GSE161581
A role for condensin in mediating transcriptional adaptation to environmental stimuli. [TT-Seq]
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. 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.