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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
...and other eukaryotic cells using engineered zinc finger nucleases (ZFNs). We found that ZFNs designed to target two different sites in a human chromosome could introduce two concurrent DNA double-strand breaks (DSBs) in the chromosome and give rise to targeted deletions of the genomic segment between...
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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
..., Kim E, Kim S, Kim JS. 2012. Targeted chromosomal duplications and inversions in the human using zinc finger nucleases. Genome Res 22: 539–548. Ma S, Zhang S, Wang F, Liu Y, Liu Y, Xu H, Liu C, Lin Y, Zhao P, Xia Q. 2012. Highly efficient and specific editing in silkworm using custom TALENs. PLoS ONE 7...
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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
..., Tomishima M, DeKelver R, Choi VM, Gregory P, Urnov F, Weinstock DM, Jasin M. 2009. Chromosomal translocations induced at specified loci in human stem cells. Proc Natl Acad Sci 106: 10620–10625. Carroll D. 2011. Genome engineering with zinc-finger nucleases. Genetics 188: 773–782. Chansky HA, Barahmand...
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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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Methods: An Efficient Method to Generate Chromosomal Rearrangements by Targeted DNA Double-Strand Breaks in Drosophila melanogaster
- Dieter Egli,
- Ernst Hafen,
- and Walter Schaffner
Genome Res. July 2004 14: 1382-1393; Published in Advance June 14, 2004, doi:10.1101/gr.2279804
...compared with chromosomal inversion. Because we did not recover any targeted event at the endogenous y locus, we conclude that the DSB at the target gene strongly stimulated targeting. Other groups using either zinc finger nucleases in Drosophila , or I-SceI in mammalian cell culture, obtained similar...
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Method: Precision genome engineering with programmable DNA-nicking enzymes
- Eunji Kim,
- Sojung Kim,
- Duk Hyoung Kim,
- Beom-Soon Choi,
- Ik-Young Choi,
- and Jin-Soo Kim
Genome Res. July 2012 22: 1327-1333; Published in Advance April 20, 2012, doi:10.1101/gr.138792.112
.... Trends Biotechnol 28: 445–446. Lee HJ, Kim E, Kim JS. 2010b. Targeted chromosomal deletions in human cells using zinc finger nucleases. Genome Res 20: 81–89. Lee HJ, Kweon J, Kim E, Kim S, Kim JS. 2011. Targeted chromosomal duplications and inversions in the human using zinc finger nucleases. Genome Res...
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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
.... Genotyping with CRISPR-Cas-derived RNA-guided endonucleases. Nat Commun 5: 3157. LeeHJ, KimE, Kim JS. 2010. Targeted chromosomal deletions in human cells using zinc finger nucleases. Genome Res 20: 81–89. Lee HJ, Kweon J, Kim E, Kim S, Kim JS. 2012. Targeted chromosomal duplications and inversions...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...this, we optimized a low-input cell-type-specific chromatin profiling method using updtumor testes, which employs micrococcal nuclease (MNase) digestion of targeted chromatin (Fig. 3A). In this method, we coexpressed the Upd ligand and histone H3-GFP fusion protein in either GSC-like cells (nanos > upd...
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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
..., among several key activities, catalyze genomic DNA nicking and reverse transcription of the L1 mRNA (Feng et al. 1996; Moran et al. 1996; Kazazian and Moran 2017; Scott and Devine 2017). New L1 insertions typically carry retrotransposition hallmarks, including target site duplications (TSDs) and a long...
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Method: Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases
- Seung Woo Cho,
- Sojung Kim,
- Yongsub Kim,
- Jiyeon Kweon,
- Heon Seok Kim,
- Sangsu Bae,
- and Jin-Soo Kim
Genome Res. January 2014 24: 132-141; Published in Advance November 19, 2013, doi:10.1101/gr.162339.113
...Methods 10: 185. LeeHJ, KimE, Kim JS. 2010. Targeted chromosomal deletions in human cells using zinc finger nucleases. Genome Res 20: 81–89. Lee HJ, Kweon J, Kim E, Kim S, Kim JS. 2012. Targeted chromosomal duplications and inversions in the human using zinc finger nucleases. Genome Res 22: 539–548. Mali...
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