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Prevalence of transcription promoters within archaeal operons and coding sequences.

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

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