{"gene":"TCF25","run_date":"2026-04-28T21:42:58","timeline":{"discoveries":[{"year":2018,"finding":"TCF25 is a component of the ribosome-associated quality control (RQC) pathway and ensures preferential formation of K48-ubiquitin linkage on nascent chains ubiquitinated by Listerin on stalled 60S ribosomal complexes.","method":"In vitro reconstitution of RQC pathway with mammalian components; ubiquitin linkage analysis","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution with defined components, replicated and extended by subsequent studies","pmids":["30244831"],"is_preprint":false},{"year":2025,"finding":"TCF25 imposes K48 ubiquitin-linkage specificity on Listerin-mediated ubiquitination by directly interacting with both the RING domain of Listerin and the acceptor ubiquitin (UbA), orienting UbA so that its K48 is positioned to attack the thioester bond of the Ube2D1~Ub conjugate. TCF25 itself is also subject to K48-specific ubiquitination by Listerin, leading to its proteasomal degradation in vivo.","method":"Functional biochemical reconstitution, AlphaFold3 structural modeling, site-directed mutagenesis, ubiquitin linkage assays","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution with mutagenesis plus structural modeling, mechanistic detail rigorously established","pmids":["40169231"],"is_preprint":false},{"year":2024,"finding":"TCF25 (preprint version of the same study as PMID 40169231): TCF25 specifically interacts with the RING domain of Listerin and acceptor ubiquitin to impose K48-linkage specificity; TCF25 itself undergoes K48-specific ubiquitination by Listerin and is degraded by the proteasome.","method":"Functional biochemical reconstitution, AlphaFold3 modeling, ubiquitin linkage assays","journal":"bioRxiv","confidence":"High","confidence_rationale":"Tier 1 — same data as peer-reviewed version; preprint precedes publication","pmids":["39464025"],"is_preprint":true},{"year":2024,"finding":"TCF25 protein levels are substantially lower than its mRNA levels in mammalian cells due to post-translational degradation by the proteasome, confirming that TCF25 itself is a proteasome substrate in vivo.","method":"Proteasome inhibitor treatment, immunoblot, comparison of mRNA and protein levels across cell lines","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — direct pharmacological inhibition experiment with clear functional readout, single lab","pmids":["38228636"],"is_preprint":false},{"year":2006,"finding":"Human NULP1 (TCF25) contains a bHLH domain and a C-terminal DUF654 domain; it functions as a transcriptional repressor, with the DUF654 motif mediating basal repressive activity via histone deacetylase activity. Overexpression of NULP1 inhibits the transcriptional activity of serum response factor (SRF).","method":"GAL4-fusion transcriptional reporter assays, co-transfection with VP-16, trichostatin A treatment, SRF reporter assay in COS-7 cells","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — multiple reporter assays with pharmacological validation, single lab","pmids":["16574069"],"is_preprint":false},{"year":2002,"finding":"Mouse Nulp1 (ortholog of TCF25) localizes to the nucleus when expressed as an EGFP fusion in human embryonic kidney cells, consistent with its function as a transcription factor.","method":"Transfection of Nulp1-EGFP fusion into HEK cells, fluorescence microscopy","journal":"Cell and tissue research","confidence":"Medium","confidence_rationale":"Tier 3 — direct localization experiment, single lab, foundational characterization","pmids":["12107429"],"is_preprint":false},{"year":2007,"finding":"NULP1 (TCF25) localizes predominantly to the cell nucleus, induces cell death with DNA fragmentation upon overexpression in human osteosarcoma Saos2 cells, and physically binds XIAP (X-linked inhibitor of apoptosis protein); this interaction is enhanced during cell death.","method":"Immunostaining with novel antibody, overexpression assays, co-immunoprecipitation with XIAP","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 — Co-IP plus localization and functional overexpression, single lab","pmids":["18068114"],"is_preprint":false},{"year":2020,"finding":"NULP1 (TCF25) directly interacts with the topologically associating domain (TAD) of NFAT3 via its C-terminal region, suppressing NFAT3 transcriptional activity; Nulp1 knockout exacerbates aortic banding-induced cardiac hypertrophy, and NFAT pathway inactivation rescues this phenotype in vivo.","method":"Co-immunoprecipitation, domain mapping, Nulp1 