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The transcription unit architecture of the Escherichia coli genome

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.

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Figure 1: Flowchart of the systematic iterative integration process.
Figure 2: Integration of the organizational components.
Figure 3: Modular units.
Figure 4: Determination of transcription units and use of alternative TSSs.

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Acknowledgements

The authors thank Derek Lovley at the University of Massachusetts, Amherst for his insightful discussion and Marc Abrams for editing the manuscript. Proteomics experiments were performed using EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. This work was supported by the US National Institutes of Health Grant GM062791 and by the Office of Science (BER), US Department of Energy, cooperative agreement DE-FC02-02ER63446.

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B.-K.C., K.Z., Y.Q., E.M.K. and B.Ø.P. conceived and designed experiments. B.-K.C., Y.S.P., Y.G. and E.M.K. performed genome-scale experiments. All data analyses were performed by B.-K.C., K.Z., Y.Q., Y.S.P. and C.L.B. The manuscript was written by B.-K.C., K.Z. and B.Ø.P.

Corresponding author

Correspondence to Bernhard Ø Palsson.

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Supplementary Figs. 1–9 and Supplementary Tables 1–14 (PDF 26256 kb)

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Cho, BK., Zengler, K., Qiu, Y. et al. The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol 27, 1043–1049 (2009). https://doi.org/10.1038/nbt.1582

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