"Synthetic Approaches to Deciphering Cis-Regulatory Codes”

Seminar series
Tue, Apr 9 2:00pm
Boyer Hall 159
Speaker Dr. Sriram Kosuri
Church Lab, Wyss Institute
Harvard University

Special Biochemistry Seminar

Next-generation sequencing technologies have enabled simple genome-wide measurements of a variety of biological processes. 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 data sets. However, proving that particular sequences have causative effects on gene expression requires 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.

For more information, please contact Todd Yeates, yeates@mbi.ucla.edu, 310-206-4866.