The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
The transcription unit architecture of the Escherichia coli genome
Open accessAbstract
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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Cites
Central Dogma of Molecular Biology
CRICK, F. (1970) · Nature · doi:10.1038/227561a0 · Cited by 3,444
Structural Mechanism for Rifampicin Inhibition of Bacterial RNA Polymerase
Campbell, E. A., Korzheva, N., Mustaev, A., Murakami, K., Nair, S., Goldfarb, A., & Darst, S. A. (2001) · Cell · doi:10.1016/s0092-8674(01)00286-0 · Cited by 1,556 · cited 1×
“coli K-12 MG1655 grown in the presence or absence of rifampicin (a small-molecular inhibitor that traps RNAP at promoters) under multiple growth condition”
A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell
Choi, P. J., Cai, L., Frieda, K., & Xie, X. S. (2008) · Science · doi:10.1126/science.1161427 · Cited by 438
EcoCyc: A comprehensive view of Escherichia coli biology
Keseler, I. M., Bonavides-Martinez, C., Collado-Vides, J., Gama-Castro, S., Gunsalus, R. P., Johnson, D. A., Krummenacker, M., Nolan, L. M., Paley, S., Paulsen, I. T., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn751 · Cited by 373 · cited 1×
“Within the known genes, several, such as rhaBADM , tynA and speF , are functional only under specific growth condition”
Application of 'next-generation' sequencing technologies to microbial genetics
MacLean, D., Jones, J. D. G., & Studholme, D. J. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2088 · Cited by 293
Cited by
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Nicolas, P., Mäder, U., Dervyn, E., Rochat, T., Leduc, A., Pigeonneau, N., Bidnenko, E., Marchadier, E., Hoebeke, M., Aymerich, S., et al. (2012) · Science · doi:10.1126/science.1206848 · Cited by 910
Thomason, M. K., Bischler, T., Eisenbart, S. K., Förstner, K. U., Zhang, A., Herbig, A., Nieselt, K., Sharma, C. M., & Storz, G. (2015) · Journal of Bacteriology · doi:10.1128/jb.02096-14 · Cited by 335
Identification and characterization of E. coli CRISPR‐cas promoters and their silencing by H‐NS
Pul, Ü., Wurm, R., Arslan, Z., Geißen, R., Hofmann, N., & Wagner, R. (2010) · Molecular Microbiology · doi:10.1111/j.1365-2958.2010.07073.x · Cited by 282
The challenges of integrating multi-omic data sets
Palsson, B., & Zengler, K. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.462 · Cited by 178
Self-citationEndogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype
Kurylo, C. M., Parks, M. M., Juette, M. F., Zinshteyn, B., Altman, R. B., Thibado, J. K., Vincent, C. T., & Blanchard, S. C. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.08.093 · Cited by 117
Metadata
- Authors
- Cho, B.-K., Zengler, K., Qiu, Y., Park, Y. S., Knight, E. M., Barrett, C. L., Gao, Y., & Palsson, B. Ø.
- Venue
- Nature Biotechnology
- Published
- 2009-11
- Volume
- 27
- Issue
- 11
- Pages
- 1043-1049
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W1966786968
- Cited by
- 253
- References
- 5
- FWCI
- 13.37
- Type
- journal article
- Language
- en
- Open access
- green
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- Cho, B.-K., Zengler, K., Qiu, Y., Park, Y. S., Knight, E. M., Barrett, C. L., Gao, Y., & Palsson, B. Ø. (2009). The transcription unit architecture of the Escherichia coli genome. Nature Biotechnology. https://doi.org/10.1038/nbt.1582
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