{"gene":"PLRG1","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2001,"finding":"The WD40 domain of PLRG1 directly interacts with the carboxyl-terminal region of CDC5L in vitro and in vivo. A bacterially expressed CDC5L fragment containing the PLRG1-interaction domain disrupts the CDC5L-PLRG1 interaction in HeLa nuclear extract and inhibits pre-mRNA splicing, demonstrating that this direct interaction is essential for pre-mRNA splicing progression.","method":"In vitro binding assay, co-immunoprecipitation, domain mapping by mutagenesis, in vitro splicing inhibition assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct interaction reconstituted in vitro with domain mapping and mutagenesis, functional consequence (splicing inhibition) demonstrated; replicated by independent peptide inhibitor study (PMID:14576297)","pmids":["11544257"],"is_preprint":false},{"year":2003,"finding":"Peptides derived from the WD40-containing interaction domain of PLRG1 and the C-terminal domain of CDC5L inhibit pre-mRNA splicing in vitro; this inhibition is rescued by pre-incubating the peptides with the corresponding partner protein, confirming that the CDC5L–PLRG1 interaction is essential for the splicing mechanism.","method":"In vitro splicing assay with competing peptides, rescue by recombinant protein pre-incubation","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro functional assay with competitive peptides and rescue control, orthogonally confirming the earlier interaction study","pmids":["14576297"],"is_preprint":false},{"year":2005,"finding":"PLRG1 is a core component of the Pso4/Prp19–Cdc5L–Plrg1–Spf27 complex (Pso4 complex) that is required for processing of psoralen DNA interstrand cross-links (ICLs) in a cell-free biochemical assay; the complex participates in an early stage of ICL repair alongside MutSβ, Ercc1-Xpf, RPA, and PCNA.","method":"Cell-free ICL processing assay, immunodepletion, co-immunoprecipitation showing Pso4 complex–WRN association","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cell-free biochemical assay with immunodepletion; PLRG1's individual contribution inferred from complex depletion, not individual KD","pmids":["16223718"],"is_preprint":false},{"year":2007,"finding":"The hPrp19 core complex normally includes Cdc5L, Plrg1, and Spf27; upon DNA damage, hPrp19 forms a ubiquitylated oligomeric species that fails to interact with either Cdc5L or Plrg1, indicating that DNA damage induces structural alterations that disrupt the PLRG1-containing core complex.","method":"SDS-PAGE under non-reducing conditions, co-immunoprecipitation, chromatin fractionation after DNA damage treatment","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — reciprocal co-IP showing loss of PLRG1 interaction with ubiquitylated Prp19; single lab, single method set","pmids":["17276391"],"is_preprint":false},{"year":2009,"finding":"PLRG1 is required for S-phase progression and suppression of apoptosis in vivo. PLRG1-deficient MEFs fail to progress through S phase and show increased apoptosis that is p53-dependent; PLRG1 deficiency causes enhanced p53 phosphorylation/stabilization and increased γ-H2AX, indicating an activated DNA damage response. PLRG1 is also required for nuclear retention of its binding partner CDC5L.","method":"Conditional knockout mice (heart- and neuron-specific), PLRG1-deficient MEFs, BrdU/FACS cell-cycle analysis, immunofluorescence for γ-H2AX, p53 knockdown rescue in MEFs and zebrafish, subcellular fractionation for CDC5L localization","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic KO with multiple orthogonal readouts (cell-cycle, apoptosis, DNA damage markers, localization), in vivo rescue experiment in zebrafish, replicated across mouse and fish models","pmids":["19307306"],"is_preprint":false},{"year":2009,"finding":"PLRG1 is a core component of the Prp19/Pso4–Cdc5L–Plrg1–Spf27 complex; Cdc5L within this complex interacts physically with ATR kinase and is required for ATR-mediated S-phase checkpoint signaling (Chk1, Rad17, FancD2 activation). PLRG1's role is inferred through its membership in the Cdc5L complex that mediates this checkpoint.","method":"Co-immunoprecipitation (Cdc5L–ATR), siRNA depletion of Cdc5L, checkpoint kinase activation assays, deletion mapping of ATR-binding region in Cdc5L","journal":"EMBO reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — PLRG1's mechanistic role is indirect; the paper focuses on Cdc5L–ATR interaction; PLRG1 contribution inferred from complex membership, not direct experiment on PLRG1","pmids":["19633697"],"is_preprint":false},{"year":2010,"finding":"PLRG1 directly interacts with CDC5L in vivo; a central region of hnRNP-M mediates direct interaction with both CDC5L and PLRG1. This interaction is inhibited during heat-shock stress. An hnRNP-M mutant lacking the CDC5L/PLRG1 interaction domain cannot modulate alternative 5′ and 3′ splice site choice, placing PLRG1 in the pathway of alternative splicing regulation via hnRNP-M.","method":"Co-immunoprecipitation in vivo, domain mapping by deletion mutants, adeno-E1A minigene alternative splicing assay","journal":"EMBO reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP and functional splicing assay with deletion mutant; single lab, two orthogonal methods","pmids":["20467437"],"is_preprint":false},{"year":2014,"finding":"PLRG1 (as part of the PSO4 core complex) is required for efficient recruitment of ATRIP to DNA damage sites and subsequent CHK1 activation and RPA2 phosphorylation; PLRG1 colocalizes with RPA at damage sites. Both the RPA1-binding ability of BCAS2 and the E3 ligase activity of PSO4 within the PLRG1-containing complex are required for these functions.","method":"siRNA depletion of complex subunits, immunofluorescence colocalization, co-immunoprecipitation of PLRG1-complex with RPA, in vitro ATR activation assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — depletion plus colocalization and functional ATR-pathway assays; PLRG1's individual contribution partially inferred from complex-level experiments","pmids":["24443570"],"is_preprint":false},{"year":2018,"finding":"PLRG1 is essential for activation of the Prp19 (NTC) E3 ubiquitin ligase. Prp19 is autoinhibited on its own; stepwise assembly of SPF27, CDC5L, and PLRG1 onto the Prp19 tetramer enables ubiquitin ligation activity. Cross-linking/MS and functional assays defined the communication between PLRG1 and Prp19 that enables E3 activity, and crystal structure revealed the autoinhibition mechanism.","method":"X-ray crystallography of Prp19, mutational analysis of autoinhibition, stepwise reconstitution of NTC core, in vitro ubiquitin ligation assay, protein-protein crosslinking coupled to mass spectrometry","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus in vitro reconstitution, mutagenesis, and functional ubiquitin ligation assay; multiple orthogonal methods in a single rigorous study","pmids":["29547724"],"is_preprint":false},{"year":2020,"finding":"The crystal structure of the WD40 domain of human PLRG1 was solved by X-ray crystallography. Comparison with cryo-EM structures of PLRG1 within the spliceosome showed that two loops of the WD40 domain become resolved upon binding to other splicing factors, revealing dynamic conformational changes during spliceosome assembly.","method":"X-ray crystallography (apo WD40 domain), comparison with cryo-EM spliceosome structures","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — crystal structure of isolated domain with structural comparison; single lab, limited functional validation beyond structural observation","pmids":["33239170"],"is_preprint":false},{"year":2021,"finding":"USP42 (a deubiquitylase) directs the integration of PLRG1 into nuclear speckles (SC35-positive) in a phase-separation-dependent manner; depletion of USP42 displaces PLRG1 from nuclear speckles and deregulates mRNA splicing events phenocopying PLRG1 repression, placing USP42-mediated deubiquitylation upstream of PLRG1 nuclear speckle localization and splicing function.","method":"Immunofluorescence colocalization, USP42 siRNA knockdown, mRNA splicing assays, phase separation assays, subcellular fractionation","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiment with functional consequence (splicing deregulation), two orthogonal methods; single lab","pmids":["33731873"],"is_preprint":false},{"year":2022,"finding":"DHX37 interacts with PLRG1 and together they co-occupy the promoter and superenhancer elements of cyclin D1 (CCND1) to transcriptionally activate CCND1 expression, promoting liver cancer cell proliferation. This reveals a non-canonical transcriptional/epigenomic function for PLRG1 beyond splicing.","method":"Co-immunoprecipitation (DHX37–PLRG1), ChIP-seq epigenomic profiling of DHX37-knockdown cells, ChIP showing co-occupancy at CCND1 promoter/superenhancer, siRNA knockdown proliferation assays","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP plus ChIP-seq with functional proliferation assay; single lab, two orthogonal methods","pmids":["35290436"],"is_preprint":false},{"year":2023,"finding":"PLRG1 knockdown in cancer cells (but not normal cells) causes mitotic arrest, microtubule instability, ER stress, autophagy accumulation, DNA damage, and ultimately apoptosis; in normal cells PLRG1 depletion induces G1 arrest as a self-protective mechanism, distinguishing tumor-specific from normal cell responses to PLRG1 loss.","method":"siRNA knockdown, cell-cycle FACS analysis, immunofluorescence for microtubule stability and DNA damage markers (γ-H2AX), apoptosis assays","journal":"BMB reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KD with multiple defined cellular phenotype readouts; single lab","pmids":["37817442"],"is_preprint":false},{"year":2024,"finding":"YBX1 directly binds to the PLRG1 promoter and transcriptionally activates PLRG1 expression; overexpression of YBX1 upregulates PLRG1 and promotes EMT (increased N-cadherin, Snail, migration, invasion) in HCC cells, and these effects are abolished by PLRG1 knockdown, placing PLRG1 downstream of YBX1 in the EMT pathway.","method":"Chromatin immunoprecipitation (ChIP) of YBX1 at PLRG1 promoter, luciferase reporter assay, siRNA knockdown of PLRG1, YBX1 overexpression, EMT marker immunoblotting, migration/invasion assays","journal":"Medical oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP plus luciferase assay for direct transcriptional regulation, epistasis via KD rescue; single lab","pmids":["39400789"],"is_preprint":false}],"current_model":"PLRG1 is an evolutionarily conserved WD40-domain protein that functions as an essential structural and regulatory subunit of the NineTeen Complex (NTC/Pso4 complex), where its stepwise assembly with Prp19, SPF27, and CDC5L is required to relieve Prp19 autoinhibition and activate its E3 ubiquitin ligase activity; through its direct interaction with CDC5L (mediated by the PLRG1 WD40 domain and the CDC5L C-terminus), it is essential for pre-mRNA splicing, and the complex additionally participates in DNA interstrand cross-link repair, ATR-mediated DNA damage checkpoint signaling (via RPA binding and ATRIP recruitment), and nuclear speckle phase-separation-dependent splicing regulated by USP42-mediated deubiquitylation; PLRG1 is also required for nuclear retention of CDC5L, p53-dependent cell-cycle progression, and has a non-canonical role in transcriptional activation of cyclin D1 via cooperation with DHX37 at superenhancer elements."