Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

MSN2-mCherry vs. msn2 microarray

ABSTRACT: Transcriptional profiling of Msn2 regulated genes. Both strains are PKAas (TPK1M164G TPK2M147G TPK3M165G) and msn4-delta. One strain has Msn2 C-terminally tagged with mCherry and the other strain is msn2-delta. In this experiment, both strains were exposed to 3 uM 1-NM-PP1, which leads to Msn2 nuclear localization, for 0, 10, 20 and 40 min. The goal was to determine the genes that show a strong upregulation in the presence of Msn2, but no expression change in the absence of Msn2.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Anders Hansen

PROVIDER: E-MTAB-1945 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression.

Hansen Anders S AS O'Shea Erin K EK

Molecular systems biology 20131105

Numerous transcription factors (TFs) encode information about upstream signals in the dynamics of their activation, but how downstream genes decode these dynamics remains poorly understood. Using microfluidics to control the nucleocytoplasmic translocation dynamics of the budding yeast TF Msn2, we elucidate the principles that govern how different promoters convert dynamical Msn2 input into gene expression output in single cells. Combining modeling and experiments, we classify promoters accordin ...[more]

PMID: 24189399

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Project description:Binding of transcription factors to DNA is a key regulatory step in the control of gene expression. DNA sequences with high affinity for transcription factors occur more frequently in the genome than instances of genes bound or regulated by these factors. How specific gene regulation is achieved by transcription factors remains unclear. We used genome-wide approaches to study how trans factors shape the binding and regulatory landscape of Pho4, a budding yeast transcription factor that activates gene expression in response to phosphate limitation. In no phosphate (0mM phosphate) medium, Pho4 is transported into the nucleus and activates transcription of a set of genes (PHO) that are necessary for cell survival in phosphate limited environment. In high phosphate (10mM phosphate) medium, Pho4 is transported outside of the nucleus and the transcription program of PHO genes are turned off. Here we examined the transcription profiling of S. cerevisiae (W303) in various strains treated in media with 10mM or 0mM inorganic phosphate, to study the the transcription activation by Pho4 its cooperative binding factor Pho2, and its competitive binding factor Cbf1. (I) To infer how much Pho4 itself, Pho2 itself, and the interaction between Pho2 and Pho4 contribute to transcriptional activation in response to Pi starvation, we applied mutant cycle analysis to compare wild type, pho2Δ, pho4Δ and pho2Δ pho4Δ strains in both 10 mM and 0 mM Pi conditions. Mutant cycle analysis is a cyclic comparison among all various mutants. For example, by comparing pho2Δ and pho2Δ pho4Δ, we can directly infer the contribution from Pho4 alone to gene activation. And by comparing wild type and pho2Δ, we can infer the contribution from Pho2 alone together with that from the interaction between Pho2 and Pho4. (II) Compare two strains or one strain in two treatments in multiple replicates with dye-swap method. wt no vs high Pi, to identify genes that are induced in response to Pi starvation. cbf1Δ vs wt in high Pi, to identify the influence of Cbf1 on gene expression in high Pi condition. cbf1Δpho4Δ vs wt in high Pi, to identify the influence of Cbf1 on gene expression that is mediated through Pho4, in high Pi condition. rtg3Δtye7Δ vs wt in high Pi, to identify the influence of Rtg3 and Tye7 on gene expression in high Pi condition. pho80Δ vs pho80Δpho4Δ, to identify the genes that are activated Pho4 when Pho4 is fully nuclear localized. pho80Δcbf1Δ vs pho80Δcbf1Δpho4Δ, to identify the influence of Cbf1 on gene expression that is mediated through Pho4, when Pho4 is fully nuclear localized.

Dataset Information

MSN2-mCherry vs. msn2 microarray

Publications

Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression.

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