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

Author:

Berenson Anna,Lane Ryan,Soto Luis,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.

Abstract

ABSTRACTCooperativity 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 sequence-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. pY1H assays provide a broadly applicable framework to study how different functional relationships affect protein occupancy at regulatory DNA regions.

Publisher

Cold Spring Harbor Laboratory

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