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| Status |
Public on Apr 15, 2017 |
| Title |
Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway [Scer ChIP-seq] |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are jointly required for induction of phosphate response genes and survival in phosphate starvation conditions. In the related human commensal and pathogen C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate-limited conditions and is only partially required for inducing the phosphate response genes. This reduced dependence on Pho2 evolved in C. glabrata and closely related species. Pho4 orthologs that are less dependent on Pho2 induce more genes when introduced into the S. cerevisiae background, and Pho4 in C. glabrata both binds to more sites and induces more genes with expanded functional roles compared to Pho4 in S. cerevisiae. We used Biotin-assisted Chromatin-ImmunoPrecipitation followed by high-throughput sequencing (BioChIP-seq) to identify the binding locations of Pho4 from both S. cerevisiae and C. glabrata in the S. cerevisiae background lacking the negative regulator Pho80, and either with or without Pho2.
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| Overall design |
First, we made S. cerevisiae strains carrying an epitope (AVItag) tagged version of Pho4 from either S. cerevisiae (ScPho4) or C. glabrata (CgPho4), in a genetic background where the negative regulator of Pho4, Pho80 is deleted, and either with or without S. cerevisiae Pho2 (ScPho2). A total of four strains were made and subject to the Bio-ChIP profiling, with one biological sample for each strain. In addition, two strains carrying an untagged version of either ScPho4 or CgPho4 in the same S. cerevisiae background (pho80∆ ScPHO2) were made to serve as mock samples. For both experiment and mock samples, a corresponding "input" sample (sonicated cell lysates prior to immuno-precipitation) was prepared and subject to sequencing.
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| Contributor(s) |
HE BZ, ZHOU X, O'Shea EK |
| Citation(s) |
28485712 |
| |
| Submission date |
Apr 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Bin He |
| E-mail(s) |
emptyhb@gmail.com, bin-he@uiowa.edu
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| Organization name |
the University of Iowa
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| Department |
Biology
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| Lab |
Gene Regulatory Evolution
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| Street address |
129 East Jefferson St., Biology Building 450
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| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
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| Platforms (1) |
| GPL13821 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (9)
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| This SubSeries is part of SuperSeries: |
| GSE97801 |
Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway |
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| Relations |
| BioProject |
PRJNA382952 |
| SRA |
SRP103927 |
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