Chromatin Remodeler RSC2 Modulates Binding of the Transcriptional Activator Ace1p and Improves the Transcription of CUP1 by Fast Cycles of Remodeling

Little is known about how dynamic binding of Transcription Factors (TF) is coordinated with chromatin remodeling. Using Single Molecule Tracking (SMT) we show that a chromatin remodeler (RSC2 complex) speeds up the search process of the TF Ace1p for its Response Elements (RE) in CUP1 promoter, ensuring a homogeneous response of the cell population to heavy metal stress. By SMT and MNase-seq, RSC2 binds to activated promoter transiently indicating that preinitiation at CUP1 is dependent on short repetitive remodeling events. Using smFISH, we demonstrate that RSC2 improves the search by increasing (a) the fraction of accessible RE, and (b) the molecular 'on' rate of the TF. Thus 'on' rates of binding can play a key role in gene regulation. Nucleosome occupancy was determined for the following four conditions: (1) Rsc2+ (No Auxin), no Cu activation, (2) Rsc2+ (No Auxin), with Cu activation, (3) Rsc2- (With Auxin), no Cu activation, (4) Rsc2- (With Auxin), with Cu activation.