Prevalence of transcription promoters within archaeal operons and coding sequences

Tie Koide, David J. Reiss, J. Christopher Bare, Wyming Lee Pang, Marc T. Facciotti, Amy K. Schmid, Min Pan, Bruz Marzolf, Phu T. Van, Fang Yin Lo, Abhishek Pratap, Eric W. Deutsch, Amelia Peterson, Dan Martin, Nitin S. Baliga

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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 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 genesevents 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.

Original languageEnglish
Article number285
JournalMolecular Systems Biology
Volume5
DOIs
Publication statusPublished - 20 Jan 2009
Externally publishedYes

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