Affinage

ATR

Alpha-1-antitrypsin-related protein · UniProt P20848

Length
421 aa
Mass
47.7 kDa
Annotated
2026-06-09
100 papers in source corpus 49 papers cited in narrative 49 extracted findings
Cross-family judge faithfulness: 9/9 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

ATR is the apical serine/threonine kinase of the replication-stress and DNA-damage checkpoint, sensing single-stranded DNA at stalled forks and lesions to coordinate origin firing, fork stability, and cell-cycle transitions (PMID:24267891, PMID:11484057). It functions as an obligate heterodimer with ATRIP (yeast Pie1/Ddc2), a mutually dependent partner required for checkpoint signaling, with cryo-EM revealing a two-monomer 'heart'-shaped complex whose catalytic pockets are held in a low-basal-activity conformation released by a single conserved activating substitution (PMID:11721054, PMID:29271416, PMID:33169019, PMID:11154263). ATR is recruited to RPA-coated ssDNA and activated through two parallel routes: TopBP1 (yeast Dpb11), which stimulates kinase activity via a conserved ATR-activation domain amplified by liquid-liquid phase-separated condensates, and ETAA1, which engages ATR through dual RPA-binding motifs and a structurally analogous coiled-coil AAD that is TopBP1-independent (PMID:16530042, PMID:27723717, PMID:33503405, PMID:30940728, PMID:18922789, PMID:19028869). The 9-1-1 clamp loaded at primer-template junctions independently and synergistically stimulates ATR/Mec1 (PMID:17189191). Phosphoproteomic separation of the two activators established TopBP1 as the dominant activator of the replication-stress response and ETAA1 as the activator of mitotic ATR signaling required for Aurora B activity and the spindle assembly checkpoint (PMID:30755469). Once active, ATR phosphorylates Chk1—relieving its C-terminal autoinhibition—to suppress global origin firing and prevent RPA exhaustion and 'replication catastrophe,' while also directly stabilizing forks by restraining MRE11/EXO1/CtIP-mediated nucleolytic degradation of nascent and template DNA (PMID:24267891, PMID:14767054, PMID:37454295, PMID:9783589). ATR drives homologous recombination by phosphorylating PALB2 (S59) to promote BRCA1-PALB2 binding and RAD51 loading, and sustains the Fanconi anemia pathway by phosphorylating FANCI to stabilize FANCI-FANCD2 mono-ubiquitination against USP1:UAF1 (PMID:28089683, PMID:32117957, PMID:27113759). Beyond the canonical checkpoint, ATR enforces an intrinsic S/G2 checkpoint by blocking CDK1-FOXM1 activation (PMID:30139873), phosphorylates Lamin A/C (S395) to promote S-phase micronucleus rupture and cGAS-dependent clearance (PMID:37788673), protects against R-loop/transcription-replication conflicts through a MUS81-dependent feedback loop (PMID:31708417), and is essential in meiosis for synapsis and RAD51/DMC1 loading at recombination sites (PMID:29976923, PMID:29977027). Substrates of the conserved Mec1/Rad53 axis include RPA, the 9-1-1 clamp, and effector adaptors, with checkpoint output shaped by adaptor proteins (Mrc1, Rad9) and reversed by PP4 phosphatase (PMID:17189191, PMID:19457865, PMID:21946560, PMID:14642562, PMID:25533186).

Mechanistic history

Synthesis pass · year-by-year structured walk · 14 steps
  1. 1998 High

    Established that the checkpoint kinase axis governs the intra-S-phase response by restraining late-origin firing under replication stress, defining ATR/Mec1's core physiological output.

    Evidence 2D gel analysis of replication intermediates in mec1/rad53 yeast mutants under hydroxyurea

    PMID:9783589

    Open questions at the time
    • Did not identify the direct kinase substrates mediating origin suppression
    • Yeast genetics; human ATR-specific mechanism not addressed
  2. 1999 High

    Identified caffeine as a direct catalytic inhibitor of ATR (and ATM) blocking p53 Ser15 phosphorylation, providing the first pharmacological handle distinguishing these kinases from DNA-PKcs.

    Evidence In vitro kinase assays on immunoprecipitated ATM/ATR plus cell-based phosphorylation readouts

    PMID:10485486

    Open questions at the time
    • Caffeine is non-selective between ATM and ATR
    • Did not define ATR's full substrate repertoire
  3. 2001 High

    Defined ATR-ATRIP (Mec1-Pie1) as an obligate, mutually dependent heterodimer essential for checkpoint signaling and damage-induced focus formation.

    Evidence Reciprocal Co-IP, siRNA, Cre-mediated deletion and immunofluorescence in human cells; two-hybrid and genetics in yeast

    PMID:11154263 PMID:11721054

    Open questions at the time
    • ATRIP's precise role beyond stabilizing the complex (does not regulate intrinsic kinase activity) left open
    • Recruitment mechanism to ssDNA not yet defined
  4. 2006 High

    Discovered TopBP1/Dpb11 as a direct allosteric activator of ATR kinase via a discrete ATR-activation domain, identifying the central activation switch.

    Evidence Recombinant protein activation assays, Xenopus extracts, point mutagenesis, human cells; in vitro Mec1 reconstitution with Dpb11

    PMID:16530042 PMID:18922789 PMID:19028869

    Open questions at the time
    • How TopBP1 is itself recruited and amplified at lesions not resolved
    • Whether a second activator existed remained unknown
  5. 2006 High

    Showed the 9-1-1 clamp loaded on partial-duplex DNA potently and independently stimulates Mec1/ATR, defining a DNA-structure-coupled activation route parallel to TopBP1.

    Evidence In vitro kinase reconstitution with purified 9-1-1 clamp on defined DNA substrates

    PMID:17189191

    Open questions at the time
    • Relative in vivo contribution versus TopBP1 not quantified at this stage
    • Human 9-1-1 dependence not directly tested
  6. 2013 High

    Established the physiological purpose of origin suppression: ATR prevents RPA-pool exhaustion and nucleus-wide fork breakage ('replication catastrophe').

