Downloaded from genome. cshlp org on November 3, 2010- Published by Cold Spring Harbor Laboratory Press Research Coevolution within a transcriptional network by compensatory trans and cis mutations Justin Catalana, Timothy Ravasi, Kai Tan, , and Irey ldeker1, g ang> Dwight Kuo, Katherine Licon, Sourav Bandyopadhyay, Ryan Ch ' Departments of Bioengineering and Medicine, University of Califonia, San Diego, La Jolla, California 92093, USA; 'Red Sea Laboratory of Integrative Systems Biology, Division of Chemical and Life Sciences and Engineering, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia; Departments of Internal Medicine and Biomedical Engineering, University of lowa, lowa City, lowa 52242, USA Transcriptional networks have been shown to evolve very rapidly prompting questions as to how such changes arise and ire tolerated Recent comparisons of transcriptional networks across species have implicated variations in the cis-actin DNA sequences near genes as the main cause of divergence what is less clear is how these changes interact with trans-acting hanges occurring elsewhere in the genetic circuit. Here, we report the discovery of a system of compensatory trans and cis mutations in the yeast AP-l transcriptional network that allows for conserved transcriptional regulation despite continued genetic change We pinpoint a single species, the fungal pathogen Candida glabrata, in which a trans mutation has occurred very recently in a single ap-l family member distinguishing it from its Saccharomyces ortholog. Comparison of chromatin immunoprecipitation profiles between Candida and Saccharomyces shows that despite their different dna-binding domains, the Ap-l orthologs regulate a conserved block of genes. this conservation is enabled by concomitant changes in the cis- regulatory motifs upstream of each gene. Thus, both trans and cis mutations have perturbed the yeast AP-l regulatory ystem in such a way as to compensate for one another this demonstrates an example of "coevolution"between a dna- binding transcription factor and its cis-regulatory site, reminiscent of the coevolution of protein binding partners upplementalmaterialisavailableonlineathttp.www.genome.orgthesequencedatafromthisstudyhavebeen submittedtoheNcblGeneExpressionOmnibus(http://www.ncbi.nlmnihgov/geo/underaccessionno.Gsel5818.] Transcriptional networks are central to understanding both evo- identified transcriptional programs that are dramatically rewired lution and phenotypic diversity among organisms. Of the many over short evolutionary time scales. As with earlier work, many of ways in which transcriptional networks can evolve, much atten- the observed differences in binding and expression have been n has been given to changes in the so-called cis-regulatory re- linked to changes in cis-regulatory regions. For example, Borneman gions of gene promoters (Wray 2007: Wagner and Lynch 2008). et al.(2007)found that the TF Tecl binds only 20% of the same Such changes include gain, loss, or modification of DNA sequence target genes in comparisons between Saccharomyces cerevisiae and motifs(Cliften et al. 2003; Kelliset aL 2003; Gasch et al. 2004; Stark the closely related Saccharomyces bayanus and saccharomyces et al. 2007) as well as alterations in motif spacing relative to the mikatae, and that this difference is due to gain and loss of canonical start of transcription, or to other motifs (Ihmels et al. 2005; Tanay Tecl cis-regulatory motifs. While some recent studies have asso- et al. 2005). In addition to changes in cis, transcriptional networks ciated genetic variants in TEs with gene expression changes ob- can also evolve through alterations to transcription factor (TF) served in interspecies hybrids(wilson et al. 2008; Wittkopp et al. proteins and other trans-acting factors(Wagner and Lynch 2008). 2008; Tirosh et al. 2009; Bullard et al. 2010; Emerson et al. 2010), in trans, potential mechanisms include mutations to protein struc- Gerke et al. 2009; Sung et al. 2009; Zheng et al. 2010), or in human ture impacting transcriptional activation or DNA-binding do- populations(Kasowski et al. 2010), the picture that emerges is that mains(Wagner and Lynch 2008), modulation of TF expression cis-regulatory regions are incredibly plastic over evolutionary time, Sankaran et al. 2009) or post-translational modifications(Holt while TFs(trans)evolve at a comparatively slower rate(Wray 2007) et al. 2009), or gain and loss of protein-protein interactions amo Given the dramatic changes that appear to be occurring in TFs (Tuch et al. 2008; Lavoie et al. 2010). transcriptional networks, a key question is how such systems re- Recently, a number of genome-scale studies have performed tain essential functions over evolutionary time (Wray 2007).One systematic comparisons of TF-binding patterns(Borneman et al. solution is that changes in cis can occur by replacement of one TI 08: Bra Lavoie et al. 2010: cofactor with another, thereby maintaining regulatory control Schmidt et al. 2010)or mRNA expression profiles across species (Tsong et al. 2006). Alternatively, rather than replacing specific Ihmels et al. 2005; Tanayet al 2005; Hogues et al. 2008; Fieldet al. cofactors, it is conceivable that the DNA-binding domains of the 2009; Wapinski et al. 2010). Almost universally, these studies have TFs that bind these cis-regulatory sequences might be altered in lock-step with changes in cis, similarly to the evolution of protein binding partners(Pazos and Valencia 2008). However, such a mechanism of evolution has yet to be observed Here, we present rticle published or Article and publication date are at a direct example of such"coevolution, " where a specific change to http://www.genome.org/cgi/doi/10.1101/gr.111765.110.Freelyavailable DNA-binding transcription factor and its cis-regulatory site have online through the Genome Research Open Access option. occurred in compensatory fashion. 