Bioengineering Lecture

Abstract:
Consortiums like ENCODE seek to identify all functional DNA elements in humans and other model
organisms by correlating functional outputs with sequence using genome-wide measurements of
particular cell types. However, proving that particular sequences have causative effects on gene expression
and regulation requires usually carefully controlled transgene expression or gene editing studies.
Conducting such experiments on genome-wide scales is difficult because of our inability to (1) rapidly alter
the sequence and context of individual genetic elements and (2) quantify the consequences of thousands
of such changes.

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 ongoing and future efforts of both increasing scale of DNA
syntheses and applying these methodologies to human cell lines.