    Evidence ATR inhibition/depletion with RPA manipulation, DNA fiber assays and imaging

    PMID:24267891

    Open questions at the time
    • Did not resolve which ATR substrates execute origin suppression
    • Direct fork-protection (non-checkpoint) functions not separated here
  7. 2016 High

    Identified ETAA1 as a second, RPA-anchored, TopBP1-independent ATR activator, revealing two parallel activation pathways whose combined loss is synthetically lethal.

    Evidence Co-IP, in vitro ATR activation assays, siRNA, synthetic lethality genetics

    PMID:27723717 PMID:30940728

    Open questions at the time
    • Functional division of labor between the two activators not yet defined
    • Structural basis of AAD-ATR engagement only partially mapped
  8. 2017 High

    Connected ATR checkpoint activity to homologous recombination by phosphorylating PALB2 to drive BRCA1-PALB2 binding and RAD51 loading, coupling cell-cycle control to repair pathway choice.

    Evidence Co-IP, phospho-site mutagenesis, HR reporter and RAD51 foci assays

    PMID:27113759 PMID:28089683

    Open questions at the time
    • In vivo kinetics of the CDK-to-ATR PALB2 phospho-switch not fully resolved
    • Whether other recombination factors are co-regulated unknown
  9. 2018 High

    Defined the functional partition of ATR's two activators: ETAA1 enforces an intrinsic S/G2 checkpoint via the CDK1-FOXM1 switch and governs mitotic ATR signaling, while TopBP1 dominates the replication-stress response.

    Evidence ATR inhibition, ETAA1/TOPBP1 depletion, live-cell imaging, phospho-flow, quantitative phosphoproteomics, mitotic kinase assays

    PMID:30139873 PMID:30755469

    Open questions at the time
    • Molecular basis for activator selection at distinct cell-cycle stages incomplete
    • How mitotic ATR signaling intersects Aurora B mechanistically not fully detailed
  10. 2018 High

    Established an essential meiotic role for ATR in chromosome synapsis and RAD51/DMC1 recombinase loading, distinct from its somatic checkpoint function.

    Evidence Conditional and hypomorphic Atr mouse models, pharmacological inhibition, chromosome-spread immunofluorescence

    PMID:29976923 PMID:29977027

    Open questions at the time
    • Meiotic ATR activator (TopBP1 vs ETAA1 vs 9-1-1) not defined
    • Direct meiotic substrates beyond the CHK1 axis unmapped
  11. 2019 High

    Expanded ATR function beyond checkpoint signaling to direct fork protection and genome surveillance: restraining MUS81 cleavage of R-loop-induced reversed forks, sustaining the FA pathway via FANCI phosphorylation, and driving micronucleus rupture via Lamin A/C.

    Evidence R-loop induction, FANCI in vitro reconstitution, Lamin A/C phospho-mutagenesis, fiber assays and imaging

    PMID:31708417 PMID:32117957 PMID:37788673

    Open questions at the time
    • Integration of these parallel ATR outputs into a unified spatiotemporal model unclear
    • Lamin A/C study is single-source within this corpus
  12. 2020 High

    Provided the structural basis for ATR/Mec1 autoinhibition and activation, showing a single conserved substitution locks the kinase constitutively active.

    Evidence Cryo-EM of Mec1(F2244L)-Ddc2 and wild-type complexes with biochemical and genetic validation

    PMID:29271416 PMID:33169019

    Open questions at the time
    • How TopBP1/ETAA1 AAD binding triggers the activating conformational change not directly captured
    • Substrate-bound active-state structure absent
  13. 2021 High

    Revealed that TopBP1 liquid-liquid phase separation amplifies ATR activation, providing a biophysical mechanism for signal amplification at replication stress.

    Evidence Optogenetics, in vitro phase separation of purified TopBP1, point mutagenesis, Chk1/fork assays

    PMID:33503405

    Open questions at the time
    • Whether ETAA1-driven activation involves condensation untested
    • In vivo physiological dimensions and regulation of condensates not fully defined
  14. 2023 High

    Dissected ATR's direct, checkpoint-independent fork-protection mechanisms, distinguishing protection of ongoing versus newly assembled forks against distinct nucleases.

    Evidence DNA fiber, iPOND, electron microscopy, MRE11/EXO1/CtIP/PrimPol knockdowns with ATR inhibition

    PMID:37454295

    Open questions at the time
    • Direct ATR substrates restraining each nuclease not identified
    • Relationship to Chk1-mediated outputs not resolved

Open questions

Synthesis pass · forward-looking unresolved questions
  • How ATR activator choice (TopBP1, ETAA1, 9-1-1, condensates) is selected and integrated across distinct genomic contexts and cell-cycle stages to produce specific substrate outputs remains unresolved.
  • No unified model linking activation route to substrate selection
  • Substrate-bound active ATR structure lacking
  • In vivo spatiotemporal coordination of checkpoint vs fork-protection functions undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 7 GO:0016740 transferase activity 4 GO:0140657 ATP-dependent activity 2 GO:0140110 transcription regulator activity 1
Localization
GO:0005654 nucleoplasm 3 GO:0000228 nuclear chromosome 2 GO:0005634 nucleus 2
Pathway
R-HSA-1474165 Reproduction 4 R-HSA-1640170 Cell Cycle 4 R-HSA-73894 DNA Repair 4 R-HSA-69306 DNA Replication 3 R-HSA-8953897 Cellular responses to stimuli 2
Partners
ATRIPCHK1ETAA1FANCIMRC1PALB2RPATOPBP1
Complex memberships
9-1-1 clamp (Rad17/Mec3/Ddc1)ATR-ATRIPMec1-Ddc2

