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

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 predic...

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Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10584920/
https://www.ncbi.nlm.nih.gov/pubmed/37853017
http://dx.doi.org/10.1038/s41467-023-42445-6
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author 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.
author_facet 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.
author_sort Berenson, Anna
collection PubMed
description 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.
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spelling pubmed-105849202023-10-20 Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors 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. Nat Commun Article 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. Nature Publishing Group UK 2023-10-18 /pmc/articles/PMC10584920/ /pubmed/37853017 http://dx.doi.org/10.1038/s41467-023-42445-6 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
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.
Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors
title Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors
title_full Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors
title_fullStr Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors
title_full_unstemmed Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors
title_short Paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism across transcription factors
title_sort paired yeast one-hybrid assays to detect dna-binding cooperativity and antagonism across transcription factors
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10584920/
https://www.ncbi.nlm.nih.gov/pubmed/37853017
http://dx.doi.org/10.1038/s41467-023-42445-6
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