Genetic analysis of variation in transcription factor binding in yeast

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Variation in transcriptional regulation is thought to be a major cause of phenotypic diversity1,2. Although widespread differences in gene expression among individuals of a species have been observed3,4,5,6,7,8, studies to examine the variability of transcription factor binding on a global scale have not been performed, and thus the extent and underlying genetic basis of transcription factor binding diversity is unknown. By mapping differences in transcription factor binding among individuals, here we present the genetic basis of such variation on a genome-wide scale. Whole-genome Ste12-binding profiles were determined using chromatin immunoprecipitation coupled with DNA sequencing in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains and their parental lines. We identified extensive Ste12-binding variation among individuals, and mapped underlying cis- and trans-acting loci responsible for such variation. We showed that most transcription factor binding variation is cis-linked, and that many variations are associated with polymorphisms residing in the binding motifs of Ste12 as well as those of several proposed Ste12 cofactors. We also identified two trans-factors, AMN1 and FLO8, that modulate Ste12 binding to promoters of more than ten genes under α-factor treatment. Neither of these two genes was previously known to regulate Ste12, and we suggest that they may be mediators of gene activity and phenotypic diversity. Ste12 binding strongly correlates with gene expression for more than 200 genes, indicating that binding variation is functional. Many of the variable-bound genes are involved in cell wall organization and biogenesis. Overall, these studies identified genetic regulators of molecular diversity among individuals and provide new insights into mechanisms of gene regulation.

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Figure 1: Extensive Ste12-binding variations among S288c × YJM789 derivatives.
Figure 2: Whole-genome linkage analysis of variable Ste12-binding traits.
Figure 3: Motif analysis of cis-variable binding regions.
Figure 4: Validation of two causative quantitative trait genes.
Figure 5: Ste12 binding significantly correlates with downstream gene expression.

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Gene Expression Omnibus

Data deposits

Raw data are deposited in the Gene Expression Omnibus (GEO) database ( under accession number GSE19636.


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We thank J. Gagneur for comments on data analysis, the Cornell Microarray Facility for helping with the gene expression experiments, A. Lin for preprocessing of microarray data, C. Yellman for technical help, and Yale University Biomedical High Performance Computing Center (NIH grant RR19895) for providing computation resources. Research was funded by National Institutes of Health (NIH) grants to M.S., H.Z. and L.M.S.

Author Contributions W.Z. and M.S. designed the study, E.M. and L.S. provided yeast strains, W.Z. performed experiments, W.Z. and H.Z. analysed the data, E.M., L.M.S. and M.S. provided suggestions in data analysis, and all authors co-wrote the paper.

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Correspondence to Michael Snyder.

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The authors declare no competing financial interests.

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Zheng, W., Zhao, H., Mancera, E. et al. Genetic analysis of variation in transcription factor binding in yeast. Nature 464, 1187–1191 (2010) doi:10.1038/nature08934

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