knockout and transgenic mouse models, aortic banding surgery, VIVIT peptide treatment, NFAT reporter assays","journal":"Journal of the American Heart Association","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP with domain mapping, KO and transgenic rescue in vivo, epistasis via VIVIT peptide, multiple orthogonal methods","pmids":["32805187"],"is_preprint":false},{"year":2018,"finding":"Drosophila Nulp1 (dNulp1, ortholog of TCF25) is required for femur development and survival; dNulp1 mutants generated by CRISPR/Cas9 targeting the DUF654 domain show bent femurs, and dNulp1 acts as a positive cofactor in the Wnt/Wingless signaling pathway, activating Wg target genes and the TopFlash reporter.","method":"CRISPR/Cas9 knockout, overexpression rescue, qRT-PCR of Wg target genes, TopFlash luciferase reporter assay in Drosophila","journal":"Current molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 — genetic KO with rescue, reporter assay, epistasis with sgg/GSK3β; Drosophila ortholog","pmids":["29437009"],"is_preprint":false},{"year":2025,"finding":"TCF25 acts as a nutrient sensor that enhances lysosomal acidification by targeting V-ATPase, promoting autophagy and ATP generation under glucose starvation. Prolonged glucose starvation leads TCF25 to constitutively activate ferritinophagy, increasing lysosomal membrane permeability and causing lysosome-dependent cell death (LDCD). TCF25 or V-ATPase KO prevents this cell death, and TCF25 deficiency protects mice from hepatic ischemia-reperfusion injury.","method":"Genome-wide CRISPR-Cas9 screen, TCF25 knockout in cell lines and mice, lysosomal acidification assays, V-ATPase interaction studies, autophagy flux assays, hepatic ischemia-reperfusion injury mouse model","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 — genome-wide screen followed by mechanistic KO studies in vitro and in vivo with multiple orthogonal readouts","pmids":["40844875"],"is_preprint":false}],"current_model":"TCF25 (also known as NULP1) is a multifunctional nuclear protein: in the ribosome-associated quality control (RQC) pathway, it imposes K48-specific ubiquitin-linkage on stalled nascent chains by binding the RING domain of the E3 ligase Listerin and the acceptor ubiquitin to orient K48 for attack on the E2~Ub thioester, while also serving as a Listerin substrate itself; independently, it acts as a transcriptional repressor (via its DUF654/bHLH domains) that suppresses SRF and NFAT3 signaling and interacts with XIAP to modulate apoptosis; and it functions as a lysosomal nutrient sensor that targets V-ATPase to regulate lysosomal acidification, autophagy, and glucose-starvation-induced lysosome-dependent cell death."},"narrative":{"teleology":[{"year":2002,"claim":"Establishing TCF25 as a nuclear protein resolved its likely compartment of action and was consistent with a transcriptional role for this uncharacterized bHLH-containing factor.","evidence":"EGFP-fusion of mouse Nulp1 expressed in HEK cells, fluorescence microscopy","pmids":["12107429"],"confidence":"Medium","gaps":["Overexpression of fusion protein; endogenous localization not confirmed","No functional assay beyond localization"]},{"year":2006,"claim":"Demonstrating that the DUF654 domain mediates transcriptional repression through HDAC activity and that TCF25 inhibits SRF signaling established its first mechanistic role as a transcriptional repressor.","evidence":"GAL4-fusion reporter assays, trichostatin A derepression, SRF reporter co-transfection in COS-7 cells","pmids":["16574069"],"confidence":"Medium","gaps":["No direct HDAC binding or recruitment shown","Endogenous target genes not identified","Reporter-based assays only"]},{"year":2007,"claim":"Identifying a physical interaction between TCF25 and the anti-apoptotic protein XIAP, enhanced during cell death, linked TCF25 to apoptotic regulation beyond transcription.","evidence":"Co-immunoprecipitation, immunostaining, overexpression-induced DNA fragmentation in Saos2 cells","pmids":["18068114"],"confidence":"Medium","gaps":["Single co-IP direction reported; no reciprocal validation described","Mechanism by which XIAP binding modulates cell death not determined","Overexpression artifacts not excluded"]},{"year":2018,"claim":"Reconstitution of the mammalian RQC pathway revealed a completely unexpected role for TCF25 as the factor that ensures K48-linkage specificity on nascent chains ubiquitinated by Listerin on stalled 60S complexes, establishing TCF25 as a core RQC component.","evidence":"In vitro reconstitution