20: 000-000@ 2010 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/10,Research Coevolution within a transcriptional network by compensatory trans and cis mutations Dwight Kuo,1 Katherine Licon,1 Sourav Bandyopadhyay,1 Ryan Chuang,1 Colin Luo,1 Justin Catalana,1 Timothy Ravasi,1,2 Kai Tan,3,4 and Trey Ideker1,4 1 Departments of Bioengineering and Medicine, University of California, San Diego, La Jolla, California 92093, USA; 2 Red Sea Laboratory of Integrative Systems Biology, Division of Chemical and Life Sciences and Engineering, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia; 3 Departments of Internal Medicine and Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, USA Transcriptional networks have been shown to evolve very rapidly, prompting questions as to how such changes arise and are tolerated. Recent comparisons of transcriptional networks across species have implicated variations in the cis-acting DNA sequences near genes as the main cause of divergence. What is less clear is how these changes interact with trans-acting changes occurring elsewhere in the genetic circuit. Here, we report the discovery of a system of compensatory trans and cis mutations in the yeast AP-1 transcriptional network that allows for conserved transcriptional regulation despite continued genetic change. We pinpoint a single species, the fungal pathogen Candida glabrata, in which a trans mutation has occurred very recently in a single AP-1 family member, distinguishing it from its Saccharomyces ortholog. Comparison of chromatin immunoprecipitation profiles between Candida and Saccharomyces shows that, despite their different DNA-binding domains, the AP-1 orthologs regulate a conserved block of genes. This conservation is enabled by concomitant changes in the cis￾regulatory motifs upstream of each gene. Thus, both trans and cis mutations have perturbed the yeast AP-1 regulatory system in such a way as to compensate for one another. This demonstrates an example of ‘‘coevolution’’ between a DNA￾binding transcription factor and its cis-regulatory site, reminiscent of the coevolution of protein binding partners. [Supplemental material is available online at http://www.genome.org. The sequence data from this study have been submitted to he NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) under accession no. GSE15818.] Transcriptional networks are central to understanding both evo￾lution and phenotypic diversity among organisms. Of the many ways in which transcriptional networks can evolve, much atten￾tion has been given to changes in the so-called cis-regulatory re￾gions of gene promoters (Wray 2007; Wagner and Lynch 2008). Such changes include gain, loss, or modification of DNA sequence motifs (Cliften et al. 2003; Kellis et al. 2003; Gasch et al. 2004; Stark et al. 2007) as well as alterations in motif spacing relative to the start of transcription, or to other motifs (Ihmels et al. 2005; Tanay et al. 2005). In addition to changes in cis, transcriptional networks can also evolve through alterations to transcription factor (TF) proteins and other trans-acting factors (Wagner and Lynch 2008). Although there have been fewer reports of evolutionary changes in trans, potential mechanisms include mutations to protein struc￾ture impacting transcriptional activation or DNA-binding do￾mains (Wagner and Lynch 2008), modulation of TF expression (Sankaran et al. 2009) or post-translational modifications (Holt et al. 2009), or gain and loss of protein–protein interactions among TFs (Tuch et al. 2008; Lavoie et al. 2010). Recently, a number of genome-scale studies have performed systematic comparisons of TF-binding patterns (Borneman et al. 2007; Tuch et al. 2008; Bradley et al. 2010; Lavoie et al. 2010; Schmidt et al. 2010) or mRNA expression profiles across species (Ihmels et al. 2005; Tanay et al. 2005; Hogues et al. 2008; Field et al. 2009; Wapinski et al. 2010). Almost universally, these studies have identified transcriptional programs that are dramatically rewired over short evolutionary time scales. As with earlier work, many of the observed differences in binding and expression have been linked to changes in cis-regulatory regions. For example, Borneman et al. (2007) found that the TF Tec1 binds only 20% of the same target genes in comparisons between Saccharomyces cerevisiae and the closely related Saccharomyces bayanus and Saccharomyces mikatae, and that this difference is due to gain and loss of canonical Tec1 cis-regulatory motifs. While some recent studies have asso￾ciated genetic variants in TFs with gene expression changes ob￾served in interspecies hybrids (Wilson et al. 2008; Wittkopp et al. 2008; Tirosh et al. 2009; Bullard et al. 2010; Emerson et al. 2010), in outbred crosses (Brem and Kruglyak 2005; Landry et al. 2005; Gerke et al. 2009; Sung et al. 2009; Zheng et al. 2010), or in human populations (Kasowski et al. 2010), the picture that emerges is that cis-regulatory regions are incredibly plastic over evolutionary time, while TFs (trans) evolve at a comparatively slower rate (Wray 2007). Given the dramatic changes that appear to be occurring in transcriptional networks, a key question is how such systems re￾tain essential functions over evolutionary time (Wray 2007). One solution is that changes in cis can occur by replacement of one TF cofactor with another, thereby maintaining regulatory control (Tsong et al. 2006). Alternatively, rather than replacing specific cofactors, it is conceivable that the DNA-binding domains of the TFs that bind these cis-regulatory sequences might be altered in lock-step with changes in cis, similarly to the evolution of protein￾binding partners (Pazos and Valencia 2008). However, such a mechanism of evolution has yet to be observed. Here, we present a direct example of such ‘‘coevolution,’’ where a specific change to a DNA-binding transcription factor and its cis-regulatory site have occurred in compensatory fashion. 4 Corresponding authors. E-mail tideker@ucsd.edu. E-mail kai-tan@uiowa.edu. Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.111765.110. Freely available online through the Genome Research Open Access option. 20:000–000 ! 2010 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/10; www.genome.org Genome Research 1 www.genome.org Downloaded from genome.cshlp.org on November 3, 2010 - Published by Cold Spring Harbor Laboratory Press