The replication fork and RNA polymerase share the same DNA template making occasional collisions between the two machineries inevitable. In the case of head-on collisions, the front edge of RNA polymerase collides with the lagging strand synthesis components of the replication fork. In the co-directional case, in contrast, the rear edge of RNA polymerase meets with the leading strand synthesis components of the replication fork. The first data suggesting that head-on collisions can occur both in vitro and in vivo resulting in replication fork stalling were obtained more than two decades ago. The mechanisms responsible for these events remained obscure. My lab got involved in these studies as a result of two purely serendipitous developments. First, while attempting to prove that H-DNA formed by d(G)n•d(C)n runs can stall DNA replication in vivo, we found that it is, in fact, transcription in a specific direction through those runs that causes fork stalling (1). Recently, we showed that unusually stable rG/dC hybrids created during transcription of those runs trigger the formation of R-loops, which, in turn, stall replication forks moving co-directionally (2). Second, while attempting to understand the nature of some obscure replication stall sites in a bacterial plasmid, we found that direct physical collisions between transcription and replication apparata led to profound fork stalling (3). Furthermore, even when RNA polymerase has not cleared the promoter, its front edge represented a formidable obstacle for the replication forks moving toward it (4). Finally, we found that RNA polymerase trapped or backtracked at the terminator sequences stalls co-directional replication forks (4). It would be fair to say that these data revitalized the field resulting in many spectacular structural and functional discoveries to be discussed at this session.

References

1. M. M. Krasilnikova, G. M. Samadashwily, A. S. Krasilnikov, S. M. Mirkin, EMBO J 17, 5095-5102 (1998).
2. B. P. Belotserkovskii et al. Proc Natl Acad Sci USA 107: 12816-12821 (2010).
3. E. V. Mirkin, S. M. Mirkin, Mol Cell Biol 25: 888-895 (2005).
4. E. V. Mirkin, D. Castro Roa, E. Nudler, S. M. Mirkin, Proc Natl Acad Sci USA 103:7276-7781 (2006).