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Probing E. coli

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In the December Nature Biotechnology Selinger et al. use an Escherichia coli oligonucleotide array with 30-base-pair resolution to detect antisense transcripts, new open reading frames (ORFs), and transcription starts and stops (Nat Biotechnol 2000, 18:1262-1268). The 295,936 elements of the array do not come without their problems. The sheer size and complexity of the array means that there is a huge amount of cross hybridization detected by missense probes. But the use of many probes within the same gene allows Selinger et al. to identify many genes that are up- or down-regulated in stationary phase. They also confirm transcription stop and start sites for two genes. Scanning for antisense transcripts suggests that there is a low level of transcription throughout the genome, probably from replication-induced and readthrough transcription.


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Wells, W. Probing E. coli. Genome Biol 1, spotlight-20001205-02 (2000) doi:10.1186/gb-spotlight-20001205-02

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  • Stationary Phase
  • Start Site
  • Huge Amount
  • Transcription Start
  • Antisense Transcript