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| Status |
Public on May 21, 2021 |
| Title |
A role for condensin in mediating transcriptional adaptation to environmental stimuli. [TT-Seq] |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The relationship between chromatin and transcription was investigated through condensin, a key regulator of higher order chromatin structure. We use rapid conditional condensin depletion in nocodozole arrested cells in budding yeast S. cerevisiae cells to study condensin’s role in transcriptional regulation. We use TT-Chemseq to assess global RNA levels through a S. pombe spike-in, and found that condensin depletion leads to upregulation of global transcription. We also found transcriptional changes in response to environmental stimuli are subdued by condensin depletion.
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| Overall design |
RNA-Seq analysis of Saccharomyces cerevisiae W303-1A strains transformed with promoter exchange of the YCG1 promoter with the MET3 promoter, auxin-inducible degron (IAA7) tagged YCG1 with OsTIR1 ligase, or control strains . 3 biological replicates for each sample type and condition are analysed. For each biological replicate, cells were grown overnight in YNB + CSM -methioninie medium, synchronised from an OD600 of 0.2 in G1 for 2 hours then released into fresh YNB + CSM -methionine medium containing nocodozole for 1.5 hours to achieve a metaphase arrest. Methionine was added at a final concentration of 133μg/ml to shut off the MET3 promoter and indole-acetic acid (IAA, auxin) at a final concentration of 88μg/ml to degrade Ycg1. 4-TU was added to the samples at a final concentration of 5mM for 5 minutes before collection from the control and degron strains with and without methionine and auxin treatment. A sample from each strain which had undergone auxin and methionine treatment was then heat shocked for 15minutes at 37°C for 15 minutes, followed by a 5 minute 4-TU pulse before collection. Total RNA was collected for nascent RNA isolation. RNA was also obtained from 4-TU pulsed S. pombe for the spike-in.
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| Contributor(s) |
Lancaster L, Patel H, Kelly G, Uhlmann F |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Nov 16, 2020 |
| Last update date |
May 23, 2021 |
| Contact name |
Lucy Lancaster |
| E-mail(s) |
lucy.lancaster@crick.ac.uk
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| Organization name |
The Francis Crick Institute
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| Lab |
Chromosome Segregation Laboratory
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| Street address |
1 Midland Rd
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| City |
London |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL21656 |
Illumina HiSeq 4000 (Saccharomyces cerevisiae) |
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| Samples (18)
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| GSM4910510 |
Control Met + Auxin TT-seq replicate 1 |
| GSM4910511 |
Control Met + Auxin TT-seq replicate 2 |
| GSM4910512 |
Control Met + Auxin TT-seq replicate 3 |
| GSM4910513 |
Control Heat shock TT-seq replicate 1 |
| GSM4910514 |
Control Heat shock TT-seq replicate 2 |
| GSM4910515 |
Control Heat shock TT-seq replicate 3 |
| GSM4910516 |
Ycg1Degron2 Untreated TT-seq replicate 1 |
| GSM4910517 |
Ycg1Degron2 Untreated TT-seq replicate 2 |
| GSM4910518 |
Ycg1Degron2 Untreated TT-seq replicate 3 |
| GSM4910519 |
Ycg1Degron2 Met + Auxin TT-seq replicate 1 |
| GSM4910520 |
Ycg1Degron2 Met + Auxin TT-seq replicate 2 |
| GSM4910521 |
Ycg1Degron2 Met + Auxin TT-seq replicate 3 |
| GSM4910522 |
Ycg1Degron2 Heat shock TT-seq replicate 1 |
| GSM4910523 |
Ycg1Degron2 Heat shock TT-seq replicate 2 |
| GSM4910524 |
Ycg1Degron2 Heat shock TT-seq replicate 3 |
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| This SubSeries is part of SuperSeries: |
| GSE161582 |
A role for condensin in mediating transcriptional adaptation to environmental stimuli. |
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| Relations |
| BioProject |
PRJNA678751 |
| SRA |
SRP292778 |
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