Transcription and recombination: when RNA meets DNA

Abstract

A particularly relevant phenomenon in cell physiology and proliferation is the fact that spontaneous mitotic recombination is strongly enhanced by transcription. The most accepted view is that transcription increases the occurrence of double-strand breaks and/or single-stranded DNA gaps that are repaired by recombination. Most breaks would arise as a consequence of the impact that transcription has on replication fork progression, provoking its stalling and/or breakage. Here, we discuss the mechanisms responsible for the cross talk between transcription and recombination, with emphasis on (1) the transcription-replication conflicts as the main source of recombinogenic DNA breaks, and (2) the formation of cotranscriptional R-loops as a major cause of such breaks. The new emerging questions and perspectives are discussed on the basis of the interference between transcription and replication, as well as the way RNA influences genome dynamics.

Figure 1.

Transcription intermediates can compromise genome integrity in prokaryotes and eukaryotes. (A) In eukaryotes, mRNP biogenesis and export are coupled to transcription. Transcribed genes may also be anchored to the nuclear pore. Negative supercoiling (−) accumulates behind the elongating RNAPII and facilitates the separation of both strands, making the DNA more susceptible to genotoxic agents. Positive supercoiling (+) accumulates ahead of the transcription machinery, in front of a head-on oncoming replication fork. (B) The nascent messenger RNA (mRNA) might hybridize back to its DNA template behind the RNAPII, forming an R-loop. (C) In prokaryotes, cotranscriptional translation of the nascent mRNA may impede the formation of R-loop. (D) Cotranscriptional folding of nonprotein coding RNAs may reduce the probability of R-loop formation in both eukaryotes and prokaryotes.

Figure 2.

CSR. Transcription of switch (S) regions of the Ig genes generates R-loops, providing ssDNA substrates for the activation-induced cytidine deaminase (AID). Subsequent sequential enzymatic activities of different DNA repair pathways, including base excision and mismatch repair, would lead to DSBs that, by NHEJ, would complete the CSR event.

Figure 3.

Putative molecular intermediates and mechanisms responsible for TAR. (A) The negative supercoiled DNA accumulating behind the elongating transcription machinery would expose ssDNA segments that would be more susceptible to DNA damage. Unless repaired, such transcription-dependent DNA lesions could block the replicative DNA polymerase. Template switching, DSB repair (in this case, the original damage was a ssDNA nick that, after replication, is converted to a DSB), or fork reversal would be required to complete replication. Postreplicative repair by translesion synthesis polymerases is not drawn for simplification. (B) The transcription machinery can be a direct obstacle for the progression of the replication fork, whether or not mediated by a cotranscriptional R-loop. An R-loop, or any other kind of transcription-dependent obstacle, could block DNA synthesis so that template switching would be needed for replication completion. Similarly, a head-on transcription-replication collision might cause replication fork arrest and reversal. Alternatively, R-loop-primed reinitiation of DNA synthesis might occur. Replication fork arrest could also result in DSBs, whether or not catalyzed by endonucleases, that would use recombination either with the sister chromatid or homologous chromosome or an ectopically located homologous DNA sequence, which can result in a transcription-dependent hyper-recombination phenotype.