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| Status |
Public on Jun 25, 2024 |
| Title |
Nitrogen signaling factor changes gene expression and binding of transcription factors [RNA-seq] |
| Organism |
Schizosaccharomyces pombe |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
High quality nitrogen sources such as NH4+ and glutamate inhibit the uptake of poor nitrogen sources including amino acids (leucine etc.), which is called “nitrogen catabolite repression (NCR)”. We found a cell-to-cell communication system in fission yeast that inactivates NCR and enables cells to take up leucine even on high NH4+ medium (referred to as adaptive growth). Furthermore, we identified novel oxylipins responsible for the adaptive growth, which are secreted from cells and are referred to as nitrogen signaling factors (NSF). RNA-seq analyses showed that mitochondrial respiratory-related genes are differentially expressed upon addition of synthetic NSF. These results suggest that the cell-to-cell communication via NSF reprograms the metabolic preference from glycolysis to mitochondrial respiration. Moreover, we also performed ChIP-seq of transcription factors (TFs) and found that bindings of several TFs on DNA are regulated by NSF.
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| Overall design |
To investigate global changes in gene expression in response to NSF exposure, we performed total RNA sequencing with cells that were grown in the presence of high ammonium concentrations and exposed to synthetic NSF for two, four, or six hours. Two - three replicates per time-point were sequenced. Furthermore, to explore transcription factor occupancy with NSF treatment, ChIP-seq of FLAG-tagged transcription factors Adn2, Atf1, Fil1, Hsr1, Php3, and Reb1 was performed in triplicates on strains for input and FLAG-IP (108 samples).
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| Contributor(s) |
Ohsawa S, Mohn F, Bühler M |
| Citation(s) |
39256560 |
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| Submission date |
Dec 13, 2023 |
| Last update date |
Oct 09, 2024 |
| Contact name |
Fabio Mohn |
| E-mail(s) |
fabio.mohn@fmi.ch
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| Organization name |
Friedrich Miescher Institute for Biomedical Research
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| Lab |
Buehler Lab
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| Street address |
Maulbeerstrasse 66
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| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platforms (2) |
| GPL17225 |
Illumina HiSeq 2500 (Schizosaccharomyces pombe) |
| GPL28961 |
Illumina NovaSeq 6000 (Schizosaccharomyces pombe) |
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| Samples (41)
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| GSM7973865 |
RNAseq of parental strain, 2h with methanol, rep 1 |
| GSM7973866 |
RNAseq of parental strain, 2h with methanol, rep 2 |
| GSM7973867 |
RNAseq of parental strain, 2h with methanol, rep 3 |
| GSM7973868 |
RNAseq of parental strain, 2h with NSF, rep 1 |
| GSM7973869 |
RNAseq of parental strain, 2h with NSF, rep 2 |
| GSM7973870 |
RNAseq of parental strain, 2h with NSF, rep 3 |
| GSM7973871 |
RNAseq of parental strain, 4h with methanol, rep 2 |
| GSM7973872 |
RNAseq of parental strain, 4h with methanol, rep 3 |
| GSM7973873 |
RNAseq of parental strain, 4h with NSF, rep 1 |
| GSM7973874 |
RNAseq of parental strain, 4h with NSF, rep 2 |
| GSM7973875 |
RNAseq of parental strain, 4h with NSF, rep 3 |
| GSM7973876 |
RNAseq of parental strain, 6h with methanol, rep 1 |
| GSM7973877 |
RNAseq of parental strain, 6h with methanol, rep 2 |
| GSM7973878 |
RNAseq of parental strain, 6h with methanol, rep 3 |
| GSM7973879 |
RNAseq of parental strain, 6h with NSF, rep 1 |
| GSM7973880 |
RNAseq of parental strain, 6h with NSF, rep 2 |
| GSM7973881 |
RNAseq of parental strain, 6h with NSF, rep 3 |
| GSM8290470 |
RNAseq of parental strain, 0h, experiment 2, rep 1 |
| GSM8290471 |
RNAseq of parental strain, 0h, experiment 2, rep 2 |
| GSM8290472 |
RNAseq of parental strain, 0h, experiment 2, rep 3 |
| GSM8290473 |
RNAseq of parental strain, 2h with methanol, experiment 2, rep 1 |
| GSM8290474 |
RNAseq of parental strain, 2h with methanol, experiment 2, rep 2 |
| GSM8290475 |
RNAseq of parental strain, 2h with methanol, experiment 2, rep 3 |
| GSM8290476 |
RNAseq of parental strain, 2h with NSF, experiment 2, rep 1 |
| GSM8290477 |
RNAseq of parental strain, 2h with NSF, experiment 2, rep 2 |
| GSM8290478 |
RNAseq of parental strain, 2h with NSF, experiment 2, rep 3 |
| GSM8290479 |
RNAseq of parental strain, 4h with methanol, experiment 2, rep 1 |
| GSM8290480 |
RNAseq of parental strain, 4h with methanol, experiment 2, rep 2 |
| GSM8290481 |
RNAseq of parental strain, 4h with methanol, experiment 2, rep 3 |
| GSM8290482 |
RNAseq of parental strain, 4h with NSF, experiment 2, rep 1 |
| GSM8290483 |
RNAseq of parental strain, 4h with NSF, experiment 2, rep 2 |
| GSM8290484 |
RNAseq of parental strain, 4h with NSF, experiment 2, rep 3 |
| GSM8290485 |
RNAseq of parental strain, 6h with methanol, experiment 2, rep 1 |
| GSM8290486 |
RNAseq of parental strain, 6h with methanol, experiment 2, rep 2 |
| GSM8290487 |
RNAseq of parental strain, 6h with methanol, experiment 2, rep 3 |
| GSM8290488 |
RNAseq of parental strain, 6h with NSF, experiment 2, rep 1 |
| GSM8290489 |
RNAseq of parental strain, 6h with NSF, experiment 2, rep 2 |
| GSM8290490 |
RNAseq of parental strain, 6h with NSF, experiment 2, rep 3 |
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| This SubSeries is part of SuperSeries: |
| GSE250095 |
Nitrogen signaling factor changes gene expression and binding of transcription factors |
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| Relations |
| BioProject |
PRJNA1052026 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE250093_RAW.tar |
686.9 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
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