Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors
Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors
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 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.
Liu Xing、Berenson Anna、Shah Sakshi、Santoso Clarissa、Soto Luis、Vidal Marc、Hill David E.、Chen Yilin、Hao Tong、Patel Mahir、Ciausu Cosmin、Lane Ryan、Li Zhaorong、Spirohn Kerstin、Fuxman Bass Juan I.
Department of Biology, Boston UniversityDepartment of Biology, Boston UniversityDepartment of Biology, Boston UniversityDepartment of Biology, Boston UniversityTri-Institutional Program in Computational Biology and MedicineCenter for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute||Department of Cancer Biology, Dana-Farber Cancer Institute||Department of Genetics, Blavatnik Institute, Harvard Medical SchoolCenter for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute||Department of Cancer Biology, Dana-Farber Cancer Institute||Department of Genetics, Blavatnik Institute, Harvard Medical SchoolDepartment of Biology, Boston UniversityCenter for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute||Department of Cancer Biology, Dana-Farber Cancer Institute||Department of Genetics, Blavatnik Institute, Harvard Medical SchoolDepartment of Computer Science, Boston UniversityDepartment of Computer Science, Boston UniversityDepartment of Biology, Boston UniversityDepartment of Biology, Boston UniversityCenter for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute||Department of Cancer Biology, Dana-Farber Cancer Institute||Department of Genetics, Blavatnik Institute, Harvard Medical SchoolDepartment of Biology, Boston University||Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute
分子生物学遗传学生物科学研究方法、生物科学研究技术
Liu Xing,Berenson Anna,Shah Sakshi,Santoso Clarissa,Soto Luis,Vidal Marc,Hill David E.,Chen Yilin,Hao Tong,Patel Mahir,Ciausu Cosmin,Lane Ryan,Li Zhaorong,Spirohn Kerstin,Fuxman Bass Juan I..Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors[EB/OL].(2025-03-28)[2025-05-03].https://www.biorxiv.org/content/10.1101/2023.04.14.536894.点此复制
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