with purified mammalian RQC components, ubiquitin linkage analysis","pmids":["30244831"],"confidence":"High","gaps":["Structural basis for K48 specificity not resolved","In vivo relevance in mammalian cells not directly tested"]},{"year":2018,"claim":"Drosophila genetic studies showed that the TCF25 ortholog dNulp1 is required for limb development and acts as a Wnt/Wingless pathway cofactor, extending TCF25 function to developmental signaling.","evidence":"CRISPR/Cas9 knockout, overexpression rescue, qRT-PCR of Wg targets, TopFlash reporter in Drosophila","pmids":["29437009"],"confidence":"Medium","gaps":["Conservation of Wnt cofactor role in mammals not tested","Direct binding partner in Wnt pathway not identified","Mechanism of transcriptional activation versus known repressor activity unresolved"]},{"year":2020,"claim":"Mapping the direct TCF25–NFAT3 interaction to the NFAT3 transactivation domain and demonstrating that Nulp1 knockout worsens cardiac hypertrophy (rescued by NFAT inhibition) established TCF25 as a physiologically relevant negative regulator of NFAT signaling in the heart.","evidence":"Reciprocal co-IP, domain mapping, Nulp1 KO and transgenic mice, aortic banding, VIVIT peptide rescue, NFAT reporter assays","pmids":["32805187"],"confidence":"High","gaps":["Whether TCF25 represses NFAT3 through HDAC recruitment or a distinct mechanism not resolved","Cardiac-specific versus systemic functions not dissected"]},{"year":2024,"claim":"Confirming that endogenous TCF25 protein is maintained at low levels by proteasomal degradation validated the in vitro finding that TCF25 is itself a ubiquitin-proteasome substrate.","evidence":"Proteasome inhibitor treatment, immunoblotting, mRNA-protein level comparison across cell lines","pmids":["38228636"],"confidence":"Medium","gaps":["Which E3 ligase(s) mediate endogenous TCF25 turnover not fully established in vivo","Functional consequence of TCF25 stabilization not tested"]},{"year":2025,"claim":"Structural and biochemical dissection revealed the precise mechanism by which TCF25 enforces K48 specificity: it simultaneously contacts the Listerin RING domain and the acceptor ubiquitin to position K48 for thioester attack, and TCF25 itself undergoes the same K48-specific modification by Listerin.","evidence":"In vitro reconstitution, AlphaFold3 structural modeling, site-directed mutagenesis, ubiquitin linkage assays","pmids":["40169231"],"confidence":"High","gaps":["No experimentally determined high-resolution structure yet","Relative contributions of TCF25 auto-ubiquitination versus substrate ubiquitination to RQC flux unknown"]},{"year":2025,"claim":"A genome-wide CRISPR screen uncovered TCF25 as a lysosomal nutrient sensor that targets V-ATPase to control lysosomal acidification, autophagy, and glucose-starvation-induced lysosome-dependent cell death, with in vivo validation in hepatic ischemia-reperfusion injury.","evidence":"Genome-wide CRISPR-Cas9 screen, TCF25 KO in cell lines and mice, lysosomal acidification assays, V-ATPase interaction studies, autophagy flux, hepatic I/R model","pmids":["40844875"],"confidence":"High","gaps":["How TCF25 senses glucose versus other nutrient signals not defined","Molecular interface between TCF25 and V-ATPase subunits not mapped","Relationship between lysosomal and RQC functions of TCF25 unexplored"]},{"year":null,"claim":"It remains unknown how the three major functions of TCF25 — RQC ubiquitin-linkage specification, transcriptional repression, and lysosomal nutrient sensing — are coordinated in cells, and whether distinct pools or post-translational modifications partition TCF25 among these pathways.","evidence":"","pmids":[],"confidence":"Low","gaps":["No integrative study connecting RQC, transcriptional, and lysosomal roles","No high-resolution experimental structure of TCF25 in any complex","Tissue-specific and developmental functions in mammals remain largely uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[4,7]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[5,6]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[9]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,3]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[4,7]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[9]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[6,9]}],"complexes":["Listerin-RQC complex"],"partners":["LTN1","XIAP","NFAT3","UBE2D1","ATP6V1A"],"other_free_text":[]},"mechanistic_narrative":"TCF25 (NULP1) is a multifunctional protein that operates in