Evidence

Reading pass · 49 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2001 ATR interacts directly with ATRIP (ATR-interacting protein); ATRIP is phosphorylated by ATR, regulates ATR expression, and is an essential component of the DNA damage checkpoint pathway. Both ATR and ATRIP localize to intranuclear foci after DNA damage or inhibition of replication. Loss of either ATR or ATRIP abolishes checkpoint responses and causes cell death, establishing that they are mutually dependent partners. Co-immunoprecipitation, siRNA knockdown, Cre-mediated ATR deletion, immunofluorescence nuclear foci Science High 11721054
1999 Caffeine inhibits the catalytic kinase activity of both ATM and ATR at concentrations that induce radiosensitization, and also inhibits UV- and gamma-radiation-induced phosphorylation of p53 Ser15, a modification directly mediated by ATM/ATR. DNA-PKcs was resistant to caffeine inhibition. In vitro kinase activity assays with immunoprecipitated ATM and ATR, cell-based checkpoint and phosphorylation assays Cancer research High 10485486
2006 TopBP1 (vertebrate homolog of yeast Cut5/Dpb11) directly activates ATR-ATRIP kinase activity through a conserved ATR-activating domain distinct from its BRCT repeats. The isolated ATR-activating domain induces ectopic ATR signaling in Xenopus egg extracts and human cells; a point mutation in this domain abolishes checkpoint regulation. Recombinant protein kinase activation assay, Xenopus egg extract checkpoint assays, point mutagenesis, human cell transfection Cell High 16530042
2013 ATR, activated by replication stress, suppresses global origin firing to prevent exhaustion of nuclear RPA. In ATR-deficient cells, unscheduled origin firing generates excess ssDNA that depletes the RPA pool, causing stalled forks to undergo nucleus-wide breakage ('replication catastrophe'). Partial RPA reduction accelerates fork breakage; forced RPA elevation delays catastrophe even without ATR activity. ATR inhibition/depletion, RPA manipulation (partial reduction and forced overexpression), DNA fiber assays, immunofluorescence Cell High 24267891
2016 ETAA1, via dual RPA-binding motifs, accumulates at DNA damage sites and stimulates ATR kinase activity through a conserved ATR-activation domain that functions independently of TopBP1. Simultaneous loss of ETAA1 and TopBP1 causes synthetic lethality with massive genome instability and abrogation of ATR-dependent signaling. Co-immunoprecipitation, in vitro ATR kinase activation assay, siRNA knockdown, immunofluorescence, synthetic lethality experiments Nature cell biology High 27723717
2017 Cryo-EM structure of the human ATR-ATRIP complex resolved at 4.7 Å (overall) and 3.9 Å (ATR catalytic core). The complex forms a hollow 'heart' shape with two ATR monomers in distinct conformations. ATRIP contains 14 HEAT repeats in an extended 'S' shape and locks the N-termini of the two ATR monomers. Catalytic pockets face outward and are not restricted by inhibitory elements. Cryo-electron microscopy, atomic model building Cell research High 29271416
2018 During normal DNA replication, ATR is activated by ETAA1 to block the CDK1-directed FOXM1 phosphorylation switch that drives S/G2 transition. ATR inhibition prematurely activates FOXM1, deregulating the S/G2 transition and leading to early mitosis, underreplicated DNA, and DNA damage, establishing an intrinsic S/G2 checkpoint enforced by ATR. ATR inhibition, ETAA1 depletion, live-cell imaging, phospho-flow cytometry, CDK1/FOXM1 phosphorylation assays Science High 30139873
2017 ATR promotes homologous recombination (HR) post-resection by stimulating the BRCA1-PALB2 interaction. ATR phosphorylates PALB2 at S59, and inhibition of CDK (which phosphorylates PALB2 S64) by ATR-mediated checkpoint facilitates BRCA1-PALB2 binding. PALB2-S59A/S64E mutant is defective for HR; S59E/S64A partially bypasses ATR requirement, establishing a CDK-to-ATR switch that couples checkpoint to HR. Co-immunoprecipitation, phospho-site mutagenesis, HR reporter assays, immunofluorescence of damage foci Molecular cell High 28089683
2003 ATR kinase activity is required for the irradiation-induced relocalization of ATR and RPA from PML nuclear bodies to nuclear foci. A kinase-inactive ATR mutant fails to relocalize after damage and blocks RPA translocation in a cell-cycle-dependent manner. Fluorescence microscopy, expression of kinase-dead ATR mutant, cell-cycle analysis Current biology Medium 12814551
2021 TopBP1 self-assembles into micrometer-sized nuclear condensates via liquid-liquid phase separation; this condensation amplifies ATR activity to phosphorylate Chk1 and slow replication forks. Single amino acid substitutions in the intrinsically disordered ATR activation domain disrupt TopBP1 condensation and ATR/Chk1 signaling. In vitro, purified TopBP1 undergoes phase separation at physiological conditions. Optogenetics, in vitro phase separation of purified TopBP1, point mutagenesis, Chk1 phosphorylation assays, replication fork assays Molecular cell High 33503405
2019 ATR promotes the rupture of micronuclei (MN) during S phase by phosphorylating Lamin A/C at Ser395, which primes Ser392 for CDK1 phosphorylation and destabilizes the MN envelope. ATR or CDK1 inhibition reduces MN rupture, reduces cGAS activation, and compromises autophagic clearance of micronuclear DNA and NK cell-mediated killing of MN-bearing cells. ATR inhibition, phospho-site mutagenesis of Lamin A/C, immunofluorescence, live-cell imaging, cGAS activation assays Molecular cell High 37788673
2019 ATR activates the MUS81 endonuclease-triggered feedback loop to protect the genome against R loops: R loop-induced reversed replication forks activate ATR-Chk1 in a MUS81-dependent manner (unlike activation by replication inhibitors). ATR then prevents excessive MUS81 cleavage of reversed forks, suppresses transcription-replication collisions, and promotes fork recovery and G2/M arrest. R-loop induction, ATR/Chk1 inhibition, siRNA knockdown of MUS81, DNA fiber assays, immunofluorescence Molecular cell High 31708417
