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High-resolution DNA-binding specificity analysis of yeast transcription factors
Open accessAbstract
Transcription factors (TFs) regulate the expression of genes through sequence-specific interactions with DNA-binding sites. However, despite recent progress in identifying in vivo TF binding sites by microarray readout of chromatin immunoprecipitation (ChIP-chip), nearly half of all known yeast TFs are of unknown DNA-binding specificities, and many additional predicted TFs remain uncharacterized. To address these gaps in our knowledge of yeast TFs and their cis regulatory sequences, we have determined high-resolution binding profiles for 89 known and predicted yeast TFs, over more than 2.3 million gapped and ungapped 8-bp sequences (“k-mers”). We report 50 new or significantly different direct DNA-binding site motifs for yeast DNA-binding proteins and motifs for eight proteins for which only a consensus sequence was previously known; in total, this corresponds to over a 50% increase in the number of yeast DNA-binding proteins with experimentally determined DNA-binding specificities. Among other novel regulators, we discovered proteins that bind the PAC (P olymerase A and C) motif (GATGAG) and regulate ribosomal RNA (rRNA) transcription and processing, core cellular processes that are constituent to ribosome biogenesis. In contrast to earlier data types, these comprehensive k-mer binding data permit us to consider the regulatory potential of genomic sequence at the individual word level. These k-mer data allowed us to reannotate in vivo TF binding targets as direct or indirect and to examine TFs' potential effects on gene expression in ∼1700 environmental and cellular conditions. These approaches could be adapted to identify TFs and cis regulatory elements in higher eukaryotes.
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Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes
Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., Botstein, D., & Brown, P. O. (2000) · Molecular Biology of the Cell · doi:10.1091/mbc.11.12.4241 · Cited by 4,815
A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome
Wei, C.-L., Wu, Q., Vega, V. B., Chiu, K. P., Ng, P., Zhang, T., Shahab, A., Yong, H. C., Fu, Y., Weng, Z., et al. (2006) · Cell · doi:10.1016/j.cell.2005.10.043 · Cited by 1,141
Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences
Berger, M. F., Badis, G., Gehrke, A. R., Talukder, S., Philippakis, A. A., Peña-Castillo, L., Alleyne, T. M., Mnaimneh, S., Botvinnik, O. B., Chan, E. T., et al. (2008) · Cell · doi:10.1016/j.cell.2008.05.024 · Cited by 606
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Nobile, C. J., Fox, E. P., Nett, J. E., Sorrells, T. R., Mitrovich, Q. M., Hernday, A. D., Tuch, B. B., Andes, D. R., & Johnson, A. D. (2012) · Cell · doi:10.1016/j.cell.2011.10.048 · Cited by 711
Sharon, E., Kalma, Y., Sharp, A., Raveh-Sadka, T., Levo, M., Zeevi, D., Keren, L., Yakhini, Z., Weinberger, A., & Segal, E. (2012) · Nature Biotechnology · doi:10.1038/nbt.2205 · Cited by 457
Evaluation of methods for modeling transcription factor sequence specificity
DREAM5 Consortium, Weirauch, M. T., Cote, A., Norel, R., Annala, M., Zhao, Y., Riley, T. R., Saez-Rodriguez, J., Cokelaer, T., Vedenko, A., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2486 · Cited by 381
Self-citationA dynamic model of proteome changes reveals new roles for transcript alteration in yeast
Lee, M. V., Topper, S. E., Hubler, S. L., Hose, J., Wenger, C. D., Coon, J. J., & Gasch, A. P. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.48 · Cited by 290
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Nutiu, R., Friedman, R. C., Luo, S., Khrebtukova, I., Silva, D., Li, R., Zhang, L., Schroth, G. P., & Burge, C. B. (2011) · Nature Biotechnology · doi:10.1038/nbt.1882 · Cited by 194
Grossman, S. R., Zhang, X., Wang, L., Engreitz, J., Melnikov, A., Rogov, P., Tewhey, R., Isakova, A., Deplancke, B., Bernstein, B. E., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1621150114 · Cited by 165
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Hernday, A. D., Lohse, M. B., Fordyce, P. M., Nobile, C. J., DeRisi, J. L., & Johnson, A. D. (2013) · Molecular Microbiology · doi:10.1111/mmi.12329 · Cited by 131
Evolutionary principles of modular gene regulation in yeasts
Thompson, D. A., Roy, S., Chan, M., Styczynsky, M. P., Pfiffner, J., French, C., Socha, A., Thielke, A., Napolitano, S., Muller, P., et al. (2013) · eLife · doi:10.7554/elife.00603 · Cited by 78
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Habib, N., Wapinski, I., Margalit, H., Regev, A., & Friedman, N. (2012) · Molecular Systems Biology · doi:10.1038/msb.2012.50 · Cited by 50
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Yu, X., Bian, X., Throop, A., Song, L., Moral, L. D., Park, J., Seiler, C., Fiacco, M., Steel, J., Hunter, P., et al. (2014) · Theranostics · doi:10.7150/thno.8255 · Cited by 34
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He, B. Z., Zhou, X., & O’Shea, E. K. (2017) · eLife · doi:10.7554/elife.25157 · Cited by 27
Marotta, D. H., Nantel, A., Sukala, L., Teubl, J. R., & Rauceo, J. M. (2013) · Genomics · doi:10.1016/j.ygeno.2013.06.002 · Cited by 19
Sun, Y., Li, J., Huang, J., Li, S., Li, Y., Lu, B., & Deng, X. (2025) · eLife · doi:10.7554/elife.96172.3 · Cited by 6
Metadata
- Authors
- 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., Philippakis, A. A., Hu, Y., De Masi, F., Pacek, M., Rolfs, A., Murthy, T., LaBaer, J., & Bulyk, M. L.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2009-01-21
- Volume
- 19
- Issue
- 4
- Pages
- 556-566
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2110037042
- Cited by
- 398
- References
- 3
- Type
- posted content
- Language
- en
- Open access
- bronze
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