Chemically regulated transcription factors reveal the persistence of repressor-resistant transcription after disrupting activator function

Control of gene expression often requires that transcription terminates rapidly after destruction, inactivation, or nuclear export of transcription factors. However, the role of transcription factor inactivation in terminating transcription is unclear. We have developed a means of conducting order of addition and co-occupancy experiments in living cells by rapidly exchanging proteins bound to promoters. Using this approach, we found that, following specific disruption of activator function, transcription from active promoters decayed slowly, persisting through multiple cell divisions. This persistent transcriptional activity raised the question of what mechanisms return promoters to inactive states. By exchanging or directing co-occupancy of protein complexes bound to a promoter, we found that the transcriptional inhibitor, Ssn6-Tup1, lost its effectiveness as a repressor following activator dissociation. Similar experiments with another repressor, the histone deacetylase Sin3-Rpd3, reinforced this distinction between repression in the presence and absence of an activator. These results suggest that although repressors such as Ssn6-Tup1 and Sin3-Rpd3 prevent activation of gene expression, other mechanisms of repression return promoters to inactive states following the dissociation or inactivation of a transcriptional activator.