Structural basis of gap-filling DNA synthesis in the nucleosome by DNA Polymerase β

Tyler M. Weaver, Benjamin J. Ryan, Spencer H. Thompson, Adil S. Hussen, Jonah J. Spencer, Zhen Xu, Nicholas J. Schnicker and Bret D. Freudenthal ()
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Tyler M. Weaver: University of Kansas Medical Center
Benjamin J. Ryan: University of Kansas Medical Center
Spencer H. Thompson: University of Kansas Medical Center
Adil S. Hussen: University of Kansas Medical Center
Jonah J. Spencer: University of Kansas Medical Center
Zhen Xu: University of Iowa Carver College of Medicine
Nicholas J. Schnicker: University of Iowa Carver College of Medicine
Bret D. Freudenthal: University of Kansas Medical Center

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract Single-strand breaks (SSBs) are one of the most prevalent forms of DNA damage found in the chromatinized genome and are repaired by single-strand break repair (SSBR) or base excision repair (BER). DNA polymerase beta (Pol β) is the primary enzyme responsible for processing the 1-nt gap intermediate in chromatin during SSBR and BER. To date, the mechanism used by Pol β to process a 1-nt gap in the context of chromatin remains poorly understood. Here, we use biochemical assays and cryogenic electron microscopy (cryo-EM) to determine the kinetic and structural basis of gap-filling DNA synthesis in the nucleosome by Pol β. This work establishes that Pol β uses a global DNA sculpting mechanism for processing 1-nt gaps in the nucleosome during SSBR and BER, providing fundamental insight into DNA repair in chromatin.

Date: 2025
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DOI: 10.1038/s41467-025-57915-2

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