2003 In Xenopus egg extracts, an ATR-dependent (but not ATM-dependent) DNA damage checkpoint blocks initiation of DNA replication by inhibiting Cdc7/Dbf4 kinase activity and preventing Cdc45 binding to chromatin. The checkpoint requires RPA loading on chromatin but not pre-RC assembly. Xenopus egg extract reconstitution, caffeine abrogation, immunodepletion of ATR, Cdc7 kinase activity assays, chromatin binding assays Molecular cell High 12535533
2019 ATR directly phosphorylates FANCI at serine residues 556, 559, and 565, stabilizing FANCI association with DNA and FANCD2. This phosphorylation stimulates mono-ubiquitination of both FANCI and FANCD2 while also inhibiting deubiquitination by USP1:UAF1, maintaining the active FA pathway. Phosphomimetic S559E/S565E mutants resist USP1:UAF1 deubiquitination. Biochemical reconstitution with recombinant proteins, in vitro ATR kinase assay, phosphomimetic and phosphodead FANCI mutants, ubiquitination/deubiquitination assays Frontiers in cell and developmental biology High 32117957
2016 ATM and ATR kinases directly phosphorylate PALB2 at three N-terminal S/Q sites in response to genotoxic stress. A phospho-deficient PALB2 mutant fails to support RAD51 foci formation and is deficient in HDR, while a phosphomimetic version supports both, establishing PALB2 phosphorylation as a regulatory step in homology-directed repair downstream of ATR. In vitro kinase assay, phospho-deficient and phosphomimetic mutant expression, RAD51 foci immunofluorescence, HDR reporter assay EMBO reports High 27113759
2004 ATR-mediated phosphorylation of Chk1 C-terminal residues relieves autoinhibition by disrupting an intramolecular interaction between the C-terminal autoinhibitory region (AIR) and the kinase domain, constituting the mechanism of Chk1 activation at the DNA replication checkpoint. Domain deletion/mutation analysis in Xenopus oocytes and embryos, co-expression interaction assays, phospho-mimetic mutations Molecular biology of the cell Medium 14767054
2017 DNA damage induces rapid accumulation of phosphoinositides (PPIs) at damage sites; nuclear PIP3 in complex with SF1, phosphorylated by IPMK, promotes nuclear actin assembly required for ATR recruitment. Sequestration of PPIs with nuclear-targeted PH domains, or depletion of IPMK or SF1, inhibits ATR recruitment and Chk1 activation after DNA damage, while ATM and DNA-PKcs are unaffected. Expression of nuclear PH-domain PPI sequesters, IPMK/SF1 depletion, live-cell imaging of PPI accumulation, pharmacological inhibition (latrunculin A, wortmannin), ATR/Chk1 phosphorylation assays Nature communications Medium 29242514
2016 Centromeric repetitive DNA suppresses ATR checkpoint activation by preventing RPA hyper-loading on chromatin, as shown in Xenopus egg extract reconstitution of centromeric replication. Electron microscopy revealed topoisomerase I-dependent DNA loops embedded in an SMC2-4 protein matrix that prevent RPA accumulation and thus ATR signaling. Xenopus egg extract reconstitution, proteomic analysis, electron microscopy, RPA chromatin-binding assays Nature cell biology Medium 27111843
2013 In Xenopus egg extracts, juxtaposition of a double-stranded DNA end with a short ssDNA gap triggers robust endogenous ATR and Chk1 activation in a manner dependent on both DNA-PKcs and ATR. DNA-PKcs primes ATR/Chk1 activation through phosphorylation of RPA32 and TopBP1 on this gapped-duplex structure. Cell-free Xenopus extract with defined DNA substrates, immunodepletion of DNA-PKcs/ATR, phosphorylation assays of RPA32 and TopBP1 The Journal of cell biology Medium 23897887
2019 ETAA1 and TOPBP1 share common structural motifs required for ATR activation: both AADs contain a predicted coiled-coil motif that is required for ATR activation in vitro and in cells, and for binding of the AADs to ATR. A conserved tryptophan in both AADs is also required for activation. In vitro ATR kinase assays, co-immunoprecipitation, immunofluorescence of Chk1 phosphorylation, bioinformatic analysis, mutagenesis The Journal of biological chemistry Medium 30940728
2019 Quantitative phosphoproteomics in ETAA1- vs TOPBP1-deficient cells established that TOPBP1 is the primary ATR activator for replication stress responses, while ETAA1 specifically regulates mitotic ATR signaling. ETAA1-dependent ATR activation during mitosis is required for proper Aurora B kinase activity, chromosome alignment, and spindle assembly checkpoint function. Quantitative mass spectrometry phosphoproteomics, ETAA1/TOPBP1 depletion, mitotic kinase assays, chromosome alignment imaging The Journal of cell biology High 30755469
2020 ATR inhibition in ETAA1-depleted cells (partial CDC7 inhibition model) unleashes CDK- and CDC7-dependent origin firing, driving cells into premature and defective mitosis. This establishes that ATR, activated mainly by ETAA1 under partial CDC7 inhibition, mediates an origin-firing checkpoint. CRISPR-Cas9 screen, ETAA1/TOPBP1 co-depletion, CDC7 inhibitor, origin firing assays, mitotic entry readouts Cell reports Medium 32877678
2023 ATR protects ongoing and newly assembled replication forks through mechanistically distinct pathways: at ongoing forks, ATR inhibition increases MRE11- and EXO1-mediated nascent DNA degradation from PrimPol-generated ssDNA gaps and increases gap-dependent fork uncoupling; at new forks, ATR inhibition triggers MRE11- and CtIP-initiated template DNA degradation by EXO1. Electron microscopy showed ATR inhibition reduces reversed forks by increasing gap-dependent nascent DNA degradation. DNA fiber assays, iPOND, electron microscopy, siRNA knockdown of MRE11/EXO1/CtIP/PrimPol, ATR inhibitor treatment Cell reports High 37454295
2009 Estrogen receptor alpha (ERα) inhibits ATR activity by activating PI3K/AKT signaling; AKT phosphorylates TopBP1 at Ser1159, preventing enhanced ATR-TopBP1 association after DNA damage. Estrogen also inhibits Claspin-Chk1 association via AKT phosphorylation of Chk1, blocking checkpoint signaling. Co-immunoprecipitation of ATR-TopBP1, AKT kinase assays, phospho-specific antibodies, pharmacological inhibitors Molecular biology of the cell Medium 19477925
