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| Status |
Public on May 13, 2013 |
| Title |
Expression data from Saccharomyces cerevisiae Dnup60, Dada2, and Dnup60 Dada2 cells |
| Platform organisms |
Schizosaccharomyces pombe; Saccharomyces cerevisiae |
| Sample organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by array
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| Summary |
In Saccharomyces cerevisiae, specific genes physically relocate from the nucleoplasm to the nuclear periphery concomitant with transcriptional activation, where they associate with the nuclear pore complex (NPC). We took a genomics approach in order to gain insight into the universality and physiological relevance of the interaction between active genes and the NPC. Using synthetic genetic array (SGA) approach, we identified interactions between components of the SAGA histone acetyltransferase complex and the Mlp and Nup60 subunits of the NPC. Cells lacking these SAGA and NPC components display growth defects under optimal growth conditions, in which cells are grown on rich medium containing the preferred sugar glucose as a carbon source and incubated at their optimal temperature. That growth defects were observed under these non-stress conditions suggests that these interactions are indicative of defects in normal cell physiology. These results are consistent with a model where physical interactions between the NPC and SAGA are important for transcription of constitutively expressed genes. To test this hypothesis, we used microarray analysis to assess changes global transcript levels in the absence of Nup60, Ada2, or Nup60 and Ada2. Microarray analysis reveals that the growth defect in these double mutants is correlated with a synthetic reduction in steady-state transcript levels for numerous genes that are strongly expressed in wildtype cells. These results suggest that SAGA and Nup60 cooperate in transcriptional regulation, and are consistent with a model for global regulation of SAGA-dependent transcription at the NPC.
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| Overall design |
Wildype, single deletion, and double deletion cells were inoculated to equal starting ODs in 50 mL YEPD media and grown at 30C with shaking. Cells were collected at mid-log phase, washed with chilled water, and stored at -80C for later processing. RNA was isolated using TRIzol reagent according to the manufacturer's protocol, with modification for yeast cells.
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| Contributor(s) |
Kerr SC, Haley TM, Fasken MB, Barbara-Haley KE, Santangelo GM, Corbett AH, Willis KA |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
May 17, 2010 |
| Last update date |
Feb 21, 2017 |
| Contact name |
Kristine Willis |
| E-mail(s) |
kaw85@georgetown.edu
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| Organization name |
Georgetown University
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| Department |
Biology
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| Street address |
37 & O Sts. NW
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| City |
Washington |
| State/province |
DC |
| ZIP/Postal code |
20057 |
| Country |
USA |
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| Platforms (1) |
| GPL2529 |
[Yeast_2] Affymetrix Yeast Genome 2.0 Array |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA127059 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE21870_RAW.tar |
12.4 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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