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Development of a novel oligonucleotide array-based transcription factor assay platform for genome-wide active transcription factor profiling in Saccharomyces cerevisiae.
J Proteome Res. 2008 Mar; 7(3):1315-25.JP

Abstract

Transcription factors (TFs) play a central role in regulating gene expression and in providing interconnecting regulatory networks between related pathway elements. Although single TF assays provide some insights into pathway regulation, a method that allows the parallel investigation of all active TFs is highly desired to elucidate the complex inter-regulated cellular mechanisms. We have developed a novel oligonucleotide array-based transcription factor assay platform for genome-wide active TF profiling of Saccharomyces cerevisiae, which can simultaneously analyze the activities of 93 different TFs. The platform has been validated using 28 purified TFs produced in Escherichia coli, cell extracts from yeast strains overexpressing particular TFs, and by detailed control experiments. We then used the platform to examine the activity changes of all yeast TFs during diauxic shift, and results showed, in good agreement with previous studies, that the Sip4 was induced specifically. Other individual TFs required for growth in synthetic complete medium were also identified. Genome-wide analysis of TF activity is extremely useful in investigating complex gene regulatory networks and for the development of systematic understanding of the complexity of genomic functions. These results obtained in this report demonstrate the validity, and for the first time the utility, of this technology for genome-wide investigation of TF activities.

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Publisher Full Text (DOI)

Authors+Show Affiliations

Zhao Y
Medical Systems Biology Research Center, Tsinghua University, Beijing 100084, China.
Shao W
No affiliation info available
Wei H
No affiliation info available
Qiao J
No affiliation info available
Lu Y
No affiliation info available
Sun Y
No affiliation info available
Mitchelson K
No affiliation info available
Cheng J
No affiliation info available
Zhou Y
No affiliation info available

MeSH

Gene Expression ProfilingGenome, FungalOligonucleotide Array Sequence AnalysisSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTranscription Factors

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

18220337

Citation

Zhao, Yongchao, et al. "Development of a Novel Oligonucleotide Array-based Transcription Factor Assay Platform for Genome-wide Active Transcription Factor Profiling in Saccharomyces Cerevisiae." Journal of Proteome Research, vol. 7, no. 3, 2008, pp. 1315-25.
Zhao Y, Shao W, Wei H, et al. Development of a novel oligonucleotide array-based transcription factor assay platform for genome-wide active transcription factor profiling in Saccharomyces cerevisiae. J Proteome Res. 2008;7(3):1315-25.
Zhao, Y., Shao, W., Wei, H., Qiao, J., Lu, Y., Sun, Y., Mitchelson, K., Cheng, J., & Zhou, Y. (2008). Development of a novel oligonucleotide array-based transcription factor assay platform for genome-wide active transcription factor profiling in Saccharomyces cerevisiae. Journal of Proteome Research, 7(3), 1315-25. https://doi.org/10.1021/pr700642g
Zhao Y, et al. Development of a Novel Oligonucleotide Array-based Transcription Factor Assay Platform for Genome-wide Active Transcription Factor Profiling in Saccharomyces Cerevisiae. J Proteome Res. 2008;7(3):1315-25. PubMed PMID: 18220337.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Development of a novel oligonucleotide array-based transcription factor assay platform for genome-wide active transcription factor profiling in Saccharomyces cerevisiae. AU - Zhao,Yongchao, AU - Shao,Wei, AU - Wei,Huajiang, AU - Qiao,Jiying, AU - Lu,Ying, AU - Sun,Yimin, AU - Mitchelson,Keith, AU - Cheng,Jing, AU - Zhou,Yuxiang, Y1 - 2008/01/26/ PY - 2008/1/29/pubmed PY - 2008/6/5/medline PY - 2008/1/29/entrez SP - 1315 EP - 25 JF - Journal of proteome research JO - J Proteome Res VL - 7 IS - 3 N2 - Transcription factors (TFs) play a central role in regulating gene expression and in providing interconnecting regulatory networks between related pathway elements. Although single TF assays provide some insights into pathway regulation, a method that allows the parallel investigation of all active TFs is highly desired to elucidate the complex inter-regulated cellular mechanisms. We have developed a novel oligonucleotide array-based transcription factor assay platform for genome-wide active TF profiling of Saccharomyces cerevisiae, which can simultaneously analyze the activities of 93 different TFs. The platform has been validated using 28 purified TFs produced in Escherichia coli, cell extracts from yeast strains overexpressing particular TFs, and by detailed control experiments. We then used the platform to examine the activity changes of all yeast TFs during diauxic shift, and results showed, in good agreement with previous studies, that the Sip4 was induced specifically. Other individual TFs required for growth in synthetic complete medium were also identified. Genome-wide analysis of TF activity is extremely useful in investigating complex gene regulatory networks and for the development of systematic understanding of the complexity of genomic functions. These results obtained in this report demonstrate the validity, and for the first time the utility, of this technology for genome-wide investigation of TF activities. SN - 1535-3893 UR - https://www.unboundmedicine.com/medline/citation/18220337/Development_of_a_novel_oligonucleotide_array_based_transcription_factor_assay_platform_for_genome_wide_active_transcription_factor_profiling_in_Saccharomyces_cerevisiae_ DB - PRIME DP - Unbound Medicine ER -