Probing E. coli

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.