Yra1-bound RNA–DNA hybrids cause orientation-independent transcription–replication collisions and telomere instability

García-Rubio, María L.; Aguilera, Paula; Lafuente-Barquero, Juan; Ruiz, José F.; Simon, Marie‐Noëlle; Geli, Vicent; Rondón, Ana G.; Aguilera, Andrés

doi:10.1101/gad.311274.117

Cited by 60 publications

(81 citation statements)

References 58 publications

(100 reference statements)

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“…This study certainly opens a new view on R loop formation ( Fig 7B). Whereas DNA-RNA hybrids are formed in any cell cycle phase regardless of replication, but causing instability as a consequence of their posterior impact on replication fork progression [8,11,[19][20][21][22][23][24]52], they may also form after the passage of the replication fork. Supporting the de novo formation of DNA-RNA hybrids, we detected an increased S9.6 signal in cells in S-G2 ( Fig 6).…”

Section: Discussionmentioning

confidence: 99%

The DNA damage response acts as a safeguard against harmful DNA–RNA hybrids of different origins

et al. 2019

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Despite playing physiological roles in specific situations, DNA–RNA hybrids threat genome integrity. To investigate how cells do counteract spontaneous DNA–RNA hybrids, here we screen an siRNA library covering 240 human DNA damage response (DDR) genes and select siRNAs causing DNA–RNA hybrid accumulation and a significant increase in hybrid‐dependent DNA breakage. We identify post‐replicative repair and DNA damage checkpoint factors, including those of the ATM/CHK2 and ATR/CHK1 pathways. Thus, spontaneous DNA–RNA hybrids are likely a major source of replication stress, but they can also accumulate and menace genome integrity as a consequence of unrepaired DSBs and post‐replicative ssDNA gaps in normal cells. We show that DNA–RNA hybrid accumulation correlates with increased DNA damage and chromatin compaction marks. Our results suggest that different mechanisms can lead to DNA–RNA hybrids with distinct consequences for replication and DNA dynamics at each cell cycle stage and support the conclusion that DNA–RNA hybrids are a common source of spontaneous DNA damage that remains unsolved under a deficient DDR.

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Section: Discussionmentioning

confidence: 99%

The DNA damage response acts as a safeguard against harmful DNA–RNA hybrids of different origins

et al. 2019

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“…Using this system we demonstrate that the FX genome has increased susceptibility to chromosome breakage induced by replication stress, particularly at R-loop forming sites (RLFSs), where the RNA transcript hybridizes to homologous DNA on the chromosome, yielding a DNA:RNA hybrid and a displaced DNA single strand. Despite their many roles in normal cellular functions, R-loops can initiate conflicts between transcription and replication by creating a barrier to replication fork progression, causing chromosome breakage (Garcia-Rubio et al, 2018;Hamperl et al, 2017). We present evidence that FMRP is also a genome maintenance protein that prevents chromosome breakage by mediating R-loop accumulation, possibly through direct interaction with the gene substrates that are prone to R-loop formation during transcription and further enhanced by replication stress.…”

Section: Introductionmentioning

confidence: 89%

Fragile X Mental Retardation Protein regulates R-loop formation and prevents global chromosome fragility

Chakraborty

Jenjaroenpun

McCulley

et al. 2019

Preprint

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Fragile X syndrome (FXS) is the most prevalent inherited intellectual disability caused by mutations in the Fragile X Mental Retardation 1 (FMR1) gene. The protein product of FMR1, FMRP, is known as a translational repressor whose nuclear function is not understood. Here we report that FMRP is a genome maintenance protein. We show that FX cells exhibit elevated level of chromosome breaks, both spontaneous and replication stress-induced. We demonstrate that FMRP is required for abating R-loop accumulation, thereby preventing chromosome breakage. Through mapping FMRP-bound chromatin loci in normal cells and correlating with FX-specific chromosome breaks, we identified novel FXS-susceptible genes. We show that FX cells have reduced expression of the uridine diphosphoglucuronosyl transferase 1 family enzymes, suggesting defective xenobiotics glucuronidation and consequential neurotoxicity in FXS. RUNNING TITLEFMRP deficiency induces DNA breaks at R-loops.

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“…The accumulation of proteins bound to the nascent transcript may have the effect of preventing access of RNA–DNA hybrid removal factors. In this respect, Npl3 behaves similar to other yeast hnRNP‐like protein, Yra1, that can also regulate R‐loop levels in two opposing manners .…”

Section: Resultsmentioning

confidence: 94%

Npl3 stabilizes R‐loops at telomeres to prevent accelerated replicative senescence

et al. 2020

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Telomere shortening rates must be regulated to prevent premature replicative senescence. TERRA R‐loops become stabilized at critically short telomeres to promote their elongation through homology‐directed repair (HDR), thereby counteracting senescence onset. Using a non‐bias proteomic approach to detect telomere binding factors, we identified Npl3, an RNA‐binding protein previously implicated in multiple RNA biogenesis processes. Using chromatin immunoprecipitation and RNA immunoprecipitation, we demonstrate that Npl3 interacts with TERRA and telomeres. Furthermore, we show that Npl3 associates with telomeres in an R‐loop‐dependent manner, as changes in R‐loop levels, for example, at short telomeres, modulate the recruitment of Npl3 to chromosome ends. Through a series of genetic and biochemical approaches, we reveal that Npl3 binds to TERRA and stabilizes R‐loops at short telomeres, which in turn promotes HDR and prevents premature replicative senescence onset. This may have implications for diseases associated with excessive telomere shortening.

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Yra1-bound RNA–DNA hybrids cause orientation-independent transcription–replication collisions and telomere instability

Cited by 60 publications

References 58 publications

The DNA damage response acts as a safeguard against harmful DNA–RNA hybrids of different origins

The DNA damage response acts as a safeguard against harmful DNA–RNA hybrids of different origins

Fragile X Mental Retardation Protein regulates R-loop formation and prevents global chromosome fragility

Npl3 stabilizes R‐loops at telomeres to prevent accelerated replicative senescence

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