ribosome-associated quality control (RQC), transcriptional regulation, and lysosomal nutrient sensing. In the RQC pathway, TCF25 imposes K48-ubiquitin linkage specificity on nascent chains ubiquitinated by the E3 ligase Listerin by directly binding the Listerin RING domain and the acceptor ubiquitin to orient K48 for nucleophilic attack on the E2~Ub thioester; TCF25 itself is a K48-ubiquitinated Listerin substrate subject to proteasomal degradation [PMID:30244831, PMID:40169231, PMID:38228636]. As a nuclear bHLH/DUF654-containing transcriptional repressor, TCF25 suppresses SRF transcriptional activity through HDAC-dependent mechanisms and inhibits NFAT3 signaling via direct interaction with the NFAT3 transactivation domain, with Nulp1 knockout exacerbating pressure-overload cardiac hypertrophy in mice [PMID:16574069, PMID:32805187]. TCF25 also functions as a lysosomal nutrient sensor that targets V-ATPase to enhance lysosomal acidification and autophagy under glucose starvation, and its sustained activation drives ferritinophagy and lysosome-dependent cell death, with TCF25 deficiency protecting against hepatic ischemia-reperfusion injury in vivo [PMID:40844875]."},"prefetch_data":{"uniprot":{"accession":"Q9BQ70","full_name":"Ribosome quality control complex subunit TCF25","aliases":["Nuclear localized protein 1","Transcription factor 25","TCF-25"],"length_aa":676,"mass_kda":76.7,"function":"Component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation (PubMed:30244831). In the RQC complex, required to promote formation of 'Lys-48'-linked polyubiquitin chains during ubiquitination of incompletely synthesized proteins by LTN1 (PubMed:30244831). May negatively regulate the calcineurin-NFAT signaling cascade by suppressing the activity of transcription factor NFATC4 (By similarity). May play a role in cell death control (By similarity)","subcellular_location":"Nucleus; Cytoplasm, cytosol","url":"https://www.uniprot.org/uniprotkb/Q9BQ70/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TCF25","classification":"Not Classified","n_dependent_lines":31,"n_total_lines":1208,"dependency_fraction":0.02566225165562914},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000141002","cell_line_id":"CID001826","localizations":[{"compartment":"cytoplasmic","grade":3}],"interactors":[{"gene":"GPRASP2","stoichiometry":10.0},{"gene":"RBM14","stoichiometry":0.2},{"gene":"USP9X","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001826","total_profiled":1310},"omim":[{"mim_id":"621047","title":"PEPTIDYL-tRNA HYDROLASE 1; PTRH1","url":"https://www.omim.org/entry/621047"},{"mim_id":"617541","title":"ANKYRIN REPEAT- AND ZINC FINGER DOMAIN-CONTAINING 1; ANKZF1","url":"https://www.omim.org/entry/617541"},{"mim_id":"612326","title":"TRANSCRIPTION FACTOR 25; TCF25","url":"https://www.omim.org/entry/612326"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TCF25"},"hgnc":{"alias_symbol":["Nulp1","KIAA1049"],"prev_symbol":[]},"alphafold":{"accession":"Q9BQ70","domains":[{"cath_id":"-","chopping":"177-199_217-380_591-597_641-653","consensus_level":"medium","plddt":89.7825,"start":177,"end":653},{"cath_id":"-","chopping":"381-588","consensus_level":"medium","plddt":91.8959,"start":381,"end":588}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BQ70","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BQ70-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BQ70-F1-predicted_aligned_error_v6.png","plddt_mean":72.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TCF25","jax_strain_url":"https://www.jax.org/strain/search?query=TCF25"},"sequence":{"accession":"Q9BQ70","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9BQ70.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9BQ70/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BQ70"}},"corpus_meta":[{"pmid":"30244831","id":"PMC_30244831","title":"Release of Ubiquitinated and Non-ubiquitinated Nascent Chains from Stalled Mammalian Ribosomal Complexes by ANKZF1 and Ptrh1.","date":"2018","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/30244831","citation_count":96,"is_preprint":false},{"pmid":"11750130","id":"PMC_11750130","title":"The human melanocortin-1 receptor locus: analysis of transcription unit, locus polymorphism and haplotype evolution.","date":"2001","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/11750130","citation_count":31,"is_preprint":false},{"pmid":"37752425","id":"PMC_37752425","title":"Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds.","date":"2023","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/37752425","citation_count":26,"is_preprint":false},{"pmid":"37170524","id":"PMC_37170524","title":"Genetic