XPF interacts with TOP2B for R-loop processing and DNA looping on actively transcribed genes

• Published in: Science advances Vol. 9; no. 45; p. eadi2095
• Main Authors: Chatzinikolaou, Georgia, Stratigi, Kalliopi, Siametis, Athanasios, Goulielmaki, Evi, Akalestou-Clocher, Alexia, Tsamardinos, Ioannis, Topalis, Pantelis, Austin, Caroline, Bouwman, Britta A. M., Crosetto, Nicola, Altmüller, Janine, Garinis, George A.
• Format: Journal Article
• Language: English
• Published: American Association for the Advancement of Science 10.11.2023
• Subjects: Biomedicine and Life Sciences; Genetics; Medicin och hälsovetenskap; Molecular Biology; SciAdv r-articles
• ISSN: 2375-2548; 2375-2548
• DOI: 10.1126/sciadv.adi2095

Co-transcriptional RNA-DNA hybrids can not only cause DNA damage threatening genome integrity but also regulate gene activity in a mechanism that remains unclear. Here, we show that the nucleotide excision repair factor XPF interacts with the insulator binding protein CTCF and the cohesin subunits SMC1A and SMC3, leading to R-loop–dependent DNA looping upon transcription activation. To facilitate R-loop processing, XPF interacts and recruits with TOP2B on active gene promoters, leading to double-strand break accumulation and the activation of a DNA damage response. Abrogation of TOP2B leads to the diminished recruitment of XPF, CTCF, and the cohesin subunits to promoters of actively transcribed genes and R-loops and the concurrent impairment of CTCF-mediated DNA looping. Together, our findings disclose an essential role for XPF with TOP2B and the CTCF/cohesin complex in R-loop processing for transcription activation with important ramifications for DNA repair–deficient syndromes associated with transcription-associated DNA damage. XPF/TOP2B-mediated R-loop processing is required for DNA looping during transcription activation.