{"gene":"ATAD5","run_date":"2026-06-09T22:02:44","timeline":{"discoveries":[{"year":2003,"finding":"ELG1/ATAD5 encodes the major subunit of a novel RFC-like complex (RLC) formed with RFC2-5 subunits, distinct from the Rad24-RFC and Ctf18-RFC complexes, and this complex is required for genome stability, S-phase progression, and Rad53 checkpoint kinase activation in response to replication stress.","method":"Genetic interaction screens, co-immunoprecipitation, biochemical fractionation, genetic epistasis with rad24 and ctf18 mutants","journal":"The EMBO journal / Current biology / PNAS","confidence":"High","confidence_rationale":"Tier 2 / Strong — independently replicated across three labs in the same year using reciprocal Co-IP and genetic epistasis","pmids":["12912927","13678589","12909721"],"is_preprint":false},{"year":2003,"finding":"Elg1 physically interacts with PCNA (Pol30) and the FEN-1 homolog Rad27, suggesting a role in Okazaki fragment maturation.","method":"Physical interaction assay (pulldown/two-hybrid), genetic interaction analysis","journal":"Current biology : CB","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single lab pulldown/two-hybrid supported by genetic interactions, replicated in context by multiple labs","pmids":["13678589"],"is_preprint":false},{"year":2004,"finding":"Elg1 participates in negative control of telomere length and telomeric silencing through a replication-mediated pathway that is dependent on yKu, DNA polymerase, and active telomerase, but independent of recombination.","method":"Genetic epistasis with telomerase, yKu, and recombination mutants; telomere length assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis in single lab with multiple genetic backgrounds, functional pathway placement","pmids":["14745004"],"is_preprint":false},{"year":2006,"finding":"Elg1 is involved in homologous recombination (HR)-mediated DSB repair; it associates with both the DSB site (MAT locus) and the homologous donor locus (HML) in a Rad52-dependent manner at HML, and its loss reduces efficiency of primer extension after strand invasion and ligation steps of HR.","method":"Chromatin immunoprecipitation (ChIP), HR repair assays with HO endonuclease-induced DSBs, genetic epistasis","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and direct repair assays in single lab with defined mechanistic steps identified","pmids":["17170004"],"is_preprint":false},{"year":2008,"finding":"The unique C-terminus of Elg1 mediates oligomerization with Rfc2-5, nuclear import, and chromatin association; the Walker A motif in the conserved RFC region is dispensable for Elg1 function in vivo; the N-terminus contributes to genome stability and promotes nuclear localization.","method":"Mutational analysis, chromatin fractionation, nuclear localization assays","journal":"DNA repair","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — systematic structure-function mutagenesis with functional readouts in single lab","pmids":["18482875"],"is_preprint":false},{"year":2009,"finding":"Elg1-RLC plays a role in sister chromatid cohesion; elg1 mutants show elevated precocious sister chromatid separation and Elg1 is required for recruitment of Ctf18 to chromatin. Genetic interactions with cohesin subunits (Mcd1/Scc1) and cohesin loader (Scc2) were identified.","method":"Genetic suppressor screen, sister chromatid cohesion assays, chromatin localization by fractionation, genetic epistasis","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two independent labs (Parnas et al. and Maradeo/Skibbens) reported Elg1-RLC cohesion roles using orthogonal methods","pmids":["19430531","19262753"],"is_preprint":false},{"year":2010,"finding":"Elg1 preferentially interacts with SUMOylated PCNA via three SUMO-interacting motifs (SIMs) and a PIP box near its N-terminus; in the absence of Elg1, SUMOylated PCNA and the helicase Srs2 accumulate on chromatin.","method":"Physical interaction assays, chromatin fractionation, SIM and PIP box mutagenesis, genetic epistasis with srs2 and PCNA modification mutants","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — mutagenesis of defined motifs combined with chromatin fractionation and genetic epistasis in single rigorous study","pmids":["20571511"],"is_preprint":false},{"year":2010,"finding":"Human ELG1/ATAD5 interacts with the USP1-UAF1 deubiquitinating enzyme complex and directs it to deubiquitinate monoubiquitinated PCNA at stalled replication forks; the N-terminal domain of ELG1 is responsible for USP1-UAF1 interaction and PCNA deubiquitination activity. ELG1 knockdown specifically increases PCNA monoubiquitination without affecting FANCD2 ubiquitination.","method":"Co-immunoprecipitation, siRNA knockdown, western blot for ubiquitinated PCNA, N-terminal domain mapping","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, domain mapping, and knockdown with specific biochemical readout in single rigorous study","pmids":["20147293"],"is_preprint":false},{"year":2011,"finding":"Elg1 N-terminus physically interacts with SUMO-pathway proteins Slx5 and Slx8 (an E3 SUMO-targeted ubiquitin ligase complex), mediated by poly-SUMO chains requiring Siz2 activity, in a PCNA modification-independent manner.","method":"Yeast two-hybrid screen, physical interaction assays, genetic epistasis with SUMO pathway mutants","journal":"Cell cycle (Georgetown, Tex.)","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — two-hybrid and genetic evidence from single lab with domain specificity established","pmids":["21869594"],"is_preprint":false},{"year":2011,"finding":"Atad5 haploinsufficiency in mice leads to defective PCNA deubiquitination in response to DNA damage in MEFs, demonstrating the in vivo tumor suppressor function of mammalian ATAD5 is linked to its PCNA deubiquitination activity.","method":"Mouse genetics (Atad5+/m heterozygous mice), MEF PCNA deubiquitination assays, tumor incidence monitoring","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo mouse model combined with direct biochemical assay for PCNA deubiquitination, with functional cancer phenotype","pmids":["21901109"],"is_preprint":false},{"year":2012,"finding":"ATAD5 regulates the lifespan of replication factories by unloading PCNA from chromatin during and after DNA synthesis; ATAD5 depletion extends replication factory lifespan, retains PCNA and replisome proteins on chromatin, decreases overall replication rate, and causes PCNA foci persistence into G2. The ATPase domain of ATAD5 is required for these activities.","method":"siRNA knockdown, PCNA chromatin fractionation, live imaging of replication factories, ATPase domain mutagenesis, flow cytometry","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (fractionation, live imaging, mutagenesis) in single rigorous study with defined mechanistic readouts","pmids":["23277426"],"is_preprint":false},{"year":2013,"finding":"The yeast Elg1-RLC directly unloads PCNA from chromatin during DNA replication in vivo and in vitro; without Elg1, PCNA accumulates on chromatin during replication and can be removed by switching Elg1 expression back on. Purified Elg1-RLC causes PCNA unloading in vitro and unloads both unmodified and SUMOylated PCNA.","method":"Improved auxin-inducible degron system, chromatin fractionation, in vitro PCNA unloading assay with purified Elg1-RLC","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with purified complex plus in vivo validation; replicated independently (Shiomi & Nishitani 2013)","pmids":["23499004"],"is_preprint":false},{"year":2013,"finding":"Human Elg1/ATAD5 depletion causes accumulation of chromatin-bound PCNA during S phase, increases PCNA foci, causes chromatin loop size increase, and leads to aberrant/lagging chromosomes in mitosis, confirming ATAD5 as a PCNA unloading factor in human cells.","method":"siRNA knockdown, chromatin fractionation, immunofluorescence imaging of PCNA foci, chromosome analysis","journal":"Genes to cells : devoted to molecular & cellular mechanisms","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods confirming PCNA unloading function in human cells, consistent with parallel yeast studies","pmids":["23937667"],"is_preprint":false},{"year":2015,"finding":"The Elg1-RLC unloads PCNA genome-wide following Okazaki fragment ligation; in elg1Δ cells PCNA is retained on chromosomes in the wake of replication forks rather than at specific sites; Okazaki fragment ligation by Cdc9 is a prerequisite for PCNA unloading, as Chlorella virus ligase substituting for Cdc9 also promotes PCNA unloading.","method":"ChIP-seq genome-wide PCNA profiling, degron-mediated depletion of Cdc9 ligase, heterologous ligase complementation, chromatin fractionation","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — genome-wide ChIP-seq plus genetic epistasis with ligase replacement, defining mechanistic prerequisite for PCNA unloading","pmids":["26212319"],"is_preprint":false},{"year":2015,"finding":"Phosphorylation of Elg1 at S112 is dependent on the ATR ortholog Mec1 and is important for Elg1's role at telomeres and in regulation of DNA repair; Elg1 phosphorylation mutants unable to undergo phosphorylation suppress the DNA damage sensitivity of rad5Δ mutants.","method":"Mass spectrometry identification of phosphorylation sites, phosphorylation mutant analysis, epistasis with rad5Δ, telomere length assays","journal":"Cell cycle (Georgetown, Tex.