},"narrative":{"mechanistic_narrative":"PLRG1 is a conserved WD40-domain protein that functions as an essential structural and regulatory subunit of the Prp19/Pso4 (NineTeen) complex, coupling pre-mRNA splicing to genome maintenance [PMID:11544257, PMID:29547724]. Within this complex, PLRG1 directly binds the C-terminus of CDC5L via its WD40 domain, and this interaction is required for pre-mRNA splicing progression: peptides disrupting the CDC5L–PLRG1 interface inhibit in vitro splicing, an effect rescued by the partner protein [PMID:11544257, PMID:14576297]. Stepwise assembly of SPF27, CDC5L, and PLRG1 onto the autoinhibited Prp19 tetramer relieves autoinhibition and activates Prp19 E3 ubiquitin ligase activity, with PLRG1's WD40 surface communicating with Prp19 to enable ligation [PMID:29547724]; two WD40 loops become ordered upon engagement of other splicing factors during spliceosome assembly [PMID:33239170]. PLRG1 is integrated into SC35-positive nuclear speckles in a phase-separation-dependent manner under control of USP42-mediated deubiquitylation, linking its localization to splicing fidelity [PMID:33731873]. Beyond splicing, the PLRG1-containing Pso4 complex acts in DNA interstrand cross-link repair and in ATR-mediated S-phase checkpoint signaling, where it colocalizes with RPA at damage sites and is required for ATRIP recruitment, CHK1 activation, and RPA2 phosphorylation [PMID:16223718, PMID:24443570]. Genetic loss of PLRG1 blocks S-phase progression, drives p53-dependent apoptosis with elevated γ-H2AX, and abolishes nuclear retention of CDC5L [PMID:19307306]. PLRG1 also has a non-canonical transcriptional role, co-occupying the CCND1 promoter and superenhancer with DHX37 to activate cyclin D1 and promote proliferation [PMID:35290436].","teleology":[{"year":2001,"claim":"Established the direct molecular contact underlying PLRG1's splicing function by mapping a WD40-domain interaction with the CDC5L C-terminus and showing it is essential for splicing.","evidence":"In vitro binding, co-IP, domain mapping, and splicing inhibition in HeLa nuclear extract","pmids":["11544257"],"confidence":"High","gaps":["Does not define how this interaction nucleates the larger complex","No structural model of the bound interface at this stage"]},{"year":2003,"claim":"Confirmed the functional necessity of the CDC5L–PLRG1 interface for splicing using competitive peptides and a recombinant-protein rescue control.","evidence":"In vitro splicing assay with competing peptides and rescue","pmids":["14576297"],"confidence":"High","gaps":["Step in the splicing cycle blocked not defined","PLRG1 catalytic or scaffolding mechanism still unknown"]},{"year":2005,"claim":"Extended PLRG1 beyond splicing by placing the Pso4 complex in an early stage of DNA interstrand cross-link repair.","evidence":"Cell-free ICL processing assay with immunodepletion and co-IP","pmids":["16223718"],"confidence":"Medium","gaps":["PLRG1's individual contribution inferred from complex depletion, not isolated knockdown","Direct enzymatic role of PLRG1 in ICL processing unresolved"]},{"year":2007,"claim":"Showed DNA damage remodels the complex, as ubiquitylated oligomeric Prp19 loses interaction with both CDC5L and PLRG1.","evidence":"Non-reducing SDS-PAGE, co-IP, and chromatin fractionation after damage","pmids":["17276391"],"confidence":"Medium","gaps":["Single lab, single method set","Functional consequence of complex disassembly not directly tested"]},{"year":2009,"claim":"Defined PLRG1 as essential in vivo for S-phase progression, suppression of p53-dependent apoptosis, and nuclear retention of CDC5L.","evidence":"Conditional knockout mice, PLRG1-deficient MEFs, cell-cycle/apoptosis assays, p53 knockdown rescue in MEFs and zebrafish","pmids":["19307306"],"confidence":"High","gaps":["Whether the phenotype reflects splicing loss or a distinct activity not separated","Mechanism linking PLRG1 loss to p53 activation unresolved"]},{"year":2009,"claim":"Connected the PLRG1-containing complex to ATR-mediated checkpoint signaling through a CDC5L–ATR interaction.","evidence":"Co-IP, Cdc5L siRNA depletion, checkpoint kinase activation assays","pmids":["19633697"],"confidence":"Low","gaps":["PLRG1's role inferred from complex membership, not a direct PLRG1 experiment","PLRG1 not shown to contact ATR"]},{"year":2010,"claim":"Placed PLRG1 in alternative splicing regulation via hnRNP-M, which bridges CDC5L and PLRG1 to influence splice-site choice.","evidence":"In vivo co-IP, deletion mapping, adeno-E1A minigene alternative splicing assay","pmids":["20467437"],"confidence":"Medium","gaps":["Single lab","Direct PLRG1 contribution versus CDC5L not dissected"]},{"year":2014,"claim":"Resolved the checkpoint role by showing the PLRG1-containing Pso4 complex recruits ATRIP to damage sites and drives CHK1/RPA2 activation, with PLRG1 colocalizing with RPA.","evidence":"siRNA depletion, immunofluorescence colocalization, complex–RPA co-IP, in vitro ATR activation","pmids":["24443570"],"confidence":"Medium","gaps":["PLRG1's individual requirement partly inferred from complex-level depletion","Direct PLRG1–RPA contact not mapped"]},{"year":2018,"claim":"Established the activation mechanism: PLRG1 is required to relieve Prp19 autoinhibition and switch on its E3 ubiquitin ligase activity through stepwise complex assembly.","evidence":"Crystallography of Prp19, mutagenesis, stepwise NTC reconstitution, in vitro ubiquitin ligation, crosslinking-MS","pmids":["29547724"],"confidence":"High","gaps":["Physiological substrates of the activated ligase not enumerated here","How PLRG1 transmits the activating signal structurally only partially defined"]},{"year":2020,"claim":"Provided structural detail of the PLRG1 WD40 domain and showed conformational ordering of loops upon binding partners during spliceosome assembly.","evidence":"X-ray crystallography of apo WD40 domain, comparison with cryo-EM spliceosome structures","pmids":["33239170"],"confidence":"Medium","gaps":["Limited functional validation beyond structural observation","Full-length PLRG1 context not