title: Transcription start site associated RNAs in bacteria.
abstract: Here, we report the genome-wide identification of small RNAs associated with transcription start sites (TSSs), 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 RNAs. ssRNAs have an average size of 45 bases and map exactly to the beginning of cognate full-length transcripts and to cryptic TSSs. Expression of bacterial tssRNAs requires factors other than the standard RNA polymerase holoenzyme. We have 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.
authors.affiliation: Center for Genomic Regulation (CRG), UPF, Barcelona, Spain.
authors.forename: Eva
authors.initials: E
authors.lastname: Yus
authors.forename: Marc
authors.initials: M
authors.lastname: Güell
authors.forename: Ana P
authors.initials: AP
authors.lastname: Vivancos
authors.forename: Wei-Hua
authors.initials: WH
authors.lastname: Chen
authors.forename: María
authors.initials: M
authors.lastname: Lluch-Senar
authors.forename: Javier
authors.initials: J
authors.lastname: Delgado
authors.forename: Anne-Claude
authors.initials: AC
authors.lastname: Gavin
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.forename: Luis
authors.initials: L
authors.lastname: Serrano
mesh_terms: D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D008969:Molecular Sequence Data; D011019:Pneumonia, Mycoplasma / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012329:RNA, Bacterial; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D012329:RNA, Bacterial; D012321:DNA-Directed RNA Polymerases