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS-identified phosphorylation with functional validation by mutant analysis in single lab","pmids":["26177013"],"is_preprint":false},{"year":2016,"finding":"Prolonged retention of PCNA on DNA into G2/M phase is the major cause of genome instability in elg1Δ yeast; disassembly-prone PCNA mutants that relieve PCNA accumulation rescue genome instability of elg1Δ; PCNA retention specifically through G2/M exacerbates genome instability beyond that caused by S-phase retention alone.","method":"Cell-cycle-regulated ELG1 alleles engineering, disassembly-prone PCNA mutants, genome instability assays, overexpression-induced PCNA accumulation","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — engineered cell-cycle-controlled alleles plus PCNA mutant rescue, multiple orthogonal genetic approaches in single rigorous study","pmids":["27373149"],"is_preprint":false},{"year":2016,"finding":"The Drosophila Enok KAT6 acetyltransferase complex physically interacts with the Elg1 PCNA-unloader complex and negatively regulates its PCNA-unloading function to promote G1/S transition; Enok depletion reduces chromatin-bound PCNA levels and causes a G1/S block that is partially rescued by Elg1 co-depletion.","method":"Co-immunoprecipitation, siRNA depletion, cell cycle analysis, chromatin-bound PCNA quantification in S2 cells and embryos","journal":"Genes & development","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus epistatic rescue of cell cycle phenotype in single lab study","pmids":["27198229"],"is_preprint":false},{"year":2017,"finding":"Structure-function analysis of yeast Elg1 shows that the sensitivity to DNA damaging agents and hyper-recombination of ELG1 alleles correlate with their ability to unload PCNA; purified Elg1 complex inhibits DNA synthesis by unloading SUMOylated PCNA from DNA; ELG1 mutations suppress rad5Δ sensitivity by allowing trans-lesion synthesis.","method":"Homology modeling-guided site-specific mutagenesis, in vitro DNA synthesis inhibition assay with purified proteins, genetic epistasis","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with purified proteins plus systematic mutagenesis with correlation of PCNA unloading to phenotype in single lab","pmids":["28108661"],"is_preprint":false},{"year":2018,"finding":"Elg1 interacts with the histone chaperone Rtt106 (identified by proteomics); the major cause of chromatin organization defects in elg1Δ is PCNA retention on DNA, with the Rtt106-Elg1 interaction playing a contributory role in post-replication nucleosome assembly.","method":"Proteomic interaction screen, Okazaki fragment length measurement, MNase sensitivity assay of newly replicated DNA, genetic epistasis","journal":"PLoS genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — proteomic identification of binding partner plus functional chromatin assays in single lab","pmids":["30418970"],"is_preprint":false},{"year":2019,"finding":"Timely removal of PCNA from DNA by the Elg1 complex is important for efficient mismatch repair (MMR); over-retained PCNA in elg1Δ hyper-recruits Msh2-Msh6 through its PIP motif and causes accumulation of MMR intermediates. PCNA mutants that spontaneously fall off DNA attenuate the elg1Δ mutator phenotype, while PCNA mutants with enhanced DNA interactions exacerbate it.","method":"Epistasis analysis with PCNA mutants, mutation rate assays, Msh2-Msh6 chromatin recruitment assays","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple PCNA mutant alleles with defined DNA-binding properties used in epistasis, with direct MMR intermediate accumulation measured","pmids":["31114918"],"is_preprint":false},{"year":2019,"finding":"ATAD5 promotes replication restart at stalled forks by recruiting RAD51 in an ATR-dependent manner; ATAD5 also removes PCNA from stalled forks to enable RAD51 recruitment. PCNA itself acts as a mechanical barrier to fork regression as shown by single-molecule FRET; ATAD5 depletion inhibits fork regression and reduces DNA breaks required for fork restart.","method":"Co-immunoprecipitation of ATAD5-RAD51, chromatin fractionation, hydroxyurea treatment, single-molecule FRET with PCNA, native BrdU assay for fork regression, mouse HU treatment model","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — single-molecule FRET, Co-IP, chromatin fractionation, and in vivo mouse data providing multiple orthogonal mechanistic lines","pmids":["31844045"],"is_preprint":false},{"year":2019,"finding":"Elg1 is essential for eliciting the DNA damage checkpoint (DC branch); in elg1 mutants, the adaptor proteins Rad9 (53BP1) and Dpb11 (TopBP1) are recruited to damage sites but fail to be phosphorylated by Mec1 (ATR), preventing checkpoint signal amplification. Local PCNA accumulation at damage sites in elg1 mutants correlates with checkpoint failure.","method":"Checkpoint-inducible strains, phosphorylation assays for Rad9/Dpb11, ChIP of PCNA at Lac operator sites, genetic epistasis","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — defined biochemical checkpoint readout with ChIP validation in single lab study","pmids":["31186330"],"is_preprint":false},{"year":2019,"finding":"The Elg1 PCNA unloader is necessary for efficient recruitment/retention of Rad51 and Rad52 at collapsed replication forks (RTS1 barrier) in fission yeast; PCNA unloading by Elg1 limits activity of anti-recombinogenic helicases Fbh1 and Srs2 to allow recombination to proceed.","method":"Replication fork collapse assays at RTS1 barrier, Rad51/Rad52 foci quantification, genetic epistasis with fbh1 and srs2 deletions","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct measurement of recombination protein recruitment combined with genetic epistasis in single lab study","pmids":["31149897"],"is_preprint":false},{"year":2020,"finding":"ATAD5 interacts with RNA helicases DDX1, DDX5, DDX21, and DHX9, increasing their abundance at replication forks to facilitate R-loop resolution; additionally, ATAD5-mediated PCNA unloading prevents new R-loop generation behind replication forks by removing PCNA that would otherwise cause collision with transcription machinery.","method":"Co-immunoprecipitation, iPOND (isolation of proteins on nascent DNA), siRNA knockdown, R-loop detection (S9.6 antibody), replication rate assays","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP of specific RNA helicase partners plus iPOND localization, combined with functional R-loop and replication assays in single rigorous study","pmids":["32542338"],"is_preprint":false},{"year":2020,"finding":"ATAD5 suppresses centrosome over-duplication; ATAD5 localizes to the base of mother and daughter centrioles. UAF1 (ATAD5 interactor) also localizes at the centrosome. ATAD5 depletion increases cells with over-duplicated centrosomes and multipolar chromosome segregation. The centrosomal function of ATAD5 does not require other RLC subunits. ATAD5 depletion reduces UAF1-ID1 interactions and increases ID1 centrosomal signal.","method":"Immunofluorescence co-localization, siRNA knockdown, centrosome counting, co-immunoprecipitation of UAF1-ID1, ATAD5 overexpression","journal":"Cell cycle (Georgetown, Tex.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct co-localization and Co-IP with functional phenotype in single lab study","pmids":["32594826"],"is_preprint":false},{"year":2020,"finding":"Access to PCNA by Srs2 and Elg1 controls the choice between DDT pathways; SUMOylated PCNA recruits Srs2 to repress a 'salvage recombination' pathway; overexpression of Elg1 (the PCNA unloader) activates salvage recombination by removing SUMOylated PCNA and thereby limiting Srs2 recruitment.","method":"Genetic epistasis with PCNA modification mutants (pol30-K164R, pol30-KK127,164RR), recombination assays, Elg1 overexpression","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis with defined PCNA modification alleles, functional pathway placement in single lab","pmids":["32371600"],"is_preprint":false},{"year":2021,"finding":"ATAD5-mediated PCNA unloading is important for timely termination of repair DNA synthesis at ROS-induced single-strand breaks (SSBs); ATAD5 depletion causes increased repair DNA synthesis and greater DNA polymerase stalling (measured by PCNA monoubiquitination) at H2O2-induced SSBs but not at MMS-induced base damage. PCNA is loaded at direct SSBs after 3'-end processing but rarely during BER of oxidized/alkylated bases.","method":"siRNA knockdown, H2O2 and MMS sensitivity assays, repair DNA synthesis measurement, PCNA monoubiquitination western blot, SSBR protein chromatin enrichment","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple biochemical readouts in single lab with defined substrate specificity (SSB vs. BER)","pmids":["34718749"],"is_preprint":false},{"year":2022,"finding":"The minimal PCNA-unloading domain (ULD) of ATAD5 was defined; the C-terminus of ULD is required for stable RFC2-5 association for active RLC formation; the N-terminus of ULD participates in opening the PCNA