Prevalence of transcription promoters within archaeal operons and coding sequences

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.

doi:10.1038/msb.2009.42

Title: Prevalence of transcription promoters within archaeal operons and coding sequences

Journal Article · Thu Jan 01 00:00:00 EST 2009 · Molecular Systems Biology

DOI:https://doi.org/10.1038/msb.2009.42· OSTI ID:1623794

Koide, Tie ^[1]; Reiss, David J. ^[1]; Bare, J. Christopher ^[1]; Pang, Wyming Lee ^[1]; Facciotti, Marc T. ^[2]; Schmid, Amy K. ^[1]; Pan, Min ^[1]; Marzolf, Bruz ^[1]; Van, Phu T. ^[1]; Lo, Fang‐Yin ^[1]; Pratap, Abhishek ^[1]; Deutsch, Eric W. ^[1]; Peterson, Amelia ^[3]; Martin, Dan ^[4]; Baliga, Nitin S. ^[4]

Inst. for Systems Biology, Seattle, WA (United States)
Inst. for Systems Biology, Seattle, WA (United States); Univ. of California, Davis, CA (United States). UC Davis Genome Center. Dept. of Biomedical Engineering
Fred Hutchinson Cancer Research Center, Seattle, WA (United States). Divisions of Human Biology and Clinical Research
Inst. for Systems Biology, Seattle, WA (United States); Fred Hutchinson Cancer Research Center, Seattle, WA (United States). Divisions of Human Biology and Clinical Research

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 B64% 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 30 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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Research Organization:: Institute for Systems Biology, Seattle, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: FG02-07ER64327

OSTI ID:: 1623794

Journal Information:: Molecular Systems Biology, Vol. 5, Issue 1; ISSN 1744-4292

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
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archaea
ChIP–chip
non-coding RNA
tiling array
transcription

Title: Prevalence of transcription promoters within archaeal operons and coding sequences

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