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

Abstract

Abstract We demonstrate a universal transcriptional regulatory design algorithm that can boost expression in a non-induced fashion for any constitutive promoter in eukaryotic cell lines. The system consists of a simplified transcriptional architecture composed of a minimal core promoter and a synthetic upstream regulatory region (sURS). The sURS was encoded by an oligo-library containing 189,990 variants, where each variant contained up to three motifs encoded with mixed-base synthesis technology. Motifs were chosen from a list of 41 transcription factor (TF) binding motifs conserved in the eukaryotic lineage. Using a machine learning and oligo library (OL-ML) approach, we identified at least 16 motifs which were associated with either a statistically significant expression boost or attenuation effect. We validated the boost and attenuation potential of these motifs using a set of unseen sURS designs, which contained multiple copies of them. The validation sURS experiments further indicated that a modular and generic set of grammar rules for boosting and attenuation may exist in yeast enabling a simple design algorithm for boosting the expression of any promoter. Finally, we demonstrated that this modular and generic set of grammar rules functions similarly in mammalian CHO-K1 and Hela cells. Our work provides a resource for the characterization of conserved regulatory grammar, as well as a tool for the design of functional promoters for industrially relevant alternative protein expression in various Eukaryotic cell lines.