ring; ATAD5-RLC binds more robustly to open-labile PCNA than wild-type PCNA.","method":"Deletion/mutagenesis analysis of ATAD5 ULD, Co-IP of RFC2-5, PCNA unloading assays, binding assays with PCNA mutants","journal":"Cells","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — systematic domain mutagenesis with functional PCNA unloading and binding assays in single lab","pmids":["35681528"],"is_preprint":false},{"year":2023,"finding":"ATAD5 is required for short-range end resection at DSBs; PCNA is rapidly loaded at DSB sites in an RFC and MRE11-RAD50-NBS1/CtIP-dependent manner, and ATAD5-mediated PCNA unloading is required for completion of short-range resection and removal of KU70/80 from DSB termini, facilitating DNA repair synthesis and HR completion.","method":"Cytological analysis of resection markers, in vitro short-range end resection system, siRNA knockdown, chromatin fractionation, HR repair assays, camptothecin sensitivity","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro reconstitution system plus cytological and genetic assays in single lab study","pmids":["37739427"],"is_preprint":false},{"year":2023,"finding":"Atad5-RLC is the major PCNA unloader in Xenopus egg extracts, providing the dominant PCNA unloading activity despite comprising only ~3% of RFC/RLCs; RFC and Ctf18-RLC immunodepletion do not detectably affect PCNA unloading rate. Atad5 PCNA unloading is dependent on ATP-binding, independent of DNA nicks and chromatin assembly, and inhibited by PCNA-interacting peptides.","method":"Xenopus egg extract PCNA unloading system, immunodepletion of Atad5/Rfc1/Ctf18, ATPase motif mutants, PCNA-interacting peptide inhibition assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution system with immunodepletion and multiple biochemical controls definitively establishing Atad5 as the major unloader","pmids":["38141767"],"is_preprint":false},{"year":2023,"finding":"ATAD5 (N-terminal domain) functions as a scaffold for Ub-PCNA deubiquitination by forming a heterotrimeric complex with UAF1-USP1; ATAD5 recognizes DNA-loaded Ub-PCNA through distinct DNA-binding and PCNA-binding motifs; ATAD5 also enhances Ub-PCNA deubiquitination by USP7 and USP11 through specific interactions, and promotes deubiquitination of poly-Ub-PCNA by all three USPs.","method":"Co-immunoprecipitation, in vitro deubiquitination assay, DNA-binding and PCNA-binding domain mapping, ATAD5 UAF1-binding mutants, sensitivity assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vitro deubiquitination reconstitution plus multiple Co-IP interactions with domain mapping and functional validation in single rigorous study","pmids":["39145935"],"is_preprint":false},{"year":2023,"finding":"ATAD5 removal of non-ubiquitinated PAF15 (PAF15Ub0) from chromatin is part of the termination mechanism for UHRF1-dependent maintenance DNA methylation; USP7 specifically deubiquitinates PAF15Ub2 in complex with DNMT1, and completion of DNA methylation by DNMT1 catalytic activity is required for termination of UHRF1-mediated ubiquitin signaling.","method":"Co-immunoprecipitation, siRNA depletion of ATAD5/USP7, chromatin fractionation, DNMT1 inhibition, interaction mapping","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and depletion experiments with defined biochemical readout of PAF15 chromatin retention in single lab study","pmids":["36734974"],"is_preprint":false},{"year":2023,"finding":"SUMOylated PCNA acts as a positive signal for telomerase activity; Elg1 physically interacts with the CST complex (Cdc13-Stn1-Ten) and, together with Stn1, negatively regulates telomere elongation in a SUMO-coordinated manner.","method":"Telomere length assays, genetic epistasis with PCNA modification mutants, physical interaction assays between Elg1 and CST complex","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — physical interaction assays combined with epistasis using defined PCNA modification alleles in single lab","pmids":["37530521"],"is_preprint":false},{"year":2024,"finding":"Cryo-EM structures of ATAD5-RFC/Elg1-RFC reveal two unique 'locking loops' that tie the complex into a rigid structure and a 'plug' domain filling the DNA-binding chamber, explaining why ATAD5-RFC exclusively unloads PCNA rather than loading it; ATAD5-RFC opens a PCNA gap between protomers 2 and 3 (distinct from gap between protomers 1 and 3 used by all known clamp loaders); ATAD5-RFC can unload PCNA using non-hydrolyzable AMP-PNP and can remove PCNA from covalently closed circular DNA, indicating unloading occurs by a mechanism distinct from loading.","method":"Cryo-EM structure determination, AMP-PNP non-hydrolyzable ATP analog experiments, PCNA unloading from covalently closed circular DNA","journal":"Nature structural & molecular biology / Science advances","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structures from two independent labs with functional validation experiments (AMP-PNP, covalently closed DNA)","pmids":["38871854","38427736"],"is_preprint":false},{"year":2024,"finding":"BAZ1B (regulatory subunit of the WICH chromatin-remodeling complex) binds ATAD5 at a region encompassing the UAF1-binding domain; disruption of ATAD5-BAZ1B interaction causes premature Ub-PCNA deubiquitination after H2O2 treatment, suggesting BAZ1B prevents premature Ub-PCNA deubiquitination to safeguard genome integrity.","method":"Co-immunoprecipitation of BAZ1B-ATAD5, ATAD5 mutants disrupting BAZ1B binding, Ub-PCNA deubiquitination assays, H2O2 sensitivity","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP with domain mapping and functional deubiquitination assay in single lab","pmids":["39627214"],"is_preprint":false}],"current_model":"ATAD5 (human ortholog of yeast Elg1) is the major subunit of an RFC-like complex (ATAD5-RLC/Elg1-RLC) that functions primarily as a dedicated PCNA unloader: structural studies show two unique locking loops and a plug domain prevent DNA binding and restrict the complex to unloading activity, mechanistically distinct from PCNA loading by RFC; genome-wide, ATAD5-RLC unloads PCNA following Okazaki fragment ligation; ATAD5's N-terminal domain additionally serves as a scaffold that recruits the USP1-UAF1 deubiquitinase complex (and USP7/USP11) to deubiquitinate Ub-PCNA on DNA before its release, and directs RNA helicases to replication forks to suppress R-loops, while also promoting RAD51 recruitment and fork regression at stalled forks, participating in short-range DSB end resection, sister chromatid cohesion, mismatch repair, centrosome duplication, and the DNA damage checkpoint through its core function of timely PCNA removal from chromatin."},"narrative":{"mechanistic_narrative":"ATAD5 (yeast Elg1) is the major subunit of an RFC-like clamp-unloader complex (ATAD5/Elg1-RLC) that maintains genome stability by enforcing the timely removal of the PCNA sliding clamp from chromatin during and after DNA replication [PMID:12912927, PMID:13678589, PMID:12909721, PMID:23277426, PMID:26212319]. Unlike the clamp-loading RFC complexes, ATAD5-RLC is a dedicated PCNA unloader: cryo-EM structures reveal unique 'locking loops' and a 'plug' domain that fill the DNA-binding chamber, restricting the complex to unloading and allowing it to remove PCNA even from covalently closed DNA via an ATP-binding (non-hydrolysis-dependent) mechanism distinct from loading [PMID:38871854, PMID:38427736]. In vitro reconstitution with purified complex and in Xenopus extracts established that ATAD5/Elg1-RLC directly unloads both unmodified and SUMOylated PCNA and provides the dominant cellular unloading activity, with Okazaki fragment ligation serving as the genome-wide trigger for unloading behind replication forks [PMID:23499004, PMID:26212319, PMID:38141767]. Beyond its core enzymatic role, the ATAD5 N-terminus is a scaffold that recruits the USP1-UAF1 deubiquitinase (and USP7/USP11) to deubiquitinate DNA-loaded ubiquitinated PCNA prior to its release [PMID:20147293, PMID:39145935], and recruits RNA helicases (DDX1, DDX5, DDX21, DHX9) to forks to resolve and suppress R-loops [PMID:32542338]. Through this control of PCNA residence time, ATAD5 governs replication factory lifespan [PMID:23277426], mismatch repair [PMID:31114918], replication fork restart and RAD51 recruitment at stalled forks [PMID:31844045], short-range DSB end resection [PMID:37739427], sister chromatid cohesion [PMID:19430531, PMID:19262753], and the DNA damage checkpoint [PMID:31186330]; failure to clear PCNA—particularly its retention into G2/M—is the principal source of genome instability in its absence [PMID:27373149]. Mouse Atad5 haploinsufficiency causes defective PCNA deubiquitination and tumor predisposition, defining its in vivo tumor-suppressor function [PMID:21901109].","teleology":[{"year":2003,"claim":"Established that ELG1/ATAD5 nucleates a distinct RFC-like complex, defining a new genome-stability factor separate from the known Rad24- and Ctf18-RFC clamp loaders.","evidence":"Genetic interaction screens, reciprocal Co-IP, and epistasis in yeast across three independent labs","pmids":["12912927","13678589","12909721"],"confidence":"High","gaps":["Biochemical activity of the complex on PCNA not yet defined","Mechanistic