The transcription unit architecture of the Escherichia coli genome Export

@article{citeulike:6083922, 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.}, author = {Cho, Byung-Kwan and Zengler, Karsten and Qiu, Yu and Park, Young S. and Knight, Eric M. and Barrett, Christian L. and Gao, Yuan and Palsson, Bernhard O.}, booktitle = {Nat Biotech}, citeulike-article-id = {6083922}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt.1582}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nbt.1582}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19881496}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19881496}, day = {01}, doi = {10.1038/nbt.1582}, issn = {1087-0156}, journal = {Nature Biotechnology}, keywords = {ecoli, transcriptional-regulatory-networks}, month = {November}, number = {11}, pages = {1043--1049}, posted-at = {2009-11-09 22:26:39}, priority = {2}, publisher = {Nature Publishing Group}, title = {The transcription unit architecture of the Escherichia coli genome}, url = {http://dx.doi.org/10.1038/nbt.1582}, volume = {27}, year = {2009} }

TY - JOUR ID - citeulike:6083922 L3 - citeulike-article-id:6083922 N2 - 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. IS - 11 JF - Nature Biotechnology SN - 1087-0156 EP - 1049 TI - The transcription unit architecture of the Escherichia coli genome PB - Nature Publishing Group VL - 27 T2 - Nat Biotech SP - 1043 KW - ecoli KW - transcriptional-regulatory-networks AU - Cho, Byung-Kwan AU - Zengler, Karsten AU - Qiu, Yu AU - Park, Young AU - Knight, Eric AU - Barrett, Christian AU - Gao, Yuan AU - Palsson, Bernhard PY - 2009/11/01/ UR - http://dx.doi.org/10.1038/nbt.1582 ER -