Mot1 regulation of promoter binding by TBP varies with gene expression levels and stress independently of coactivator-dependence [ChIP-Seq]

Mot1 is an essential Snf2-family ATPase in budding yeast that regulates transcription by dissociating the general initiation factor TBP (TATA-binding protein) from DNA. Previous studies showed that in optimum growth conditions Mot1 preferentially removes TBP from stress-responsive promoters that utilize the coactivator SAGA to enhance TBP binding at TFIID-dependent promoters of “housekeeping” genes. In stress conditions of amino acid starvation, by contrast, we found that Mot1 promotes high-level TBP occupancy at genes activated by transcription factor Gcn4, enriched for SAGA-dependent promoters, and at highly-transcribed subsets of constitutively expressed SAGA- and TFIID-dependent genes, while suppressing TBP occupancies at lowly transcribed genes regardless of SAGA/TFIID dependence. Importantly, the response to Mot1 depletion for genes induced by starvation or oxidative stress switched from decreased to increased TBP occupancies when transcribed at low basal levels in non-stressed cells. Notably, reduced TBP binding on Mot1 depletion impairs transcription of highly expressed TFIID genes but not highly expressed SAGA/stress-activated genes, implying that promoter activation by SAGA produces a surfeit of incomplete preinitiation complexes dependent on Mot1 for their formation. Immunopurification of formaledhyde-fixed and sonicated DNA fragments that were subjected to paired-end sequencing