distinction from loading RFCs unresolved"]},{"year":2003,"claim":"Linked Elg1 physically to PCNA and the Okazaki fragment maturation machinery, providing the first clue that its substrate is the sliding clamp.","evidence":"Pulldown/two-hybrid and genetic interaction with Pol30 (PCNA) and Rad27/FEN-1 in yeast","pmids":["13678589"],"confidence":"Medium","gaps":["Direction of PCNA regulation (load vs unload) not determined","Interaction not reconstituted with purified components"]},{"year":2010,"claim":"Defined ATAD5's scaffolding role by showing its N-terminus recruits the USP1-UAF1 deubiquitinase to remove monoubiquitin from PCNA, coupling clamp regulation to the ubiquitin pathway.","evidence":"Co-IP, siRNA knockdown, ubiquitin-PCNA western blot, and domain mapping in human cells; plus SUMO-PCNA/SIM-PIP recognition in yeast","pmids":["20147293","20571511"],"confidence":"High","gaps":["Whether deubiquitination is mechanistically coupled to unloading not resolved","Roles of additional DUBs not yet explored"]},{"year":2011,"claim":"Demonstrated in vivo physiological relevance and disease link by showing Atad5 haploinsufficiency impairs PCNA deubiquitination and predisposes mice to tumors.","evidence":"Atad5+/m heterozygous mouse model, MEF deubiquitination assays, tumor incidence","pmids":["21901109"],"confidence":"High","gaps":["Molecular link between PCNA deubiquitination defect and tumorigenesis indirect","Human disease mutation spectrum not addressed"]},{"year":2013,"claim":"Proved the core activity—that the complex directly unloads PCNA from chromatin—resolving the long-standing question of its enzymatic function.","evidence":"In vitro PCNA unloading with purified Elg1-RLC plus auxin degron in vivo (yeast); chromatin fractionation and ATPase mutants in human cells regulating replication factory lifespan","pmids":["23499004","23277426","23937667"],"confidence":"High","gaps":["Trigger that times unloading not yet identified","Structural basis for unloading-only activity unknown"]},{"year":2015,"claim":"Identified the physiological signal for unloading by showing Okazaki fragment ligation is a prerequisite for genome-wide PCNA removal behind forks.","evidence":"ChIP-seq PCNA profiling, Cdc9 ligase degron, and heterologous Chlorella ligase complementation in yeast","pmids":["26212319"],"confidence":"High","gaps":["How ligation status is sensed by the complex unclear","Lagging- vs leading-strand specificity not fully mapped"]},{"year":2016,"claim":"Established that the timing of PCNA clearance is critical, showing retention into G2/M—not S-phase retention alone—is the major driver of genome instability.","evidence":"Cell-cycle-regulated ELG1 alleles and disassembly-prone PCNA mutant rescue of genome instability in yeast","pmids":["27373149"],"confidence":"High","gaps":["Downstream lesion caused by retained PCNA not pinpointed","Mammalian generalization of G2/M effect untested here"]},{"year":2019,"claim":"Expanded the functional reach of PCNA unloading to mismatch repair, fork restart, checkpoint signaling, and recombination, showing clamp residence time gates multiple genome-maintenance pathways.","evidence":"PCNA-mutant epistasis and MMR intermediate assays (yeast), ATAD5-RAD51 Co-IP and single-molecule FRET fork regression (human/mouse), Rad9/Dpb11 phosphorylation and ChIP (yeast), Rad51/Rad52 recruitment at collapsed forks (fission yeast)","pmids":["31114918","31844045","31186330","31149897"],"confidence":"High","gaps":["Whether each pathway role is direct or a secondary consequence of PCNA retention varies by study","Cross-species mechanistic conservation not uniformly tested"]},{"year":2020,"claim":"Revealed a transcription-replication coordination role by showing ATAD5 recruits RNA helicases to forks and that PCNA unloading itself prevents R-loop accumulation, plus an RLC-independent centrosomal function.","evidence":"Co-IP and iPOND with DDX1/DDX5/DDX21/DHX9, S9.6 R-loop detection (human cells); immunofluorescence and centrosome counting with UAF1/ID1","pmids":["32542338","32594826"],"confidence":"Medium","gaps":["Helicase recruitment mechanism not structurally defined","Whether centrosomal role uses deubiquitination scaffolding unclear"]},{"year":2023,"claim":"Defined ATAD5 as the dominant cellular unloader and a multi-DUB scaffold, and extended its substrate-clearance role to DSB end resection and DNA-methylation termination.","evidence":"Xenopus extract immunodepletion and ATPase mutants; in vitro DUB reconstitution with UAF1-USP1/USP7/USP11 and domain mapping; in vitro short-range resection system; PAF15 chromatin fractionation","pmids":["38141767","39145935","37739427","36734974"],"confidence":"High","gaps":["Coordination between unloading and deubiquitination scaffolding not fully integrated","Substrate selectivity among PCNA-clamped processes incomplete"]},{"year":2024,"claim":"Provided the structural mechanism for why ATAD5-RFC unloads rather than loads PCNA, identifying locking loops and a plug domain and a unique protomer 2-3 gate.","evidence":"Cryo-EM structures from two independent labs with AMP-PNP and covalently closed circular DNA functional tests; BAZ1B Co-IP regulating deubiquitination timing","pmids":["38871854","38427736","39627214"],"confidence":"High","gaps":["Structural state of the bound PCNA during ring opening not captured","How regulatory partners (BAZ1B) modulate the structural cycle unknown"]},{"year":null,"claim":"How ATAD5 integrates and prioritizes its multiple substrate-clearance functions (unloading, deubiquitination, helicase recruitment) at a single fork or lesion in real time remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model coupling unloading kinetics to DUB scaffolding and helicase delivery","Spectrum and functional consequences of human ATAD5 disease alleles not defined in the corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[10,29,33]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[7,30]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[7,23,30]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[30,33]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[11,13,29]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[4]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[10,12,13]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[24]}],"pathway":[{"term_id":"R-HSA-69306","term_label":"DNA Replication","supporting_discovery_ids":[10,11,13]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[19,20,28]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[15,16,24]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[7,30]}],"complexes":["ATAD5/Elg1-RFC-like complex (RLC)","USP1-UAF1 deubiquitinase complex (heterotrimer with ATAD5)"],"partners":["PCNA","RFC2-5","USP1","UAF1","USP7","USP11","RAD51","BAZ1B"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96QE3","full_name":"ATPase family AAA domain-containing protein 5","aliases":["Chromosome fragility-associated gene 1 protein"],"length_aa":1844,"mass_kda":207.6,"function":"Has an important role in DNA replication and in maintaining genome integrity during replication stress (PubMed:15983387, PubMed:19755857). Involved in a RAD9A-related damage checkpoint, a pathway that is important in determining whether DNA damage is compatible with cell survival or whether it requires cell elimination by apoptosis (PubMed:15983387). Modulates the RAD9A interaction with BCL2 and thereby induces DNA damage-induced apoptosis (PubMed:15983387). Promotes PCNA deubiquitination by recruiting the ubiquitin-specific protease 1 (USP1) and WDR48 thereby down-regulating the error-prone damage bypass pathway (PubMed:20147293). As component of the ATAD5 RFC-like complex, regulates the function of the DNA polymerase processivity factor PCNA by unloading the ring-shaped PCNA homotrimer from DNA after replication during the S phase of the cell cycle (PubMed:23277426, PubMed:23937667). This seems to be dependent on its ATPase activity (PubMed:23277426). Plays important roles in restarting stalled replication forks under replication stress, by unloading the PCNA homotrimer from DNA and recruiting RAD51 possibly through an ATR-dependent manner (PubMed:31844045). Ultimately this enables replication fork regression, breakage, and eventual fork restart (PubMed:31844045). Both the PCNA unloading activity and the interaction with WDR48 are required to efficiently recruit RAD51 to stalled replication forks (PubMed:31844045). 