Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors

• Published in: Nature communications Vol. 14; no. 1; pp. 6570 - 16
• Main Authors: Berenson, Anna, Lane, Ryan, Soto-Ugaldi, Luis F., Patel, Mahir, Ciausu, Cosmin, Li, Zhaorong, Chen, Yilin, Shah, Sakshi, Santoso, Clarissa, Liu, Xing, Spirohn, Kerstin, Hao, Tong, Hill, David E., Vidal, Marc, Fuxman Bass, Juan I.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 18.10.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 49; 631/337/572; 631/553/2710; 631/553/2711; Assaying; Binding; Binding Sites; Cooperativity; Deoxyribonucleic acid; DNA; DNA - metabolism; Epstein-Barr virus; Epstein-Barr Virus Infections; Gene expression; Herpesvirus 4, Human - genetics; Herpesvirus 4, Human - metabolism; Human papillomavirus; Humanities and Social Sciences; Humans; Isoforms; multidisciplinary; Protein Binding; Proteins; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Science; Science (multidisciplinary); Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Yeast
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-42445-6

Cooperativity 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. Combinations of transcription factors (TFs) bind DNA to fine-tune gene expression. Here, the authors map cooperative and antagonistic DNA binding across hundreds of TF-pairs. TF-TF relationships vary depending on DNA targets and TF isoforms.