title: Genome-wide antisense transcription drives mRNA processing in bacteria.
abstract: RNA deep sequencing technologies are revealing unexpected levels of complexity in bacterial transcriptomes with the discovery of abundant noncoding RNAs, antisense RNAs, long 5' and 3' untranslated regions, and alternative operon structures. Here, by applying deep RNA sequencing to both the long and short RNA fractions (<50 nucleotides) obtained from the major human pathogen Staphylococcus aureus, we have detected a collection of short RNAs that is generated genome-wide through the digestion of overlapping sense/antisense transcripts by RNase III endoribonuclease. At least 75% of sense RNAs from annotated genes are subject to this mechanism of antisense processing. Removal of RNase III activity reduces the amount of short RNAs and is accompanied by the accumulation of discrete antisense transcripts. These results suggest the production of pervasive but hidden antisense transcription used to process sense transcripts by means of creating double-stranded substrates. This process of RNase III-mediated digestion of overlapping transcripts can be observed in several evolutionarily diverse Gram-positive bacteria and is capable of providing a unique genome-wide posttranscriptional mechanism to adjust mRNA levels.
authors: Laboratory of Microbial Biofilms, Instituto de Agrobiotecnología, Consejo Superior de Investigaciones Científicas-Universidad Pública de Navarra-Gobierno de Navarra, 31006 Pamplona, Spain. ilasa@unavarra.es
authors: Iñigo
authors: I
authors: Lasa
authors: Alejandro
authors: A
authors: Toledo-Arana
authors: Alexander
authors: A
authors: Dobin
authors: Maite
authors: M
authors: Villanueva
authors: Igor Ruiz
authors: IR
authors: de los Mozos
authors: Marta
authors: M
authors: Vergara-Irigaray
authors: Víctor
authors: V
authors: Segura
authors: Delphine
authors: D
authors: Fagegaltier
authors: José R
authors: JR
authors: Penadés
authors: Jaione
authors: J
authors: Valle
authors: Cristina
authors: C
authors: Solano
authors: Thomas R
authors: TR
authors: Gingeras
mesh_terms: D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial / Q000235:genetics*; D006801:Humans; D016366:Open Reading Frames / Q000235:genetics; D012323:RNA Processing, Post-Transcriptional / Q000235:genetics*; D016372:RNA, Antisense / Q000235:genetics* / Q000378:metabolism; D012329:RNA, Bacterial / Q000235:genetics; D012330:RNA, Double-Stranded / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D043244:Ribonuclease III / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D013211:Staphylococcus aureus / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D016372:RNA, Antisense; D012329:RNA, Bacterial; D012330:RNA, Double-Stranded; D012333:RNA, Messenger; D043244:Ribonuclease III