crystallized"]},{"year":2021,"claim":"Identified an upstream regulatory layer: USP42-mediated deubiquitylation controls phase-separation-dependent integration of PLRG1 into nuclear speckles and thereby splicing function.","evidence":"Immunofluorescence colocalization, USP42 knockdown, splicing assays, phase separation assays, fractionation","pmids":["33731873"],"confidence":"Medium","gaps":["Direct ubiquitylation sites on PLRG1 not mapped","Single lab"]},{"year":2022,"claim":"Revealed a non-canonical transcriptional function for PLRG1, co-occupying the CCND1 promoter and superenhancer with DHX37 to activate cyclin D1.","evidence":"Co-IP, ChIP-seq, ChIP at CCND1, proliferation assays in liver cancer cells","pmids":["35290436"],"confidence":"Medium","gaps":["How a splicing factor is recruited to chromatin not defined","Single lab"]},{"year":2023,"claim":"Distinguished tumor-specific from normal-cell responses to PLRG1 loss, with cancer cells undergoing mitotic catastrophe and apoptosis versus protective G1 arrest in normal cells.","evidence":"siRNA knockdown, cell-cycle FACS, microtubule/DNA-damage immunofluorescence, apoptosis assays","pmids":["37817442"],"confidence":"Medium","gaps":["Molecular basis of the tumor-versus-normal difference unresolved","Single lab"]},{"year":2024,"claim":"Placed PLRG1 downstream of YBX1 transcriptional control in promoting EMT in hepatocellular carcinoma.","evidence":"ChIP and luciferase at PLRG1 promoter, YBX1 overexpression, PLRG1 knockdown rescue, EMT marker and migration/invasion assays","pmids":["39400789"],"confidence":"Medium","gaps":["Mechanism by which PLRG1 drives EMT downstream not defined","Single lab"]},{"year":null,"claim":"How PLRG1 partitions between its canonical splicing/E3-activation role and its chromatin-associated transcriptional function, and what governs that switch, remains unresolved.","evidence":"No single study reconciles the spliceosomal and transcriptional activities","pmids":[],"confidence":"Medium","gaps":["No unified model linking splicing and transcriptional roles","Substrate spectrum of the PLRG1-activated Prp19 ligase incomplete","Chromatin recruitment mechanism unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[8]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0,1]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[8]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[9]}],"localization":[{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[10]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[4,10]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[7]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1,8]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[2,7]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[4,5]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[11]}],"complexes":["Prp19/Pso4 complex (NineTeen Complex, NTC)","spliceosome"],"partners":["CDC5L","PRPF19","SPF27","HNRNP-M","USP42","DHX37","RPA1","YBX1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O43660","full_name":"Pleiotropic regulator 1","aliases":[],"length_aa":514,"mass_kda":57.2,"function":"Involved in pre-mRNA splicing as component of the spliceosome (PubMed:28076346, PubMed:28502770). Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing (PubMed:11101529, PubMed:11544257). As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs (Probable)","subcellular_location":"Nucleus; Nucleus speckle","url":"https://www.uniprot.org/uniprotkb/O43660/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/PLRG1","classification":"Common Essential","n_dependent_lines":1179,"n_total_lines":1208,"dependency_fraction":0.9759933774834437},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CTNNBL1","stoichiometry":10.0},{"gene":"PRPF19","stoichiometry":4.0},{"gene":"PRPF4B","stoichiometry":4.0},{"gene":"TOP1","stoichiometry":4.0},{"gene":"CPSF6","stoichiometry":0.2},{"gene":"RBM39","stoichiometry":0.2},{"gene":"RBM6","stoichiometry":0.2},{"gene":"RNF40","stoichiometry":0.2},{"gene":"SF3A1","stoichiometry":0.2},{"gene":"SF3A2","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/PLRG1","total_profiled":1310},"omim":[{"mim_id":"605961","title":"PLEIOTROPIC REGULATOR 1; PLRG1","url":"https://www.omim.org/entry/605961"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nuclear speckles","reliability":"Supported"},{"location":"Nuclear membrane","reliability":"Additional"},{"location":"Nucleoli fibrillar center","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PLRG1"},"hgnc":{"alias_symbol":["PRL1","Prp46","PRPF46","Cwc1","TANGO4"],"prev_symbol":[]},"alphafold":{"accession":"O43660","domains":[{"cath_id":"2.40.10,2.40.128","chopping":"287-370","consensus_level":"medium","plddt":96.123,"start":287,"end":370}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O43660","model_url":"https://alphafold.ebi.ac.uk/files/AF-O43660-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O43660-F1-predicted_aligned_error_v6.png","plddt_mean":77.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PLRG1","jax_strain_url":"https://www.jax.org/strain/search?query=PLRG1"},"sequence":{"accession":"O43660","fasta_url":"https://rest.uniprot.org/uniprotkb/O43660.