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ATAD5","url":"https://www.omim.org/entry/609534"},{"mim_id":"176740","title":"PROLIFERATING CELL NUCLEAR ANTIGEN; PCNA","url":"https://www.omim.org/entry/176740"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Cytokinetic bridge","reliability":"Additional"},{"location":"Centriolar satellite","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"bone 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\"Reverse Yeast Two-Hybrid Array\" (RYTHA), Identifies Mutants that Dissociate the Physical Interaction Between Elg1 and Slx5.","date":"2017","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28476868","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.11.25.625248","title":"Insights into the causes and consequences of DNA repeat expansions from 700,000 biobank participants","date":"2024-11-26","source":"bioRxiv","url":"https://doi.org/10.1101/2024.11.25.625248","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.05.29.656775","title":"The Elg1 Replication Factor C-like complex safeguards cells from replication stress through a noncanonical pathway independent of the Mec1-Rad53 axis","date":"2025-05-30","source":"bioRxiv","url":"https://doi.org/10.1101/2025.05.29.656775","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":26346,"output_tokens":8763,"usd":0.105242,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":18531,"output_tokens":4251,"usd":0.099465,"stage2_stop_reason":"end_turn"},"total_usd":0.204707,"stage1_batch_id":"msgbatch_0179Z2pxRYBsXi2xADneafRw","stage2_batch_id":"msgbatch_01LaY9ZaVdgjWArcZo9eqQE5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2003,\n      \"finding\": \"ELG1/ATAD5 encodes the major subunit of a novel RFC-like complex (RLC) formed with RFC2-5 subunits, distinct from the Rad24-RFC and Ctf18-RFC complexes, and this complex is required for genome stability, S-phase progression, and Rad53 checkpoint kinase activation in response to replication stress.\",\n      \"method\": \"Genetic interaction screens, co-immunoprecipitation, biochemical fractionation, genetic epistasis with rad24 and ctf18 mutants\",\n      \"journal\": \"The EMBO journal / Current biology / PNAS\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — independently replicated across three labs in the same year using reciprocal Co-IP and genetic epistasis\",\n      \"pmids\": [\"12912927\", \"13678589\", \"12909721\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Elg1 physically interacts with PCNA (Pol30) and the FEN-1 homolog Rad27, suggesting a role in Okazaki fragment maturation.\",\n      \"method\": \"Physical interaction assay (pulldown/two-hybrid), genetic interaction analysis\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single lab pulldown/two-hybrid supported by genetic interactions, replicated in context by multiple labs\",\n      \"pmids\": [\"13678589\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Elg1 participates in negative control of telomere length and telomeric silencing through a replication-mediated pathway that is dependent on yKu, DNA polymerase, and active telomerase, but independent of recombination.\",\n      \"method\": \"Genetic epistasis with telomerase, yKu, and recombination mutants; telomere length assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis in single lab with multiple genetic backgrounds, functional pathway placement\",\n      \"pmids\": [\"14745004\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Elg1 is involved in homologous recombination (HR)-mediated DSB repair; it associates with both the DSB site (MAT locus) and the homologous donor locus (HML) in a Rad52-dependent manner at HML, and its loss reduces efficiency of primer extension after strand invasion and ligation steps of HR.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP), HR repair assays with HO endonuclease-induced DSBs, genetic epistasis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and direct repair assays in single lab with defined mechanistic steps identified\",\n      \"pmids\": [\"17170004\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"The unique C-terminus of Elg1 mediates oligomerization with Rfc2-5, nuclear import, and chromatin association; the Walker A motif in the conserved RFC region is dispensable for Elg1 function in vivo; the N-terminus contributes to genome stability and promotes nuclear localization.\",\n      \"method\": \"Mutational analysis, chromatin fractionation, nuclear localization assays\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — systematic structure-function mutagenesis with functional readouts in single lab\",\n      \"pmids\": [\"18482875\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Elg1-RLC plays a role in sister chromatid cohesion; elg1 mutants show elevated precocious sister chromatid separation and Elg1 is required for recruitment of Ctf18 to chromatin. Genetic interactions with cohesin subunits (Mcd1/Scc1) and cohesin loader (Scc2) were identified.\",\n      \"method\": \"Genetic suppressor screen, sister chromatid cohesion assays, chromatin localization by fractionation, genetic epistasis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two independent labs (Parnas et al. and Maradeo/Skibbens) reported Elg1-RLC cohesion roles using orthogonal methods\",\n      \"pmids\": [\"19430531\", \"19262753\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Elg1 preferentially interacts with SUMOylated PCNA via three SUMO-interacting motifs (SIMs) and a PIP box near its N-terminus; in the absence of Elg1, SUMOylated PCNA and the helicase Srs2 accumulate on chromatin.\",\n      \"method\": \"Physical interaction assays, chromatin fractionation, SIM and PIP box mutagenesis, genetic epistasis with srs2 and PCNA modification mutants\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — mutagenesis of defined motifs combined with chromatin fractionation and genetic epistasis in single rigorous study\",\n      \"pmids\": [\"20571511\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Human ELG1/ATAD5 interacts with the USP1-UAF1 deubiquitinating enzyme complex and directs it to deubiquitinate monoubiquitinated PCNA at stalled replication forks; the N-terminal domain of ELG1 is responsible for USP1-UAF1 interaction and PCNA deubiquitination activity. ELG1 knockdown specifically increases PCNA monoubiquitination without affecting FANCD2 ubiquitination.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, western blot for ubiquitinated PCNA, N-terminal domain mapping\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, domain mapping, and knockdown with specific biochemical readout in single rigorous study\",\n      \"pmids\": [\"20147293\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Elg1 N-terminus physically interacts with SUMO-pathway proteins Slx5 and Slx8 (an E3 SUMO-targeted ubiquitin ligase complex), mediated by poly-SUMO chains requiring Siz2 activity, in a PCNA modification-independent manner.\",\n      \"method\": \"Yeast two-hybrid screen, physical interaction assays, genetic epistasis with SUMO pathway mutants\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — two-hybrid and genetic evidence from single lab with domain specificity established\",\n      \"pmids\": [\"21869594\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Atad5 haploinsufficiency in mice leads to defective PCNA deubiquitination in response to DNA damage in MEFs, demonstrating the in vivo tumor suppressor function of mammalian ATAD5 is linked to its PCNA deubiquitination activity.\",\n      \"method\": \"Mouse genetics (Atad5+/m heterozygous mice), MEF PCNA deubiquitination assays, tumor incidence monitoring\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo mouse model combined with direct biochemical assay for PCNA deubiquitination, with functional cancer phenotype\",\n      \"pmids\": [\"21901109\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"ATAD5 regulates the lifespan of replication factories by unloading PCNA from chromatin during and after DNA synthesis; ATAD5 depletion extends replication factory lifespan, retains PCNA and replisome proteins on chromatin, decreases overall replication rate, and causes PCNA foci persistence into G2. The ATPase domain of ATAD5 is required for these activities.\",\n      \"method\": \"siRNA knockdown, PCNA chromatin fractionation, live imaging of replication factories, ATPase domain mutagenesis, flow cytometry\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (fractionation, live imaging, mutagenesis) in single rigorous study with defined mechanistic readouts\",\n      \"pmids\": [\"23277426\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"The yeast Elg1-RLC directly unloads PCNA from chromatin during DNA replication in vivo and in vitro; without Elg1, PCNA accumulates on chromatin during replication and can be removed by switching Elg1 expression back on. Purified Elg1-RLC causes PCNA unloading in vitro and unloads both unmodified and SUMOylated PCNA.\",\n      \"method\": \"Improved auxin-inducible degron system, chromatin fractionation, in vitro PCNA unloading assay with purified Elg1-RLC\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with purified complex plus in vivo validation; replicated independently (Shiomi & Nishitani 2013)\",\n      \"pmids\": [\"23499004\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Human Elg1/ATAD5 depletion causes accumulation of chromatin-bound PCNA during S phase, increases PCNA foci, causes chromatin loop size increase, and leads to aberrant/lagging chromosomes in mitosis, confirming ATAD5 as a PCNA unloading factor in human cells.