Automating Assays for Mapping Genome Supercoiling to Transcriptomics

The transcriptome-wide profile of bacteria define a cellular state of genes that are on or off, depending on external stimuli and conditions. Our recent work in soil bacteria has elucidated a complex cellular state that is highly sensitive to external stimuli, even in the absence of direct binding of transcription factors. In this project we explore how extreme environmental cues link directly to a broad, global control mechanism of transcriptomic dynamics, namely supercoiling of DNA in the bacterial chromosome.  We have developed a novel assay for mapping topoisomerase binding and supercoiling density that allows us to quantify local topoisomerase activity, and by proxy, the extent of positive supercoiling. By simultaneously measuring transcriptomic dynamics, we propose to develop whole-cell models directly from our experimental data, that link extremal environmental signals to transcriptomic cell state.This biotechnology will enable the development of a new generation of biological circuit devices, that rely on a mixture of genome and synthetic gene circuit signals to perform computation.This project will leverage the establishment of a UCSB biofoundry and automation lab, by developing and optimizing robotic protocols for sequencing and quantifying genome-wide supercoiling density maps and transcriptomic response.