title: Prevalence of transcription promoters within archaeal operons and coding sequences.
abstract: Despite the knowledge of complex prokaryotic-transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have had a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of approximately 64% of all genes, including putative non-coding RNAs in Halobacterium salinarum NRC-1. Our integrative analysis of transcriptome dynamics and protein-DNA interaction data sets showed widespread environment-dependent modulation of operon architectures, transcription initiation and termination inside coding sequences, and extensive overlap in 3' ends of transcripts for many convergently transcribed genes. A significant fraction of these alternate transcriptional events correlate to binding locations of 11 transcription factors and regulators (TFs) inside operons and annotated genes-events usually considered spurious or non-functional. Using experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements.
authors.affiliation: Institute for Systems Biology, Seattle, WA 98103, USA.
authors.forename: Tie
authors.initials: T
authors.lastname: Koide
authors.forename: David J
authors.initials: DJ
authors.lastname: Reiss
authors.forename: J Christopher
authors.initials: JC
authors.lastname: Bare
authors.forename: Wyming Lee
authors.initials: WL
authors.lastname: Pang
authors.forename: Marc T
authors.initials: MT
authors.lastname: Facciotti
authors.forename: Amy K
authors.initials: AK
authors.lastname: Schmid
authors.forename: Min
authors.initials: M
authors.lastname: Pan
authors.forename: Bruz
authors.initials: B
authors.lastname: Marzolf
authors.forename: Phu T
authors.initials: PT
authors.lastname: Van
authors.forename: Fang-Yin
authors.initials: FY
authors.lastname: Lo
authors.forename: Abhishek
authors.initials: A
authors.lastname: Pratap
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.forename: Amelia
authors.initials: A
authors.lastname: Peterson
authors.forename: Dan
authors.initials: D
authors.lastname: Martin
authors.forename: Nitin S
authors.initials: NS
authors.lastname: Baliga
mesh_terms: D003198:Computer Simulation; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D019766:Genes, Archaeal; D016680:Genome, Bacterial; D019617:Halobacterium salinarum / Q000235:genetics / Q000502:physiology; D008957:Models, Genetic; D009010:Monte Carlo Method; D009876:Operon; D011401:Promoter Regions, Genetic; D012313:RNA / Q000235:genetics; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors; D012313:RNA