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O43660/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O43660"}},"corpus_meta":[{"pmid":"16223718","id":"PMC_16223718","title":"The Pso4 mRNA splicing and DNA repair complex interacts with WRN for processing of DNA interstrand cross-links.","date":"2005","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16223718","citation_count":112,"is_preprint":false},{"pmid":"19633697","id":"PMC_19633697","title":"Cdc5L interacts with ATR and is required for the S-phase cell-cycle checkpoint.","date":"2009","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/19633697","citation_count":83,"is_preprint":false},{"pmid":"20467437","id":"PMC_20467437","title":"Direct interaction between hnRNP-M and CDC5L/PLRG1 proteins affects alternative splice site choice.","date":"2010","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/20467437","citation_count":59,"is_preprint":false},{"pmid":"17276391","id":"PMC_17276391","title":"The Prp19/Pso4 core complex undergoes ubiquitylation and structural alterations in response to DNA damage.","date":"2007","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/17276391","citation_count":58,"is_preprint":false},{"pmid":"33731873","id":"PMC_33731873","title":"USP42 drives nuclear speckle mRNA splicing via directing dynamic phase separation to promote tumorigenesis.","date":"2021","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/33731873","citation_count":57,"is_preprint":false},{"pmid":"19307306","id":"PMC_19307306","title":"PLRG1 is an essential regulator of cell proliferation and apoptosis during vertebrate development and tissue homeostasis.","date":"2009","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/19307306","citation_count":51,"is_preprint":false},{"pmid":"24443570","id":"PMC_24443570","title":"The PSO4 protein complex associates with replication protein A (RPA) and modulates the activation of ataxia telangiectasia-mutated and Rad3-related (ATR).","date":"2014","source":"The Journal of biological 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reports","url":"https://pubmed.ncbi.nlm.nih.gov/41631214","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":14539,"output_tokens":3996,"usd":0.051778,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11746,"output_tokens":4304,"usd":0.083165,"stage2_stop_reason":"end_turn"},"total_usd":0.134943,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2001,\n      \"finding\": \"The WD40 domain of PLRG1 directly interacts with the carboxyl-terminal region of CDC5L in vitro and in vivo. A bacterially expressed CDC5L fragment containing the PLRG1-interaction domain disrupts the CDC5L-PLRG1 interaction in HeLa nuclear extract and inhibits pre-mRNA splicing, demonstrating that this direct interaction is essential for pre-mRNA splicing progression.\",\n      \"method\": \"In vitro binding assay, co-immunoprecipitation, domain mapping by mutagenesis, in vitro splicing inhibition assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct interaction reconstituted in vitro with domain mapping and mutagenesis, functional consequence (splicing inhibition) demonstrated; replicated by independent peptide inhibitor study (PMID:14576297)\",\n      \"pmids\": [\"11544257\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Peptides derived from the WD40-containing interaction domain of PLRG1 and the C-terminal domain of CDC5L inhibit pre-mRNA splicing in vitro; this inhibition is rescued by pre-incubating the peptides with the corresponding partner protein, confirming that the CDC5L–PLRG1 interaction is essential for the splicing mechanism.\",\n      \"method\": \"In vitro splicing assay with competing peptides, rescue by recombinant protein pre-incubation\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro functional assay with competitive peptides and rescue control, orthogonally confirming the earlier interaction study\",\n      \"pmids\": [\"14576297\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"PLRG1 is a core component of the Pso4/Prp19–Cdc5L–Plrg1–Spf27 complex (Pso4 complex) that is required for processing of psoralen DNA interstrand cross-links (ICLs) in a cell-free biochemical assay; the complex participates in an early stage of ICL repair alongside MutSβ, Ercc1-Xpf, RPA, and PCNA.\",\n      \"method\": \"Cell-free ICL processing assay, immunodepletion, co-immunoprecipitation showing Pso4 complex–WRN association\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cell-free biochemical assay with immunodepletion; PLRG1's individual contribution inferred from complex depletion, not individual KD\",\n      \"pmids\": [\"16223718\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"The hPrp19 core complex normally includes Cdc5L, Plrg1, and Spf27; upon DNA damage, hPrp19 forms a ubiquitylated oligomeric species that fails to interact with either Cdc5L or Plrg1, indicating that DNA damage induces structural alterations that disrupt the PLRG1-containing core complex.\",\n      \"method\": \"SDS-PAGE under non-reducing conditions, co-immunoprecipitation, chromatin fractionation after DNA damage treatment\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — reciprocal co-IP showing loss of PLRG1 interaction with ubiquitylated Prp19; single lab, single method set\",\n      \"pmids\": [\"17276391\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"PLRG1 is required for S-phase progression and suppression of apoptosis in vivo. PLRG1-deficient MEFs fail to progress through S phase and show increased apoptosis that is p53-dependent; PLRG1 deficiency causes enhanced p53 phosphorylation/stabilization and increased γ-H2AX, indicating an activated DNA damage response. PLRG1 is also required for nuclear retention of its binding partner CDC5L.\",\n      \"method\": \"Conditional knockout mice (heart- and neuron-specific), PLRG1-deficient MEFs, BrdU/FACS cell-cycle analysis, immunofluorescence for γ-H2AX, p53 knockdown rescue in MEFs and zebrafish, subcellular fractionation for CDC5L localization\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic KO with multiple orthogonal readouts (cell-cycle, apoptosis, DNA damage markers, localization), in vivo rescue experiment in zebrafish, replicated across mouse and fish models\",\n      \"pmids\": [\"19307306\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"PLRG1 is a core component of the Prp19/Pso4–Cdc5L–Plrg1–Spf27 complex; Cdc5L within this complex interacts physically with ATR kinase and is required for ATR-mediated S-phase checkpoint signaling (Chk1, Rad17, FancD2 activation). PLRG1's role is inferred through its membership in the Cdc5L complex that mediates this checkpoint.