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ChIP-chip of MG1655 with antibody against E. coli RNAP beta subunit under various conditions

ABSTRACT: We integrated RNAP binding regions (RBRs) and mRNA transcript abundance to determine segments of contiguous transcription originating from promoter regions. To measure RBRs at a genome scale, we employed a ChIP-chip method to E. coli K-12 MG1655 grown in the presence or absence of rifampicin under multiple growth conditions using antibody against E. coli RNAP beta subunit. A twelve ChIP-chip study using immunoprecipitated DNA (IP-DNA) from four separate culture conditions with and/or without rifampicin treatment. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide probes spaced 25 bp apart (25-bp overlap between two probes) across the E. coli genome (NimbleGen). Experiments were conducted as biological duplicates or triplicates (different cultures).

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

SUBMITTER: Bernhard Palsson

PROVIDER: E-GEOD-15588 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The transcription unit architecture of the Escherichia coli genome.

Cho Byung-Kwan BK Zengler Karsten K Qiu Yu Y Park Young Seoub YS Knight Eric M EM Barrett Christian L CL Gao Yuan Y Palsson Bernhard Ø BØ

Nature biotechnology 20091101 11

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. ...[more]

PMID: 19881496

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