Berenson, AnnaLane, RyanSoto-Ugaldi, Luis F.Patel, MahirCiausu, CosminLi, ZhaorongChen, YilinShah, SakshiSantoso, ClarissaLiu, XingSpirohn, KerstinHao, TongHill, David E.Vidal, MarcFuxman Bass, Juan I.2024-02-292024-02-292023-10-18A. Berenson, R. Lane, L.F. Soto-Ugaldi, M. Patel, C. Ciausu, Z. Li, Y. Chen, S. Shah, C. Santoso, X. Liu, K. Spirohn, T. Hao, D.E. Hill, M. Vidal, J.I. Fuxman Bass. 2023. "Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors." Nature Communications, Volume 14, Issue 1, pp.6570-. https://doi.org/10.1038/s41467-023-42445-62041-1723https://hdl.handle.net/2144/48248Cooperativity and antagonism between transcription factors (TFs) can drastically modify their binding to regulatory DNA elements. While mapping these relationships between TFs is important for understanding their context-specific functions, existing approaches either rely on DNA binding motif predictions, interrogate one TF at a time, or study individual TFs in parallel. Here, we introduce paired yeast one-hybrid (pY1H) assays to detect cooperativity and antagonism across hundreds of TF-pairs at DNA regions of interest. We provide evidence that a wide variety of TFs are subject to modulation by other TFs in a DNA region-specific manner. We also demonstrate that TF-TF relationships are often affected by alternative isoform usage and identify cooperativity and antagonism between human TFs and viral proteins from human papillomaviruses, Epstein-Barr virus, and other viruses. Altogether, pY1H assays provide a broadly applicable framework to study how different functional relationships affect protein occupancy at regulatory DNA regions.6570-Electronicen© The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.http://creativecommons.org/licenses/by/4.0/HumansTranscription factorsSaccharomyces cerevisiaeEpstein-Barr virus infectionsProtein bindingHerpesvirus 4, humanDNABinding sitesArticle2024-01-1810.1038/s41467-023-42445-60000-0002-3782-6186 (Berenson, Anna)0009-0009-0513-9849 (Lane, Ryan)0000-0002-3370-4595 (Patel, Mahir)0000-0002-2071-1606 (Spirohn, Kerstin)0000-0001-7908-3256 (Hao, Tong)0000-0001-5192-0921 (Hill, David E)0000-0001-9457-1207 (Fuxman Bass, Juan I)861234