\",\n      \"method\": \"Co-immunoprecipitation (Cdc5L–ATR), siRNA depletion of Cdc5L, checkpoint kinase activation assays, deletion mapping of ATR-binding region in Cdc5L\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — PLRG1's mechanistic role is indirect; the paper focuses on Cdc5L–ATR interaction; PLRG1 contribution inferred from complex membership, not direct experiment on PLRG1\",\n      \"pmids\": [\"19633697\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"PLRG1 directly interacts with CDC5L in vivo; a central region of hnRNP-M mediates direct interaction with both CDC5L and PLRG1. This interaction is inhibited during heat-shock stress. An hnRNP-M mutant lacking the CDC5L/PLRG1 interaction domain cannot modulate alternative 5′ and 3′ splice site choice, placing PLRG1 in the pathway of alternative splicing regulation via hnRNP-M.\",\n      \"method\": \"Co-immunoprecipitation in vivo, domain mapping by deletion mutants, adeno-E1A minigene alternative splicing assay\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP and functional splicing assay with deletion mutant; single lab, two orthogonal methods\",\n      \"pmids\": [\"20467437\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"PLRG1 (as part of the PSO4 core complex) is required for efficient recruitment of ATRIP to DNA damage sites and subsequent CHK1 activation and RPA2 phosphorylation; PLRG1 colocalizes with RPA at damage sites. Both the RPA1-binding ability of BCAS2 and the E3 ligase activity of PSO4 within the PLRG1-containing complex are required for these functions.\",\n      \"method\": \"siRNA depletion of complex subunits, immunofluorescence colocalization, co-immunoprecipitation of PLRG1-complex with RPA, in vitro ATR activation assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — depletion plus colocalization and functional ATR-pathway assays; PLRG1's individual contribution partially inferred from complex-level experiments\",\n      \"pmids\": [\"24443570\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PLRG1 is essential for activation of the Prp19 (NTC) E3 ubiquitin ligase. Prp19 is autoinhibited on its own; stepwise assembly of SPF27, CDC5L, and PLRG1 onto the Prp19 tetramer enables ubiquitin ligation activity. Cross-linking/MS and functional assays defined the communication between PLRG1 and Prp19 that enables E3 activity, and crystal structure revealed the autoinhibition mechanism.\",\n      \"method\": \"X-ray crystallography of Prp19, mutational analysis of autoinhibition, stepwise reconstitution of NTC core, in vitro ubiquitin ligation assay, protein-protein crosslinking coupled to mass spectrometry\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus in vitro reconstitution, mutagenesis, and functional ubiquitin ligation assay; multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"29547724\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The crystal structure of the WD40 domain of human PLRG1 was solved by X-ray crystallography. Comparison with cryo-EM structures of PLRG1 within the spliceosome showed that two loops of the WD40 domain become resolved upon binding to other splicing factors, revealing dynamic conformational changes during spliceosome assembly.\",\n      \"method\": \"X-ray crystallography (apo WD40 domain), comparison with cryo-EM spliceosome structures\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — crystal structure of isolated domain with structural comparison; single lab, limited functional validation beyond structural observation\",\n      \"pmids\": [\"33239170\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"USP42 (a deubiquitylase) directs the integration of PLRG1 into nuclear speckles (SC35-positive) in a phase-separation-dependent manner; depletion of USP42 displaces PLRG1 from nuclear speckles and deregulates mRNA splicing events phenocopying PLRG1 repression, placing USP42-mediated deubiquitylation upstream of PLRG1 nuclear speckle localization and splicing function.\",\n      \"method\": \"Immunofluorescence colocalization, USP42 siRNA knockdown, mRNA splicing assays, phase separation assays, subcellular fractionation\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment with functional consequence (splicing deregulation), two orthogonal methods; single lab\",\n      \"pmids\": [\"33731873\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DHX37 interacts with PLRG1 and together they co-occupy the promoter and superenhancer elements of cyclin D1 (CCND1) to transcriptionally activate CCND1 expression, promoting liver cancer cell proliferation. This reveals a non-canonical transcriptional/epigenomic function for PLRG1 beyond splicing.\",\n      \"method\": \"Co-immunoprecipitation (DHX37–PLRG1), ChIP-seq epigenomic profiling of DHX37-knockdown cells, ChIP showing co-occupancy at CCND1 promoter/superenhancer, siRNA knockdown proliferation assays\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP plus ChIP-seq with functional proliferation assay; single lab, two orthogonal methods\",\n      \"pmids\": [\"35290436\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PLRG1 knockdown in cancer cells (but not normal cells) causes mitotic arrest, microtubule instability, ER stress, autophagy accumulation, DNA damage, and ultimately apoptosis; in normal cells PLRG1 depletion induces G1 arrest as a self-protective mechanism, distinguishing tumor-specific from normal cell responses to PLRG1 loss.