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Genome-scale reconstruction of the sigma factor network in E. coli

ABSTRACT: We report the application of single-molecule-based sequencing technology for high-throughput profiling of transcription start sites for Escherichia coli under different conditions. By obtaining sequence from 5' RACE (rapid amplification of cDNA ends) followed by deep sequencing, we generated genome-wide TSS (transcription start site) maps for E. coli. This TSS-map was integrated with ChIP-chip data generated for 6 sigma factors in E. coli, resulting in reconstruction of sigma factor network in E. coli. Examination of transcription start sites by biological duplicates from E. coli for 3 different conditions

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Donghyuk Kim

PROVIDER: E-GEOD-46737 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states.

Cho Byung-Kwan BK Kim Donghyuk D Knight Eric M EM Zengler Karsten K Palsson Bernhard O BO

BMC biology 20140124

<h4>Background</h4>At the beginning of the transcription process, the RNA polymerase (RNAP) core enzyme requires a σ-factor to recognize the genomic location at which the process initiates. Although the crucial role of σ-factors has long been appreciated and characterized for many individual promoters, we do not yet have a genome-scale assessment of their function.<h4>Results</h4>Using multiple genome-scale measurements, we elucidated the network of σ-factor and promoter interactions in Escheric ...[more]

PMID: 24461193

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