DDX17 is required for efficient DSB repair at DNA:RNA hybrid deficient loci

Abstract

Proteins with RNA-binding activity are increasingly being implicated in DNA damage responses (DDR). Additionally, DNA:RNA-hybrids are rapidly generated around DNA double-strand breaks (DSBs), and are essential for effective repair. Here, using a meta-analysis of proteomic data, we identify novel DNA repair proteins and characterise a novel role for DDX17 in DNA repair. We found DDX17 to be required for both cell survival and DNA repair in response to numerous agents that induce DSBs. Analysis of DSB repair factor recruitment to damage sites suggested a role for DDX17 early in the DSB ubiquitin cascade. Genome-wide mapping of R-loops revealed that while DDX17 promotes the formation of DNA:RNA-hybrids around DSB sites, this role is specific to loci that have low levels of pre-existing hybrids. We propose that DDX17 facilitates DSB repair at loci that are inefficient at forming DNA:RNA-hybrids by catalysing the formation of DSB-induced hybrids, thereby allowing propagation of the damage response.

R-Loops and R-Loop-Binding Proteins in Cancer Progression and Drug Resistance

“…In addition to specific degradation of the RNA strand, the helicase Senataxin (SETX) unwinds R-loops and enables subsequent cleavage [ 19 ]. Other helicases, such as RNA helicase aquarius (AQR) and the DEAD Box helicase also resolve R-loops [ 1 , 5 , 9 , 17 , 20 , 21 ]. Similarly, topoisomerase I resolves supercoils, which prevents the formation of transcription-induced R-loops.…”

“…Once formed, aberrant R-loops can be resolved through degradation of the RNA component by RNAse H1 or H2, which specifically degrade RNA-DNA hybrids. R-loops can also be resolved by unwinding the RNA-DNA hybrid through the helicase activity of SETX, DHX9, DDX5, DDX17, DDX21, and AQR [ 1 , 20 , 21 ]; ( B ) Physiological and pathological processes that promote R-loop formation. R-loops preferentially form when Pol II is stalling.…”

Break‐induced RNA–DNA hybrids (BIRDHs) in homologous recombination: friend or foe?

“…Similarly, other helicases have been later reported to impact BIRDH formation or resolution, based on either the fact that they were directly detected at DSBs by live‐cell microscopy, immunofluorescence or ChIP, or because their loss caused changes in BIRDH levels and affected HR repair. These include SETX (Cohen et al , 2018; Rawal et al , 2020), DHX9 (Chakraborty & Hiom, 2021), DDX5 (Mersaoui et al , 2019; Yu et al , 2020; Sessa et al , 2021), DDX17 (Bader et al , 2022), and UPF1 (Ngo et al , 2021). It is likely that other helicases known to protect cells from harmful R‐loops could also have similar role on BIRDHs, but studies are still lacking.…”

“…In contrast, the loss of the DEAD‐box helicase DDX17 was recently reported to reduce the levels of BIRDHs (Bader et al , 2022). Since this reduction was observed exclusively in DSBs occurring at regions that are not R‐loop prone in undamaged conditions, and DDX17 depletion affected the DSB signaling cascade at the step of RNF168 ubiquitylation of γH2AX and the subsequent steps of 53BP1 and BRCA1 recruitment, it has been proposed that BIRDHs are required to enable proper DSB signaling (Bader et al , 2022).…”

“…In contrast, the loss of the DEAD‐box helicase DDX17 was recently reported to reduce the levels of BIRDHs (Bader et al , 2022). Since this reduction was observed exclusively in DSBs occurring at regions that are not R‐loop prone in undamaged conditions, and DDX17 depletion affected the DSB signaling cascade at the step of RNF168 ubiquitylation of γH2AX and the subsequent steps of 53BP1 and BRCA1 recruitment, it has been proposed that BIRDHs are required to enable proper DSB signaling (Bader et al , 2022). However, given the potential impact of most RNA helicases on transcription and RNA metabolism, it would be useful to show that these helicases do not affect the processing and termination of nascent RNAs trapped around DNA breaks, thus potentially having an indirect impact on repair by altering 3′‐end resection or the loading of HR factors.…”