\",\n      \"method\": \"siRNA knockdown, chromatin fractionation, immunofluorescence imaging of PCNA foci, chromosome analysis\",\n      \"journal\": \"Genes to cells : devoted to molecular & cellular mechanisms\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods confirming PCNA unloading function in human cells, consistent with parallel yeast studies\",\n      \"pmids\": [\"23937667\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The Elg1-RLC unloads PCNA genome-wide following Okazaki fragment ligation; in elg1Δ cells PCNA is retained on chromosomes in the wake of replication forks rather than at specific sites; Okazaki fragment ligation by Cdc9 is a prerequisite for PCNA unloading, as Chlorella virus ligase substituting for Cdc9 also promotes PCNA unloading.\",\n      \"method\": \"ChIP-seq genome-wide PCNA profiling, degron-mediated depletion of Cdc9 ligase, heterologous ligase complementation, chromatin fractionation\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genome-wide ChIP-seq plus genetic epistasis with ligase replacement, defining mechanistic prerequisite for PCNA unloading\",\n      \"pmids\": [\"26212319\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Phosphorylation of Elg1 at S112 is dependent on the ATR ortholog Mec1 and is important for Elg1's role at telomeres and in regulation of DNA repair; Elg1 phosphorylation mutants unable to undergo phosphorylation suppress the DNA damage sensitivity of rad5Δ mutants.\",\n      \"method\": \"Mass spectrometry identification of phosphorylation sites, phosphorylation mutant analysis, epistasis with rad5Δ, telomere length assays\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS-identified phosphorylation with functional validation by mutant analysis in single lab\",\n      \"pmids\": [\"26177013\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Prolonged retention of PCNA on DNA into G2/M phase is the major cause of genome instability in elg1Δ yeast; disassembly-prone PCNA mutants that relieve PCNA accumulation rescue genome instability of elg1Δ; PCNA retention specifically through G2/M exacerbates genome instability beyond that caused by S-phase retention alone.\",\n      \"method\": \"Cell-cycle-regulated ELG1 alleles engineering, disassembly-prone PCNA mutants, genome instability assays, overexpression-induced PCNA accumulation\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — engineered cell-cycle-controlled alleles plus PCNA mutant rescue, multiple orthogonal genetic approaches in single rigorous study\",\n      \"pmids\": [\"27373149\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"The Drosophila Enok KAT6 acetyltransferase complex physically interacts with the Elg1 PCNA-unloader complex and negatively regulates its PCNA-unloading function to promote G1/S transition; Enok depletion reduces chromatin-bound PCNA levels and causes a G1/S block that is partially rescued by Elg1 co-depletion.\",\n      \"method\": \"Co-immunoprecipitation, siRNA depletion, cell cycle analysis, chromatin-bound PCNA quantification in S2 cells and embryos\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus epistatic rescue of cell cycle phenotype in single lab study\",\n      \"pmids\": [\"27198229\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Structure-function analysis of yeast Elg1 shows that the sensitivity to DNA damaging agents and hyper-recombination of ELG1 alleles correlate with their ability to unload PCNA; purified Elg1 complex inhibits DNA synthesis by unloading SUMOylated PCNA from DNA; ELG1 mutations suppress rad5Δ sensitivity by allowing trans-lesion synthesis.\",\n      \"method\": \"Homology modeling-guided site-specific mutagenesis, in vitro DNA synthesis inhibition assay with purified proteins, genetic epistasis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with purified proteins plus systematic mutagenesis with correlation of PCNA unloading to phenotype in single lab\",\n      \"pmids\": [\"28108661\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Elg1 interacts with the histone chaperone Rtt106 (identified by proteomics); the major cause of chromatin organization defects in elg1Δ is PCNA retention on DNA, with the Rtt106-Elg1 interaction playing a contributory role in post-replication nucleosome assembly.\",\n      \"method\": \"Proteomic interaction screen, Okazaki fragment length measurement, MNase sensitivity assay of newly replicated DNA, genetic epistasis\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — proteomic identification of binding partner plus functional chromatin assays in single lab\",\n      \"pmids\": [\"30418970\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Timely removal of PCNA from DNA by the Elg1 complex is important for efficient mismatch repair (MMR); over-retained PCNA in elg1Δ hyper-recruits Msh2-Msh6 through its PIP motif and causes accumulation of MMR intermediates. PCNA mutants that spontaneously fall off DNA attenuate the elg1Δ mutator phenotype, while PCNA mutants with enhanced DNA interactions exacerbate it.\",\n      \"method\": \"Epistasis analysis with PCNA mutants, mutation rate assays, Msh2-Msh6 chromatin recruitment assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple PCNA mutant alleles with defined DNA-binding properties used in epistasis, with direct MMR intermediate accumulation measured\",\n      \"pmids\": [\"31114918\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"ATAD5 promotes replication restart at stalled forks by recruiting RAD51 in an ATR-dependent manner; ATAD5 also removes PCNA from stalled forks to enable RAD51 recruitment. PCNA itself acts as a mechanical barrier to fork regression as shown by single-molecule FRET; ATAD5 depletion inhibits fork regression and reduces DNA breaks required for fork restart.\",\n      \"method\": \"Co-immunoprecipitation of ATAD5-RAD51, chromatin fractionation, hydroxyurea treatment, single-molecule FRET with PCNA, native BrdU assay for fork regression, mouse HU treatment model\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — single-molecule FRET, Co-IP, chromatin fractionation, and in vivo mouse data providing multiple orthogonal mechanistic lines\",\n      \"pmids\": [\"31844045\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Elg1 is essential for eliciting the DNA damage checkpoint (DC branch); in elg1 mutants, the adaptor proteins Rad9 (53BP1) and Dpb11 (TopBP1) are recruited to damage sites but fail to be phosphorylated by Mec1 (ATR), preventing checkpoint signal amplification. Local PCNA accumulation at damage sites in elg1 mutants correlates with checkpoint failure.\",\n      \"method\": \"Checkpoint-inducible strains, phosphorylation assays for Rad9/Dpb11, ChIP of PCNA at Lac operator sites, genetic epistasis\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — defined biochemical checkpoint readout with ChIP validation in single lab study\",\n      \"pmids\": [\"31186330\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The Elg1 PCNA unloader is necessary for efficient recruitment/retention of Rad51 and Rad52 at collapsed replication forks (RTS1 barrier) in fission yeast; PCNA unloading by Elg1 limits activity of anti-recombinogenic helicases Fbh1 and Srs2 to allow recombination to proceed.\",\n      \"method\": \"Replication fork collapse assays at RTS1 barrier, Rad51/Rad52 foci quantification, genetic epistasis with fbh1 and srs2 deletions\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct measurement of recombination protein recruitment combined with genetic epistasis in single lab study\",\n      \"pmids\": [\"31149897\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ATAD5 interacts with RNA helicases DDX1, DDX5, DDX21, and DHX9, increasing their abundance at replication forks to facilitate R-loop resolution; additionally, ATAD5-mediated PCNA unloading prevents new R-loop generation behind replication forks by removing PCNA that would otherwise cause collision with transcription machinery.\",\n      \"method\": \"Co-immunoprecipitation, iPOND (isolation of proteins on nascent DNA), siRNA knockdown, R-loop detection (S9.6 antibody), replication rate assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP of specific RNA helicase partners plus iPOND localization, combined with functional R-loop and replication assays in single rigorous study\",\n      \"pmids\": [\"32542338\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ATAD5 suppresses centrosome over-duplication; ATAD5 localizes to the base of mother and daughter centrioles. UAF1 (ATAD5 interactor) also localizes at the centrosome. ATAD5 depletion increases cells with over-duplicated centrosomes and multipolar chromosome segregation. The centrosomal function of ATAD5 does not require other RLC subunits. ATAD5 depletion reduces UAF1-ID1 interactions and increases ID1 centrosomal signal.\",\n      \"method\": \"Immunofluorescence co-localization, siRNA knockdown, centrosome counting, co-immunoprecipitation of UAF1-ID1, ATAD5 overexpression\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct co-localization and Co-IP with functional phenotype in single lab study\",\n      \"pmids\": [\"32594826\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Access to PCNA by Srs2 and Elg1 controls the choice between DDT pathways; SUMOylated PCNA recruits Srs2 to repress a 'salvage recombination' pathway; overexpression of Elg1 (the PCNA unloader) activates salvage recombination by removing SUMOylated PCNA and thereby limiting Srs2 recruitment.