title: Design of synthetic yeast promoters via tuning of nucleosome architecture.
abstract: Model-based design of biological parts is a critical goal of synthetic biology, especially for eukaryotes. Here we demonstrate that nucleosome architecture can have a role in defining yeast promoter activity and utilize a computationally-guided approach that can enable both the redesign of endogenous promoter sequences and the de novo design of synthetic promoters. Initially, we use our approach to reprogram native promoters for increased expression and evaluate their performance in various genetic contexts. Increases in expression ranging from 1.5- to nearly 6-fold in a plasmid-based system and up to 16-fold in a genomic context were obtained. Next, we demonstrate that, in a single design cycle, it is possible to create functional, purely synthetic yeast promoters that achieve substantial expression levels (within the top sixth percentile among native yeast promoters). In doing so, this work establishes a unique DNA-level specification of promoter activity and demonstrates predictive design of synthetic parts.
authors.affiliation: Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712.
authors.forename: Kathleen A
authors.initials: KA
authors.lastname: Curran
authors.affiliation: Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712.
authors.forename: Nathan C
authors.initials: NC
authors.lastname: Crook
authors.affiliation: Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712.
authors.forename: Ashty S
authors.initials: AS
authors.lastname: Karim
authors.affiliation: Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712.
authors.forename: Akash
authors.initials: A
authors.lastname: Gupta
authors.affiliation: Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712.
authors.forename: Allison M
authors.initials: AM
authors.lastname: Wagman
authors.affiliation: Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712.|Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712.
authors.forename: Hal S
authors.initials: HS
authors.lastname: Alper
mesh_terms: D015966:Gene Expression Regulation, Fungal; D008957:Models, Genetic; D009154:Mutation / Q000235:genetics; D009707:Nucleosomes / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D012441:Saccharomyces cerevisiae / Q000235:genetics
chemical_list: D009707:Nucleosomes