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Methods: Efficient target-selected mutagenesis in Caenorhabditis elegans: Toward a knockout for every gene
- Edwin Cuppen,
- Eelke Gort,
- Esther Hazendonk,
- Josine Mudde,
- José van de Belt,
- Isaäc J. Nijman,
- Victor Guryev,
- and Ronald H.A. Plasterk
Genome Res. May 2007 17: 649-658; Published in Advance April 6, 2007, doi:10.1101/gr.6080607
...inactivation of the zebrafish rag1 gene . Science 297 : 99 – 102 . ↵ Wienholds, E. , van Eeden, F. , Kosters, M. , Mudde, J. , Plasterk, R.H. , Cuppen, E. ( 2003 ) Efficient target-selected mutagenesis in zebrafish . Genome Res. 13 : 2700 – 2707 . ↵ Winkler, S. , Schwabedissen, A. , Backasch, D. , Bokel, C...
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Methods: Target-selected mutant screen by TILLING in Drosophila
- Sylke Winkler,
- Anja Schwabedissen,
- Dana Backasch,
- Christian Bökel,
- Claudia Seidel,
- Stefanie Bönisch,
- Maximilian Fürthauer,
- Antje Kuhrs,
- Laura Cobreros,
- Michael Brand,
- and Marcos González-Gaitán
Genome Res. May 2005 15: 718-723; doi:10.1101/gr.3721805
...—a high-throughput harvest for functional genomics. Nat. Rev. Genet. 5 : 145 –150. ↵ Wienholds, E., van Eeden, F., Kosters, M., Mudde, J., Plasterk, R.H., and Cuppen, E. 2003 . Efficient target-selected mutagenesis in zebrafish. Genome Res. 13 : 2700 –2707. Web site references http...
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Resource: Systematic genome editing of the genes on zebrafish Chromosome 1 by CRISPR/Cas9
- Yonghua Sun,
- Bo Zhang,
- Lingfei Luo,
- De-Li Shi,
- Han Wang,
- Zongbin Cui,
- Honghui Huang,
- Ying Cao,
- Xiaodong Shu,
- Wenqing Zhang,
- Jianfeng Zhou,
- Yun Li,
- Jiulin Du,
- Qingshun Zhao,
- Jun Chen,
- Hanbing Zhong,
- Tao P. Zhong,
- Li Li,
- Jing-Wei Xiong,
- Jinrong Peng,
- Wuhan Xiao,
- Jian Zhang,
- Jihua Yao,
- Zhan Yin,
- Xianming Mo,
- Gang Peng,
- Jun Zhu,
- Yan Chen,
- Yong Zhou,
- Dong Liu,
- Weijun Pan,
- Yiyue Zhang,
- Hua Ruan,
- Feng Liu,
- Zuoyan Zhu,
- Anming Meng,
- and The ZAKOC Consortium
Genome Res. January 2020 30: 118-126; Published in Advance December 12, 2019, doi:10.1101/gr.248559.119
..., such as the sequence bias of targetable or highly efficient sites, remain elusive and need to be substantially characterized.To generate a comprehensive genetic resource to facilitate zebrafish research for the community, we aim to knock out all the annotated genes in zebrafish Chromosome 1, a project involving 38...
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Method: Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases
- Christine Merlin,
- Lauren E. Beaver,
- Orley R. Taylor,
- Scot A. Wolfe,
- and Steven M. Reppert
Genome Res. January 2013 23: 159-168; Published in Advance September 25, 2012, doi:10.1101/gr.145599.112
...Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases Christine Merlin 1 , 5 , Lauren E. Beaver 1 , Orley R. Taylor 2 , Scot A. Wolfe 3 , 4 and Steven M. Reppert 1 , 5 1 Department...
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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
...-directed mutagenesis (Doyon et al. 2008; Meng et al. 2008; Bedell et al. 2012; Hwang et al. 2013), are highly efficient for coding sequences, but they are hard to apply to the noncoding , mostly because of our limited ability to predict the outcome of small changes in noncoding sequences. Classical random insertional...
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Method: Discovery and assessment of conserved Pax6 target genes and enhancers
- Pedro Coutinho,
- Sofia Pavlou,
- Shipra Bhatia,
- Kevin J. Chalmers,
- Dirk A. Kleinjan,
- and Veronica van Heyningen
Genome Res. August 2011 21: 1349-1359; Published in Advance May 26, 2011, doi:10.1101/gr.124115.111
...of predicted target gene Tcf7l2 (Cho and Dressler 1998), the collected data allow us to conclude that our target selection procedure is highly efficient in finding Pax6 regulated genes and simultaneously delivers (part of) the evolutionarily conserved regulatory network that centers around this important...
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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
...an actual biological process, while pharmacological and genetic perturbations of DNMTs cause undesired global depletion of mCG. Thus, these techniques suffer from confounding secondary effects due to a lack of target selectivity and are therefore unable to accurately address the role of mCG in regulating m...
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LETTER: Genetic Variation in Coding Regions Between and Within Commonly Used Inbred Rat Strains
- Bart M.G. Smits,
- Bert F.M. van Zutphen,
- Ronald H.A. Plasterk,
- and Edwin Cuppen
Genome Res. July 2004 14: 1285-1290; doi:10.1101/gr.2155004
..., M., Mudde, J., Plasterk, R.H., and Cuppen, E. 2003 . Efficient target-selected mutagenesis in zebrafish. Genome Res. 13 : 2700 –2707. ↵ Wong, G.K., Yang, Z., Passey, D.A., Kibukawa, M., Paddock, M., Liu, C.R., Bolund, L., and Yu, J. 2003 . A population threshold for functional polymorphisms. Genome...

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