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ATR and TopBP1 oppose to control dormant origin activity and overall replication dynamics, providing a first defense against replication stress [OK-seq]

ABSTRACT: Replication stress, a major feature of cancers, and ensuing genomic instability stem from perturbations of replication fork progression. The first line of defense against this stress is the recruitment of extra-origins, called dormant, which assists constitutive origins in completing replication. To determine how the DNA replication checkpoint contributes to this compensation process in human cells, we set a dose-response assay that allows quantification of the compensation efficiencies, enabling accurate comparison of cells depleted of relevant proteins. Results show that ATR activity is essential to dormant origin mobilization. In stark contradiction to what would be expected from its ATR-activating function, TopBP1 represses compensation and acts downstream of ATR. Therefore, our results instead design the TopBP1 function in replisome assembly as key to dormancy. Furthermore, Repli-seq and OK-seq data collectively confirm that ATR inactivation prevents dormant origins from firing under stress. Conversely, constitutive origin activity significantly rises in these conditions, attesting of intrinsic differences between dormant and constitutive origins. Altogether, our results elicit a model positing that TopBP1 specifically locks dormant origins at the pre-initiation stage, an intermediate complex in the replisome assembly process. ATR activation would trigger eviction of TopBP1 from this complex, allowing assembly to proceed and compensation to occur.

ORGANISM(S): Homo sapiens

PROVIDER: GSE314900 | GEO | 2026/03/16

REPOSITORIES: GEO

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ATR and TopBP1 oppose to control dormant origin activity and overall replication dynamics, providing a first defense against replication stress [Repli-Seq]

Project description:Replication stress, a major feature of cancers, and ensuing genomic instability stem from perturbations of replication fork progression. The first line of defense against this stress is the recruitment of extra-origins, called dormant, which assists constitutive origins in completing replication. To determine how the DNA replication checkpoint contributes to this compensation process in human cells, we set a dose-response assay that allows quantification of the compensation efficiencies, enabling accurate comparison of cells depleted of relevant proteins. Results show that ATR activity is essential to dormant origin mobilization. In stark contradiction to what would be expected from its ATR-activating function, TopBP1 represses compensation and acts downstream of ATR. Therefore, our results instead design the TopBP1 function in replisome assembly as key to dormancy. Furthermore, Repli-seq and OK-seq data collectively confirm that ATR inactivation prevents dormant origins from firing under stress. Conversely, constitutive origin activity significantly rises in these conditions, attesting of intrinsic differences between dormant and constitutive origins. Altogether, our results elicit a model positing that TopBP1 specifically locks dormant origins at the pre-initiation stage, an intermediate complex in the replisome assembly process. ATR activation would trigger eviction of TopBP1 from this complex, allowing assembly to proceed and compensation to occur.

2026-03-16 | GSE302744 | GEO

Convergence of SIRT1 and ATR signaling to modulate replication origin dormancy

Project description:During routine genome duplication, many potential replication origins remain inactive, or dormant. Such origin dormancy is achieved, in part, by an interaction with the metabolic sensor SIRT1 deacetylase. We report here that dormant origins are a group of consistent, pre-determined genomic sequences that can be distinguished from baseline (i.e. ordinarily active) origins by their preferential association with MCM2, a component of the replicative helicase, phosphorylated on serine 108 (pS108-MCM2). pS108-MCM2 is a substrate of the ATR kinase, which is recruited to chromatin via an interaction with hyperacetylated TOPBP1 in cells undergoing replication stress or in cells devoid of SIRT1 deacetylase activity. In turn, S108-MCM2 phosphorylation enhances a second, DDK-dependent, S139-MCM2 phosphorylation, which triggers initiation of DNA replication at dormant origins. These observations suggest that replication origin dormancy and activation are regulated by distinct post-translational modifications on the MCM helicase that reflect a balance between SIRT1 activity and ATR signaling.

