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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
...of offtarget effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res 24: 132–141. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, et al. 2013. Multiplex engineering using CRISPR/ Cas systems. Science 339: 819–823. Cradick TJ, Fine EJ, Antico CJ...
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Method: Arrayed CRISPR screen with image-based assay reliably uncovers host genes required for coxsackievirus infection
- Heon Seok Kim,
- Kyungjin Lee,
- Seong-Jun Kim,
- Sungchan Cho,
- Hye Jin Shin,
- Chonsaeng Kim,
- and Jin-Soo Kim
Genome Res. June 2018 28: 859-868; Published in Advance April 30, 2018, doi:10.1101/gr.230250.117
...-level control for sequence specific siRNA off-target effects. PLoS One 7: e51942. ↵Cho SW, Kim S, Kim Y, Kweon J, Kim HS, Bae S, Kim JS. 2014. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res 24: 132–141. ↵Coyne CB, Bergelson JM. 2006. Virus-induced Abl...
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Method: Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq
- Daesik Kim,
- Sojung Kim,
- Sunghyun Kim,
- Jeongbin Park,
- and Jin-Soo Kim
Genome Res. March 2016 26: 406-415; Published in Advance January 19, 2016, doi:10.1101/gr.199588.115
...: 1177–1180. Cho SW, Kim S, Kim Y, Kweon J, KimHS, Bae S, Kim JS. 2014. Analysis of offtarget effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res 24: 132–141. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, et al. 2013.Multiplex...
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Research: Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators
- Lauren R. Polstein,
- Pablo Perez-Pinera,
- D. Dewran Kocak,
- Christopher M. Vockley,
- Peggy Bledsoe,
- Lingyun Song,
- Alexias Safi,
- Gregory E. Crawford,
- Timothy E. Reddy,
- and Charles A. Gersbach
Genome Res. August 2015 25: 1158-1169; Published in Advance May 29, 2015, doi:10.1101/gr.179044.114
.... 2014; Fu et al. 2014). These studies of CRISPR/Cas9 specificity have used various methods to determine off-target sites, including bioinformatic prediction (Fu et al. 2013; Hsu et al. 2013), high-throughput reporter assays (Mali et al. 2013a), and profiling activity of a purified CRISPR system in vitro...
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Method: Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line
- Patrick Essletzbichler,
- Tomasz Konopka,
- Federica Santoro,
- Doris Chen,
- Bianca V. Gapp,
- Robert Kralovics,
- Thijn R. Brummelkamp,
- Sebastian M.B. Nijman,
- and Tilmann Bürckstümmer
Genome Res. December 2014 24: 2059-2065; Published in Advance November 4, 2014, doi:10.1101/gr.177220.114
...effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases. Genome Res 24: 132–141. Choi PS, Meyerson M. 2014. Targeted genomic rearrangements using CRISPR/Cas technology. Nat Commun 5: 3728. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, et al. 2013...
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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
..., Iyer V, Huang X, et al. 2014. Efficient modification by CRISPR-Cas9 nickase with minimal off-target effects. Nat Methods 11: 399–402. Sung YH, Kim JM, Kim HT, Lee J, Jeon J, Jin Y, Choi JH, Ban YH, Ha SJ, Kim CH, et al. 2014. Highly efficient gene knockout in mice and zebrafish with RNA-guided...
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Research: Mechanisms of precise genome editing using oligonucleotide donors
- Yinan Kan,
- Brian Ruis,
- Taylor Takasugi,
- and Eric A. Hendrickson
Genome Res. July 2017 27: 1099-1111; Published in Advance March 29, 2017, doi:10.1101/gr.214775.116
...lesions could then be introduced near the chromophore (TY residues) of the EGFP sequence using CRISPR/ Cas9 cleavase, nickases, or dual nickases. HDR repair of the genomic lesions using ODN donors containing the sequence of the SH residues leads to the conversion of EGFP to BFP. The ODN donors also...
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Research: Genome surgery using Cas9 ribonucleoproteins for the treatment of age-related macular degeneration
- Kyoungmi Kim,
- Sung Wook Park,
- Jin Hyoung Kim,
- Seung Hwan Lee,
- Daesik Kim,
- Taeyoung Koo,
- Kwang-eun Kim,
- Jeong Hun Kim,
- and Jin-Soo Kim
Genome Res. March 2017 27: 419-426; Published in Advance February 16, 2017, doi:10.1101/gr.219089.116
..., Tabebordbar M, Cheng JK, Mali P, Wu EY, Ng AH, Zhu K, Wagers AJ, Church GM. 2016. A multifunctional AAV–CRISPR–Cas9 and its host response. Nat Methods 13: 868–874. ↵Cho SW, Kim S, Kim Y, Kweon J, Kim HS, Bae S, Kim JS. 2014. Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases...
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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
...). The use of large sets of negative control gRNAs in high-throughput CRISPR/Cas9-based screening applications is also enabling reproducible and highly quantitative analyses of off-target gRNA activity (Gilbert et al. 2014; Sanjana et al. 2014). However, despite the importance of these advances...
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