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Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting

View ORCID ProfileIneke Brouwer, Emma Kerklingh, View ORCID ProfileFred van Leeuwen, View ORCID ProfileTineke Laura Lenstra
doi: https://doi.org/10.1101/2021.12.15.472793
Ineke Brouwer
1Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, 1066 CX Amsterdam, the Netherlands
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Emma Kerklingh
1Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, 1066 CX Amsterdam, the Netherlands
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Fred van Leeuwen
2Division of Gene Regulation, the Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Department of Medical Biology, Amsterdam UMC, University of Amsterdam, 1105AZ Amsterdam, the Netherlands
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Tineke Laura Lenstra
1Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, 1066 CX Amsterdam, the Netherlands
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  • For correspondence: t.lenstra@nki.nl
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Summary

Transcriptional bursting has been linked to the stochastic positioning of nucleosomes. However, how bursting is regulated by remodeling of promoter nucleosomes is unknown. Here, we use single-molecule live-cell imaging of GAL10 transcription in budding yeast to measure how transcriptional bursting changes upon single and double perturbations of chromatin remodeling factors, the transcription factor Gal4 and preinitiation complex (PIC) components. Using dynamic epistasis analysis, we reveal how remodeling of different nucleosomes regulates individual transcriptional bursting parameters. At the nucleosome covering the Gal4 binding sites, RSC acts synergistically with Gal4 binding to facilitate each burst. Conversely, nucleosome remodeling at the TATA box controls only the first burst upon galactose induction. In the absence of remodelers, nucleosomes at canonical TATA boxes are displaced by TBP binding to allow for transcription activation. Overall, our results reveal how promoter nucleosome remodeling, together with transcription factor and PIC binding regulates the kinetics of transcriptional bursting.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵3 Lead contact

  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190737

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 15, 2021.
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Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting
Ineke Brouwer, Emma Kerklingh, Fred van Leeuwen, Tineke Laura Lenstra
bioRxiv 2021.12.15.472793; doi: https://doi.org/10.1101/2021.12.15.472793
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Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting
Ineke Brouwer, Emma Kerklingh, Fred van Leeuwen, Tineke Laura Lenstra
bioRxiv 2021.12.15.472793; doi: https://doi.org/10.1101/2021.12.15.472793

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