| MSV000088134 | MassIVE

Convergence of SIRT1 and ATR signaling to modulate replication origin dormancy

Project description:During routine genome duplication, many potential replication origins remain inactive, or 'dormant'. Such origin dormancy is achieved, in part, by an interaction with the metabolic sensor SIRT1 deacetylase. We report here that dormant origins are a group of consistent, pre-determined genomic sequences that can be distinguished from baseline (i.e. ordinarily active) origins by their preferential association with MCM2, a component of the replicative helicase, phosphorylated on serine 108 (pS108-MCM2). pS108-MCM2 is a substrate of the ATR kinase, which is recruited to chromatin via an interaction with hyperacetylated TOPBP1 in cells undergoing replication stress or in cells devoid of SIRT1 deacetylase activity. In turn, S108-MCM2 phosphorylation enhances a second, DDK-dependent, S139-MCM2 phosphorylation, which triggers initiation of DNA replication at dormant origins. These observations suggest that replication origin dormancy and activation are regulated by distinct post-translational modifications on the MCM helicase that reflect a balance between SIRT1 activity and ATR signaling.

2022-05-09 | GSE184353 | GEO

ADAR1 Links R-Loop Homeostasis to ATR Activation in Replication Stress Response

Project description:Unscheduled R-loops are a major source of replication stress and DNA damage. R-loop-induced replication defects are sensed and suppressed by ATR kinase, whereas it is not known whether R-loop itself is actively involved in ATR activation and, if so, how this is achieved. Here, we report that the nuclear form of RNA-editing enzyme ADAR1 promotes ATR activation and resolves genome-wide R-loops, a process that requires its double-stranded RNA-binding domains. Mechanistically, ADAR1 interacts with TOPBP1 and facilitates its loading on perturbed replication forks by enhancing the association of TOPBP1 with RAD9 of the 9-1-1 complex. When replication is inhibited, DNA-RNA hybrid competes with TOPBP1 for ADAR1 binding to promote the translocation of ADAR1 from damaged fork to R-loop region. There, ADAR1 recruits RNA helicases DHX9 and DDX21 to unwind R-loops, simultaneously allowing TOPBP1 to stimulate ATR more efficiently. Collectively, we propose that the tempo-spatially regulated assembly of ADAR1-nucleated protein complexes link R-loop clearance and ATR activation, while R-loops crosstalk with blocked replication forks by transposing ADAR1 to finetune ATR activity and safeguard the genome.

2023-09-01 | GSE217878 | GEO

Selective interactions at pre-replication complexes categorize baseline and dormant origins

Project description:The initiation of DNA synthesis in metazoans is restricted to a group of baseline replication origins, whereas other (dormant) origins do not initiate replication despite recruiting apparently indistinguishable pre-replication complexes. Dormant origins are activated as backups when DNA synthesis stalls. We report that dormant origins selectively bind CDK-phosphorylated RecQL4 (pRecQL4), a helicase mutated in Rothmund-Thomson, RAPADILINO and Baller-Gerold syndromes. In unperturbed cells, pRecQL4 restricts replication initiation to baseline origins by preventing dormant origins from binding the essential initiation factor MTBP. When cells encounter replication stress, pRecQL4 first promotes the dissociation of MTBP from chromatin, and then enables its redistribution to both baseline and dormant origins, facilitating compensatory initiation to complete genome duplication. Thus, MTBP-pRecQL4 interactions modulate replication origin choice and facilitate recovery from replication stress.

2025-04-06 | GSE276856 | GEO

FAM111A regulates replication origin activation and cell fitness

Project description:FAM111A is a replisome associated protein and dominant mutations within its trypsin-like peptidase domain are linked to severe human developmental syndrome, the Kenny-Caffey syndrome. However, FAM111A functions remain unclear. Here, we show that FAM111A facilitates efficient activation of DNA replication origins. Upon replication fork stalling, FAM111A promotes dormant origin activation and ssDNA exposure. Furthermore, unrestrained expression of FAM111A wild-type as well as patient mutants causes accumulation of DNA damage and cell death, only when the peptidase domain remains intact. The peptidase domain is responsible for ssDNA exposure during S phase, which is not caused by caspase dependent apoptosis. Altogether, these data unveil how FAM111A promotes DNA replication in normal conditions and becomes harmful in a disease context.

