Insights on the effect of macromolecular crowding on transcription and its regulation
Transcription of DNA into RNA is a fundamental cellular process upon which life depends. It is tightly regulated in several different ways, and among the most important mechanisms are protein-induced topological changes in DNA such as looping. In vivo neither transcription, nor protein-induced loopi...
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| Format: | Article |
| Language: | English |
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Cambridge University Press
2025-01-01
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| Series: | QRB Discovery |
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| Online Access: | https://www.cambridge.org/core/product/identifier/S2633289225000080/type/journal_article |
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| author | Wenxuan Xu Dylan Collette Jin Qian Laura Finzi David Dunlap |
| author_facet | Wenxuan Xu Dylan Collette Jin Qian Laura Finzi David Dunlap |
| author_sort | Wenxuan Xu |
| collection | DOAJ |
| description | Transcription of DNA into RNA is a fundamental cellular process upon which life depends. It is tightly regulated in several different ways, and among the most important mechanisms are protein-induced topological changes in DNA such as looping. In vivo neither transcription, nor protein-induced looping dynamics exhibited by individual molecules are easily monitored. In vitro single-molecule approaches do offer that possibility, but assays are conducted in rarefied, saline buffer conditions which greatly differ from the crowded intracellular environment. In the following, we describe monitoring both transcription and lac repressor-mediated DNA looping of single DNA molecules in the presence of different concentrations of crowders to bridge the gap between in vitro and in vivo experimentation. We found that crowding shifts the preferred orientation of DNA strands in the looped complex. Crowding also attenuates the rate of transcript elongation and enhances readthrough at the terminator. Clearly, the activities of proteins involved in gene regulation are modified in surprising ways by crowding. |
| format | Article |
| id | doaj-art-22dd39c9ad184c639b46e987b34b38c1 |
| institution | Kabale University |
| issn | 2633-2892 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Cambridge University Press |
| record_format | Article |
| series | QRB Discovery |
| spelling | doaj-art-22dd39c9ad184c639b46e987b34b38c12025-08-20T03:49:33ZengCambridge University PressQRB Discovery2633-28922025-01-01610.1017/qrd.2025.8Insights on the effect of macromolecular crowding on transcription and its regulationWenxuan Xu0Dylan Collette1Jin Qian2Laura Finzi3https://orcid.org/0000-0003-1173-5339David Dunlap4Physics Department, Emory University, Atlanta, GA, USA Institute of STEM Cells and Regenerative Medicine, University of Washington, Seattle, WA, USAPhysics Department, Emory University, Atlanta, GA, USA Physics Department, Oglethorpe University, Atlanta, GA, USAPhysics Department, Emory University, Atlanta, GA, USA National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USAPhysics Department, Emory University, Atlanta, GA, USA Department of Physics & Astronomy, Clemson University, SC, USAPhysics Department, Emory University, Atlanta, GA, USA Department of Physics & Astronomy, Clemson University, SC, USATranscription of DNA into RNA is a fundamental cellular process upon which life depends. It is tightly regulated in several different ways, and among the most important mechanisms are protein-induced topological changes in DNA such as looping. In vivo neither transcription, nor protein-induced looping dynamics exhibited by individual molecules are easily monitored. In vitro single-molecule approaches do offer that possibility, but assays are conducted in rarefied, saline buffer conditions which greatly differ from the crowded intracellular environment. In the following, we describe monitoring both transcription and lac repressor-mediated DNA looping of single DNA molecules in the presence of different concentrations of crowders to bridge the gap between in vitro and in vivo experimentation. We found that crowding shifts the preferred orientation of DNA strands in the looped complex. Crowding also attenuates the rate of transcript elongation and enhances readthrough at the terminator. Clearly, the activities of proteins involved in gene regulation are modified in surprising ways by crowding.https://www.cambridge.org/core/product/identifier/S2633289225000080/type/journal_articleMacromolecular crowdingDNA looping and transcriptionTranscription recyclingtethered particle motion technique (TPM)magnetic tweezers |
| spellingShingle | Wenxuan Xu Dylan Collette Jin Qian Laura Finzi David Dunlap Insights on the effect of macromolecular crowding on transcription and its regulation QRB Discovery Macromolecular crowding DNA looping and transcription Transcription recycling tethered particle motion technique (TPM) magnetic tweezers |
| title | Insights on the effect of macromolecular crowding on transcription and its regulation |
| title_full | Insights on the effect of macromolecular crowding on transcription and its regulation |
| title_fullStr | Insights on the effect of macromolecular crowding on transcription and its regulation |
| title_full_unstemmed | Insights on the effect of macromolecular crowding on transcription and its regulation |
| title_short | Insights on the effect of macromolecular crowding on transcription and its regulation |
| title_sort | insights on the effect of macromolecular crowding on transcription and its regulation |
| topic | Macromolecular crowding DNA looping and transcription Transcription recycling tethered particle motion technique (TPM) magnetic tweezers |
| url | https://www.cambridge.org/core/product/identifier/S2633289225000080/type/journal_article |
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