XRN2 Links Transcription Termination to DNA Damage and Replication Stress

Abstract

XRN2 is a 5’-3’ exoribonuclease implicated in transcription termination. Here we demonstrate an unexpected role for XRN2 in the DNA damage response involving resolution of R-loop structures and prevention of DNA double-strand breaks (DSBs). We show that XRN2 undergoes DNA damage-inducible nuclear re-localization, co-localizing with 53BP1 and R loops, in a transcription and R-loop-dependent process. XRN2 loss leads to increased R loops, genomic instability, replication stress, DSBs and hypersensitivity of cells to various DNA damaging agents. We demonstrate that the DSBs that arise with XRN2 loss occur at transcriptional pause sites. XRN2-deficient cells also exhibited an R-loop- and transcription-dependent delay in DSB repair after ionizing radiation, suggesting a novel role for XRN2 in R-loop resolution, suppression of replication stress, and maintenance of genomic stability. Our study highlights the importance of regulating transcription-related activities as a critical component in maintaining genetic stability.

Human THO coordinates transcription termination and subsequent transcript release from the HSP70 locus

“…Aberrant R‐loops formed in the absence of THO interrupt DNA replication and induce genome instability (Gómez‐González et al, ; Santos‐Pereira & Aguilera, ). It has also been shown that various DNA and RNA helicases as well as XRN2 prevent the formation of transcriptional R‐loops (Boulé & Zakian, ; Cristini et al, ; Hodroj et al, ; Kim, Choe, & Seo, ; Morales et al, ). To test the possibility that aberrant R‐loop formation contributes to transcript accumulation of the human HSPA1A gene, we over‐expressed RNase H in THOC5‐ and DDX5/DDX17‐depleted cells, and HSP70 mRNA localization was analyzed by in situ hybridization.…”

Nascent Connections: R-Loops and Chromatin Patterning

“…Interestingly, increased PAF1 recruitment over terminal R-loops may also account for H3K4me1 deposition over these regions and for efficient transcription termination given the ability of the PAF1 complex to recruit termination factors [60]. R-loops may also favor the recruitment of the XRN2 “torpedo” ribonuclease at terminal pause sites, triggering the release of the RNAP machinery upon degradation of the residual transcript downstream of the PAS [30, 31, 62]. …”

“…This association is clearest in the context of defects in a variety of factors involved in co-transcriptional processes such as splicing, mRNA export, 3’ RNA processing, and transcription elongation, among others. Defects in other factors such as topoisomerases that are thought to prevent R-loop formation [83], or in enzymes such as Ribonucleases H [84] and RNA/DNA helicases that are thought to mediate R-loop resolution, also associate with DSBs and genomic instability [62, 85–89]. Not surprisingly, dysfunctional R-loop metabolism has been implicated in multiple human disorders, particularly cancers and neurological diseases (a topic reviewed in [71, 90, 91]).…”

Arginine methylation of the DDX 5 helicase RGG / RG motif by PRMT 5 regulates resolution of RNA:DNA hybrids

“…The RNA helicase Senataxin has been shown to resolve R‐loops in vitro , and its deficiency in cells leads to R‐loop accumulation (Skourti‐Stathaki et al , ; Sollier et al , ; Hatchi et al , ). Senataxin is reported to function with the 5′–3′ exonuclease XRN2 to resolve a subset of R‐loops at transcription termination sites of actively transcribed genes (Skourti‐Stathaki et al , ; Morales et al , ; Aymard et al , ). The DNA helicase RECQ5 and RNA helicases DDX1 (Li et al , , ; Ribeiro de Almeida et al , ), DDX19 (Hodroj et al , ), DDX21 (Song et al , ), DDX23 (Sridhara et al , ), and DHX9 (Cristini et al , ) were also found to be functionally involved in suppression of R‐loops.…”