Reprogramming genetic circuits using space

Abstract

Genetic circuits confer computing abilities to living cells, performing novel transformations of input stimuli into output responses. These genetic circuits are routinely engineered for insertion into bacterial plasmids and chromosomes, using a design paradigm whose only spatial consideration is a linear ordering of the individual components. However, chromosomal DNA has a complex three dimensional conformation which alters the mechanics of gene expression, leading to dynamics that are specific to chromosomal location. Here we demonstrate that because of this, position in the bacterial chromosome is crucial to the function of synthetic genetic circuits, and that three dimensional space should not be overlooked in their design. Our results show that genetically identical circuits can be reprogrammed to produce different outputs by changing their spatial positioning and configuration. We engineer 221 spatially unique genetic circuits of four different types, three regulatory cascades and a toggle switch, by either inserting the entire circuit in a specific chromosomal position or separating and distributing circuit modules. Their analysis reveals that spatial positioning can be used not only to optimize circuits but also to switch circuits between modes of operation, giving rise to new functions. Alongside a comprehensive characterization of chromosomal space using single-cell RNA-seq profiles and Hi-C interaction maps, we offer baseline information for leveraging intracellular space as a design parameter in bioengineering.