RNA sequencing unveils very small RNAs with potential regulatory functions in bacteria

RNA sequencing (RNA-seq) is the gold standard for the discovery of small non-coding RNAs. Following a long-standing approach, reads shorter than 16 nucleotides (nt) are removed from the small RNA sequencing libraries or datasets. The serendipitous discovery of a 12 nt-long RNA species capable of modulating the microRNA from which they derive prompted us to challenge this dogma, and by expanding the window of RNA sizes down to 8 nt, to confirm the existence of functional very small RNAs (vsRNAs <16nt). Here we report the profiling of vsRNAs in Escherichia coli (with different experimental conditions), E. coli-derived outer membrane vesicles (OMVs) and five other bacterial strains (Pseudomonas aeruginosa PA7, P. aeruginosa PAO1, Salmonella Typhimurium 14028S, Legionella pneumophila JR32 Philadelphia-1 and Staphylococcus aureus HG001). Overall design: We analyzed by small RNA-seq the 8- to 30-nt window of RNA length of the gram-negative E. coli MG1655 model organism and 5 other bacterial strains (P. aeruginosa PA7, P. aeruginosa PAO1, S. Typhimurium 14028S, L. pneumophila JR32 Philadelphia-1 and S. aureus HG001).