Department of Biology, Boston University, Boston, MA, 02215, USA.
Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA.
Nat Commun. 2023 Oct 18;14(1):6570. 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.
转录因子 (TFs) 之间的协同作用和拮抗作用可以极大地改变它们与调控 DNA 元件的结合。虽然绘制这些 TF 之间的关系对于理解它们特定于上下文的功能很重要，但现有的方法要么依赖于 DNA 结合基序预测，要么一次检测一个 TF，要么平行研究单个 TF。在这里，我们引入了配对酵母单杂交 (pY1H) 测定法，以检测数百个 TF 对在感兴趣的 DNA 区域中的协同作用和拮抗作用。我们提供的证据表明，广泛的 TF 受到 DNA 区域特异性的其他 TF 的调节。我们还证明，TF-TF 关系通常受到替代同工型使用的影响，并鉴定了人类 TF 与人类乳头瘤病毒、 Epstein-Barr 病毒和其他病毒的病毒蛋白之间的协同作用和拮抗作用。总之，pY1H 测定法为研究不同功能关系如何影响调节 DNA 区域的蛋白质占据提供了一个广泛适用的框架。
