Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.


Logo for

Science 319 (5871): 1797-1799

Copyright © 2008 by the American Association for the Advancement of Science

Evolution of Eukaryotic Transcription Circuits

Brian B. Tuch,1,2 Hao Li,1 Alexander D. Johnson1,2*

Abstract: The gradual modification of transcription circuits over evolutionary time scales is an important source of the diversity of life. Over the past decade, studies in animals have shown how seemingly small molecular changes in gene regulation can have large effects on morphology and physiology and how selective pressures can act on these changes. More recently, genome-wide studies, particularly those in single-cell yeasts, have uncovered evidence of extensive transcriptional rewiring, indicating that even closely related organisms regulate their genes using markedly different circuitries.

1 Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
2 Department of Microbiology and Immunology, University of California, San Francisco, CA, USA.

* To whom correspondence should be addressed. E-mail: ajohnson{at}

Epistatic relationships reveal the functional organization of yeast transcription factors.
J. Zheng, J. J. Benschop, M. Shales, P. Kemmeren, J. Greenblatt, G. Cagney, F. Holstege, H. Li, and N. J. Krogan (2014)
Mol Syst Biol 6, 420
   Abstract »    Full Text »    PDF »
Evolution and functional cross-talk of protein post-translational modifications.
P. Beltrao, P. Bork, N. J. Krogan, and V. van Noort (2014)
Mol Syst Biol 9, 714
   Abstract »    Full Text »    PDF »
Transcription Factor RFX1 Is Crucial for Maintenance of Genome Integrity in Fusarium graminearum.
K. Min, H. Son, J. Y. Lim, G. J. Choi, J.-C. Kim, S. D. Harris, and Y.-W. Lee (2014)
Eukaryot. Cell 13, 427-436
   Abstract »    Full Text »    PDF »
WetA Is Required for Conidiogenesis and Conidium Maturation in the Ascomycete Fungus Fusarium graminearum.
H. Son, M.-G. Kim, K. Min, J. Y. Lim, G. J. Choi, J.-C. Kim, S.-K. Chae, and Y.-W. Lee (2014)
Eukaryot. Cell 13, 87-98
   Abstract »    Full Text »    PDF »
Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution.
A. I. Ramos and S. Barolo (2013)
Phil Trans R Soc B 368, 20130018
   Abstract »    Full Text »    PDF »
Mitochondria Influence CDR1 Efflux Pump Activity, Hog1-Mediated Oxidative Stress Pathway, Iron Homeostasis, and Ergosterol Levels in Candida albicans.
E. Thomas, E. Roman, S. Claypool, N. Manzoor, J. Pla, and S. L. Panwar (2013)
Antimicrob. Agents Chemother. 57, 5580-5599
   Abstract »    Full Text »    PDF »
The evolution of complex gene regulation by low-specificity binding sites.
A. J. Stewart and J. B. Plotkin (2013)
Proc R Soc B 280, 20131313
   Abstract »    Full Text »    PDF »
Multiple Genomic Changes Associated with Reorganization of Gene Regulation and Adaptation in Yeast.
L. David, Y. Ben-Harosh, E. Stolovicki, L. S. Moore, M. Nguyen, R. Tamse, J. Dean, E. Mancera, L. M. Steinmetz, and E. Braun (2013)
Mol. Biol. Evol. 30, 1514-1526
   Abstract »    Full Text »    PDF »
Identifying Cis-Regulatory Changes Involved in the Evolution of Aerobic Fermentation in Yeasts.
Z. Lin, T.-Y. Wang, B.-S. Tsai, F.-T. Wu, F.-J. Yu, Y.-J. Tseng, H.-M. Sung, and W.-H. Li (2013)
Genome Biol Evol 5, 1065-1078
   Abstract »    Full Text »    PDF »
Evolutionary principles of modular gene regulation in yeasts.
D. A. Thompson, S. Roy, M. Chan, M. P. Styczynsky, J. Pfiffner, C. French, A. Socha, A. Thielke, S. Napolitano, P. Muller, et al. (2013)
eLife Sci 2, e00603
   Abstract »    Full Text »    PDF »
Promoter propagation in prokaryotes.
M. Matus-Garcia, H. Nijveen, and M. W. J. van Passel (2012)
Nucleic Acids Res. 40, 10032-10040
   Abstract »    Full Text »    PDF »
Why Transcription Factor Binding Sites Are Ten Nucleotides Long.
A. J. Stewart, S. Hannenhalli, and J. B. Plotkin (2012)
Genetics 192, 973-985
   Abstract »    Full Text »    PDF »
Reshaping of global gene expression networks and sex-biased gene expression by integration of a young gene.
