Transcription of Nearly All Yeast RNA Polymerase II-Transcribed Genes Is Dependent on Transcription Factor TFIID

RNA Pol II transcription has been implied to be either regulated by the general transcription factor TFIID or the co-activator SAGA. Also, this dominancy of either SAGA or TFIID might be according to the existance, or not, of a TATA consensus sequence. We used microarrays to analyse newly-synthesized RNA in two mutants that allow conditional nuclear depletion of Taf4 or Taf5 to reevaluate whether some genes are more affected than others. The genotype of yeast strains was modified to allow nuclear depletion of either Taf4 or Taf5. Taf4 (or Taf5) was depleted from the nucleus by adding either 5uM rapamycin to the cells. To the control cultures only DMSO was added (in these cells Tafs are not depleted from the nucleus and thus were used as the control samples). Newly synthesized mRNA were labeled using 4tU labeling 30 min after the addition of rapamycin. Labeling occured for 6 min. mRNA levels and synthesis rates were measured using Affymetrix GeneChip Yeast Genome 2.0 Array.