Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors
Date
2023-10-18
Authors
Berenson, Anna
Lane, Ryan
Soto-Ugaldi, Luis F.
Patel, Mahir
Ciausu, Cosmin
Li, Zhaorong
Chen, Yilin
Shah, Sakshi
Santoso, Clarissa
Liu, Xing
Version
Published version
OA Version
Citation
A. 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/s41467-023-42445-6
Abstract
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.
Description
License
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