Replication and transcription on a collision course: eukaryotic regulation mechanisms and implications for DNA stability

Abstract

DNA replication and transcription are vital cellular processes during which the genetic information is copied into complementary DNA and RNA molecules. Highly complex machineries required for DNA and RNA synthesis compete for the same DNA template, therefore being on a collision course. Unscheduled replication-transcription clashes alter the gene transcription program and generate replication stress, reducing fork speed. Molecular pathways and mechanisms that minimize the conflict between replication and transcription have been extensively characterized in prokaryotic cells and recently identified also in eukaryotes. A pathological outcome of replication-transcription collisions is the formation of stable RNA:DNA hybrids in molecular structures called R-loops. Growing evidence suggests that R-loop accumulation promotes both genetic and epigenetic instability, thus severely affecting genome functionality. In the present review, we summarize the current knowledge related to replication and transcription conflicts in eukaryotes, their consequences on genome stability and the pathways involved in their resolution. These findings are relevant to clarify the molecular basis of cancer and neurodegenerative diseases.

Keywords: R-loops; cancer; epigenetic instability; genetic instability; neurodegeneration; replication stress; replication–transcription conflicts.

FIGURE 1

Eukaryotic mechanisms that manage replication– transcription conflicts. Schematic representation of a head-on encounter between the replisome and RNAPII. The cotrascriptional processing of nascent RNA, including its export through the nuclear envelope mediated by the THO/TREX and TREX2 complexes, can impede replication forks progression. The ATR checkpoint pathway temporarily inhibits RNA export by phosphorylating nucleoporins, thus allowing fork advancement. However, this process may generate harmful R-loop structures, more likely in head-on replication–transcription encounters. Multiple factors, including the accessory DNA/RNA helicases of the replisome Sen1/SETX and Pif1, the RNA exosome, RNaseH2, and Toposomerase I, may cooperate in limiting R-loop accumulation at the fork. The FACT complex, which interacts with SETX, could be involved in the re-establishment of chromatin status upon replication–transcription collisions. R-loops can be also processed into DSBs by XPG and XPF endonucleases. Hog1-dependent Mrc1 phosphorylation and RecQL5 modulate the speed of the replisome or RNAPII, respectively, while Dicer dislodges RNAPII at fork passage. Failure to promptly remove R-loops (gray box) causes not only DSBs, but also chromatin condensation through the accumulation of H3S10P and H3K9me2 markers, which contributes to fork arrest and gene silencing. Unrestrained R-loop accumulation has been also linked to repeats expansion and inflammation events, thus contributing to cancer and neurodegeneration (refer to text for further details).