The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Identifying transcription factor functions and targets by phenotypic activation
Abstract
Mapping transcriptional regulatory networks is difficult because many transcription factors (TFs) are activated only under specific conditions. We describe a generic strategy for identifying genes and pathways induced by individual TFs that does not require knowledge of their normal activation cues. Microarray analysis of 55 yeast TFs that caused a growth phenotype when overexpressed showed that the majority caused increased transcript levels of genes in specific physiological categories, suggesting a mechanism for growth inhibition. Induced genes typically included established targets and genes with consensus promoter motifs, if known, indicating that these data are useful for identifying potential new target genes and binding sites. We identified the sequence 5′-TCACGCAA as a binding sequence for Hms1p, a TF that positively regulates pseudohyphal growth and previously had no known motif. The general strategy outlined here presents a straightforward approach to discovery of TF activities and mapping targets that could be adapted to any organism with transgenic technology.
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Cites
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971
Exploration of Essential Gene Functions via Titratable Promoter Alleles
Mnaimneh, S., Davierwala, A. P., Haynes, J., Moffat, J., Peng, W.-T., Zhang, W., Yang, X., Pootoolal, J., Chua, G., Lopez, A., et al. (2004) · Cell · doi:10.1016/j.cell.2004.06.013 · Cited by 604
Self-citationUpc2p and Ecm22p, Dual Regulators of Sterol Biosynthesis in Saccharomyces cerevisiae
Vik, Å., & Rine, J. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.19.6395-6405.2001 · Cited by 277
Cited by
Intrinsically disordered proteins: regulation and disease
Babu, M. M., van der Lee, R., de Groot, N. S., & Gsponer, J. (2011) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2011.03.011 · Cited by 601
High-resolution DNA-binding specificity analysis of yeast transcription factors
Zhu, C., Byers, K. J. R. P., McCord, R. P., Shi, Z., Berger, M. F., Newburger, D. E., Saulrieta, K., Smith, Z., Shah, M. V., Radhakrishnan, M., et al. (2009) · Genome Research · doi:10.1101/gr.090233.108 · Cited by 398
Universality in network dynamics
Barzel, B., & Barabási, A.-L. (2013) · Nature Physics · doi:10.1038/nphys2741 · Cited by 396
Deciphering eukaryotic gene-regulatory logic with 100 million random promoters
de Boer, C. G., Vaishnav, E. D., Sadeh, R., Abeyta, E. L., Friedman, N., & Regev, A. (2020) · Nature Biotechnology · doi:10.1038/s41587-019-0315-8 · Cited by 283
Kemmeren, P., Sameith, K., van de Pasch, L. A. L., Benschop, J. J., Lenstra, T. L., Margaritis, T., O’Duibhir, E., Apweiler, E., van Wageningen, S., Ko, C. W., et al. (2014) · Cell · doi:10.1016/j.cell.2014.02.054 · Cited by 277
Metadata
- Authors
- Chua, G., Morris, Q. D., Sopko, R., Robinson, M. D., Ryan, O., Chan, E. T., Frey, B. J., Andrews, B. J., Boone, C., & Hughes, T. R.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2006-08-08
- Volume
- 103
- Issue
- 32
- Pages
- 12045-12050
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2158107150
- Cited by
- 183
- References
- 3
- FWCI
- 4.54
- Type
- journal article
- Language
- en
- Open access
- closed
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- Chua, G., Morris, Q. D., Sopko, R., Robinson, M. D., Ryan, O., Chan, E. T., Frey, B. J., Andrews, B. J., Boone, C., & Hughes, T. R. (2006). Identifying transcription factor functions and targets by phenotypic activation. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0605140103
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