Reconciling competing models on the roles of condensates and soluble complexes in transcription factor function

Abstract

Phase separation regulates many biological processes, but the role of transcription factor (TF)-mediated condensates in gene regulation is contentious. We used Gcn4, a prototypical budding yeast TF, to assess two competing models for transcription activation, i.e., mediated via soluble complexes or through transcriptional condensates. We find that the ability of Gcn4 to form soluble complexes with coactivator subunit Med15 closely mirrors its propensity to recruit Med15 into condensates. Both properties are predictive of in vivo activity, cautioning against interpretation of mutational data without direct comparisons. Unexpectedly, Gcn4 variants with the highest affinities for Med15 do not function as per expectation. Instead, their lower activities reflect their ability to phase separate with Med15, suggesting that condensate formation tempers their activity. Our results show that TFs can function as soluble complexes as well as condensates, reconciling two seemingly opposing models, with implications for other phase-separating systems.