CDT1

Summary: The inherited checkpoint-signaling assertion remains unresolved.

Reason: PAINT node PANTHER:PTN002008627 is an ancestral functional assertion, not a pairwise transfer. Current descendant records include genuine human, mouse and fly experimental annotations. The mouse and human cited binding/licensing experiments do not independently resolve signal-transduction participation, while the fly checkpoint IMP and complete PAINT node were not re-adjudicated here. Retain uncertainty rather than infer an erroneous node from donor count or the target appearing among its own supporting descendants.

Summary: The cited study establishes regulated licensing interactions, not checkpoint signaling.

Reason: PMID:14672932 Experimental Procedures and Results/Figs. 1–6 assay Cdt1–Cdc6/MCM association, chromatin MCM loading, serum regulation and geminin inhibition. Human CDT1 rescues geminin-blocked MCM loading in rat REF52 cells; human HeLa/293 and mouse NIH/3T3 assays have distinct scopes. These experiments do not establish the signal-transduction step required by GO:0000076. This is a source-specific overextension from replication control, not a claim that CDT1 can never affect checkpoints.

Summary: The mouse donor is identifiable, but the complete combined inference is unresolved.

Reason: The current Q8R4E9 GO:0000076 IDA cites PMID:12192004. Its actual murine cDNA, purified-protein, yeast-two-hybrid, DNA-cellulose and mobility-shift assays establish binding and geminin-dependent inhibition, rather than checkpoint signal transduction. However this human electronic assertion combines ARBA:ARBA00090203 and orthology sources; the complete rule and any independent supporting chain have not been reconstructed. Preserve the exact source entities and uncertainty rather than assert that one questionable donor interpretation disproves the whole inference.

Summary: CDT1 participates in the mitotic cell cycle.

Reason: Conserved licensing supplies loaded MCM helicases for S phase; independent human G2-specific perturbations and rescue establish a second contribution to mitotic kinetochore–microtubule attachment. Both are performed functions, consistent with the PAINT assertion.

Summary: CDT1 localizes to kinetochores during mitosis.

Reason: The original full study detects endogenous CDT1 at kinetochores with independent antibodies and depletion controls. Human HeLa evidence is distinguished from PTK2 and LLCPK1 observations; Hec1-loop perturbation reduces CDT1 recruitment.

Summary: DNA binding is a conserved CDT1 activity.

Reason: The PAINT assertion is consistent with directly assayed mouse Cdt1 binding to single- and double-stranded DNA and with human recombinant CDT1 DNA-cellulose assays. Neither source establishes sequence-specific origin recognition; the broad DNA-binding term is appropriate.

Summary: The electronic DNA-binding assertion is supported.

Reason: The exact orthology/InterPro source is retained. Mouse full-length Cdt1 and deletions were assayed by DNA-cellulose and mobility shift; independent human recombinant-protein experiments also measure DNA binding. This is an intrinsic binding activity, not inferred solely from chromatin residence.

Summary: The mouse-to-human DNA-binding inference is sound.

Reason: The Q8R4E9 donor has direct biochemical grounding in the mouse study. Human CDT1 protein assays independently corroborate binding to both DNA forms, without establishing a sequence preference.

Summary: Chromatin association is central to replication licensing.

Reason: The original human study reports chromatin association and MCM loading. Live-cell work independently establishes dynamic G1 chromatin binding, while purified human licensing reactions place CDT1 in the MCM recruitment step. These support chromatin binding without assigning DNA-unwinding catalysis to CDT1.

Summary: CDT1 associates with geminin.

Reason: The original human study and exact positive records EBI-456960/456966/456975 support reciprocal 293T co-IP and pull-down. Retain the association under the ClinGen binding instruction; being bound and inhibited by geminin does not give CDT1 geminin’s inhibitory activity.

Summary: CDT1 binds CDC6 in licensing assays.

Reason: Full primary Results/Figs. 3–5 and EBI-457031/457078 support CDC6 association, including its N-terminal 1–192 region. Human constructs, in-vitro translation and mammalian-cell experiments have distinct scopes. Retain binding without transferring CDC6 ATPase activity.

Summary: Geminin association persists in the tested phosphorylation context.

Reason: The authentic abstract explicitly distinguishes impaired CDT1 DNA binding from retained geminin binding, and EBI-457118 records the positive in-vitro GST-geminin pull-down. This supports association, not a kinase activity of CDT1.

Summary: The protein-array study supports CDT1–geminin association.

Reason: Exact human-pair records EBI-371683/375115 are positive array assays. The original abstract describes in-situ expression of replication factors in a mammalian translation system. Retain this assay-scoped interaction; it does not establish an endogenous complex or a new catalytic activity.

Summary: The protein-array study supports CDT1–CDC6 association.

