The Role of Replication-Associated Repair Factors on R-Loops

Abstract

The nascent RNA can reinvade the DNA double helix to form a structure termed the R-loop, where a single-stranded DNA (ssDNA) is accompanied by a DNA-RNA hybrid. Unresolved R-loops can impede transcription and replication processes and lead to genomic instability by a mechanism still not fully understood. In this sense, a connection between R-loops and certain chromatin markers has been reported that might play a key role in R-loop homeostasis and genome instability. To counteract the potential harmful effect of R-loops, different conserved messenger ribonucleoprotein (mRNP) biogenesis and nuclear export factors prevent R-loop formation, while ubiquitously-expressed specific ribonucleases and DNA-RNA helicases resolve DNA-RNA hybrids. However, the molecular events associated with R-loop sensing and processing are not yet known. Given that R-loops hinder replication progression, it is plausible that some DNA replication-associated factors contribute to dissolve R-loops or prevent R-loop mediated genome instability. In support of this, R-loops accumulate in cells depleted of the BRCA1, BRCA2 or the Fanconi anemia (FA) DNA repair factors, indicating that they play an active role in R-loop dissolution. In light of these results, we review our current view of the role of replication-associated DNA repair pathways in preventing the harmful consequences of R-loops.

Keywords: BRCA; DNA-RNA hybrids; Fanconi anemia; cancer; genetic instability; replication stress.

Figure 1

Multiple factors either prevent the accumulation of harmful R-loops or contribute to their resolution and dissolution. (A) The alleviation of negative supercoiling by topoisomerase I (TopoI) together with the cotranscriptional processes of messenger ribonucleoprotein (mRNP) biogenesis and several RNA binding factors contribute to preventing DNA-RNA hybridization. (B) In the absence of either of these factors, the nascent RNA can reinvade the DNA double helix to form a structure termed the R-loop, where a single-stranded (ssDNA) is accompanied by a DNA-RNA hybrid. R-loops and/or their associated chromatin alterations constitute a roadblock for incoming replication forks. (C) Ribonuclease (RNase) H and helicases, such as Senataxin (SETX), control R-loop levels in the cells by degrading the RNA moiety of the R-loops or unwinding DNA-RNA hybrids, respectively. BRCA1 recruits SETX to R-loop sites. FACT, PIF1, BRCA2 and Fanconi anemia (FA) factors help the replisome to overcome R-loops. XPG and XPF nucleases can also target R-loops, thus generating DNA breaks.