Extrinsic factors, like differing RNA polymerase concentrations and nucleotide availability, affect transcription equally within the cell, regardless of what cis-regulatory elements drive transcription of the genes in question. Intrinsic components, like DNA-protein binding kinetics, are promoter-specific contributions to noise. Our project aims to tease apart the extrinsic and intrinsic components of gene expression noise, and characterize the noise inherent to commonly used promoters in synthetic biology.
Original work done by Michael Elowitz investigated stochasticity in gene expression at the single cell level using a dual-reporter fluorescent system [1]. In this method two constructs are created that both drive expression of a fluorescent protein using the same promoter, RBS, and terminator. One of these reporter constructs uses YFP and the other CFP. This dual reporter system is what allows the investigator to differentiate between the extrinsic factors of noise, which should affect both constructs equally, and the intrinsic factors, which will result in a difference in the ratio of CFP: YFP fluorescence. These constructs are then integrated (notebook link here) into specific sites on the genome and the fluorescence output measured using fluorescent imaging.
Panel A shows an example of intrinsic and extrinsic noise; both the ratio of the fluorescence of the two reporters (intrinsic) and the absolute fluorescence of the two reporters (extrinsic) changes. Panel B shows an example of extrinsic noise only; the ratio of the fluorescence of the two reporters stays constant while the absolute fluorescence changes. Figure taken from:[2].
References
1: Elowitz, Michael B., et al. "Stochastic gene expression in a single cell." Science 297.5584 (2002): 1183-1186.
2: Raser, Jonathan M., and Erin K. O'Shea. "Noise in gene expression: origins, consequences, and control." Science 309.5743 (2005): 2010-2013.