Reason: EBI-375401 is the exact positive in-vitro protein-array record for the human pair. This is compatible with independent licensing biochemistry, but the array itself is not evidence that CDT1 supplies CDC6 ATPase activity.

Summary: Geminin is recovered with CDT1 in the original binding experiment.

Reason: Full Fig. 7 uses geminin as a positive control in GST-CDT1 pull-down from HeLa nuclear extracts. Keep the correct association separately from the E3 ligases that target CDT1 for degradation.

Summary: CDT1 associates with PCNA.

Reason: Full Fig. 7 combines HeLa nuclear-extract GST pull-down and human 293T co-IP of WT and altered CDT1 constructs. Disruption of the PCNA-binding region impairs association. CDT1 is a regulated substrate in this context, not a ubiquitin ligase.

Summary: CDT1 recruits its binding partner geminin to chromatin.

Reason: The authentic abstract directly reports CDT1-dependent geminin recruitment and altered CDT1 residence time. The original full body was not recovered, so retain the established association with independent human structural evidence rather than inventing its detailed assay conditions.

Summary: Human CDT1 forms a physical complex with geminin.

Reason: The full primary structural experiment uses human CDT1 158–356 and geminin 82–160; solution measurements corroborate association. Licensing assays use different CDT1 constructs and Xenopus extracts. Retain binding without treating one oligomeric model as universal.

Summary: CDT1 contacts the C-terminal MCM6 region.

Reason: The inspected primary Methods use human CDT1 410–445 and MCM6 708–821 in pull-down/NMR experiments. This establishes a mapped interaction rather than a full-length complex structure or a helicase activity of CDT1.

Summary: CDT1 associates with an ORCA/LRWD1-containing complex.

Reason: Full Fig. 1E detects CDT1 in endogenous ORCA immunoprecipitates from human cells. Co-complex association supports generic binding; it does not establish a purified binary interface or transfer ORCA’s chromatin-recruitment functions.

Summary: The cited study supports the geminin–CDT1 interaction.

Reason: The original partner is geminin, not Idas. The authentic abstract explicitly distinguishes Idas–geminin binding from the established geminin–CDT1 complex and reports competition. Independent human structural evidence supports retaining the correct pair.

Summary: CDT1 associates with geminin and HBO1/KAT7 under the tested conditions.

Reason: The genuine full primary text/Fig. 2B shows baseline Flag-CDT1–HBO1 association that decreases after osmotic stress, whereas geminin association persists. Preserve both original partners and the condition dependence; do not transfer HBO1 acetyltransferase activity.

Summary: CDT1 associates with PCNA and SKP2.

Reason: The original full main text describes PCNA and SKP2 in CDT1 immunoprecipitates, unchanged by osmotic stress; supplementary Fig. S4 itself was not independently inspected. Keep the association with that access boundary and the independent PCNA/turnover experiments, without assigning substrate ubiquitination to CDT1.

Summary: CDT1 physically associates with Hec1/NDC80.

Reason: The full study reports human Hec1 fragments in the CDT1 two-hybrid screen, GST-CDT1 pull-down from HeLa lysate and endogenous co-IP. The kinetochore role is represented separately; Hec1 association alone is not the direct microtubule-binding assay.

Summary: The CDT1–geminin interaction is independently established.

Reason: This source’s inspected main text does not resolve the exact geminin-positive assay behind the original IPI record; lack of mitotic kinetochore geminin is not a binding-negative result. Independent human structural and pull-down evidence establishes the same pair, so retain correct binding while leaving the original assay linkage explicit.

Summary: CDT1 associates with NUF2 in the kinetochore complex.

Reason: The full GST-CDT1 pull-down retrieves NUF2 from HeLa lysate together with Hec1. This supports a complex association; it is not a demonstrated purified binary CDT1–NUF2 interaction.

Summary: CDT1 directly binds GRWD1 in purified-protein assays.

Reason: Full Fig. 2 includes purified GST-CDT1/GRWD1 binding and tagged-CDT1 co-IP with endogenous GRWD1. The authors did not observe endogenous CDT1 co-IP in that experiment. Preserve those distinctions and do not transfer GRWD1 histone-binding activity.

Summary: The quantitative interactome supports CDT1–geminin association.

Reason: EBI-11145627 is an exact positive human HeLa affinity-purification record with C-terminally tagged CDT1 bait. This is cellular complex association, not proof of a purified binary interface; its partner-specific function is not inferred from the screen.

Summary: The quantitative interactome supports CDT1–MCM6 association.

Reason: EBI-11144956 records the exact positive human pair in the HeLa CDT1-bait experiment. Retain the association and its tag/context limits; direct domain evidence independently corroborates the pair without making CDT1 a helicase.

Summary: CDT1 associates with FAF1 in human nuclear extracts.

