Dynamic landscape of transcription initiation by yeast RNA polymerase I

Abstract

<p>RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA, a key step in ribosome biogenesis. Elevated Pol I activity supports rapid cell growth—a hallmark of cancer—making Pol I a therapeutic target. The initial step in synthesis involves assembly of the Pol I transcription initiation complex on the gene promoter; however, its quantitative and dynamic parameters remain poorly defined. Here, we integrate biochemical, biophysical, and molecular dynamics approaches to dissect promoter and transcription start site (TSS) recognition by the <em>Saccharomyces cerevisiae</em> Pol I machinery. We show that core factor (CF) identifies the promoter through a two–step mechanism: a rapid encounter is followed by a slower conformational transition that establishes stabilizing interactions. In contrast, CF binds nonpromoter DNA in a single step without such transitions, forming nonspecific complexes that dissociate quickly. Correct promoter binding allows CF to recruit and position Pol I near the TSS, inducing DNA bending, helix distortion, and melting as the preinitiation complex converts into an active state. These functional and dynamic parameters contribute to a quantitative framework for elucidating the molecular mechanisms of Pol I regulation and inhibition.</p>