Datasets and code supporting Jacobson 2026

Recent work reported that chromosomal gene positions determines mRNA localization within <i>Escherichia coli</i> (<i>E. coli</i>) cells, implying a widespread genome-guided organizing mechanism. Yet this interpretation contrasts with biophysical expectations based on translation and diffusion and may be confounded by nascent transcription.

Here, we examine this phenomenon by analyzing intracellular spatial transcriptomics datasets spanning different methods, bacterial species, growth conditions, and thousands of genes. We confirm the presence of genome-associated localization signatures that track chromosome macrodomain dynamics across the cell cycle and establish causality by repositioning a gene at distinct chromosomal loci. Quantitative analysis, however, shows that these signatures generally involve only a minority of transcripts and are of magnitudes consistent with reported rates of nascent transcription.