Reason: Full Fig. 6j uses human HEK nuclear lysate, an ATPase-defective p97 substrate trap and HA-FAF1 co-IP to recover CDT1. Earlier worm experiments are separate. The association does not give CDT1 FAF1 adaptor or p97 ATPase activity.

Summary: The barcode-fusion screen supports CDT1–geminin association.

Reason: EBI-11781378 and EBI-11772432 are exact positive human-protein two-hybrid records in yeast, respectively validated and barcode-fusion formats. Preserve that heterologous assay scope and the correct generic binding assertion.

Summary: CDT1 associates with USP37.

Reason: Full Results section 3.2 detects endogenous CDT1 in Flag-USP37 immunoprecipitates from human cells. The study characterizes CDT1 as a deubiquitination substrate; the upper phosphorylated band does not establish another source isoform or CDT1 deubiquitinase activity.

Summary: BioPlex supports CDT1–geminin complex association.

Reason: EBI-21621073 is the exact positive human 293T record from C-terminally tagged CDT1 affinity purification. Retain the association with AP-MS scope, without claiming purified direct binding or assigning the partner’s activity.

Summary: The expanded BioPlex network corroborates CDT1–geminin association.

Reason: EBI-54578340 is the exact positive human 293T CDT1-bait record. Its affinity-purification context supports complex association; the separate HCT116 network is not silently substituted for this recorded experiment.

Summary: CDT1 performs replication functions in the nucleus.

Reason: Nuclear localization is accompanied by actual licensing/MCM-loading activity and early-S-phase restraint of synthesis in human cells. These activities, rather than location alone, support the PAINT nuclear functional assertion.

Summary: Nuclear localization fits CDT1’s licensing role.

Reason: The original human study supports nuclear/chromatin association. Later human-cell chromatin-binding work corroborates this central compartment; the abstract-only original cache is not treated as a full localization-methods inspection.

Summary: The nucleus is a correct core location with a reporter-specific source limitation.

Reason: The original full paper uses a CDT1-derived FUCCI fluorescent fragment to mark cell-cycle phase; that reporter is not a direct assay of full-length endogenous CDT1. Independent full-protein human evidence establishes nuclear localization and activity, so preserve the correct location without transferring LSD1 functions.

Summary: Human nuclear extracts contain CDT1.

Reason: The original human experiments recover CDT1 from nuclear lysates and test chromatin-associated turnover, independently of the worm experiments in earlier sections. This supports the core nuclear location without assigning the degradation machinery’s activities to CDT1.

Summary: The electronic nucleus annotation is supported.

Reason: Independent human chromatin-binding, nuclear-extract and replication experiments establish the nuclear compartment. Retain the electronic source unchanged; location is not inferred solely from sequence prediction.

Summary: Nuclear residence is consistent with the original licensing context.

Reason: The original structural/licensing article is not itself treated as a definitive localization assay. Independent human nuclear and chromatin evidence supports the same core compartment while the original NAS source remains intact.

Summary: CDT1 is present in the nucleoplasm.

Reason: The HPA immunofluorescence assertion and current official CDT1 record specify nucleoplasm. This accords with nuclear licensing and synthesis control; no new independent image quantification is claimed.

Summary: The nucleoplasm is a core location during licensing control.

Reason: The Reactome event describes geminin ubiquitination releasing CDT1. Its location assertion agrees with HPA and human nuclear evidence; it does not identify CDT1 as the ubiquitinating enzyme.

Summary: Nucleoplasmic licensing is consistent with the pathway assertion.

Reason: The cached Reactome event concerns MCM10 association and MCM stabilization, not a separate CDT1 localization experiment. HPA and human licensing studies independently support the same core compartment; MCM10 activity is not transferred.

Summary: The pre-RC displacement event occurs in the established nuclear compartment.

Reason: Reactome models CDT1 release after helicase loading. Retain its nucleoplasm assertion using independent HPA/nuclear evidence, without treating release from a complex as loss of nuclear localization.

Summary: Nucleoplasmic location remains correct in this pathway context.

Reason: The cached event assigns ORC1 phosphorylation to cyclin A/CDK2; its CDT1 location assertion is independently supported by HPA and nuclear licensing work. It does not establish kinase activity of CDT1.

Summary: Geminin binding is compatible with the core nucleoplasmic compartment.

Reason: The Reactome event represents CDT1–geminin association. Independent HPA/nuclear evidence supports location; newer reconstitution qualifies the older oligomeric mechanism without invalidating the compartment or interaction.

Summary: The nucleoplasm is supported independently of the expression event.

Reason: This Reactome event concerns E2F1-driven CDT1 gene expression. HPA and direct human nuclear evidence support the protein’s location; being the expressed product does not make CDT1 an E2F-like transcription regulator.

Summary: Nuclear-body localization is an additional cellular context.

Reason: HPA reports nuclear bodies in addition to nucleoplasm. Retain this observed subnuclear pattern without assigning a specific nuclear-body function or making that structure the general site of licensing.

