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Differential binding of the related transcription factors Pho4 and Cbf1 can tune the sensitivity of promoters to different levels of an induction signal.

Aow JS, Xue X, Run JQ, Lim GF, Goh WS, Clarke ND - Nucleic Acids Res. (2013)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Computational and Systems Biology, Genome Institute of Singapore, 60 Biopolis St., Singapore 138672, Singapore.

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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Reporters with high Cbf1: Pho4 affinity ratios show a sensitivity to induction that is anomalously high based on the simple Pho4 + Cbf1 model (X’s), but are explained well a model that assumes a role for bound Cbf1 in shifting promoter chromatin structures toward a more accessible state (circles). Sensitivities were calculated as described in the text. Colors indicate the NA (green), NC (blue), NG (yellow) and NT (red) reporters as in other figures.
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gkt210-F5: Reporters with high Cbf1: Pho4 affinity ratios show a sensitivity to induction that is anomalously high based on the simple Pho4 + Cbf1 model (X’s), but are explained well a model that assumes a role for bound Cbf1 in shifting promoter chromatin structures toward a more accessible state (circles). Sensitivities were calculated as described in the text. Colors indicate the NA (green), NC (blue), NG (yellow) and NT (red) reporters as in other figures.

Mentions: For a family of promoters with a single binding site, and which are otherwise identical, we can expect a monotonic relationship between the affinity for the binding site and the sensitivity to induction (Supplementary Figure S8). While the precise shape of this relationship depends on the concentrations of the transcription factor with respect to the affinities, the overall trend is robust to these differences. We therefore calculated sensitivity values from the experimental GFP expression values for the 16 reporter constructs and compared these values with the in vitro affinities of the binding sites (Methods). For 12 of the 16 promoters, those with sites flanked by [N][ACG], we find a strong linear correlation between Pho4 affinity and induction sensitivity (R = 0.85). The correlation is improved to R = 0.92 if, instead of using Pho4 affinity, we use predicted induction sensitivity (Figure 5). This can be done using the predicted expression levels obtained previously from the model, with no additional parameterization.Figure 5.


Differential binding of the related transcription factors Pho4 and Cbf1 can tune the sensitivity of promoters to different levels of an induction signal.

Aow JS, Xue X, Run JQ, Lim GF, Goh WS, Clarke ND - Nucleic Acids Res. (2013)

Reporters with high Cbf1: Pho4 affinity ratios show a sensitivity to induction that is anomalously high based on the simple Pho4 + Cbf1 model (X’s), but are explained well a model that assumes a role for bound Cbf1 in shifting promoter chromatin structures toward a more accessible state (circles). Sensitivities were calculated as described in the text. Colors indicate the NA (green), NC (blue), NG (yellow) and NT (red) reporters as in other figures.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3643608&req=5

gkt210-F5: Reporters with high Cbf1: Pho4 affinity ratios show a sensitivity to induction that is anomalously high based on the simple Pho4 + Cbf1 model (X’s), but are explained well a model that assumes a role for bound Cbf1 in shifting promoter chromatin structures toward a more accessible state (circles). Sensitivities were calculated as described in the text. Colors indicate the NA (green), NC (blue), NG (yellow) and NT (red) reporters as in other figures.
Mentions: For a family of promoters with a single binding site, and which are otherwise identical, we can expect a monotonic relationship between the affinity for the binding site and the sensitivity to induction (Supplementary Figure S8). While the precise shape of this relationship depends on the concentrations of the transcription factor with respect to the affinities, the overall trend is robust to these differences. We therefore calculated sensitivity values from the experimental GFP expression values for the 16 reporter constructs and compared these values with the in vitro affinities of the binding sites (Methods). For 12 of the 16 promoters, those with sites flanked by [N][ACG], we find a strong linear correlation between Pho4 affinity and induction sensitivity (R = 0.85). The correlation is improved to R = 0.92 if, instead of using Pho4 affinity, we use predicted induction sensitivity (Figure 5). This can be done using the predicted expression levels obtained previously from the model, with no additional parameterization.Figure 5.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Computational and Systems Biology, Genome Institute of Singapore, 60 Biopolis St., Singapore 138672, Singapore.

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.

Show MeSH
Related in: MedlinePlus