title: Bacterial antisense RNAs are mainly the product of transcriptional noise.
abstract: cis-Encoded antisense RNAs (asRNAs) are widespread along bacterial transcriptomes. However, the role of most of these RNAs remains unknown, and there is an ongoing discussion as to what extent these transcripts are the result of transcriptional noise. We show, by comparative transcriptomics of 20 bacterial species and one chloroplast, that the number of asRNAs is exponentially dependent on the genomic AT content and that expression of asRNA at low levels exerts little impact in terms of energy consumption. A transcription model simulating mRNA and asRNA production indicates that the asRNA regulatory effect is only observed above certain expression thresholds, substantially higher than physiological transcript levels. These predictions were verified experimentally by overexpressing nine different asRNAs in Mycoplasma pneumoniae. Our results suggest that most of the antisense transcripts found in bacteria are the consequence of transcriptional noise, arising at spurious promoters throughout the genome.
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.
authors.forename: Verónica
authors.initials: V
authors.lastname: Lloréns-Rico
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.
authors.forename: Jaime
authors.identifier: 0000-0003-2458-9609
authors.initials: J
authors.lastname: Cano
authors.affiliation: MSD Animal Health, Bioprocess Technology and Support, 5830 AB Boxmeer, Netherlands.; Laboratory of Systems and Synthetic Biology, Wageningen University, 6700 EJ Wageningen, Netherlands.
authors.forename: Tjerko
authors.initials: T
authors.lastname: Kamminga
authors.affiliation: Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46980 Paterna, València, Spain.
authors.forename: Rosario
authors.identifier: 0000-0002-9397-1003
authors.initials: R
authors.lastname: Gil
authors.affiliation: Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46980 Paterna, València, Spain.; Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, 46020 Valencia, Spain.
authors.forename: Amparo
authors.identifier: 0000-0002-9146-7284
authors.initials: A
authors.lastname: Latorre
authors.affiliation: European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
authors.forename: Wei-Hua
authors.initials: WH
authors.lastname: Chen
authors.affiliation: European Molecular Biology Laboratory, 69117 Heidelberg, Germany.; Max Delbrück Centre (MDC) for Molecular Medicine, 13125 Berlin, Germany.
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.affiliation: Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, La Jolla, CA 92037, USA.; Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD 20850, USA.
authors.forename: John I
authors.identifier: 0000-0002-3784-5301
authors.initials: JI
authors.lastname: Glass
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain.
authors.forename: Luis
authors.initials: L
authors.lastname: Serrano
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain.
authors.forename: Maria
authors.initials: M
authors.lastname: Lluch-Senar
mesh_terms: D016372:RNA, Antisense / Q000235:genetics*; D012329:RNA, Bacterial / Q000235:genetics*; D013045:Species Specificity; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D016372:RNA, Antisense; D012329:RNA, Bacterial
keywords: RNA; bacterial antisense RNAs