Summary: CDT1 directly regulates replication initiation through licensing.

Reason: The PAINT assertion is consistent with CDT1-mediated MCM recruitment/loading and geminin-sensitive regulation. Human reconstitution establishes an actual loading contribution rather than necessity alone.

Summary: The electronic initiation-regulation assertion is biologically supported.

Reason: Human purified-protein omission and mutant experiments establish CDT1-dependent helicase recruitment/loading, and geminin alters that step. Preserve the combined source while grounding the process in performed licensing activity.

Summary: CDT1 positively supports DNA replication through licensing.

Reason: The original human experiments show impaired fork progression after CDT1 depletion in the FAF1 study. Independent reconstitution resolves the performed role: CDT1 helps recruit and load MCM2–7, supplying a licensing step required for subsequent synthesis. It is not merely a substrate whose removal changes the phenotype.

Summary: CDT1 can restrict cell-cycle progression in the tested context.

Reason: PMID:19906994 main Results, Validation in Mammalian Cell Lines, explicitly reports WT CDT1 overexpression causing G2 arrest in human U2OS cells, with R198/R210 mutants less effective. This is an actual target-dependent phenotype, not simply geminin acting on CDT1. The authors interpret arrest as checkpoint activation; Fig. S9 itself and detailed SI methods were not inspected. Retain this broad contextual process outside the core without presenting overexpression-induced arrest as normal checkpoint-transducer activity.

Summary: CDT1 supports stable kinetochore–microtubule attachment.

Reason: G2-specific human-cell depletion, rescue, Hec1-loop experiments and cold-stable attachment measurements separate the mitotic role from a prior replication failure. Independent purified human CDT1 microtubule-binding assays provide a molecular basis for its contribution.

Summary: The polymerase-binding PAINT assertion has direct plant grounding.

Reason: The exact Arabidopsis donor loci encode CDT1a/b: their original study recovers POL2A and DPB2 by TAP, with direct DPB2 two-hybrid interaction. This is polymerase-complex association, not a human purified catalytic-subunit assay. Retain the ancestral judgment absent evidence of human loss; the complete historical node was not reconstructed, and no donor-count or self-donor objection is made.

Summary: Refine the licensing assembly claim to the demonstrated pre-RC step.

Reason: CDT1 supports MCM recruitment/loading into a mitotic pre-replicative complex. The current preinitiation-complex definition instead encompasses the downstream assembly that enables origin opening/helicase activation. Human loading experiments support GO:1902985 as the precise replacement for the InterPro-derived assertion. This is a stage-specific semantic correction between distinct ontology branches, not a claimed direct-parent move.

Proposed replacements: mitotic pre-replicative complex assembly

Summary: CDT1 participates in the tested osmotic-stress response.

Reason: Full primary experiments show sorbitol/JNK1-dependent CDT1 phosphorylation and decreased HBO1 recruitment; a CDT1 phosphosite mutant alters that response. This supports a contextual change in CDT1 recruitment activity without making sorbitol response its defining role or assigning JNK1 kinase activity to it.

Summary: CDT1 directly regulates DNA replication in both directions.

Reason: MCM loading promotes licensing, whereas independent purified human replisome and cellular experiments establish restraint of early DNA synthesis. These performed functions support the broad ARBA assertion; being inhibited by geminin alone would not suffice.

Summary: CDT1 participates in mitotic replication initiation through licensing.

Reason: The original human work links CDT1 to MCM loading, and purified human systems directly demonstrate that contribution. The broad initiation process encompasses licensing; no intrinsic origin-melting or helicase catalytic activity is assigned.

Summary: Pre-replicative complex assembly is a central CDT1 function.

Reason: The original human study and later purified reconstitutions establish MCM recruitment/loading with ORC and CDC6. CDT1 supplies protein/DNA contacts in this assembly rather than merely being consumed or modified by it.

Summary: Independent human experiments support CDT1-mediated inhibition of DNA synthesis.

Reason: The original PMID:19906994 links an inhibitory CDT1–geminin assembly to licensing; CDT1 interface mutants also lose positive licensing, so that experiment does not isolate an inhibitory CDT1 role. Independently, PMID:36608667 demonstrates CDT1 inhibition of purified human CMG-dependent fork synthesis, including established forks, with an unaffected Pol epsilon-only control and corresponding human-cell experiments. PMID:41004347 supports MCM-contact-dependent synthesis restraint in engineered human MCF-7 cells. PMID:41365879 shows geminin inhibition need not require the older heterohexamer. Retain the existing biological assertion with independent support, preserving the original IDA/reference and avoiding a universal inhibitory-assembly claim. The 2023 paper explicitly leaves altered helicase–polymerase coupling as an alternative; the experiments do not isolate inhibition of CMG alone.