Sensing R-Loop-Associated DNA Damage to Safeguard Genome Stability

Abstract

DNA transcription and replication are two essential physiological processes that can turn into a threat for genome integrity when they compete for the same DNA substrate. During transcription, the nascent RNA strongly binds the template DNA strand, leading to the formation of a peculiar RNA–DNA hybrid structure that displaces the non-template single-stranded DNA. This three-stranded nucleic acid transition is called R-loop. Although a programed formation of R-loops plays important physiological functions, these structures can turn into sources of DNA damage and genome instability when their homeostasis is altered. Indeed, both R-loop level and distribution in the genome are tightly controlled, and the list of factors involved in these regulatory mechanisms is continuously growing. Over the last years, our knowledge of R-loop homeostasis regulation (formation, stabilization, and resolution) has definitely increased. However, how R-loops affect genome stability and how the cellular response to their unscheduled formation is orchestrated are still not fully understood. In this review, we will report and discuss recent findings about these questions and we will focus on the role of ATM- and Rad3-related (ATR) and Ataxia–telangiectasia-mutated (ATM) kinases in the activation of an R-loop-dependent DNA damage response.

Emerging Role of Chimeric RNAs in Cell Plasticity and Adaptive Evolution of Cancer Cells

“…The interplay of splicing factors and RNA-binding proteins (RBPs) are found to play an important role in DNA-RNA hybrid (R-loop) formation during transcription to prevent RNA-induced genome instability [59]. In cancers, mutations in the spliceosome machinery can affect R-loop formation, promoting genomic instability [60][61][62].…”

A Fibrinogen Alpha Fragment Mitigates Chemotherapy-Induced MLL Rearrangements

“…While both drugs are topoisomerase II inhibitors, etoposide forms topoisomerase poisoning complexes, blocking DNA resealing during the enzymatic reaction, whereas doxorubicin intercalates into the double helix compromising topoisomerase functions, RNA-and DNA synthesis as well as generating free oxygen radicals (38,39). Therefore, etoposide primarily induces DSBs, while doxorubicin additionally causes formation of oxidative DNA lesions, DNA adducts and RNA-DNA hybrids, representing obstacles for nascent DNA synthesis (74). Interestingly, when we studied MLLbcr rearrangements following a short (4 h) treatment period and a long (72 h) recovery period versus uninterrupted treatment, a recovery period was necessary to unveil the protective effect of Fa27 during doxorubicin but not etoposide treatment.…”

Non-Coding RNAs and Splicing Activity in Testicular Germ Cell Tumors

“…This is further confirmed by the accumulation of R-loops in mitotic germ cells of the testis in mice deleted for Atm or Tdp1, two DNA-damage response genes required for repair of DNA breaks [ 136 , 137 , 138 ]. In this regard, it has been also demonstrated that defects in the homologous recombination (HR) proteins BRCA1 and BRCA2 [ 139 , 140 ], in the nucleotide excision repair (NER) proteins XPG and XPF [ 141 ] and in the Fanconi anemia (FA) pathway [ 142 , 143 , 144 ], lead to R-loop accumulation, thus indicating that several DNA repair pathways contribute to R-loop regulation [ 145 ].…”