Surprising features of nuclear receptor interaction networks revealed by live-cell single-molecule imaging
Type II nuclear receptors (T2NRs) require heterodimerization with a common partner, the retinoid X receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and overexpression studies, binding of T2NRs to chromatin is proposed to be regulated by competition fo...
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2025-01-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/92979 |
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| author | Liza Dahal Thomas GW Graham Gina M Dailey Alec Heckert Robert Tjian Xavier Darzacq |
| author_facet | Liza Dahal Thomas GW Graham Gina M Dailey Alec Heckert Robert Tjian Xavier Darzacq |
| author_sort | Liza Dahal |
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| description | Type II nuclear receptors (T2NRs) require heterodimerization with a common partner, the retinoid X receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and overexpression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells. Using single-molecule tracking (SMT) and proximity-assisted photoactivation (PAPA), we monitored interactions between endogenously tagged RXR and retinoic acid receptor (RAR) in live cells. Unexpectedly, we find that higher expression of RAR, but not RXR, increases heterodimerization and chromatin binding in U2OS cells. This surprising finding indicates the limiting factor is not RXR but likely its cadre of obligate dimer binding partners. SMT and PAPA thus provide a direct way to probe which components are functionally limiting within a complex TF interaction network providing new insights into mechanisms of gene regulation in vivo with implications for drug development targeting nuclear receptors. |
| format | Article |
| id | doaj-art-2c1b6e3cf95a4b119427484b4dc403d2 |
| institution | Kabale University |
| issn | 2050-084X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj-art-2c1b6e3cf95a4b119427484b4dc403d22025-01-10T15:49:00ZengeLife Sciences Publications LtdeLife2050-084X2025-01-011210.7554/eLife.92979Surprising features of nuclear receptor interaction networks revealed by live-cell single-molecule imagingLiza Dahal0https://orcid.org/0000-0002-5600-1673Thomas GW Graham1https://orcid.org/0000-0001-5189-4313Gina M Dailey2https://orcid.org/0000-0002-8988-963XAlec Heckert3https://orcid.org/0000-0001-8748-6645Robert Tjian4Xavier Darzacq5https://orcid.org/0000-0003-2537-8395Department of Molecular and Cell Biology, Berkeley, United States; Howard Hughes Medical Institute, University of California, Berkeley, United StatesDepartment of Molecular and Cell Biology, Berkeley, United States; Howard Hughes Medical Institute, University of California, Berkeley, United StatesDepartment of Molecular and Cell Biology, Berkeley, United StatesEikon Therapeutics Inc, Hayward, California, Berkeley, United StatesDepartment of Molecular and Cell Biology, Berkeley, United States; Howard Hughes Medical Institute, University of California, Berkeley, United StatesDepartment of Molecular and Cell Biology, Berkeley, United StatesType II nuclear receptors (T2NRs) require heterodimerization with a common partner, the retinoid X receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and overexpression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells. Using single-molecule tracking (SMT) and proximity-assisted photoactivation (PAPA), we monitored interactions between endogenously tagged RXR and retinoic acid receptor (RAR) in live cells. Unexpectedly, we find that higher expression of RAR, but not RXR, increases heterodimerization and chromatin binding in U2OS cells. This surprising finding indicates the limiting factor is not RXR but likely its cadre of obligate dimer binding partners. SMT and PAPA thus provide a direct way to probe which components are functionally limiting within a complex TF interaction network providing new insights into mechanisms of gene regulation in vivo with implications for drug development targeting nuclear receptors.https://elifesciences.org/articles/92979single-molecule trackingnuclear receptorstranscription factorsgene regulatory networksmolecular biophysicsprotein-protein interactions |
| spellingShingle | Liza Dahal Thomas GW Graham Gina M Dailey Alec Heckert Robert Tjian Xavier Darzacq Surprising features of nuclear receptor interaction networks revealed by live-cell single-molecule imaging eLife single-molecule tracking nuclear receptors transcription factors gene regulatory networks molecular biophysics protein-protein interactions |
| title | Surprising features of nuclear receptor interaction networks revealed by live-cell single-molecule imaging |
| title_full | Surprising features of nuclear receptor interaction networks revealed by live-cell single-molecule imaging |
| title_fullStr | Surprising features of nuclear receptor interaction networks revealed by live-cell single-molecule imaging |
| title_full_unstemmed | Surprising features of nuclear receptor interaction networks revealed by live-cell single-molecule imaging |
| title_short | Surprising features of nuclear receptor interaction networks revealed by live-cell single-molecule imaging |
| title_sort | surprising features of nuclear receptor interaction networks revealed by live cell single molecule imaging |
| topic | single-molecule tracking nuclear receptors transcription factors gene regulatory networks molecular biophysics protein-protein interactions |
| url | https://elifesciences.org/articles/92979 |
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