2017 In vaccinia virus-infected cells, ATR is activated in the cytoplasm early during infection at viral DNA factories. Canonical ATR pathway components (RPA, INTS7, Chk1, TOPBP1) are recruited to cytoplasmic viral factories. Pharmacological and RNAi inhibition of ATR or TOPBP1 suppresses viral genome replication; RPA and PCNA interact with the viral polymerase E9. RNAi knockdown, pharmacological inhibition, co-immunoprecipitation of viral polymerase with RPA/PCNA, immunofluorescence Cell reports Medium 28467896
2023 ADAR1 promotes ATR activation by interacting with TOPBP1 and facilitating its loading on perturbed replication forks by enhancing TOPBP1 association with RAD9 of the 9-1-1 complex. During replication inhibition, DNA-RNA hybrids compete with TOPBP1 for ADAR1 binding, translocating ADAR1 to R-loop regions where it recruits RNA helicases DHX9 and DDX21 to resolve R-loops, allowing TOPBP1 to stimulate ATR more efficiently. Co-immunoprecipitation, siRNA knockdown, replication fork assays, R-loop detection, ATR/Chk1 phosphorylation assays Nucleic acids research Medium 37831098
1999 In mouse meiosis, ATR protein associates with chromosome cores and synaptonemal complexes, forming dense aggregates on the last chromosomes to complete pairing at the zygotene-pachytene transition. ATM-deficient spermatocytes accumulate large amounts of ATR. ATR does not co-localize with RAD51/DMC1 recombination foci, distinguishing its meiotic role from recombinase function. Immunofluorescence on meiotic chromosome spreads, electron microscopy, ATM-null mouse analysis Chromosoma Medium 10382071
2018 Germline-specific ATR deletion in male mice causes chromosome axis fragmentation and germ cell elimination at mid-pachynema. ATR is required for synapsis (independently of DSB formation), loading of RAD51 and DMC1 recombinases to DSBs, and regulation of recombination focus dynamics on synapsed and asynapsed chromosomes. Conditional ATR knockout, chromosome spread immunofluorescence, recombination focus quantification Nature communications High 29976923
2018 ATR, through its effector kinase CHK1, promotes efficient RAD51 and DMC1 assembly at RPA-coated resected DSB sites during meiosis. Hypomorphic ATR mutation and pharmacological ATR inhibition in cultured spermatocytes impair interhomolog connections and synapsis, and ATR promotes local accumulation of recombination markers on unsynapsed axes to favor homologous chromosome synapsis. Hypomorphic Atr mouse model, pharmacological ATR inhibition in vivo and in cultured spermatocytes, immunofluorescence chromosome spreads Nature communications High 29977027
2020 Cryo-EM structures of constitutively active Mec1(F2244L)-Ddc2 at 2.8 Å and wild-type Mec1-Ddc2 at 3.8 Å reveal the molecular basis for low basal activity (auto-inhibition) and the conformational changes required for Mec1/ATR activation. A single conserved mutation (F2244L in Mec1, corresponding to a conserved ATR residue) results in constitutive kinase activity. Cryo-electron microscopy structure determination, biochemical kinase assays, mutagenesis, genetic complementation Nature structural & molecular biology High 33169019
2006 The yeast 9-1-1 checkpoint clamp (Rad17/Mec3/Ddc1) loaded onto partial duplex DNA greatly activates Mec1 (ATR) kinase activity. Activated Mec1 phosphorylates Ddc1 and Mec3 subunits of the clamp, the Rad24 loader subunit, RPA subunits Rpa1 and Rpa2, and the effector kinase Rad53. The Ddc1 subunit mediates functional interactions with Mec1. In vitro kinase reconstitution with purified components on defined DNA substrates, subunit-specific binding studies, phosphorylation assays Molecular cell High 17189191
2008 Dpb11 (yeast TopBP1 ortholog) directly activates Mec1 (ATR) kinase in phosphorylating downstream effectors including Rad53 and RPA. DNA is not required for Dpb11-mediated activation. Dpb11 and yeast 9-1-1 independently activate Mec1 but show substantial synergism when combined. Mec1 phosphorylates Dpb11 in a positive feedback loop. In vitro Mec1 kinase assay with purified Dpb11, Rad53 phosphorylation assay, genetic complementation The Journal of biological chemistry High 18922789
2008 A C-terminal domain of Dpb11 (yeast TopBP1) associates with Mec1-Ddc2 and strongly stimulates Mec1 kinase activity in a Ddc2-dependent manner. Mec1 phosphorylates Dpb11, amplifying Dpb11's stimulatory effect on Mec1-Ddc2 kinase activity. Dpb11 is a functional ortholog of TopBP1, establishing conservation of the Mec1/ATR activation mechanism. Genetic and physical interaction studies, in vitro kinase assay with Mec1-Ddc2 and Dpb11, phosphorylation assays Proceedings of the National Academy of Sciences High 19028869
2009 Mrc1, a replication fork-associated adaptor protein, cooperates with Mec1 to activate Rad53 by facilitating a stronger enzyme-substrate interaction between Mec1 and Rad53, achieving >70-fold increase in Rad53 activation. Mrc1 does not increase Mec1 catalytic activity per se but promotes efficient Rad53 phosphorylation. The conserved C-terminal domain of Mrc1 is required for this function. In vitro reconstitution with purified Mec1, Mrc1, and Rad53; activity-based Rad53 kinase assay; domain deletion analysis The Journal of biological chemistry High 19457865
2011 A ternary complex of Dpb11, Mec1, and Rad9 (adaptor/mediator) is required for efficient Rad9 phosphorylation by Mec1 in vitro and for checkpoint activation in vivo. CDK-mediated phosphorylation of Rad9 at two residues generates a binding site for Dpb11 BRCT repeats, enabling Rad9 recruitment into the ternary complex and restricting checkpoint signaling to S/G2 phases when CDK is active. In vitro kinase reconstitution of ternary complex, BRCT domain binding assays, CDK phospho-site mutagenesis, in vivo checkpoint assays The EMBO journal High 21946560
2015 Mec1/ATR is highly active during normal (unperturbed) DNA replication, at levels comparable to or higher than replication stress conditions. This 'replication-correlated' Mec1 activity requires the 9-1-1 clamp and the Dna2 lagging-strand factor and is distinguishable from Mec1's checkpoint role in activating Rad53. Quantitative phosphoproteomics combined with genetic manipulation (9-1-1 and Dna2 mutants), kinase substrate profiling Molecular cell High 25752575
