Topoisomerase 1-dependent R-loop deficiency drives accelerated replication and genomic instability

Sarni, Dan; Barroso, Sónia; Shtrikman, Alon; Sinai, Michal Irony-Tur; Oren, Yifat S.; Aguilera, Andrés; Kerem, Batsheva

doi:10.1016/j.celrep.2022.111397

Cited by 8 publications

(6 citation statements)

References 96 publications

(149 reference statements)

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“…4d, f , and Fig. 5 ), which is in agreement with the observation that increased TOP1 expression causing low R-loop levels and promoting accelerated replication 69 . We propose that pol2a might promote S-phase progression, therefore, to decrease R-loops under topological stress (Fig.…”

Section: Discussionsupporting

confidence: 90%

DNA polymerase ε harmonizes topological states and R-loops formation to maintain genome integrity in Arabidopsis

Li,

Zhou,

et al. 2023

Nat Commun

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Genome topology is tied to R-loop formation and genome stability. However, the regulatory mechanism remains to be elucidated. By establishing a system to sense the connections between R-loops and genome topology states, we show that inhibiting DNA topoisomerase 1 (TOP1i) triggers the global increase of R-loops (called topoR-loops) and DNA damages, which are exacerbated in the DNA damage repair-compromised mutant atm. A suppressor screen identifies a mutation in POL2A, the catalytic subunit of DNA polymerase ε, rescuing the TOP1i-induced topoR-loop accumulation and genome instability in atm. Importantly we find that a highly conserved junction domain between the exonuclease and polymerase domains in POL2A is required for modulating topoR-loops near DNA replication origins and facilitating faithful DNA replication. Our results suggest that DNA replication acts in concert with genome topological states to fine-tune R-loops and thereby maintain genome integrity, revealing a likely conserved regulatory mechanism of TOP1i resistance in chemotherapy for ATM-deficient cancers.

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Section: Discussionsupporting

confidence: 90%

DNA polymerase ε harmonizes topological states and R-loops formation to maintain genome integrity in Arabidopsis

Li,

Zhou,

et al. 2023

Nat Commun

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“…POLι knockdown caused stalling at the two higher levels of p53 [0 and 4 nM si(p53)], and the opposite with intermediate low p53 [8 nM si(p53)] ( Supplementary Figure S3D ). As stalling was associated with longer tracks after POLι silencing at 0 and 4 nM si(p53), it might be caused by the detrimental effect of excessively high replication speed in this cellular model system ( 67 , 68 ). From these observations, we concluded that, albeit different DDT hierarchies could be established in different cells expressing p53, the levels of p53 and the expression of POLι rule on the DDT pathway choice.…”

Section: Resultsmentioning

confidence: 96%

“…Conversely, at high p53 where the POLι–p53 DDT pathway is predominant, REV1 may support nascent DNA synthesis deceleration by POLι–p53. Track ratio analysis revealed increased values only when REV1 depletion unleashed excessively fast replication, causing non-classical replication stress ( 67 , 68 ). Interestingly, POLζ down-regulation decelerated DNA synthesis not only at lower levels of p53 (2, 4500 ng/ml) but up to 0.25 ng/ml tetracycline, where the POLι–p53 complex was most prominent.…”

Section: Discussionmentioning

confidence: 99%

The levels of p53 govern the hierarchy of DNA damage tolerance pathway usage

Castaño,

Schorer,

Guo

et al. 2024

Nucleic Acids Research

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It is well-established that, through canonical functions in transcription and DNA repair, the tumor suppressor p53 plays a central role in safeguarding cells from the consequences of DNA damage. Recent data retrieved in tumor and stem cells demonstrated that p53 also carries out non-canonical functions when interacting with the translesion synthesis (TLS) polymerase iota (POLι) at DNA replication forks. This protein complex triggers a DNA damage tolerance (DDT) mechanism controlling the DNA replication rate. Given that the levels of p53 trigger non-binary rheostat-like functions in response to stress or during differentiation, we explore the relevance of the p53 levels for its DDT functions at the fork. We show that subtle changes in p53 levels modulate the contribution of some DDT factors including POLι, POLη, POLζ, REV1, PCNA, PRIMPOL, HLTF and ZRANB3 to the DNA replication rate. Our results suggest that the levels of p53 are central to coordinate the balance between DDT pathways including (i) fork-deceleration by the ZRANB3-mediated fork reversal factor, (ii) POLι-p53-mediated fork-slowing, (iii) POLι- and POLη-mediated TLS and (iv) PRIMPOL-mediated fork-acceleration. Collectively, our study reveals the relevance of p53 protein levels for the DDT pathway choice in replicating cells.

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“…Alternative causes of increased fork velocity were associated with overexpression of oncogenes, downregulation of mRNA biogenesis, or PARP1 inhibition 55 – 58 . Moreover, activation of oncogenic HRAS in pre-senescent cells was shown to accelerate forks by inducing overexpression of topoisomerase 1 (TOP1), which is known to resolve unwanted R-loops 59 . TOP1 was heavily expressed in SF3B1 MUT and SF3B1 WT erythroblasts, while senataxin and THO complex proteins, other R-loop modulators were specifically upregulated in SF3B1 MUT erythroblasts and could contribute to fork velocity 60 .…”

Section: Discussionmentioning

confidence: 99%

Accelerated DNA replication fork speed due to loss of R-loops in myelodysplastic syndromes with SF3B1 mutation

Rombaut,

Lefèvre,

Rached

et al. 2024

Nat Commun

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Myelodysplastic syndromes (MDS) with mutated SF3B1 gene present features including a favourable outcome distinct from MDS with mutations in other splicing factor genes SRSF2 or U2AF1. Molecular bases of these divergences are poorly understood. Here we find that SF3B1-mutated MDS show reduced R-loop formation predominating in gene bodies associated with intron retention reduction, not found in U2AF1- or SRSF2-mutated MDS. Compared to erythroblasts from SRSF2- or U2AF1-mutated patients, SF3B1-mutated erythroblasts exhibit augmented DNA synthesis, accelerated replication forks, and single-stranded DNA exposure upon differentiation. Importantly, histone deacetylase inhibition using vorinostat restores R-loop formation, slows down DNA replication forks and improves SF3B1-mutated erythroblast differentiation. In conclusion, loss of R-loops with associated DNA replication stress represents a hallmark of SF3B1-mutated MDS ineffective erythropoiesis, which could be used as a therapeutic target.

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Topoisomerase 1-dependent R-loop deficiency drives accelerated replication and genomic instability

Cited by 8 publications

References 96 publications

DNA polymerase ε harmonizes topological states and R-loops formation to maintain genome integrity in Arabidopsis

DNA polymerase ε harmonizes topological states and R-loops formation to maintain genome integrity in Arabidopsis

The levels of p53 govern the hierarchy of DNA damage tolerance pathway usage

Accelerated DNA replication fork speed due to loss of R-loops in myelodysplastic syndromes with SF3B1 mutation

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