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Enhancer control of transcriptional activity via modulation of burst frequency

Tünnermann, Jana. Enhancer control of transcriptional activity via modulation of burst frequency. 2024, Doctoral Thesis, University of Basel, Faculty of Science.

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Official URL: https://edoc.unibas.ch/96823/

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Abstract

In mammalian cells, transcriptional regulation strongly relies on cis-regulatory elements such as enhancers that can be located at large genomic distances from their target genes. Their action can be broadly defined as the ability to increase the amount of transcription generated at a cognate promoter. The Giorgetti laboratory and others have recently shown that this effect strongly depends on the genomic distance between the enhancer and promoter: enhancer action increases as the enhancer-promoter genomic distance decreases. However, how this is achieved at the level of single cells remains poorly understood. Within a single cell, transcription is a highly dynamic and stochastic process that occurs in bursts of promoter activity separated by periods of transcriptional inactivity. Whether different genomic distances from an enhancer translate in different promoter burst kinetics, and how this relates to the underlying mechanisms of enhancer-promoter communication remains unclear.
To answer these questions, we performed live-cell imaging of nascent transcription in mouse embryonic stem cell (mESC) lines harboring a bottom-up engineered genomic locus allowing to change enhancer-promoter distance without further regulatory confounding effects. By imaging transcription dynamics in multiple cell lines where an ectopic Sox2 promoter is located at different distances from the Sox2 control region (SCR) enhancer, we found that genomic distance from the enhancer controls the frequency, but not the duration, amplitude or size of bursts from the promoter. As a result, genomic distance from the enhancer also impacts the amount of cell-to-cell and temporal variability in transcriptional output from the promoter: a distal enhancer results in larger amounts of transcriptional noise than a proximal enhancer. Using mathematical modeling, we further show that the promoter operates as a multi-state system where the enhancer selectively increases the transition rate from a ’basal’ lowly transcribing regime to more transient, transcriptionally active regime, in a way that depends on its distance from the promoter. Our results provide quantitative insight into how an enhancer acts on a promoter in single cells, and into how the large-scale architecture of a locus determine transcription levels as well as temporal and cell-to-cell variability.
Advisors:Giorgetti, Luca
Committee Members:Bühler, Marc and Lenstra, Tineke
Faculties and Departments:05 Faculty of Science
09 Associated Institutions > Friedrich Miescher Institut FMI > Quantitative Biology > Chromosome structure and transcriptional regulation (Giorgetti)
UniBasel Contributors:Bühler, Marc
Item Type:Thesis
Thesis Subtype:Doctoral Thesis
Thesis no:15577
Thesis status:Complete
Number of Pages:xv, 81
Language:English
Identification Number:
  • urn: urn:nbn:ch:bel-bau-diss155779
edoc DOI:
Last Modified:25 Jan 2025 05:30
Deposited On:24 Jan 2025 11:57

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