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Method: Homozygous editing of multiple genes for accelerated generation of xenotransplantation pigs
- Xiaoyue Duan,
- Chaolei Chen,
- Chang Du,
- Liang Guo,
- Jun Liu,
- Naipeng Hou,
- Pan Li,
- Xiaolan Qi,
- Fei Gao,
- Xuguang Du,
- Jiangping Song,
- and Sen Wu
Genome Res. May 2025 35: 1167-1178; Published in Advance March 5, 2025, doi:10.1101/gr.279709.124
...(Supplemental Fig. S6), consistent with observations from other Cas9-mediated editing studies (Haapaniemi et al. 2018; Enache et al. 2020). Despite these changes, cell morphology and colony formation efficiency were unaffected, underscoring V2.1G's capability to generate robust multigene-targeting clones...
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Method: Versatile and robust genome editing with Streptococcus thermophilus CRISPR1-Cas9
- Daniel Agudelo,
- Sophie Carter,
- Minja Velimirovic,
- Alexis Duringer,
- Jean-François Rivest,
- Sébastien Levesque,
- Jeremy Loehr,
- Mathilde Mouchiroud,
- Denis Cyr,
- Paula J. Waters,
- Mathieu Laplante,
- Sylvain Moineau,
- Adeline Goulet,
- and Yannick Doyon
Genome Res. January 2020 30: 107-117; Published in Advance January 3, 2020, doi:10.1101/gr.255414.119
...expression of the holoenzyme from a single adeno-associated viral vector for in vivo editing applications. Delivery of St1Cas9 to the neonatal liver efficiently rewired metabolic pathways, leading to phenotypic rescue in a mouse model of hereditary tyrosinemia. These robust enzymes expand and complement...
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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
..., Kim D, Cho SW, Kim J, Kim JS. 2014. Highly efficient RNA-guided editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res 24: 1012–1019. ↵Kim D, Bae S, Park J, Kim E, Kim S, Yu HR, Hwang J, Kim JI, Kim JS. 2015. Di-seq: -wide profiling of CRISPR-Cas9 off-target effects...
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Method: Highly efficient gene knockout in mice and zebrafish with RNA-guided endonucleases
- Young Hoon Sung,
- Jong Min Kim,
- Hyun-Taek Kim,
- Jaehoon Lee,
- Jisun Jeon,
- Young Jin,
- Jung-Hwa Choi,
- Young Ho Ban,
- Sang-Jun Ha,
- Cheol-Hee Kim,
- Han-Woong Lee,
- and Jin-Soo Kim
Genome Res. January 2014 24: 125-131; Published in Advance November 19, 2013, doi:10.1101/gr.163394.113
...– 10625. ChangN, SunC, Gao L, ZhuD, Xu X, Zhu X, Xiong JW, Xi JJ. 2013. Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos. Cell Res 23: 465–472. Cho SW, Kim S, Kim JM, Kim JS. 2013a. Targeted engineering in human cells with the Cas9 RNA-guided endonuclease.Nat Biotechnol31: 230–232. Cho SW...
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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
...meganucleases is transforming editing and functional genomics. CRISPR/Cas9 was developed such that targeted genomic lesions could be introduced in vivo with unprecedented ease. In the presence of homology donors, these lesions facilitate high-efficiency precise editing (PGE) via homology-directed repair (HDR...
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Method: Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells
- Keyi Geng,
- Lara G. Merino,
- Linda Wedemann,
- Aniek Martens,
- Małgorzata Sobota,
- Yerma P. Sanchez,
- Jonas Nørskov Søndergaard,
- Robert J. White,
- and Claudia Kutter
Genome Res. October 2022 32: 1876-1891; Published in Advance September 30, 2022, doi:10.1101/gr.276901.122
...to efficiently capture and dissect the on-target sequence content in the order of kilobases. We resolved complex on-target genomic rearrangements with varying biological consequences. By introducing a powerful approach, this study contributes to a more reliable validation of CRISPR-Cas9-induced deletions...
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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
..., Li Y, Fine EJ, Wu X, Shalem O, et al. 2013. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31: 827–832. HwangWY, FuY, ReyonD,MaederML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, Joung JK. 2013. Efficient editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol 31: 227...
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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
...J, Kim JS. 2014. Highly efficient RNA-guided editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res (this issue). doi: 10.1101/gr.171322.113. Li D, Qiu Z, Shao Y, Chen Y, Guan Y, Liu M, Li Y, Gao N, Wang L, Lu X, et al. 2013a. Heritable gene targeting in themouse and rat...
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Research: Targeted delivery of CRISPR interference system against Fabp4 to white adipocytes ameliorates obesity, inflammation, hepatic steatosis, and insulin resistance
- Jee Young Chung,
- Qurrat Ul Ain,
- Yoonsung Song,
- Seok-Beom Yong,
- and Yong-Hee Kim
Genome Res. September 2019 29: 1442-1452; Published in Advance August 29, 2019, doi:10.1101/gr.246900.118
...efficient RNA-guided editing in human cells via delivery of purified Cas9 ribonucleoproteins. Genome Res 24: 1012–1019. doi:10.1101/gr.171322.113 ↵Kolonin MG, Saha PK, Chan L, Pasqualini R, Arap W. 2004. Reversal of obesity by targeted ablation of adipose tissue. Nat Med 10: 625–632. doi:10.1038/nm1048...
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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
...proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances...
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