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Research Overview

Impact of Transcription and Replication on the Organization and Stability of the Genome

Since transcription and replication share the same template, occasional collisions between the two machineries are inevitable and can interfere with both processes. We have recently found that the head-on collisions with elongating RNA polymerase is much more detrimental for the replication fork progression in vivo than the co-directional collisions. Furthermore, we have proven that these collisions are caused by the direct physical interaction of the two machineries, rather than the long-range alterations of the DNA template. These results, combined with the data on the preferred co-directional alignment of transcription units with the direction of replication in prokaryotes, have led us to suggest that the main disadvantage of the head-on collisions could be in their inhibitory effect on DNA replication.

Figure 2

Figure 2. Collisions between replication and transcription in bacteria. In case of head-on collisions, replicative DNA helicase, depicted by the green hexagon, collides with the front end of RNA polymerase (golden convex). In case of co-directional collisions, the leading strand DNA polymerase (red oval) collides with the rear end of the RNA polymerase.

Besides collisions with elongating RNA polymerases, we study the effects of the transcription initiation or termination complexes on the replication fork progression. This could be even more important, since most genes are not actively transcribed during DNA replication. We have recently found that the steadfast transcription initiation complexes inhibit the replication fork progression in an orientation-dependent manner, during head-on collisions. Transcription terminators also appeared to attenuate DNA replication, but in the opposite, co-directional orientation. Notably in both instances, the replication fork is stalled immediately after passing the coding region. Transcription regulatory signals, thus, serve as "punctuation marks" for DNA replication in vivo by attenuating the replication fork progression, as it has traversed the coding areas. This attenuation could provide an extra time for the repair or recombination machineries to clear the coding areas off the newly acquired mutations.

This project is now developing in several directions. First, we are expanding our collision studies from the E. coli into yeast S cerevisiae and, eventually, mammals. Second, we plan to experimentally determine mutation rates in the transcribed areas that are replicated head-on or co-directionally. This study will be carried out in yeast, using selectable genes driven by the S-phase-specific promoters. Finally, we are starting a major bioinformatics project, aimed at estimating the sequence divergence between genes in numerous bacterial genomes depending on their positioning relative to the direction of the replication.