title: Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation.
abstract: The transcription of genomic information in eukaryotes is regulated in large part by chromatin. How a diverse array of chromatin regulator (CR) proteins with different functions and genomic localization patterns coordinates chromatin activity to control transcription remains unclear. Here, we take a synthetic biology approach to decipher the complexity of chromatin regulation by studying emergent transcriptional behaviors from engineered combinatorial, spatial, and temporal patterns of individual CRs. We fuse 223 yeast CRs to programmable zinc finger proteins. Site-specific and combinatorial recruitment of CRs to distinct intralocus locations reveals a range of transcriptional logic and behaviors, including synergistic activation, long-range and spatial regulation, and gene expression memory. Comparing these transcriptional behaviors with annotated CR complex and function terms provides design principles for the engineering of transcriptional regulation. This work presents a bottom-up approach to investigating chromatin-mediated transcriptional regulation and introduces chromatin-based components and systems for synthetic biology and cellular engineering.
authors.affiliation: Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
authors.forename: Albert J
authors.initials: AJ
authors.lastname: Keung
authors.affiliation: Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
authors.forename: Caleb J
authors.initials: CJ
authors.lastname: Bashor
authors.affiliation: Program in Molecular Biology, Cell Biology and Biochemistry, Boston University, Boston, MA 02215, USA.
authors.forename: Szilvia
authors.initials: S
authors.lastname: Kiriakov
authors.affiliation: Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
authors.forename: James J
authors.initials: JJ
authors.lastname: Collins
authors.affiliation: Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA. Electronic address: akhalil@bu.edu.
authors.forename: Ahmad S
authors.initials: AS
authors.lastname: Khalil
mesh_terms: D002843:Chromatin / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D017930:Genes, Reporter; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D029701:Saccharomyces cerevisiae Proteins