biostudies-literatureScholz SANIH Predoctoral Training Program in GeneticsNIAID NIH HHSNIH Cellular and Molecular Biology TrainingNIHNIGMS NIH HHS10360-10375https://www.ebi.ac.uk/biostudies/studies/S-EPMC9561378biostudies-literatureUnknown50(18)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 tNucleic acids researchGenetic context effects can override canonical cis regulatory elements in Escherichia coli.PMC9561378R03-AI130610R35 GM128637T32-GM007315R03 AI130610T32 GM007544T32 GM007315R35-GM128637T32-GM007544Lindeboom CDScholz SAFreddolino LfalseGenetic context effects can override canonical cis regulatory elements in Escherichia coli.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 t2022-01-01T00:00:00Z2022 Oct2025-08-31T03:06:14.31Z2025-04-06T17:07:10.373ZS-EPMC95613783613471610.1093/nar/gkac787