S. Chen, X. Ni, B. H. Krinsky, Y. E. Zhang, M. D. Vibranovski, K. P. White, and M. Long (2012)
EMBO J. 31, 2798-2809
   Abstract »    Full Text »    PDF »
Thousands of Cis-Regulatory Sequence Combinations Are Shared by Arabidopsis and Poplar.
J. Ding, H. Hu, and X. Li (2012)
Plant Physiology 158, 145-155
   Abstract »    Full Text »    PDF »
Conservation of transcription factor binding events predicts gene expression across species.
M. Hemberg and G. Kreiman (2011)
Nucleic Acids Res. 39, 7092-7102
   Abstract »    Full Text »    PDF »
Coevolution of Morphology and Virulence in Candida Species.
D. S. Thompson, P. L. Carlisle, and D. Kadosh (2011)
Eukaryot. Cell 10, 1173-1182
   Abstract »    Full Text »    PDF »
Evolution of a derived protein-protein interaction between HoxA11 and Foxo1a in mammals caused by changes in intramolecular regulation.
K. J. Brayer, V. J. Lynch, and G. P. Wagner (2011)
PNAS 108, E414-E420
   Abstract »    Full Text »    PDF »
Cdk2-dependent phosphorylation of p21 regulates the role of Cdk2 in cisplatin cytotoxicity.
R. Hodeify, A. Tarcsafalvi, J. Megyesi, R. L. Safirstein, and P. M. Price (2011)
Am J Physiol Renal Physiol 300, F1171-F1179
   Abstract »    Full Text »    PDF »
Is Transcription Factor Binding Site Turnover a Sufficient Explanation for Cis-Regulatory Sequence Divergence?.
S. Venkataram and J. C. Fay (2010)
Genome Biol Evol 2, 851-858
   Abstract »    Full Text »    PDF »
Dissecting the expression patterns of transcription factors across conditions using an integrated network-based approach.
S. C. Janga and B. Contreras-Moreira (2010)
Nucleic Acids Res. 38, 6841-6856
   Abstract »    Full Text »    PDF »
Protein evolution in yeast transcription factor subnetworks.
Y. Wang, E. A. Franzosa, X.-S. Zhang, and Y. Xia (2010)
Nucleic Acids Res. 38, 5959-5969
   Abstract »    Full Text »    PDF »
Regulatory Factor X (RFX)-mediated transcriptional rewiring of ciliary genes in animals.
B. P. Piasecki, J. Burghoorn, and P. Swoboda (2010)
PNAS 107, 12969-12974
   Abstract »    Full Text »    PDF »
Gene duplication and the evolution of ribosomal protein gene regulation in yeast.
I. Wapinski, J. Pfiffner, C. French, A. Socha, D. A. Thompson, and A. Regev (2010)
PNAS 107, 5505-5510
   Abstract »    Full Text »    PDF »
NFIL3 and cAMP Response Element-Binding Protein Form a Transcriptional Feedforward Loop that Controls Neuronal Regeneration-Associated Gene Expression.
H. D. MacGillavry, F. J. Stam, M. M. Sassen, L. Kegel, W. T. J. Hendriks, J. Verhaagen, A. B. Smit, and R. E. van Kesteren (2009)
J. Neurosci. 29, 15542-15550
   Abstract »    Full Text »    PDF »
Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution.
L. J. Holt, B. B. Tuch, J. Villen, A. D. Johnson, S. P. Gygi, and D. O. Morgan (2009)
Science 325, 1682-1686
   Abstract »    Full Text »    PDF »
Dampened Hedgehog signaling but normal Wnt signaling in zebrafish without cilia.
P. Huang and A. F. Schier (2009)
Development 136, 3089-3098
   Abstract »    Full Text »    PDF »
Transcriptional Analysis of the Candida albicans Cell Cycle.
P. Cote, H. Hogues, and M. Whiteway (2009)
Mol. Biol. Cell 20, 3363-3373
   Abstract »    Full Text »    PDF »
Degree dependence in rates of transcription factor evolution explains the unusual structure of transcription networks.
A. J. Stewart, R. M. Seymour, and A. Pomiankowski (2009)
Proc R Soc B 276, 2493-2501
   Abstract »    Full Text »    PDF »
Transcription factor function and promoter architecture govern the evolution of bacterial regulons.
J. C. Perez and E. A. Groisman (2009)
PNAS 106, 4319-4324
   Abstract »    Full Text »    PDF »
Conserved factors Ryp2 and Ryp3 control cell morphology and infectious spore formation in the fungal pathogen Histoplasma capsulatum.
R. H. Webster and A. Sil (2008)
PNAS 105, 14573-14578
   Abstract »    Full Text »    PDF »

To Advertise     Find Products

Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882