ArticleNucleic acids research2013
Differential binding of the related transcription factors Pho4 and Cbf1 can tune the sensitivity of promoters to different levels of an induction signal.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 16 citations in OpenAlex.
- Article
- Article
- Transcription factor CBF-1 is critical for circadian gene expression by modulating WHITE COLLAR complex recruitment to the frq locus.PLoS genetics · 2018Article
- Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Predicting the impact of promoter variability on regulatory outputs.Scientific reports · 2015Article
- Core promoter sequence in yeast is a major determinant of expression level.Genome research · 2015Article
- A comprehensive protein-protein interactome for yeast PAS kinase 1 reveals direct inhibition of respiration through the phosphorylation of Cbf1.Molecular biology of the cell · 2014Article
- In pursuit of design principles of regulatory sequences.Nature reviews. Genetics · 2014Review
- Mapping the fine structure of a eukaryotic promoter input-output function.Nature genetics · 2013Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
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Abstract
Transcription factors that belong to the same family typically have similar, but not identical, binding specificities. As such, they can be expected to compete differentially for binding to different variants of their binding sites. Pho4 is a yeast factor whose nuclear concentration is up-regulated in low phosphate, while the related factor, Cbf1, is constitutively expressed. We constructed 16 GFP-reporter genes containing all palindromic variants of the motif NNCACGTGNN, and determined their activities at a range of phosphate concentrations. Pho4 affinity did not explain expression data well except under fully induced conditions. However, reporter activity was quantitatively well explained under all conditions by a model in which Cbf1 itself has modest activating activity, and Pho4 and Cbf1 compete with one another. Chromatin immunoprecipitation and computational analyses of natural Pho4 target genes, along with the activities of the reporter constructs, indicates that genes differ in their sensitivity to intermediate induction signals in part because of differences in their affinity for Cbf1. The induction sensitivity of both natural Pho4 target genes and reporter genes was well explained only by a model that assumes a role for Cbf1 in remodeling chromatin. Our analyses highlight the importance of taking into account the activities of related transcription factors in explaining system-wide gene expression data.
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