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Prevalence of transcription promoters within archaeal operons and coding sequences.

Publication ,  Journal Article
Koide, T; Reiss, DJ; Bare, JC; Pang, WL; Facciotti, MT; Schmid, AK; Pan, M; Marzolf, B; Van, PT; Lo, F-Y; Pratap, A; Deutsch, EW; Peterson, A ...
Published in: Molecular systems biology
January 2009

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.

Duke Scholars

Published In

Molecular systems biology

DOI

EISSN

1744-4292

ISSN

1744-4292

Publication Date

January 2009

Volume

5

Start / End Page

285

Related Subject Headings

  • Transcription, Genetic
  • Transcription Factors
  • Reproducibility of Results
  • RNA
  • Promoter Regions, Genetic
  • Operon
  • Monte Carlo Method
  • Models, Genetic
  • Halobacterium salinarum
  • Genome, Bacterial
 

Citation

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Koide, T., Reiss, D. J., Bare, J. C., Pang, W. L., Facciotti, M. T., Schmid, A. K., … Baliga, N. S. (2009). Prevalence of transcription promoters within archaeal operons and coding sequences. Molecular Systems Biology, 5, 285. https://doi.org/10.1038/msb.2009.42
Koide, Tie, David J. Reiss, J Christopher Bare, Wyming Lee Pang, Marc T. Facciotti, Amy K. Schmid, Min Pan, et al. “Prevalence of transcription promoters within archaeal operons and coding sequences.Molecular Systems Biology 5 (January 2009): 285. https://doi.org/10.1038/msb.2009.42.
Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, et al. Prevalence of transcription promoters within archaeal operons and coding sequences. Molecular systems biology. 2009 Jan;5:285.
Koide, Tie, et al. “Prevalence of transcription promoters within archaeal operons and coding sequences.Molecular Systems Biology, vol. 5, Jan. 2009, p. 285. Epmc, doi:10.1038/msb.2009.42.
Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo F-Y, Pratap A, Deutsch EW, Peterson A, Martin D, Baliga NS. Prevalence of transcription promoters within archaeal operons and coding sequences. Molecular systems biology. 2009 Jan;5:285.
Journal cover image

Published In

Molecular systems biology

DOI

EISSN

1744-4292

ISSN

1744-4292

Publication Date

January 2009

Volume

5

Start / End Page

285

Related Subject Headings

  • Transcription, Genetic
  • Transcription Factors
  • Reproducibility of Results
  • RNA
  • Promoter Regions, Genetic
  • Operon
  • Monte Carlo Method
  • Models, Genetic
  • Halobacterium salinarum
  • Genome, Bacterial