At the transcription level gene expression is controlled by the accessibility of the regulatory elements within DNA - promoters and enhancers. Research in yeast and mammalian cells indicates that modulation of chromatin accessibility occurs through interaction of transcription factors (TF) and chromatin remodelers. Binding of certain TF to their target DNA sequences is highly dynamic, with residence time on the scale of few seconds. Biophysical observations were recently supported by a ChIP assay with subsecond temporal resolution (CLK) and by high-resolution footprinting by deep sequencing. We are interested in molecular mechanisms of the rapid TF exchange on promoters and in the correlation of this exchange with transcription from the regulated gene. We use as a model a yeast gene CUP1 encoding metallothionein expressed in response to heavy metal stress. CUP1 is activated by copper-bound TF Ace1p. Our previous studies demonstrated that fast cycling of TF Ace1p on promoters of CUP1 is productive, i.e. it leads to the ON switch of the gene. We apply new single-molecule methods for individual cells. We measure residence times of transcription factors on chromatin by Single Molecule Tracking (SMT). We observe the dynamics of transcription in live individual cells by live fluorescent marking of mRNA and in cell populations by single-molecule FISH. We built a custom instrument for SMT and optimized SMT data interpretation. We developed methods for SMT in yeast cell nuclei and we developed approach of performing SMT on specific promoters. We measured binding parameters of a chromatin remodeler RSC and TF Ace1p on specific promoter of CUP1. We correlated the transcriptional activity of CUP1 promoter in individual wild type cells and in cells defective for specific chromatin remodelers with changes in the search for the binding sites and the specific residence time of TF. We demonstrated that the transient recruitment of TFs is regulated by fast cyclical chromatin remodeling events to ensure the best dynamic transcriptional response. Additional important information about the dynamics of the TF interaction on specific promoter may be extracted from SMT data if two TF with related functions may be tracked simultaneously. We are developing and adapting instrumentation and technology to be able to track simultaneously two interacting functionally related molecules at a time and to visualize the chromatin target with a third fluorescent label. Ultimately, these studies will lay the groundwork for the analysis of in vivo interactions of the components of the transcriptional machinery. SMT technique that we are in process of developing may be applied to a number of other problems of cellular biology where the information for molecular interactions is desired.
