  Transcription is regulated through binding factors to gene promoters to
activate or repress expression, however, the mechanisms by which factors find
targets remain unclear. Using single-molecule fluorescence microscopy, we
determined in vivo stoichiometry and spatiotemporal dynamics of a GFP tagged
repressor, Mig1, from a paradigm signaling pathway of Saccharomyces cerevisiae.
We find the repressor operates in clusters, which upon extracellular signal
detection, translocate from the cytoplasm, bind to nuclear targets and
turnover. Simulations of Mig1 configuration within a 3D yeast genome model
combined with a promoter-specific, fluorescent translation reporter confirmed
clusters are the functional unit of gene regulation. In vitro and structural
analysis on reconstituted Mig1 suggests that clusters are stabilized by
depletion forces between intrinsically disordered sequences. We observed
similar clusters of a co-regulatory activator from a different pathway,
supporting a generalized cluster model for transcription factors that reduces
promoter search times through intersegment transfer while stabilizing gene
expression.
