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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...the two probes. This distance is inversely related to chromatin compaction; a high FRET efficiency indicates close proximity (and thus compacted chromatin), whereas low FRET efficiency indicates a more relaxed chromatin state. FRET-FISH can measure chromatin compaction at selected gene loci, providing...
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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
.... In principle, paired nickases double the specificity of Cas9-mediated mutagenesis and will broaden the utility of RNA-guided enzymes in applications that require precise editing such as gene and cell therapy. One caveat to this approach is that two highly active sgRNAs are needed to make an efficient nickase...
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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
...IJ, Kim DH, Jeon J, Lee J, Lee K, Jeong D, Kim JS, Lee HW. 2013. Knockout mice created by TALEN-mediated gene targeting. Nat Biotechnol 31: 23–24. 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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Method: High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9
- Gaurav K. Varshney,
- Wuhong Pei,
- Matthew C. LaFave,
- Jennifer Idol,
- Lisha Xu,
- Viviana Gallardo,
- Blake Carrington,
- Kevin Bishop,
- MaryPat Jones,
- Mingyu Li,
- Ursula Harper,
- Sunny C. Huang,
- Anupam Prakash,
- Wenbiao Chen,
- Raman Sood,
- Johan Ledin,
- and Shawn M. Burgess
Genome Res. July 2015 25: 1030-1042; Published in Advance June 5, 2015, doi:10.1101/gr.186379.114
.../ Cas9 is by far the most efficient gene targeting method in zebrafish. At the sequence level, indel mutations generated by these gene-editing nucleases can be classified as simple insertions, simple deletions, and complex changes that include both deletion and random insertion (Fig. 3B). Our data...
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Method: Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair
- Thomas O. Auer,
- Karine Duroure,
- Anne De Cian,
- Jean-Paul Concordet,
- and Filippo Del Bene
Genome Res. January 2014 24: 142-153; Published in Advance October 31, 2013, doi:10.1101/gr.161638.113
..., as was shown nearly 20 years ago using the homing endonuclease ISceI, efficiently stimulate homologous recombination (HR) with a gene targeting vector in cultured cells and plants (Jasin 1996). Several types of artificial nucleases can now be designed to make the initial DSB that induces modification...
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Method: Cre-dependent Cas9-expressing pigs enable efficient in vivo genome editing
- Kepin Wang,
- Qin Jin,
- Degong Ruan,
- Yi Yang,
- Qishuai Liu,
- Han Wu,
- Zhiwei Zhou,
- Zhen Ouyang,
- Zhaoming Liu,
- Yu Zhao,
- Bentian Zhao,
- Quanjun Zhang,
- Jiangyun Peng,
- Chengdan Lai,
- Nana Fan,
- Yanhui Liang,
- Ting Lan,
- Nan Li,
- Xiaoshan Wang,
- Xinlu Wang,
- Yong Fan,
- Pieter A. Doevendans,
- Joost P.G. Sluijter,
- Pentao Liu,
- Xiaoping Li,
- and Liangxue Lai
Genome Res. December 2017 27: 2061-2071; Published in Advance November 16, 2017, doi:10.1101/gr.222521.117
...of principle, we were able to simultaneously inactivate five tumor suppressor genes (TP53, PTEN, APC, BRCA1, and BRCA2) and activate one oncogene (KRAS), achieved by delivering Cre recombinase and sgRNAs, which caused rapid lung tumor development. The efficient editing shown here demonstrates that these pigs...
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Method: 2C-Cas9: a versatile tool for clonal analysis of gene function
- Vincenzo Di Donato,
- Flavia De Santis,
- Thomas O. Auer,
- Noé Testa,
- Héctor Sánchez-Iranzo,
- Nadia Mercader,
- Jean-Paul Concordet,
- and Filippo Del Bene
Genome Res. May 2016 26: 681-692; Published in Advance March 8, 2016, doi:10.1101/gr.196170.115
...RNAs) specifically targeting a gene of interest. To facilitate cloning of sgRNA target sequences, BsmbI and BsaI restriction sites (red arrows) were introduced. Tol2 allows efficient transgenesis after injection into one-cell stage zebrafish embryos. (B) (Left panel) Confocal imaging of the spinal cord of 2 dpf Tg...
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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: 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
.... Targeted delivery of the CRISPRi system against Fabp4 to white adipocytes by ATS-9R induced effective silencing of Fabp4, resulting in reduction of body weight and inflammation and restoration of hepatic steatosis in obese mice. This RNA-guided DNA recognition platform provides a simple and safe approach...
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Method: A mobile insulator system to detect and disrupt cis-regulatory landscapes in vertebrates
- José Bessa,
- Mario Luengo,
- Solangel Rivero-Gil,
- Ana Ariza-Cosano,
- António H.F. Maia,
- Francisco J. Ruiz-Ruano,
- Pablo Caballero,
- Silvia Naranjo,
- Jaime J. Carvajal,
- and José Luis Gómez-Skarmeta
Genome Res. March 2014 24: 487-495; Published in Advance November 25, 2013, doi:10.1101/gr.165654.113
...Model OrganismDatabase.Nucleic Acids Res 39: D822–D829. Chang N, Sun C, Gao L, Zhu D, Xu X, Zhu X, Xiong J-W, Xi JJ. 2013. Genome editing with RNA-guided Cas9 nuclease in zebrafish embryos. Cell Res 23: 465–472. Chung JH, Whiteley M, Felsenfeld G. 1993. A 59 element of the chicken b-globin domain serves...

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