Transcriptome-wide analysis reveals sequence selection to avoid mRNA aggregation in E. coli

RNA is built from a four-nucleotide alphabet. Complementary sequences inevitably arise, creating pervasive opportunities for promiscuous RNA–RNA interactions. Here, we show that this chemistry makes the transcriptome intrinsically prone to self-association. We simulated the simultaneous interactions of ~7,500 mRNAs representing the E. coli transcriptome at physiological concentrations. These large-scale simulations predict widespread, dynamic clustering driven by RNA alone and organized by long, multivalent transcripts. Purified mRNA recapitulates this behavior in vitro , with aggregate composition mirroring model predictions. Strikingly, native mRNA sequences are markedly less prone to self-association than matched randomized controls: they fold more stably, expose shorter single-stranded regions, and form weaker intermolecular contacts. Similar signatures are observed in abundant human mRNAs, suggesting that evolution has shaped coding sequences to minimize self-association. These findings identify transcriptome solubility as an unrecognized constraint on mRNA sequence evolution and provide a framework for understanding how cells keep their transcriptomes dispersed and functional.