The transcription unit architecture of the Escherichia coli genome.

TitleThe transcription unit architecture of the Escherichia coli genome.
Publication TypeJournal Article
Year of Publication2009
AuthorsCho B-K, Zengler K, Qiu Y, Park Y S, Knight EM, Barrett CL, Gao Y, Palsson BØ
JournalNature biotechnology
Volume27
Issue11
Pagination1043-9
PubMed Date2009 Nov
ISSN1546-1696
KeywordsBase Sequence, Binding Sites, DNA-Directed RNA Polymerases, Escherichia coli, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Genome, Bacterial, High-Throughput Screening Assays, Molecular Sequence Data, Open Reading Frames, Transcription Initiation Site, Transcription, Genetic
Abstract

Bacterial genomes are organized by structural and functional elements, including promoters, transcription start and termination sites, open reading frames, regulatory noncoding regions, untranslated regions and transcription units. Here, we iteratively integrate high-throughput, genome-wide measurements of RNA polymerase binding locations and mRNA transcript abundance, 5' sequences and translation into proteins to determine the organizational structure of the Escherichia coli K-12 MG1655 genome. Integration of the organizational elements provides an experimentally annotated transcription unit architecture, including alternative transcription start sites, 5' untranslated region, boundaries and open reading frames of each transcription unit. A total of 4,661 transcription units were identified, representing an increase of >530% over current knowledge. This comprehensive transcription unit architecture allows for the elucidation of condition-specific uses of alternative sigma factors at the genome scale. Furthermore, the transcription unit architecture provides a foundation on which to construct genome-scale transcriptional and translational regulatory networks.

Alternate JournalNat. Biotechnol.
PubMed ID19881496

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