2003 Mec1 (ATR) stabilizes DNA polymerases alpha and epsilon at stalled replication forks (during HU treatment), a function requiring Sgs1 helicase but not Rad53 activation. Sgs1 is proposed to resolve aberrantly paired structures to maintain ssDNA for RPA and Mec1, promoting DNA polymerase association. Chromatin immunoprecipitation (ChIP) of DNA polymerases at stalled forks, genetic analysis with mec1 and sgs1 mutants The EMBO journal Medium 12912929
2001 Mec1 and Rad53 checkpoint kinases are required to prevent irreversible collapse of replication forks in the presence of MMS (DNA alkylation). In checkpoint mutants, replication forks collapse at high rates while wild-type cells complete replication. The accelerated S-phase in checkpoint mutants is primarily due to inappropriate origin firing, not faster fork progression. DNA combing and BrdU incorporation to monitor fork progression, genetic analysis of mec1/rad53 mutants, cell viability assays Nature High 11484057
1998 Mec1 and Rad53 checkpoint genes are required for inhibition of late-firing replication origins during S-phase stress (hydroxyurea treatment). In mec1 and rad53 mutants, late origins fire despite ongoing fork stalling from early origins, establishing these kinases as regulators of the intra-S-phase checkpoint controlling origin firing. 2D gel electrophoresis of replication intermediates, genetic analysis of mec1/rad53 mutants Nature High 9783589
1999 Mec1-dependent phosphorylation of Sir3 triggers its redistribution from telomeres to DNA double-strand breaks during S phase, enabling Sir3-mediated DSB repair. This relocalization requires both MEC1 and RAD9 and is S-phase specific. Immunofluorescence of Sir3 localization, genetic analysis with mec1 and rad9 mutants, DSB induction assays Cell Medium 10367890
2004 The Mre11 complex and Exo1 function together to activate the Mec1 signaling pathway by generating long ssDNA tails at DSB ends, promoting Mec1 association with DSBs. The Ddc1-Mec3-Rad17 clamp associates with damage sites independently of Mre11/Exo1 function, establishing a two-step mechanism for Mec1 recruitment. Genetic epistasis of mre11/exo1 mutants, chromatin immunoprecipitation of Mec1 at DSBs, checkpoint activation assays Molecular and cellular biology Medium 15509802
2001 Pie1 (yeast ATRIP ortholog) interacts physically with Mec1 in vivo; Pie1 is essential for cell growth and deletion causes checkpoint defects identical to mec1Δ, including loss of Rad53 hyperphosphorylation. Mec1 kinase activity is not affected by pie1Δ, indicating Pie1 regulates a function other than Mec1 kinase activity itself. Two-hybrid screen, co-immunoprecipitation, genetic analysis of pie1Δ mutants, Rad53 phosphorylation assays Molecular and cellular biology Medium 11154263
2003 Mec1 directly phosphorylates RPA1 (major site Ser178) and RPA2 in vitro. Mec1 and RPA are physically associated during unperturbed growth and after DNA damage. The phospho-deficient rfa1-S178A mutation reduces Mec1-RPA1 physical interaction and affects kinetics of RPA1 and Rad53 phosphorylation in vivo. Mec1 immunoprecipitate-kinase assay, phospho-site mapping, Co-IP, in vivo checkpoint phosphorylation assays DNA repair Medium 14642562
2005 The Mec1/Rad53 checkpoint pathway regulates mitochondrial DNA (mtDNA) copy number in yeast by altering dNTP pools through ribonucleotide reductase (RNR) activity. Deletion of SML1 is epistatic to rad53Δ and rrm3Δ for mtDNA copy number regulation, placing these genes in the same pathway. Genetic epistasis analysis, mtDNA copy number quantification, RNR gene dosage manipulation Molecular biology of the cell Medium 15829566
2006 Mec1-dependent phosphorylation promotes the association of the DNA polymerase zeta-Rev1 translesion synthesis complex with double-strand breaks. Rev1 plays a noncatalytic role in this association. This requires neither the Rad24 checkpoint-clamp loader nor Rad6-Rad18-mediated PCNA ubiquitination. Chromatin immunoprecipitation of Polζ-Rev1 complex at DSBs, genetic analysis with mec1 and checkpoint mutants Current biology Medium 16546083
2013 Mec1 regulates resection of DSB ends: loss of Mec1 accelerates resection and reduces Rad9 loading at DSBs. A Mec1-ad mutant that increases Rad9 recruitment inhibits DSB resection by both Rad53-dependent and Rad53-independent mechanisms. Mec1 thereby coordinates its own activation with Tel1/ATM signaling by controlling ssDNA generation at DSBs. Southern blot and qPCR ssDNA quantification at DSBs, ChIP of Rad9 and MRX, genetic analysis of mec1-ad mutant The EMBO journal Medium 24357557
2013 ATR/Mec1 prevents lethal meiotic recombination initiation on partially replicated chromosomes through three mechanisms: inhibiting Mer2 phosphorylation by Cdc7 kinase, precluding chromosomal loading of Rec114 and Mre11, and lowering Spo11 abundance. Without this checkpoint, DSBs form on unreplicated DNA and frequently fail to repair, causing rapid loss of cell viability. Genetic analysis with mec1/dbf4 mutants, meiotic DSB quantification, Mer2 phosphorylation assays, ChIP of recombination proteins eLife Medium 24137535
2014 PP4 phosphatase (Pph3/Psy2 subunits) physically interacts with Mec1-Ddc2 in a manner mediated by Psy2 and Ddc2. PP4 dephosphorylates 94% of the substrates compromised by the mec1-100 mutation, including a phosphoacceptor site within Mec1 itself. Mutation of this Mec1 auto-phosphorylation site confers DNA damage sensitivity. FRET in subnuclear repair foci, biochemical interaction studies, phosphoproteomics, genetic suppressor screens Molecular cell Medium 25533186
2005 Mec1/Ddc2 immune complexes can directly activate Rad53 through a phosphorylation-dependent mechanism at low Rad53 concentrations. Rad53 then autoactivates via an intermolecular autophosphorylation mechanism, achieving >9-fold increase in activity. DNA damage induces Rad53 oligomerization in vivo, supporting the trans-autophosphorylation model. In vitro kinase assays with immunoprecipitated Mec1/Ddc2, purified dephosphorylated Rad53, kinetic analysis, in vivo Rad53 oligomerization assay The Journal of biological chemistry Medium 16365046

