Transcription factor clusters regulate genes in eukaryotic cells

TL;DR

This study reveals that transcription factors in yeast form clusters that facilitate gene regulation by reducing search times and stabilizing expression, with evidence from live-cell imaging, simulations, and structural analysis.

Contribution

It demonstrates that transcription factor clusters are the functional units of gene regulation, a novel insight supported by multi-faceted experimental and computational approaches.

Findings

Transcription factors operate in clusters within the nucleus.

Clusters translocate, bind to targets, and turnover upon signal detection.

Clusters are stabilized by depletion forces between disordered sequences.

Abstract

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.