Genetic context effects can override canonical cis regulatory elements in Escherichia coli

Abstract

Recent experiments have shown that in addition to control by cis regulatory elements, the local chromosomal context of a gene also has a profound impact on its transcription. Although this chromosome-position dependent expression variation has been empirically mapped at high-resolution, the underlying causes of the variation have not been elucidated. Here, we demonstrate that 1 kb of flanking, non-coding synthetic sequences with a low frequency of guanosine and cytosine (GC) can dramatically reduce reporter expression compared to neutral and high GC-content flanks in Escherichia coli. Natural and artificial genetic context can have a similarly strong effect on reporter expression, regardless of cell growth phase or medium. Despite the strong reduction in the maximal expression level from the fully-induced reporter, low GC synthetic flanks do not affect the time required to reach the maximal expression level after induction. Overall, we demonstrate key determinants of transcriptional propensity that appear to act as tunable modulators of transcription, independent of regulatory sequences such as the promoter. These findings provide insight into the regulation of naturally occurring genes and an independent control for optimizing expression of synthetic biology constructs.

Graphical Abstract

Graphical Abstract

Natural variations in the transcription of a newly integrated gene exist dependent upon the genomic context into which that gene is inserted; we refer to these variations as ‘transcriptional propensity’. We show that transcriptional propensity is largely independent of promoter and growth phase, but that it can be further altered, and even over-ridden, by engineered flanking sequences (top left), giving rise to a new layer of control over artificially inserted DNA in bacterial genomes (right).