Source papers

Stage 0 corpus · 100 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2008 ATR: an essential regulator of genome integrity. Nature reviews. Molecular cell biology 1428 18594563
2013 DNA damage sensing by the ATM and ATR kinases. Cold Spring Harbor perspectives in biology 1164 24003211
1999 Inhibition of ATM and ATR kinase activities by the radiosensitizing agent, caffeine. Cancer research 921 10485486
2001 ATR and ATRIP: partners in checkpoint signaling. Science (New York, N.Y.) 793 11721054
2013 ATR prohibits replication catastrophe by preventing global exhaustion of RPA. Cell 763 24267891
2017 The essential kinase ATR: ensuring faithful duplication of a challenging genome. Nature reviews. Molecular cell biology 671 28811666
2006 TopBP1 activates the ATR-ATRIP complex. Cell 620 16530042
2001 Regulation of DNA replication fork progression through damaged DNA by the Mec1/Rad53 checkpoint. Nature 575 11484057
1998 A Mec1- and Rad53-dependent checkpoint controls late-firing origins of DNA replication. Nature 539 9783589
2014 ATM and ATR as therapeutic targets in cancer. Pharmacology & therapeutics 509 25512053
2001 ATM and ATR: networking cellular responses to DNA damage. Current opinion in genetics & development 509 11163154
2013 ATR-FTIR: a "rejuvenated" tool to investigate amyloid proteins. Biochimica et biophysica acta 334 23746423
2003 An ATR- and Cdc7-dependent DNA damage checkpoint that inhibits initiation of DNA replication. Molecular cell 295 12535533
2017 ATR/CHK1 inhibitors and cancer therapy. Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology 290 29054375
1999 MEC1-dependent redistribution of the Sir3 silencing protein from telomeres to DNA double-strand breaks. Cell 281 10367890
2003 DNA polymerase stabilization at stalled replication forks requires Mec1 and the RecQ helicase Sgs1. The EMBO journal 280 12912929
2018 Targeting ATR in cancer. Nature reviews. Cancer 271 29899559
2018 An intrinsic S/G2 checkpoint enforced by ATR. Science (New York, N.Y.) 250 30139873
2011 ATR signalling: more than meeting at the fork. The Biochemical journal 246 21615334
1999 MEC1 and MEC2: two new cell lines derived from B-chronic lymphocytic leukaemia in prolymphocytoid transformation. Leukemia research 237 10071128
2010 ATR: a master conductor of cellular responses to DNA replication stress. Trends in biochemical sciences 227 20947357
2015 Molecular Pathways: Targeting ATR in Cancer Therapy. Clinical cancer research : an official journal of the American Association for Cancer Research 222 26362996
2007 The ATR pathway: fine-tuning the fork. DNA repair 203 17531546
2016 Activation of the ATR kinase by the RPA-binding protein ETAA1. Nature cell biology 202 27723717
2015 ATM and ATR signaling at a glance. Journal of cell science 194 26567218
2017 Targeting the ATR-CHK1 Axis in Cancer Therapy. Cancers 186 28448462
2013 Targeting ATR in DNA damage response and cancer therapeutics. Cancer treatment reviews 160 23583268
2006 The checkpoint clamp activates Mec1 kinase during initiation of the DNA damage checkpoint. Molecular cell 159 17189191
2017 Coupling of Homologous Recombination and the Checkpoint by ATR. Molecular cell 154 28089683
2007 ATM and ATR: components of an integrated circuit. Cell cycle (Georgetown, Tex.) 152 17312392
2010 The ATR barrier to replication-born DNA damage. DNA repair 120 21036674
2019 ATR Protects the Genome against R Loops through a MUS81-Triggered Feedback Loop. Molecular cell 119 31708417
2009 ATR/Mec1: coordinating fork stability and repair. Current opinion in cell biology 117 19230642
2017 APOBEC3A and APOBEC3B Activities Render Cancer Cells Susceptible to ATR Inhibition. Cancer research 115 28698210
2011 Dpb11 coordinates Mec1 kinase activation with cell cycle-regulated Rad9 recruitment. The EMBO journal 106 21946560
2021 Progress towards a clinically-successful ATR inhibitor for cancer therapy. Current research in pharmacology and drug discovery 105 34909652
2008 Yeast DNA replication protein Dpb11 activates the Mec1/ATR checkpoint kinase. The Journal of biological chemistry 103 18922789
2016 Centromeric DNA replication reconstitution reveals DNA loops and ATR checkpoint suppression. Nature cell biology 101 27111843
2008 Dpb11 activates the Mec1-Ddc2 complex. Proceedings of the National Academy of Sciences of the United States of America 101 19028869
2001 Pie1, a protein interacting with Mec1, controls cell growth and checkpoint responses in Saccharomyces cerevisiae. Molecular and cellular biology 100 11154263
2015 Phosphoproteomics reveals distinct modes of Mec1/ATR signaling during DNA replication. Molecular cell 95 25752575
2021 TopBP1 assembles nuclear condensates to switch on ATR signaling. Molecular cell 92 33503405
2004 Requirement of the Mre11 complex and exonuclease 1 for activation of the Mec1 signaling pathway. Molecular and cellular biology 92 15509802
2015 Cancer-Specific Synthetic Lethality between ATR and CHK1 Kinase Activities. Cell reports 91 26748709
2018 Synthetically Lethal Interactions of ATM, ATR, and DNA-PKcs. Trends in cancer 89 30352678
2019 A consensus set of genetic vulnerabilities to ATR inhibition. Open biology 88 31506018
2004 ATM and ATR: sensing DNA damage. World journal of gastroenterology 87 14716813
2003 ATR kinase activity regulates the intranuclear translocation of ATR and RPA following ionizing radiation. Current biology : CB 85 12814551
2013 Interplays between ATM/Tel1 and ATR/Mec1 in sensing and signaling DNA double-strand breaks. DNA repair 83 23953933
2017 DNA damage causes rapid accumulation of phosphoinositides for ATR signaling. Nature communications 82 29242514
2017 Cryo-EM structure of human ATR-ATRIP complex. Cell research 82 29271416