\",\n      \"method\": \"Genetic epistasis with PCNA modification mutants (pol30-K164R, pol30-KK127,164RR), recombination assays, Elg1 overexpression\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis with defined PCNA modification alleles, functional pathway placement in single lab\",\n      \"pmids\": [\"32371600\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ATAD5-mediated PCNA unloading is important for timely termination of repair DNA synthesis at ROS-induced single-strand breaks (SSBs); ATAD5 depletion causes increased repair DNA synthesis and greater DNA polymerase stalling (measured by PCNA monoubiquitination) at H2O2-induced SSBs but not at MMS-induced base damage. PCNA is loaded at direct SSBs after 3'-end processing but rarely during BER of oxidized/alkylated bases.\",\n      \"method\": \"siRNA knockdown, H2O2 and MMS sensitivity assays, repair DNA synthesis measurement, PCNA monoubiquitination western blot, SSBR protein chromatin enrichment\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple biochemical readouts in single lab with defined substrate specificity (SSB vs. BER)\",\n      \"pmids\": [\"34718749\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The minimal PCNA-unloading domain (ULD) of ATAD5 was defined; the C-terminus of ULD is required for stable RFC2-5 association for active RLC formation; the N-terminus of ULD participates in opening the PCNA ring; ATAD5-RLC binds more robustly to open-labile PCNA than wild-type PCNA.\",\n      \"method\": \"Deletion/mutagenesis analysis of ATAD5 ULD, Co-IP of RFC2-5, PCNA unloading assays, binding assays with PCNA mutants\",\n      \"journal\": \"Cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — systematic domain mutagenesis with functional PCNA unloading and binding assays in single lab\",\n      \"pmids\": [\"35681528\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ATAD5 is required for short-range end resection at DSBs; PCNA is rapidly loaded at DSB sites in an RFC and MRE11-RAD50-NBS1/CtIP-dependent manner, and ATAD5-mediated PCNA unloading is required for completion of short-range resection and removal of KU70/80 from DSB termini, facilitating DNA repair synthesis and HR completion.\",\n      \"method\": \"Cytological analysis of resection markers, in vitro short-range end resection system, siRNA knockdown, chromatin fractionation, HR repair assays, camptothecin sensitivity\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro reconstitution system plus cytological and genetic assays in single lab study\",\n      \"pmids\": [\"37739427\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Atad5-RLC is the major PCNA unloader in Xenopus egg extracts, providing the dominant PCNA unloading activity despite comprising only ~3% of RFC/RLCs; RFC and Ctf18-RLC immunodepletion do not detectably affect PCNA unloading rate. Atad5 PCNA unloading is dependent on ATP-binding, independent of DNA nicks and chromatin assembly, and inhibited by PCNA-interacting peptides.\",\n      \"method\": \"Xenopus egg extract PCNA unloading system, immunodepletion of Atad5/Rfc1/Ctf18, ATPase motif mutants, PCNA-interacting peptide inhibition assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution system with immunodepletion and multiple biochemical controls definitively establishing Atad5 as the major unloader\",\n      \"pmids\": [\"38141767\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ATAD5 (N-terminal domain) functions as a scaffold for Ub-PCNA deubiquitination by forming a heterotrimeric complex with UAF1-USP1; ATAD5 recognizes DNA-loaded Ub-PCNA through distinct DNA-binding and PCNA-binding motifs; ATAD5 also enhances Ub-PCNA deubiquitination by USP7 and USP11 through specific interactions, and promotes deubiquitination of poly-Ub-PCNA by all three USPs.\",\n      \"method\": \"Co-immunoprecipitation, in vitro deubiquitination assay, DNA-binding and PCNA-binding domain mapping, ATAD5 UAF1-binding mutants, sensitivity assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vitro deubiquitination reconstitution plus multiple Co-IP interactions with domain mapping and functional validation in single rigorous study\",\n      \"pmids\": [\"39145935\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ATAD5 removal of non-ubiquitinated PAF15 (PAF15Ub0) from chromatin is part of the termination mechanism for UHRF1-dependent maintenance DNA methylation; USP7 specifically deubiquitinates PAF15Ub2 in complex with DNMT1, and completion of DNA methylation by DNMT1 catalytic activity is required for termination of UHRF1-mediated ubiquitin signaling.\",\n      \"method\": \"Co-immunoprecipitation, siRNA depletion of ATAD5/USP7, chromatin fractionation, DNMT1 inhibition, interaction mapping\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and depletion experiments with defined biochemical readout of PAF15 chromatin retention in single lab study\",\n      \"pmids\": [\"36734974\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SUMOylated PCNA acts as a positive signal for telomerase activity; Elg1 physically interacts with the CST complex (Cdc13-Stn1-Ten) and, together with Stn1, negatively regulates telomere elongation in a SUMO-coordinated manner.\",\n      \"method\": \"Telomere length assays, genetic epistasis with PCNA modification mutants, physical interaction assays between Elg1 and CST complex\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — physical interaction assays combined with epistasis using defined PCNA modification alleles in single lab\",\n      \"pmids\": [\"37530521\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cryo-EM structures of ATAD5-RFC/Elg1-RFC reveal two unique 'locking loops' that tie the complex into a rigid structure and a 'plug' domain filling the DNA-binding chamber, explaining why ATAD5-RFC exclusively unloads PCNA rather than loading it; ATAD5-RFC opens a PCNA gap between protomers 2 and 3 (distinct from gap between protomers 1 and 3 used by all known clamp loaders); ATAD5-RFC can unload PCNA using non-hydrolyzable AMP-PNP and can remove PCNA from covalently closed circular DNA, indicating unloading occurs by a mechanism distinct from loading.\",\n      \"method\": \"Cryo-EM structure determination, AMP-PNP non-hydrolyzable ATP analog experiments, PCNA unloading from covalently closed circular DNA\",\n      \"journal\": \"Nature structural & molecular biology / Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structures from two independent labs with functional validation experiments (AMP-PNP, covalently closed DNA)\",\n      \"pmids\": [\"38871854\", \"38427736\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"BAZ1B (regulatory subunit of the WICH chromatin-remodeling complex) binds ATAD5 at a region encompassing the UAF1-binding domain; disruption of ATAD5-BAZ1B interaction causes premature Ub-PCNA deubiquitination after H2O2 treatment, suggesting BAZ1B prevents premature Ub-PCNA deubiquitination to safeguard genome integrity.\",\n      \"method\": \"Co-immunoprecipitation of BAZ1B-ATAD5, ATAD5 mutants disrupting BAZ1B binding, Ub-PCNA deubiquitination assays, H2O2 sensitivity\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP with domain mapping and functional deubiquitination assay in single lab\",\n      \"pmids\": [\"39627214\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ATAD5 (human ortholog of yeast Elg1) is the major subunit of an RFC-like complex (ATAD5-RLC/Elg1-RLC) that functions primarily as a dedicated PCNA unloader: structural studies show two unique locking loops and a plug domain prevent DNA binding and restrict the complex to unloading activity, mechanistically distinct from PCNA loading by RFC; genome-wide, ATAD5-RLC unloads PCNA following Okazaki fragment ligation; ATAD5's N-terminal domain additionally serves as a scaffold that recruits the USP1-UAF1 deubiquitinase complex (and USP7/USP11) to deubiquitinate Ub-PCNA on DNA before its release, and directs RNA helicases to replication forks to suppress R-loops, while also promoting RAD51 recruitment and fork regression at stalled forks, participating in short-range DSB end resection, sister chromatid cohesion, mismatch repair, centrosome duplication, and the DNA damage checkpoint through its core function of timely PCNA removal from chromatin.