Critical role of R-loops in processing replication blocks

Blocks in replication result from impediments to the advancing replication machinery and are lethal if not resolved. The replication fork must be reassembled for DNA synthesis to proceed. Fork assembly outside the chromosomal origin of replication (oriC) is mediated by recombination or via a helicase-dependent pathway. ColE1 plasmid origins of replication and oriK sites initiate primosome assembly by an RNA-DNA hybrid structure known as R-loop. We review evidence suggesting that R-loops are frequent during normal cell growth and that R-loops are critical for the maintenance of genome integrity. We propose that downstream of a replication block, RNA at R-loops is extended by DNA polymerase I, opening up the DNA duplex and leading to the recruitment of the replisome. This would allow replication to proceed while the original block is repaired or bypassed. Unlike recombination and helicase-dependent fork restoration, this mechanism would operate preferentially in transcribed areas of the genome, which are known to be particularly susceptible to DNA damage. Our model emphasizes the intimate relationship between transcription and repair, offers a unifying interpretation of phenotypes attributed to bacterial strains deficient in R-loop fork assembly, and calls for a renewed focus on R-loop formation and regulation.