Revisiting genome-guided RNA localization in bacteria

Elucidating the intracellular organization of bacterial transcriptomes may reveal new modes of gene regulation. Recent work reported that chromosomal gene position determines mRNA localization within Escherichia coli 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. Moreover, genome-associated patterns preferentially occur in weakly translated and unstable mRNAs. Together, our results indicate that genome-guided localization is unlikely to be a dominant driver of transcript positioning in bacteria. Genome organization has been previously proposed to dictate mRNA localization in bacteria. Here, the authors use spatial transcriptomic analysis to show that the genomic effect involves only a minority of transcripts, mainly weakly translated and unstable mRNAs.