Prevalence of transcription promoters within archaeal operons and coding sequences.
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| Online Access: |
Full Text (via OSTI) |
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| Format: | eBook |
| Language: | English |
| Published: |
Washington, D.C. : Oak Ridge, Tenn. :
United States. Department of Energy. Office of Science ; Distributed by the Office of Scientific and Technical Information, U.S. Department of Energy,
2009.
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| Subjects: |
| 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 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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| Item Description: | Published through Scitech Connect. 01/01/2009. "Journal ID: ISSN 1744-4292." 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 ; et al; Institute for Systems Biology, Seattle, WA (United States) |
| Physical Description: | Size: Article No. 285 : digital, PDF file. |