Synthetic chromatin-based logic, spatial regulation, and memory

Albert J. Keung1,3,5, Caleb J. Bashor1,3, Szilvia Kiriakov2, James J. Collins1,3,4, Ahmad S. Khalil1,4,*

1Department of Biomedical Engineering and Center of Synthetic Biology, Boston University, Boston, MA 02215, USA

2Program in Molecular Biology, Cell Biology & Biochemistry, Boston University, Boston, MA,

02215, USA

3Howard Hughes Medical Institute

4Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA

5Presenter

*Correspondence: akhalil@bu.edu (A.S.K.)

ABSTRACT

The complex structure of chromatin vastly extends the information potential of the eukaryotic genome beyond the underlying DNA sequence. Several hundred chromatin regulators (CRs) modulate eukaryotic genome structure and function by remodeling nucleosomes and DNA. Yet, despite being the subject of extensive studies, it remains unclear how CRs operate through diverse processes to regulate gene transcription, and this powerful layer of gene regulation has yet to be exploited in engineering applications. Synthetic biology offers a unique approach to decompose and exploit the complexity of chromatin by studying emergent transcriptional behaviors from engineered combinatorial, spatial, and temporal patterns of individual CRs. Here we fuse a library of 223 yeast CRs to programmable zinc finger proteins. Site-specific and combinatorial recruitment of CRs to engineered genomic loci drives a host of transcriptional
logic functions, spatial behaviors, and epigenetic control. Analyzing these transcriptional behaviors through gene ontology provides useful design principles for CR organization in establishing and engineering chromatin-based transcriptional regulation. This work presents a bottom-up approach to investigating chromatin regulation, and introduces new, chromatin-based components, useful transcriptional behaviors, and design strategies for synthetic biology and cellular engineering.