Publications [#160641] of Amy K. Schmid

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Papers Published

  1. T Koide, DJ Reiss, JC Bare, WL Pang, MT Facciotti, AK Schmid, M Pan, B Marzolf, PT Van, FY Lo, A Pratap, EW Deutsch, A Peterson, D Martin, NS Baliga, Prevalence of transcription promoters within archaeal operons and coding sequences., Molecular systems biology, vol. 5 (2009), pp. 285 [doi] .
    (last updated on 2010/12/20)

    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.