemann et al. 2014; Clerici et al. 2017, 2018; Sun et al. 2018). Although RNA is not present in the cryo-EM structure of the S. cerevisiae polymerase module, its overall organization is very...
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Resource: A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells
- William K.M. Lai,
- Luca Mariani,
- Gerson Rothschild,
- Edwin R. Smith,
- Bryan J. Venters,
- Thomas R. Blanda,
- Prashant K. Kuntala,
- Kylie Bocklund,
- Joshua Mairose,
- Sarah N. Dweikat,
- Katelyn Mistretta,
- Matthew J. Rossi,
- Daniela James,
- James T. Anderson,
- Sabrina K. Phanor,
- Wanwei Zhang,
- Zibo Zhao,
- Avani P. Shah,
- Katherine Novitzky,
- Eileen McAnarney,
- Michael-C. Keogh,
- Ali Shilatifard,
- Uttiya Basu,
- Martha L. Bulyk,
- and B. Franklin Pugh
Genome Res. September 2021 31: 1663-1679; Published in Advance August 23, 2021, doi:10.1101/gr.275472.121
...in common use) and micrococcal nuclease (MNase). A ssTF-specific antibody is added to immobilized permeabilized cells or nuclei (under native or cross-linked conditions), where it binds to its chromatin target. pAG-MNase is next added and recruited via pAG to the target-specific antibody, and the MNase...
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Research: Exploring the DNA-recognition potential of homeodomains
- Stephanie W. Chu,
- Marcus B. Noyes,
- Ryan G. Christensen,
- Brian G. Pierce,
- Lihua J. Zhu,
- Zhiping Weng,
- Gary D. Stormo,
- and Scot A. Wolfe
Genome Res. October 2012 22: 1889-1898; Published in Advance April 26, 2012, doi:10.1101/gr.139014.112
...finger-HD chimeras (Pomerantz et al. 1995; Rivera et al. 1996), may have value in expanding the sequences that be efficiently targeted by zinc finger–based artificial nucleases. Methods Construction of the HD library A pB1H2v2-12En (pB1H2v2-12En(SB)) (Noyes et al. 2008a) construct was created...
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Method: Gene disruption by cell-penetrating peptide-mediated delivery of Cas9 protein and guide RNA
- Suresh Ramakrishna,
- Abu-Bonsrah Kwaku Dad,
- Jagadish Beloor,
- Ramu Gopalappa,
- Sang-Kyung Lee,
- and Hyongbum Kim
Genome Res. June 2014 24: 1020-1027; Published in Advance April 2, 2014, doi:10.1101/gr.171264.113
..., East A, Cheng A, Lin S, Ma E, Doudna J. 2013. RNA-programmed editing in human cells. Elife 2: e00471. 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 H, Um E, Cho SR, Jung C, Kim JS...
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