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ATAD5 (yeast Elg1) is the major subunit of an RFC-like clamp-unloader complex (ATAD5/Elg1-RLC) that maintains genome stability by enforcing the timely removal of the PCNA sliding clamp from chromatin during and after DNA replication [#0, #10, #13]. Unlike the clamp-loading RFC complexes, ATAD5-RLC is a dedicated PCNA unloader: cryo-EM structures reveal unique 'locking loops' and a 'plug' domain that fill the DNA-binding chamber, restricting the complex to unloading and allowing it to remove PCNA even from covalently closed DNA via an ATP-binding (non-hydrolysis-dependent) mechanism distinct from loading [#33]. In vitro reconstitution with purified complex and in Xenopus extracts established that ATAD5/Elg1-RLC directly unloads both unmodified and SUMOylated PCNA and provides the dominant cellular unloading activity, with Okazaki fragment ligation serving as the genome-wide trigger for unloading behind replication forks [#11, #13, #29]. Beyond its core enzymatic role, the ATAD5 N-terminus is a scaffold that recruits the USP1-UAF1 deubiquitinase (and USP7/USP11) to deubiquitinate DNA-loaded ubiquitinated PCNA prior to its release [#7, #30], and recruits RNA helicases (DDX1, DDX5, DDX21, DHX9) to forks to resolve and suppress R-loops [#23]. Through this control of PCNA residence time, ATAD5 governs replication factory lifespan [#10], mismatch repair [#19], replication fork restart and RAD51 recruitment at stalled forks [#20], short-range DSB end resection [#28], sister chromatid cohesion [#5], and the DNA damage checkpoint [#21]; failure to clear PCNA—particularly its retention into G2/M—is the principal source of genome instability in its absence [#15]. Mouse Atad5 haploinsufficiency causes defective PCNA deubiquitination and tumor predisposition, defining its in vivo tumor-suppressor function [#9].\"\n,\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Established that ELG1/ATAD5 nucleates a distinct RFC-like complex, defining a new genome-stability factor separate from the known Rad24- and Ctf18-RFC clamp loaders.\",\n      \"evidence\": \"Genetic interaction screens, reciprocal Co-IP, and epistasis in yeast across three independent labs\",\n      \"pmids\": [\"12912927\", \"13678589\", \"12909721\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Biochemical activity of the complex on PCNA not yet defined\", \"Mechanistic distinction from loading RFCs unresolved\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Linked Elg1 physically to PCNA and the Okazaki fragment maturation machinery, providing the first clue that its substrate is the sliding clamp.\",\n      \"evidence\": \"Pulldown/two-hybrid and genetic interaction with Pol30 (PCNA) and Rad27/FEN-1 in yeast\",\n      \"pmids\": [\"13678589\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direction of PCNA regulation (load vs unload) not determined\", \"Interaction not reconstituted with purified components\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Defined ATAD5's scaffolding role by showing its N-terminus recruits the USP1-UAF1 deubiquitinase to remove monoubiquitin from PCNA, coupling clamp regulation to the ubiquitin pathway.\",\n      \"evidence\": \"Co-IP, siRNA knockdown, ubiquitin-PCNA western blot, and domain mapping in human cells; plus SUMO-PCNA/SIM-PIP recognition in yeast\",\n      \"pmids\": [\"20147293\", \"20571511\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether deubiquitination is mechanistically coupled to unloading not resolved\", \"Roles of additional DUBs not yet explored\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Demonstrated in vivo physiological relevance and disease link by showing Atad5 haploinsufficiency impairs PCNA deubiquitination and predisposes mice to tumors.\",\n      \"evidence\": \"Atad5+/m heterozygous mouse model, MEF deubiquitination assays, tumor incidence\",\n      \"pmids\": [\"21901109\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular link between PCNA deubiquitination defect and tumorigenesis indirect\", \"Human disease mutation spectrum not addressed\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Proved the core activity—that the complex directly unloads PCNA from chromatin—resolving the long-standing question of its enzymatic function.\",\n      \"evidence\": \"In vitro PCNA unloading with purified Elg1-RLC plus auxin degron in vivo (yeast); chromatin fractionation and ATPase mutants in human cells regulating replication factory lifespan\",\n      \"pmids\": [\"23499004\", \"23277426\", \"23937667\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Trigger that times unloading not yet identified\", \"Structural basis for unloading-only activity unknown\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identified the physiological signal for unloading by showing Okazaki fragment ligation is a prerequisite for genome-wide PCNA removal behind forks.\",\n      \"evidence\": \"ChIP-seq PCNA profiling, Cdc9 ligase degron, and heterologous Chlorella ligase complementation in yeast\",\n      \"pmids\": [\"26212319\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How ligation status is sensed by the complex unclear\", \"Lagging- vs leading-strand specificity not fully mapped\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Established that the timing of PCNA clearance is critical, showing retention into G2/M—not S-phase retention alone—is the major driver of genome instability.\",\n      \"evidence\": \"Cell-cycle-regulated ELG1 alleles and disassembly-prone PCNA mutant rescue of genome instability in yeast\",\n      \"pmids\": [\"27373149\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream lesion caused by retained PCNA not pinpointed\", \"Mammalian generalization of G2/M effect untested here\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Expanded the functional reach of PCNA unloading to mismatch repair, fork restart, checkpoint signaling, and recombination, showing clamp residence time gates multiple genome-maintenance pathways.\",\n      \"evidence\": \"PCNA-mutant epistasis and MMR intermediate assays (yeast), ATAD5-RAD51 Co-IP and single-molecule FRET fork regression (human/mouse), Rad9/Dpb11 phosphorylation and ChIP (yeast), Rad51/Rad52 recruitment at collapsed forks (fission yeast)\",\n      \"pmids\": [\"31114918\", \"31844045\", \"31186330\", \"31149897\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether each pathway role is direct or a secondary consequence of PCNA retention varies by study\", \"Cross-species mechanistic conservation not uniformly tested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Revealed a transcription-replication coordination role by showing ATAD5 recruits RNA helicases to forks and that PCNA unloading itself prevents R-loop accumulation, plus an RLC-independent centrosomal function.\",\n      \"evidence\": \"Co-IP and iPOND with DDX1/DDX5/DDX21/DHX9, S9.6 R-loop detection (human cells); immunofluorescence and centrosome counting with UAF1/ID1\",\n      \"pmids\": [\"32542338\", \"32594826\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Helicase recruitment mechanism not structurally defined\", \"Whether centrosomal role uses deubiquitination scaffolding unclear\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined ATAD5 as the dominant cellular unloader and a multi-DUB scaffold, and extended its substrate-clearance role to DSB end resection and DNA-methylation termination.\",\n      \"evidence\": \"Xenopus extract immunodepletion and ATPase mutants; in vitro DUB reconstitution with UAF1-USP1/USP7/USP11 and domain mapping; in vitro short-range resection system; PAF15 chromatin fractionation\",\n      \"pmids\": [\"38141767\", \"39145935\", \"37739427\", \"36734974\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Coordination between unloading and deubiquitination scaffolding not fully integrated\", \"Substrate selectivity among PCNA-clamped processes incomplete\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Provided the structural mechanism for why ATAD5-RFC unloads rather than loads PCNA, identifying locking loops and a plug domain and a unique protomer 2-3 gate.\",\n      \"evidence\": \"Cryo-EM structures from two independent labs with AMP-PNP and covalently closed circular DNA functional tests; BAZ1B Co-IP regulating deubiquitination timing\",\n      \"pmids\": [\"38871854\", \"38427736\", \"39627214\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural state of the bound PCNA during ring opening not captured\", \"How regulatory partners (BAZ1B) modulate the structural cycle unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ATAD5 integrates and prioritizes its multiple substrate-clearance functions (unloading, deubiquitination, helicase recruitment) at a single fork or lesion in real time remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model coupling unloading kinetics to DUB scaffolding and helicase delivery\", \"Spectrum and functional consequences of human ATAD5 disease alleles not defined in the corpus\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [10, 29, 33]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [7, 30]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [7, 23, 30]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [30, 33]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [11, 13, 29]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [10, 12, 13]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [24]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-69306\", \"supporting_discovery_ids\": [10, 11, 13]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [19, 20, 28]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [15, 16, 24]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [7, 30]}\n    ],\n    \"complexes\": [\"ATAD5/Elg1-RFC-like complex (RLC)\", \"USP1-UAF1 deubiquitinase complex (heterotrimer with ATAD5)\"],\n    \"partners\": [\"PCNA\", \"RFC2-5\", \"USP1\", \"UAF1\", \"USP7\", \"USP11\", \"RAD51\", \"BAZ1B\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}