\",\n      \"method\": \"siRNA knockdown, cell-cycle FACS analysis, immunofluorescence for microtubule stability and DNA damage markers (γ-H2AX), apoptosis assays\",\n      \"journal\": \"BMB reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KD with multiple defined cellular phenotype readouts; single lab\",\n      \"pmids\": [\"37817442\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"YBX1 directly binds to the PLRG1 promoter and transcriptionally activates PLRG1 expression; overexpression of YBX1 upregulates PLRG1 and promotes EMT (increased N-cadherin, Snail, migration, invasion) in HCC cells, and these effects are abolished by PLRG1 knockdown, placing PLRG1 downstream of YBX1 in the EMT pathway.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP) of YBX1 at PLRG1 promoter, luciferase reporter assay, siRNA knockdown of PLRG1, YBX1 overexpression, EMT marker immunoblotting, migration/invasion assays\",\n      \"journal\": \"Medical oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP plus luciferase assay for direct transcriptional regulation, epistasis via KD rescue; single lab\",\n      \"pmids\": [\"39400789\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PLRG1 is an evolutionarily conserved WD40-domain protein that functions as an essential structural and regulatory subunit of the NineTeen Complex (NTC/Pso4 complex), where its stepwise assembly with Prp19, SPF27, and CDC5L is required to relieve Prp19 autoinhibition and activate its E3 ubiquitin ligase activity; through its direct interaction with CDC5L (mediated by the PLRG1 WD40 domain and the CDC5L C-terminus), it is essential for pre-mRNA splicing, and the complex additionally participates in DNA interstrand cross-link repair, ATR-mediated DNA damage checkpoint signaling (via RPA binding and ATRIP recruitment), and nuclear speckle phase-separation-dependent splicing regulated by USP42-mediated deubiquitylation; PLRG1 is also required for nuclear retention of CDC5L, p53-dependent cell-cycle progression, and has a non-canonical role in transcriptional activation of cyclin D1 via cooperation with DHX37 at superenhancer elements.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PLRG1 is a conserved WD40-domain protein that functions as an essential structural and regulatory subunit of the Prp19/Pso4 (NineTeen) complex, coupling pre-mRNA splicing to genome maintenance [#0, #8]. Within this complex, PLRG1 directly binds the C-terminus of CDC5L via its WD40 domain, and this interaction is required for pre-mRNA splicing progression: peptides disrupting the CDC5L–PLRG1 interface inhibit in vitro splicing, an effect rescued by the partner protein [#0, #1]. Stepwise assembly of SPF27, CDC5L, and PLRG1 onto the autoinhibited Prp19 tetramer relieves autoinhibition and activates Prp19 E3 ubiquitin ligase activity, with PLRG1's WD40 surface communicating with Prp19 to enable ligation [#8]; two WD40 loops become ordered upon engagement of other splicing factors during spliceosome assembly [#9]. PLRG1 is integrated into SC35-positive nuclear speckles in a phase-separation-dependent manner under control of USP42-mediated deubiquitylation, linking its localization to splicing fidelity [#10]. Beyond splicing, the PLRG1-containing Pso4 complex acts in DNA interstrand cross-link repair and in ATR-mediated S-phase checkpoint signaling, where it colocalizes with RPA at damage sites and is required for ATRIP recruitment, CHK1 activation, and RPA2 phosphorylation [#2, #7]. Genetic loss of PLRG1 blocks S-phase progression, drives p53-dependent apoptosis with elevated γ-H2AX, and abolishes nuclear retention of CDC5L [#4]. PLRG1 also has a non-canonical transcriptional role, co-occupying the CCND1 promoter and superenhancer with DHX37 to activate cyclin D1 and promote proliferation [#11].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Established the direct molecular contact underlying PLRG1's splicing function by mapping a WD40-domain interaction with the CDC5L C-terminus and showing it is essential for splicing.\",\n      \"evidence\": \"In vitro binding, co-IP, domain mapping, and splicing inhibition in HeLa nuclear extract\",\n      \"pmids\": [\"11544257\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define how this interaction nucleates the larger complex\", \"No structural model of the bound interface at this stage\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Confirmed the functional necessity of the CDC5L–PLRG1 interface for splicing using competitive peptides and a recombinant-protein rescue control.\",\n      \"evidence\": \"In vitro splicing assay with competing peptides and rescue\",\n      \"pmids\": [\"14576297\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Step in the splicing cycle blocked not defined\", \"PLRG1 catalytic or scaffolding mechanism still unknown\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Extended PLRG1 beyond splicing by placing the Pso4 complex in an early stage of DNA interstrand cross-link repair.\",\n      \"evidence\": \"Cell-free ICL processing assay with immunodepletion and co-IP\",\n      \"pmids\": [\"16223718\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"PLRG1's individual contribution inferred from complex depletion, not isolated knockdown\", \"Direct enzymatic role of PLRG1 in ICL processing unresolved\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Showed DNA damage remodels the complex, as ubiquitylated oligomeric Prp19 loses interaction with both CDC5L and PLRG1.\",\n      \"evidence\": \"Non-reducing SDS-PAGE, co-IP, and chromatin fractionation after damage\",\n      \"pmids\": [\"17276391\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab, single method set\", \"Functional consequence of complex disassembly not directly tested\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Defined PLRG1 as essential in vivo for S-phase progression, suppression of p53-dependent apoptosis, and nuclear retention of CDC5L.