title: Insights into the Mechanisms of Basal Coordination of Transcription Using a Genome-Reduced Bacterium.
abstract: Coordination of transcription in bacteria occurs at supra-operonic scales, but the extent, specificity, and mechanisms of such regulation are poorly understood. Here, we tackle this problem by profiling the transcriptome of the model organism Mycoplasma pneumoniae across 115 growth conditions. We identify three qualitatively different levels of co-expression corresponding to distinct relative orientations and intergenic properties of adjacent genes. We reveal that the degree of co-expression between co-directional adjacent operons, and more generally between genes, is tightly related to their capacity to be transcribed en bloc into the same mRNA. We further show that this genome-wide pervasive transcription of adjacent genes and operons is specifically repressed by DNA regions preferentially bound by RNA polymerases, by intrinsic terminators, and by large intergenic distances. Taken together, our findings suggest that the basal coordination of transcription is mediated by the physical entities and mechanical properties of the transcription process itself, and that operon-like behaviors may strongly vary from condition to condition.
authors.affiliation: CNRS & Université Grenoble Alpes TIMC-IMAG, 38000 Grenoble, France. Electronic address: ivan.junier@univ-grenoble-alpes.fr.
authors.forename: Ivan
authors.initials: I
authors.lastname: Junier
authors.affiliation: Institut für Pathologie, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany.
authors.forename: E Besray
authors.initials: EB
authors.lastname: Unal
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra, 08002 Barcelona, Spain.
authors.forename: Eva
authors.initials: E
authors.lastname: Yus
authors.affiliation: EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra, 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, The Barcelona Institute of Science and Technology, Doctor Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra, 08002 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys 23, 08010 Barcelona, Spain. Electronic address: luis.serrano@crg.eu.
authors.forename: Luis
authors.initials: L
authors.lastname: Serrano
mesh_terms: D001419:Bacteria; D012321:DNA-Directed RNA Polymerases; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D009876:Operon; D011401:Promoter Regions, Genetic; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D012321:DNA-Directed RNA Polymerases