Transcription start site RNAs (tssRNAs) in bacteria

Here we report the genome-wide identification of small RNAs associated with transcription start sites, termed tssRNAs, in Mycoplasma pneumoniae. tssRNAs were also found to be present in a different bacterial phyla, Escherichia coli. Similar to the recently identified promoter-associated tiny RNAs (tiRNAs) in eukaryotes, tssRNAs are associated with active promoters. Evidence suggests that these tssRNAs are distinct from previously described abortive transcription. ssRNAs have an average size of 45 bases, and they map exactly to the beginning of cognate full-length transcripts as well as to cryptic transcription start sites. The expression of bacterial tssRNAs requires factors other than the standard RNA polymerase holoenzyme. We found that the RNA polymerase is halted at tssRNA positions in vivo, which may indicate that a pausing mechanism exists to prevent transcription in the absence of genes. These results suggest that small RNAs associated with TSSs could be a universal feature of bacterial transcription.