title: A synthetic biology framework for programming eukaryotic transcription functions.
abstract: Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for systematically constructing eukaryotic transcription functions using artificial zinc fingers, modular DNA-binding domains found within many eukaryotic TFs. Utilizing this platform, we construct a library of orthogonal synthetic transcription factors (sTFs) and use these to wire synthetic transcriptional circuits in yeast. We engineer complex functions, such as tunable output strength and transcriptional cooperativity, by rationally adjusting a decomposed set of key component properties, e.g., DNA specificity, affinity, promoter design, protein-protein interactions. We show that subtle perturbations to these properties can transform an individual sTF between distinct roles (activator, cooperative factor, inhibitory factor) within a transcriptional complex, thus drastically altering the signal processing behavior of multi-input systems. This platform provides new genetic components for synthetic biology and enables bottom-up approaches to understanding the design principles of eukaryotic transcriptional complexes and networks.
authors.affiliation: Howard Hughes Medical Institute, Department of Biomedical Engineering, and Center for BioDynamics, Boston University, Boston, MA 02215, USA.
authors.forename: Ahmad S
authors.initials: AS
authors.lastname: Khalil
authors.forename: Timothy K
authors.initials: TK
authors.lastname: Lu
authors.forename: Caleb J
authors.initials: CJ
authors.lastname: Bashor
authors.forename: Cherie L
authors.initials: CL
authors.lastname: Ramirez
authors.forename: Nora C
authors.initials: NC
authors.lastname: Pyenson
authors.forename: J Keith
authors.initials: JK
authors.lastname: Joung
authors.forename: James J
authors.initials: JJ
authors.lastname: Collins
mesh_terms: D000595:Amino Acid Sequence; D053263:Gene Regulatory Networks; D008958:Models, Molecular; D008969:Molecular Sequence Data; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D058615:Synthetic Biology; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic; D016335:Zinc Fingers
chemical_list: D014157:Transcription Factors