A Structural Model of Transcriptional Activation by Mediator

Abstract

Mediator integrates regulatory signals from transcription factors (TFs) and controls RNA polymerase II (Pol II) activity in eukaryotes. Its Tail module serves as the primary hub for TF activation domains (ADs), but the mechanistic logic coupling this distal engagement to transcriptional output is unclear. Here we model an extensive set of human AD-Tail interactions with AlphaFold 3 and infer how they may influence the architecture of the Mediator-Pol II complex. Across the ensemble, ADs recurrently engage a restricted set of surfaces spanning multiple Tail subunits, revealing several previously unrecognized sites. The ensemble map recovers established activator-binding regions and is consistent with prior biochemical and structural data. Our modeling suggests how multivalent AD binding modulates the conformational landscape of the Tail to favor an initiation-competent Pol II state, providing a structural framework for tunable gene activation through Mediator.