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ABSTRACT: We have developed a novel, high-throughput approach to collecting randomly perturbed gene-expression profiles from the human genome.A human 293 cell library that stably expresses randomly chosen zinc-finger transcription factors was constructed, and the expression profile of each cell line was obtained using cDNA microarray technology.Gene expression profiles from a total of 132 cell lines were collected and analyzed by (1) a simple clustering method based on expression-profile similarity, and (2) the shortest-path analysis method. These analyses identified a number of gene groups, and further investigation revealed that the genes that were grouped together had close biological relationships. The artificial transcription factor-based random genome perturbation method thus provides a novel functional genomic tool for annotation and classification of genes in the human genome and those of many other organisms.
Genome Research 01/2004; 13(12):2708-16. · 13.61 Impact Factor
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Kyung-Soon Park,
Dong-ki Lee,
Horim Lee, Yangsoon Lee,
Young-Soon Jang,
Yong Ha Kim,
Hyo-Young Yang,
Seong-il Lee,
Wongi Seol,
Jin-Soo Kim,
Sung-Il Lee
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ABSTRACT: We have developed a method in which randomized libraries of zinc finger-containing artificial transcription factors are used to induce phenotypic variations in yeast and mammalian cells. By linking multiple zinc-finger domains together, we constructed more than 100,000 zinc-finger proteins with diverse DNA-binding specificities and fused each of them to either a transcription activation or repression domain. The resulting transcriptional regulatory proteins were expressed individually in cells, and the transfected cells were screened for various phenotypic changes, such as drug resistance, thermotolerance or osmotolerance in yeast, and differentiation in mammalian cells. Genes associated with the selected phenotypes were also identified. Our results show that randomized libraries of artificial transcription factors are useful tools for functional genomics and phenotypic engineering.
Nature Biotechnology 11/2003; 21(10):1208-14. · 23.27 Impact Factor
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Kwang-Hee Bae,
Young Do Kwon,
Hyun-Chul Shin,
Moon-Sun Hwang,
Eun-Hyun Ryu,
Kyung-Soon Park,
Hyo-Young Yang,
Dong-Ki Lee, Yangsoon Lee,
Jinwoo Park,
Heung Sun Kwon,
Hyun-Won Kim,
Byung-Il Yeh,
Hyean-Woo Lee,
Soon Hyung Sohn,
Joonho Yoon,
Wongi Seol,
Jin-Soo Kim
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ABSTRACT: We describe methods for generating artificial transcription factors capable of up- or downregulating the expression of genes whose promoter regions contain the target DNA sequences. To accomplish this, we screened zinc fingers derived from sequences in the human genome and isolated 56 zinc fingers with diverse DNA-binding specificities. We used these zinc fingers as modular building blocks in the construction of novel, sequence-specific DNA-binding proteins. Fusion of these zinc-finger proteins with either a transcriptional activation or repression domain yielded potent transcriptional activators or repressors, respectively. These results show that the human genome encodes zinc fingers with diverse DNA-binding specificities and that these domains can be used to design sequence-specific DNA-binding proteins and artificial transcription factors.
Nature Biotechnology 04/2003; 21(3):275-80. · 23.27 Impact Factor
