A universal system for boosting gene expression in eukaryotic cell-lines

Inbal Vaknin, Or Willinger, Jonathan Mandl, Hadar Heuberger, Dan Ben-Ami, Yi Zeng, Sarah Goldberg, Yaron Orenstein and Roee Amit ()
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Inbal Vaknin: Technion
Or Willinger: Technion
Jonathan Mandl: Bar-Ilan University
Hadar Heuberger: Ben-Gurion University of the Negev
Dan Ben-Ami: Ben-Gurion University of the Negev
Yi Zeng: Technion
Sarah Goldberg: Technion
Yaron Orenstein: Bar-Ilan University
Roee Amit: Technion

Nature Communications, 2024, vol. 15, issue 1, 1-17

Abstract: Abstract We demonstrate a transcriptional regulatory design algorithm that can boost expression in yeast and mammalian cell lines. The system consists of a simplified transcriptional architecture composed of a minimal core promoter and a synthetic upstream regulatory region (sURS) composed of up to three motifs selected from a list of 41 motifs conserved in the eukaryotic lineage. The sURS system was first characterized using an oligo-library containing 189,990 variants. We validate the resultant expression model using a set of 43 unseen sURS designs. The validation sURS experiments indicate that a generic set of grammar rules for boosting and attenuation may exist in yeast cells. Finally, we demonstrate that this generic set of grammar rules functions similarly in mammalian CHO-K1 and HeLa cells. Consequently, our work provides a design algorithm for boosting the expression of promoters used for expressing industrially relevant proteins in yeast and mammalian cell lines.

Date: 2024
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DOI: 10.1038/s41467-024-46573-5

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