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Portuguez AS, Grbesa I, Tal M, Deitch R, Raz D, Kliker L, Weismann R, Schwartz M, Loza O, Cohen L, Marchenkov-Flam L, Sung MH, Kaplan T, Hakim O. Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression. Nucleic Acids Res 2022; 50:6702-6714. [PMID: 35713523 PMCID: PMC9262608 DOI: 10.1093/nar/gkac488] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 05/18/2022] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
The rapid transcriptional response to the transcription factor, glucocorticoid receptor (GR), including gene activation or repression, is mediated by the spatial association of genes with multiple GR binding sites (GBSs) over large genomic distances. However, only a minority of the GBSs have independent GR-mediated activating capacity, and GBSs with independent repressive activity were rarely reported. To understand the positive and negative effects of GR we mapped the regulatory environment of its gene targets. We show that the chromatin interaction networks of GR-activated and repressed genes are spatially separated and vary in the features and configuration of their GBS and other non-GBS regulatory elements. The convergence of the KLF4 pathway in GR-activated domains and the STAT6 pathway in GR-repressed domains, impose opposite transcriptional effects to GR, independent of hormone application. Moreover, the ROR and Rev-erb transcription factors serve as positive and negative regulators, respectively, of GR-mediated gene activation. We found that the spatial crosstalk between GBSs and non-GBSs provides a physical platform for sequestering the Ep300 co-activator from non-GR regulatory loci in both GR-activated and -repressed gene compartments. While this allows rapid gene repression, Ep300 recruitment to GBSs is productive specifically in the activated compartments, thus providing the basis for gene induction.
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Affiliation(s)
| | | | - Moran Tal
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Rachel Deitch
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Dana Raz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Limor Kliker
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Ran Weismann
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Michal Schwartz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Olga Loza
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Leslie Cohen
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Libi Marchenkov-Flam
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Building 206, Ramat-Gan 5290002, Israel
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, NIA, National Institutes of Health, Baltimore, MD 21224, USA
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 91904, Israel,Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91121, Israel
| | - Ofir Hakim
- To whom correspondence should be addressed. Tel: +972 3 738 4295; Fax: +972 3 738 4296;
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Trümper V, von Knethen A, Preuß A, Ermilov E, Hackbarth S, Kuchler L, Gunne S, Schäfer A, Bornhütter T, Vereb G, Ujlaky-Nagy L, Brüne B, Röder B, Schindler M, Parnham MJ, Knape T. Flow cytometry-based FRET identifies binding intensities in PPARγ1 protein-protein interactions in living cells. Theranostics 2019; 9:5444-5463. [PMID: 31534496 PMCID: PMC6735382 DOI: 10.7150/thno.29367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 05/01/2019] [Indexed: 01/10/2023] Open
Abstract
PPARγ is a pharmacological target in inflammatory and metabolic diseases. Upon agonistic treatment or following antagonism, binding of co-factors is altered, which consequently affects PPARγ-dependent transactivation as well as its DNA-independent properties. Therefore, establishing techniques to characterize these interactions is an important issue in living cells. Methods: Using the FRET pair Clover/mRuby2, we set up a flow cytometry-based FRET assay by analyzing PPARγ1 binding to its heterodimerization partner RXRα. Analyses of PPARγ-reporter and co-localization studies by laser-scanning microscopy validated this system. Refining the system, we created a new readout to distinguish strong from weak interactions, focusing on PPARγ-binding to the co-repressor N-CoR2. Results: We observed high FRET in cells expressing Clover-PPARγ1 and mRuby2-RXRα, but no FRET when cells express a mRuby2-RXRα deletion mutant, lacking the PPARγ interaction domain. Focusing on the co-repressor N-CoR2, we identified in HEK293T cells the new splice variant N-CoR2-ΔID1-exon. Overexpressing this isoform tagged with mRuby2, revealed no binding to Clover-PPARγ1, nor in murine J774A.1 macrophages. In HEK293T cells, binding was even lower in comparison to N-CoR2 constructs in which domains established to mediate interaction with PPARγ binding are deleted. These data suggest a possible role of N-CoR2-ΔID1-exon as a dominant negative variant. Because binding to N-CoR2-mRuby2 was not altered following activation or antagonism of Clover-PPARγ1, we determined the effect of pharmacological treatment on FRET intensity. Therefore, we calculated flow cytometry-based FRET efficiencies based on our flow cytometry data. As with PPARγ antagonism, PPARγ agonist treatment did not prevent binding of N-CoR2. Conclusion: Our system allows the close determination of protein-protein interactions with a special focus on binding intensity, allowing this system to characterize the role of protein domains as well as the effect of pharmacological agents on protein-protein interactions.
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Affiliation(s)
- Verena Trümper
- Institute of Biochemistry I - Pathobiochemistry, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt/Main, Germany
| | - Andreas von Knethen
- Institute of Biochemistry I - Pathobiochemistry, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt/Main, Germany
- Branch for Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60596 Frankfurt/Main, Germany
| | - Annegret Preuß
- Department of Physics, Humboldt University Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - Eugeny Ermilov
- Department of Physics, Humboldt University Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - Steffen Hackbarth
- Department of Physics, Humboldt University Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - Laura Kuchler
- Institute of Biochemistry I - Pathobiochemistry, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt/Main, Germany
| | - Sandra Gunne
- Branch for Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60596 Frankfurt/Main, Germany
| | - Anne Schäfer
- Institute of Biochemistry I - Pathobiochemistry, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt/Main, Germany
| | - Tobias Bornhütter
- Department of Physics, Humboldt University Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - György Vereb
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Lázló Ujlaky-Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Bernhard Brüne
- Institute of Biochemistry I - Pathobiochemistry, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt/Main, Germany
- Branch for Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60596 Frankfurt/Main, Germany
| | - Beate Röder
- Department of Physics, Humboldt University Berlin, Newtonstraße 15, 12489 Berlin, Germany
| | - Michael Schindler
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Karls University Tübingen, Elfriede-Aulhorn-Str. 6, 72076 Tübingen
| | - Michael J. Parnham
- Branch for Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60596 Frankfurt/Main, Germany
| | - Tilo Knape
- Branch for Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, 60596 Frankfurt/Main, Germany
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