2023-10-03 | PXD044180 | Pride

Conservation of replication timing reveals global and local regulation of replication origin activity.

Project description:DNA replication initiates from defined locations called replication origins; some origins are highly active whereas others are dormant and rarely used. Origins also differ in their activation time resulting in particular genomic regions replicating at characteristic times and in a defined temporal order. Here we report the comparison of genome replication in four budding yeast species: Saccharomyces cerevisiae, S. paradoxus, S. arboricolus and S. bayanus. First, we find that the locations of active origins are predominantly conserved between species, whereas dormant origins are poorly conserved. Second, we generated genome-wide replication profiles for each of these species and discovered that the temporal order of genome replication is highly conserved. Therefore, active origins are not only conserved in location, but also activation time. Only a minority of these conserved origins show differences in activation time between these species. To gain insight as to the mechanisms by which origin activation time is regulated we generated replication profiles for a S. cerevisiae / S. bayanus hybrid strain and find that there are both local and global regulators of origin function. Measurement of genome replication time from 4 budding yeast species (Saccharomyces cerevisiae, S. paradoxus, S. arboricolus and S. bayanus) and a hybrid (between Saccharomyces cerevisiae and S. bayanus). For each strain two samples were analysed: a replicating sample (from S phase) and a non-replicating sample (from G2 phase) The reference genome sequences for each yeast species are available as Series supplementary file [sac*.fa]

2012-06-19 | E-GEOD-36045 | biostudies-arrayexpress

Phosphorylated SIRT1 associates with replication origins to prevent excess replication initiation and preserve genomic stability

Project description:Chromatin structure affects DNA replication patterns, but the role of specific chromatin modifiers in regulating the replication process is yet unclear. We report that phosphorylation of the human SIRT1 deacetylase on Threonine 530 (T530-pSIRT1) modulates DNA synthesis. T530-pSIRT1 associates with replication origins and inhibits replication from a group of ÒdormantÓ potential replication origins, which initiate replication only when cells are subject to replication stress. Although both active and dormant origins bind T530-pSIRT1, active origins are distinguished from dormant origins by their unique association with an open chromatin mark, histone H3 methylated on lysine 4. SIRT1 phosphorylation also facilitates leading and lagging strand coordination. SIRT1 T530 phosphorylation is essential to prevent DNA breakage upon replication stress and cells harboring SIRT1 that cannot be phosphorylated exhibit a high prevalence of extrachromosomal elements, hallmarks of perturbed replication. These observations suggest that SIRT1 phosphorylation modulates the distribution of replication initiation events to insure genomic stability.

2017-06-02 | GSE94403 | GEO

Conservation of replication timing reveals global and local regulation of replication origin activity.

2012-06-19 | GSE36045 | GEO

Origin-Dependent DNA Replication in vitro: Insights into DDK and S-CDK function and Replisome Assembly

Project description:Initiation of eukaryotic DNA replication requires temporal separation of helicase loading from helicase activation and replisome assembly. Using an in vitro assay for eukaryotic origin-dependent replication initiation, we investigated the control of these events. After helicase loading, we found that the Dbf4-dependent Cdc7 kinase (DDK) initially drives origin recruitment of Sld3 and the Cdc45 helicase-activating protein. Corresponding in vivo studies found that DDK was required for Cdc45 binding at early origins during G1. Upon activation of S-phase cyclin-dependent kinases (S-CDK), a second helicase-activating protein (GINS) and the remainder of the replisome are recruited to the origin. Investigation of DNA polymerase recruitment showed that Mcm10 and DNA unwinding both were critical for recruitment of the lagging but not leading strand DNA polymerases. Our studies identify distinct roles for DDK and S-CDK during helicase activation and support a model in which the leading strand DNA polymerase is recruited prior to DNA unwinding and initial RNA primer synthesis. We performed chromatin immunoprecipitation (ChIP) against Cdc45 in CDC7 and cdc7-4 cells arrested in G1 phase to assess the requirement of the Dbf4-dependent kinase on the recruitment of Cdc45 to origin DNA during G1.

2011-07-21 | E-GEOD-29646 | biostudies-arrayexpress

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