Bacterial core RNA polymerase (RNAP) must associate with a sigma factor to recognize promoter sequences. Escherichia coli encodes seven sigma factors, each believed to be specific for a largely distinct subset of promoters. Using microarrays representing the entire E. coli genome, we identify 87 in vivo targets of sigma32, the heat-shock sigma factor, and estimate that there are 120-150 sigma32 promoters in total. Unexpectedly, 25% of these sigma32 targets are located within coding regions, suggesting novel regulatory roles for sigma32. The majority of sigma32 promoter targets overlap with those of sigma70, the housekeeping sigma factor. Furthermore, their DNA sequence motifs are often interdigitated, with RNAPsigma70 and RNAPsigma32 initiating transcription in vitro with similar efficiency and from identical positions. SigmaE-regulated promoters also overlap extensively with those for sigma70. These results suggest that extensive functional overlap between sigma factors is an important phenomenon.

Collisions between DNA replication and transcription significantly affect genome organization, regulation, and stability. Previous studies have described collisions between replication forks and elongating RNA polymerases. Although replication collisions with the transcription-initiation or -termination complexes are potentially even more important because most genes are not actively transcribed during DNA replication, their existence and mechanisms remained unproven. To address this matter, we have designed a bacterial promoter that binds RNA polymerase and maintains it in the initiating mode by precluding the transition into the elongation mode. By using electrophoretic analysis of replication intermediates, we have found that this steadfast transcriptioninitiation complex inhibits replication fork progression in an orientation-dependent manner during head-on collisions. Transcription terminators also appeared to attenuate DNA replication, but in the opposite, codirectional orientation. Thus, transcription regulatory signals may serve as ''punctuation marks'' for DNA replication in vivo.collisions ͉ promoter ͉ terminator I mpairment of DNA replication is believed to be a major factor in genomic instability (1-13). Because transcription and replication share the same template, occasional collisions between the two machineries are inevitable and can interfere with replication fork progression. Collisions between the elongating RNA polymerase and the replication fork have been well documented in vitro (14-17) and in vivo in both Escherichia coli (18)(19)(20) and Saccharomyces cerevisiae (6,21,22). The consensus from those studies was that head-on collisions with elongating RNA polymerase are much more detrimental for replication fork progression than codirectional collisions. Although it was suggested that replication stalling during the head-on collisions with transcription was caused by topological stress in the DNA separating the two machineries (18,19,22,23), we have recently shown that it is caused by their direct, physical interaction (20). These results, combined with the data on preferred codirectional alignment of transcription units with the direction of replication in prokaryotes (23-27), have led to the suggestion that the main disadvantage of the head-on collisions could be their inhibitory effect on DNA replication.All of the experimental studies cited in the preceding paragraph evaluated the effects of elongating RNA polymerase on the progression of the replication fork. Is there an interplay between the replication machinery and the transcriptioninitiation complex? To the best of our knowledge, there have been few studies on this matter. One intriguing example was the detection of a polar replication fork pause site at the tRNA locus of S. cerevisiae, which depended on the functionality of both the promoter and the RNA polymerase III (pol III) (22). It was believed that the replication fork was attenuated during the encounter with the elongating RNA polymerase (22). A later study, however, suggest...