2009 A tale of two tails: activation of DNA damage checkpoint kinase Mec1/ATR by the 9-1-1 clamp and by Dpb11/TopBP1. DNA repair 80 19464966
2009 Estrogen inhibits ATR signaling to cell cycle checkpoints and DNA repair. Molecular biology of the cell 80 19477925
1999 The association of ATR protein with mouse meiotic chromosome cores. Chromosoma 79 10382071
2024 Targeting ATR in patients with cancer. Nature reviews. Clinical oncology 78 38378898
2005 The conserved Mec1/Rad53 nuclear checkpoint pathway regulates mitochondrial DNA copy number in Saccharomyces cerevisiae. Molecular biology of the cell 78 15829566
2006 ATR homolog Mec1 controls association of DNA polymerase zeta-Rev1 complex with regions near a double-strand break. Current biology : CB 67 16546083
2005 Frp1 is a Fusarium oxysporum F-box protein required for pathogenicity on tomato. Molecular microbiology 67 16091043
2004 Regulation of Chk1 kinase by autoinhibition and ATR-mediated phosphorylation. Molecular biology of the cell 67 14767054
2017 DNA-PKcs, ATM, and ATR Interplay Maintains Genome Integrity during Neurogenesis. The Journal of neuroscience : the official journal of the Society for Neuroscience 60 28123024
2023 Targeting ATM and ATR for cancer therapeutics: Inhibitors in clinic. Drug discovery today 58 37302542
2008 Activation of ATR and related PIKKs. Cell cycle (Georgetown, Tex.) 58 18769153
2021 An extending ATR-CHK1 circuitry: the replication stress response and beyond. Current opinion in genetics & development 57 34329853
2013 Mec1/ATR regulates the generation of single-stranded DNA that attenuates Tel1/ATM signaling at DNA ends. The EMBO journal 57 24357557
2022 Guiding ATR and PARP inhibitor combinationswith chemogenomic screens. Cell reports 56 35830811
2016 ATM/ATR-mediated phosphorylation of PALB2 promotes RAD51 function. EMBO reports 56 27113759
2023 ATR promotes clearance of damaged DNA and damaged cells by rupturing micronuclei. Molecular cell 53 37788673
2017 Targeting ATR in cancer medicine. Current problems in cancer 53 28662958
2017 ATR Is a Therapeutic Target in Synovial Sarcoma. Cancer research 53 29038346
2019 Quantitative phosphoproteomics reveals mitotic function of the ATR activator ETAA1. The Journal of cell biology 52 30755469
2014 Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling. Molecular cell 51 25533186
2003 Hyperoxia activates the ATR-Chk1 pathway and phosphorylates p53 at multiple sites. American journal of physiology. Lung cellular and molecular physiology 47 12959929
2023 Emerging strategies for cancer therapy by ATR inhibitors. Cancer science 46 37189251
2022 TOP1-DNA Trapping by Exatecan and Combination Therapy with ATR Inhibitor. Molecular cancer therapeutics 45 35439320
2019 Activation of ATR-related protein kinase upon DNA damage recognition. Current genetics 43 31624858
2014 Homeostatic regulation of meiotic DSB formation by ATM/ATR. Experimental cell research 43 25116420
2018 ATR is a multifunctional regulator of male mouse meiosis. Nature communications 42 29976923
2009 Mutation of CRE1 in Fusarium oxysporum reverts the pathogenicity defects of the FRP1 deletion mutant. Molecular microbiology 42 19912543
2010 Mechanisms of ATR-mediated checkpoint signalling. Frontiers in bioscience (Landmark edition) 40 20515729
2009 Reconstitution of Rad53 activation by Mec1 through adaptor protein Mrc1. The Journal of biological chemistry 39 19457865
2018 ATR is required to complete meiotic recombination in mice. Nature communications 38 29977027
2016 ATR-mediated regulation of nuclear and cellular plasticity. DNA repair 38 27283761
2018 Separable roles for Mec1/ATR in genome maintenance, DNA replication, and checkpoint signaling. Genes & development 37 29899143
2023 ATR protects ongoing and newly assembled DNA replication forks through distinct mechanisms. Cell reports 35 37454295
2020 ATR Restrains DNA Synthesis and Mitotic Catastrophe in Response to CDC7 Inhibition. Cell reports 35 32877678
2013 DNA structure-specific priming of ATR activation by DNA-PKcs. The Journal of cell biology 35 23897887
2013 ATR/Mec1 prevents lethal meiotic recombination initiation on partially replicated chromosomes in budding yeast. eLife 35 24137535
2005 Activation of the checkpoint kinase Rad53 by the phosphatidyl inositol kinase-like kinase Mec1. The Journal of biological chemistry 35 16365046
2007 Meiotic roles of Mec1, a budding yeast homolog of mammalian ATR/ATM. Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology 34 17674144
2019 Common motifs in ETAA1 and TOPBP1 required for ATR kinase activation. The Journal of biological chemistry 33 30940728
2003 MEC1-dependent phosphorylation of yeast RPA1 in vitro. DNA repair 33 14642562
2014 RNA-processing proteins regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA. EMBO reports 31 25527408
2020 ATR-Mediated FANCI Phosphorylation Regulates Both Ubiquitination and Deubiquitination of FANCD2. Frontiers in cell and developmental biology 30 32117957
2023 ADAR1 links R-loop homeostasis to ATR activation in replication stress response. Nucleic acids research 29 37831098
2009 Mouse models for ATR deficiency. DNA repair 29 19782648
2020 Mechanism of auto-inhibition and activation of Mec1ATR checkpoint kinase. Nature structural & molecular biology 27 33169019
2018 Essential Function of Mec1, the Budding Yeast ATM/ATR Checkpoint-Response Kinase, in Protein Homeostasis. Developmental cell 27 30130531
2017 Cytoplasmic ATR Activation Promotes Vaccinia Virus Genome Replication. Cell reports 27 28467896
2011 Cell-cycle-specific activators of the Mec1/ATR checkpoint kinase. Biochemical Society transactions 26 21428947
1999 Interaction between the MEC1-dependent DNA synthesis checkpoint and G1 cyclin function in Saccharomyces cerevisiae. Genetics 26 9927443

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