266: TOP1α and TOP3β Differentially Regulate HPV31 Replication via R-loops and DNA Breaks

Vatsa A et al., Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2526296123 - In HPV31-positive keratinocytes (CIN612), TOP1α and TOP3β are upregulated and required for viral transcription and replication, acting via distinct effects on R-loop accumulation and topoisomerase-mediated DNA breaks. Key terms: HPV31, TOP1α, TOP3β, R-loops, DNA breaks. Study Highlights:Using HPV31-positive CIN612 cells and primary HFK controls, the authors applied ChIP, RADAR, DRIP, alkaline COMET, RNA-seq, and shRNA knockdown to map topoisomerase binding and function. They found TOP1α and TOP3β, but not TOP3α, are elevated in HPV-positive cells and bind the viral URR, and that shRNA depletion of TOP1α or TOP3β reduced episomal viral DNA and early viral transcripts. Knockdown decreased DNA breaks (~50% reduction in COMET tail formation and reduced γH2AX) and altered R-loop levels differentially, with TOP1α depletion increasing viral R-loops by ~50% and TOP3β depletion causing >3-fold R-loop accumulation at viral and cellular loci. Transcriptome changes included reduced IL6/STAT3-AKT signaling after TOP1α loss and marked downregulation of EGR3 (>5-fold) after TOP3β loss, linking distinct mechanistic effects to impaired viral replication. Conclusion:TOP1α and TOP3β are differentially required for maintenance of HPV episomes and viral gene expression through distinct regulation of DNA breaks, R-loop dynamics, and specific host signaling pathways. Music:Enjoy the music based on this article at the end of the episode. Article title:Differential roles of type I topoisomerases in regulating HPV pathogenesis First author:Vatsa A Journal:Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2526296123 DOI:10.1073/pnas.2526296123 Reference:Vatsa A, Templeton CW, Laimins L. Differential roles of type I topoisomerases in regulating HPV pathogenesis. Proc. Natl. Acad. Sci. U.S.A. 2026.123:e2526296123. https://doi.org/10.1073/pnas.2526296123 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) - https://creativecommons.org/licenses/by/4.0/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/top1alpha-top3beta-hpv-replication QC:This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-01-21. QC Scope:- article metadata and core scientific claims from the narration- excludes analogies, intro/outro, and music- transcript coverage: Audited sections covering HPV biology and torsional stress, TOP1α/TOP3β (and TOP3α) roles, URR binding and episomal maintenance, knockdown effects on viral DNA and transcription, R-loop dynamics (DRIP), DNA breaks (COMET, γH2AX, TOP1cc/TOP3cc), DDR involvement, and host signaling changes (IL-6/STAT3-AKT, EGR3).- transcript topics: HPV-induced torsional stress and topoisomerase roles; TOP1α, TOP3β, and TOP3α expression in HPV-positive cells; Binding of TOP1α and TOP3β to the HPV URR and episomal maintenance; shRNA knockdown effects on HPV genome levels and viral transcription; R-loop dynamics and DRIP analyses; DNA damage and TOP1cc/TOP3cc formation; γH2AX and COMET results QC Summary:- factual score: 10/10- metadata score: 10/10- supported core claims: 8- claims flagged for review: 0- metadata checks passed: 4- metadata issues found: 0 Metadata Audited:- article_doi- article_title- article_journal- license Factual Items Audited:- TOP1α and TOP3β are elevated in HP... Chapters (00:00:00) - How HPV solves its torsional stress(00:02:49) - How do HPV mutations cause cancer?(00:06:16) - HPV cell cancer(00:10:12) - HPV cancer: The DNA damage crisis(00:13:54) - Untie the Loop