Synthetic Approaches to Studying Cis-Regulation

In this talk, I will discuss our efforts to bring our DNA synthesis capacities to genomic scales in order to systematically test hypotheses of cis-regulatory control. First, we have leveraged DNA microarrays to assemble gene-sized constructs to both lower costs and increase scales of gene synthesis. Second, we developed methods to characterize large libraries of synthetic DNA in multiplex using next-generation sequencing. We synthesized ~27,000 combinations of promoter, ribosome binding site, and peptide leader sequences in an effort to look at the composability of regulatory elements governing gene expression in E. coli. We are able to quantify both the transcription and translation levels of each member of the library independently, leading to insights on how regulatory elements in combination affect transcription and translation rates. Finally, I will discuss our new efforts at UCLA of both increasing scale of DNA syntheses and applying these methodologies to human cell lines.