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| Status |
Public on May 20, 2021 |
| Title |
SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH-sensing. We determined that a nucleocytoplasmic pH oscillation was required for the transcriptional response to carbon starvation in S. cerevisiae.
Methods: We performed RNA sequencing analysis to determine the extent of the requirement for theSNF5 QLC in the activation of glucose-repressed genes. Total RNA was extracted from WT, ΔQ-snf5 and HtoA-snf5 strains during exponentially growth (+Glu) and after 4 hours of glucose starvation. Next, Poly-A selection was performed using Dynabeads and libraries were performed following manufactures indications. Sequencing of the 32 samples was performed on an Illumina Hi-seq on two lanes. RNA-seq data were aligned to the University of California, Santa Cruz (UCSC), sacCer2 genome using Kallisto (0.43.0,http://www.nature.com/nbt/journal/v34/n5/full/nbt.3519.html) and downstream visualization and analysis was done using R (3.2.2). Differential gene expression analysis, heat maps and volcano plots were created using DESeq2 where a wald test was used to determine differentially expressed genes and Euclidean distance to calculate clustering for heat maps.
Conclusions: We found that pH changes and the SNF5 QLC are required for correct transcriptional reprogramming upon carbon starvation, but the dependencies are nuanced.
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| Overall design |
S.cerevisiae cells were grown in glucose or starvation conditions with the following genotypes: WT, delta-Q, HtoA-snf5 or starved at pH7.
Analysis scripts available: https://github.com/gbritt/Kallisto_DESeq2_Scripts_RNASeq_12.18.17
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| Contributor(s) |
Brittingham GP, Holt LJ, Gutierrez JI |
| Citation(s) |
35129437 |
| |
| Submission date |
May 19, 2021 |
| Last update date |
Mar 09, 2022 |
| Contact name |
Gregory Brittingham |
| E-mail(s) |
gbritt91@gmail.com
|
| Organization name |
NYU Institute for Systems Genetics
|
| Department |
Cell Biology
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| Lab |
Liam Holt Lab
|
| Street address |
435 East 30th street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platforms (1) |
| GPL17342 |
Illumina HiSeq 2500 (Saccharomyces cerevisiae) |
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| Samples (21)
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| Relations |
| BioProject |
PRJNA731118 |
| SRA |
SRP320494 |
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