\",\n      \"evidence\": \"Conditional knockout mice, PLRG1-deficient MEFs, cell-cycle/apoptosis assays, p53 knockdown rescue in MEFs and zebrafish\",\n      \"pmids\": [\"19307306\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the phenotype reflects splicing loss or a distinct activity not separated\", \"Mechanism linking PLRG1 loss to p53 activation unresolved\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Connected the PLRG1-containing complex to ATR-mediated checkpoint signaling through a CDC5L–ATR interaction.\",\n      \"evidence\": \"Co-IP, Cdc5L siRNA depletion, checkpoint kinase activation assays\",\n      \"pmids\": [\"19633697\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"PLRG1's role inferred from complex membership, not a direct PLRG1 experiment\", \"PLRG1 not shown to contact ATR\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Placed PLRG1 in alternative splicing regulation via hnRNP-M, which bridges CDC5L and PLRG1 to influence splice-site choice.\",\n      \"evidence\": \"In vivo co-IP, deletion mapping, adeno-E1A minigene alternative splicing assay\",\n      \"pmids\": [\"20467437\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Direct PLRG1 contribution versus CDC5L not dissected\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Resolved the checkpoint role by showing the PLRG1-containing Pso4 complex recruits ATRIP to damage sites and drives CHK1/RPA2 activation, with PLRG1 colocalizing with RPA.\",\n      \"evidence\": \"siRNA depletion, immunofluorescence colocalization, complex–RPA co-IP, in vitro ATR activation\",\n      \"pmids\": [\"24443570\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"PLRG1's individual requirement partly inferred from complex-level depletion\", \"Direct PLRG1–RPA contact not mapped\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Established the activation mechanism: PLRG1 is required to relieve Prp19 autoinhibition and switch on its E3 ubiquitin ligase activity through stepwise complex assembly.\",\n      \"evidence\": \"Crystallography of Prp19, mutagenesis, stepwise NTC reconstitution, in vitro ubiquitin ligation, crosslinking-MS\",\n      \"pmids\": [\"29547724\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological substrates of the activated ligase not enumerated here\", \"How PLRG1 transmits the activating signal structurally only partially defined\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Provided structural detail of the PLRG1 WD40 domain and showed conformational ordering of loops upon binding partners during spliceosome assembly.\",\n      \"evidence\": \"X-ray crystallography of apo WD40 domain, comparison with cryo-EM spliceosome structures\",\n      \"pmids\": [\"33239170\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Limited functional validation beyond structural observation\", \"Full-length PLRG1 context not crystallized\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identified an upstream regulatory layer: USP42-mediated deubiquitylation controls phase-separation-dependent integration of PLRG1 into nuclear speckles and thereby splicing function.\",\n      \"evidence\": \"Immunofluorescence colocalization, USP42 knockdown, splicing assays, phase separation assays, fractionation\",\n      \"pmids\": [\"33731873\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct ubiquitylation sites on PLRG1 not mapped\", \"Single lab\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Revealed a non-canonical transcriptional function for PLRG1, co-occupying the CCND1 promoter and superenhancer with DHX37 to activate cyclin D1.\",\n      \"evidence\": \"Co-IP, ChIP-seq, ChIP at CCND1, proliferation assays in liver cancer cells\",\n      \"pmids\": [\"35290436\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How a splicing factor is recruited to chromatin not defined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Distinguished tumor-specific from normal-cell responses to PLRG1 loss, with cancer cells undergoing mitotic catastrophe and apoptosis versus protective G1 arrest in normal cells.\",\n      \"evidence\": \"siRNA knockdown, cell-cycle FACS, microtubule/DNA-damage immunofluorescence, apoptosis assays\",\n      \"pmids\": [\"37817442\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular basis of the tumor-versus-normal difference unresolved\", \"Single lab\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Placed PLRG1 downstream of YBX1 transcriptional control in promoting EMT in hepatocellular carcinoma.\",\n      \"evidence\": \"ChIP and luciferase at PLRG1 promoter, YBX1 overexpression, PLRG1 knockdown rescue, EMT marker and migration/invasion assays\",\n      \"pmids\": [\"39400789\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which PLRG1 drives EMT downstream not defined\", \"Single lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PLRG1 partitions between its canonical splicing/E3-activation role and its chromatin-associated transcriptional function, and what governs that switch, remains unresolved.\",\n      \"evidence\": \"No single study reconciles the spliceosomal and transcriptional activities\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model linking splicing and transcriptional roles\", \"Substrate spectrum of the PLRG1-activated Prp19 ligase incomplete\", \"Chromatin recruitment mechanism unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [10]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [4, 10]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1, 8]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [2, 7]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [4, 5]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [11]}\n    ],\n    \"complexes\": [\n      \"Prp19/Pso4 complex (NineTeen Complex, NTC)\",\n      \"spliceosome\"\n    ],\n    \"partners\": [\n      \"CDC5L\",\n      \"PRPF19\",\n      \"SPF27\",\n      \"hnRNP-M\",\n      \"USP42\",\n      \"DHX37\",\n      \"RPA1\",\n      \"YBX1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}