A1 Refereed original research article in a scientific journal

Dynamic landscape of transcription initiation by yeast RNA polymerase I




AuthorsParilova, Olena; Bartos, Piia; Malinen, Anssi M.

PublisherOxford University Press (OUP)

Publication year2026

Journal: Nucleic Acids Research

Article numbergkag153

Volume54

Issue5

ISSN0305-1048

eISSN1362-4962

DOIhttps://doi.org/10.1093/nar/gkag153

Publication's open availability at the time of reportingOpen Access

Publication channel's open availability Open Access publication channel

Web address https://doi.org/10.1093/nar/gkag153

Self-archived copy’s web addresshttps://research.utu.fi/converis/portal/detail/Publication/515647872

Self-archived copy's licenceCC BY

Self-archived copy's versionPublisher`s PDF


Abstract

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 Saccharomyces cerevisiae 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.


Downloadable publication

This is an electronic reprint of the original article.
This reprint may differ from the original in pagination and typographic detail. Please cite the original version.




Funding information in the publication
The work was supported by Research Council of Finland (307775, 314100, and 335377 to A.M.M.), Sigrid Juséliuksen säätiö (to A.M.M.), Turun Yliopistosäätiö (to A.M.M.), University of Turku Graduate School (UTUGS; to O.P.), Suomen Kulttuurirahasto (to O.P.), and Emil Aaltosen Säätiö (to P.B). Funding to pay the Open Access publication charges for this article was provided by Research grant (from Sigrid Juseliuksen säätiö).


Last updated on 02/03/2026 07:38:05 AM