diversity and selection of Tibetan sheep breeds revealed by whole-genome resequencing.","date":"2023","source":"Animal bioscience","url":"https://pubmed.ncbi.nlm.nih.gov/37170524","citation_count":26,"is_preprint":false},{"pmid":"37372363","id":"PMC_37372363","title":"Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers.","date":"2023","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/37372363","citation_count":24,"is_preprint":false},{"pmid":"25184702","id":"PMC_25184702","title":"Epigenome-wide DNA methylation in hearing ability: new mechanisms for an old problem.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/25184702","citation_count":22,"is_preprint":false},{"pmid":"16574069","id":"PMC_16574069","title":"hnulp1, a basic helix-loop-helix protein with a novel transcriptional repressive domain, inhibits transcriptional activity of serum response factor.","date":"2006","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/16574069","citation_count":22,"is_preprint":false},{"pmid":"39731152","id":"PMC_39731152","title":"Distinct microbes, metabolites, and the host genome define the multi-omics profiles in right-sided and left-sided colon cancer.","date":"2024","source":"Microbiome","url":"https://pubmed.ncbi.nlm.nih.gov/39731152","citation_count":21,"is_preprint":false},{"pmid":"20465587","id":"PMC_20465587","title":"Detection of recombinant haplotypes in wild mice (Mus musculus) provides new insights into the origin of Japanese mice.","date":"2010","source":"Molecular ecology","url":"https://pubmed.ncbi.nlm.nih.gov/20465587","citation_count":19,"is_preprint":false},{"pmid":"33257475","id":"PMC_33257475","title":"Identification and characterization of distinct brown adipocyte subtypes in C57BL/6J mice.","date":"2020","source":"Life science alliance","url":"https://pubmed.ncbi.nlm.nih.gov/33257475","citation_count":18,"is_preprint":false},{"pmid":"29221435","id":"PMC_29221435","title":"Exploring digenic inheritance in arrhythmogenic cardiomyopathy.","date":"2017","source":"BMC medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/29221435","citation_count":16,"is_preprint":false},{"pmid":"35760404","id":"PMC_35760404","title":"Genome-wide association analysis of nine reproduction and morphological traits in three goat breeds from Southern China.","date":"2022","source":"Animal bioscience","url":"https://pubmed.ncbi.nlm.nih.gov/35760404","citation_count":15,"is_preprint":false},{"pmid":"12107429","id":"PMC_12107429","title":"Nulp1, a novel basic helix-loop-helix protein expressed broadly during early embryonic organogenesis and prominently in developing dorsal root ganglia.","date":"2002","source":"Cell and tissue research","url":"https://pubmed.ncbi.nlm.nih.gov/12107429","citation_count":14,"is_preprint":false},{"pmid":"36929535","id":"PMC_36929535","title":"Genetic fine-mapping reveals single nucleotide polymorphism mutations in the MC1R regulatory region associated with duck melanism.","date":"2023","source":"Molecular ecology","url":"https://pubmed.ncbi.nlm.nih.gov/36929535","citation_count":14,"is_preprint":false},{"pmid":"35092859","id":"PMC_35092859","title":"Genome-wide detection of selective signals for fecundity traits in goats (Capra hircus).","date":"2022","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/35092859","citation_count":14,"is_preprint":false},{"pmid":"32805187","id":"PMC_32805187","title":"NULP1 Alleviates Cardiac Hypertrophy by Suppressing NFAT3 Transcriptional Activity.","date":"2020","source":"Journal of the American Heart Association","url":"https://pubmed.ncbi.nlm.nih.gov/32805187","citation_count":13,"is_preprint":false},{"pmid":"18045611","id":"PMC_18045611","title":"Identification of prostate cancer antigens by automated high-throughput filter immunoscreening.","date":"2007","source":"Journal of immunological methods","url":"https://pubmed.ncbi.nlm.nih.gov/18045611","citation_count":13,"is_preprint":false},{"pmid":"18068114","id":"PMC_18068114","title":"Nuclear localized protein-1 (Nulp1) increases cell death of human osteosarcoma cells and binds the X-linked inhibitor of apoptosis protein.","date":"2007","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/18068114","citation_count":12,"is_preprint":false},{"pmid":"35384084","id":"PMC_35384084","title":"CircTCF25 serves as a sponge for miR-206 to support proliferation, migration, and invasion of glioma via the Jak2/p-Stat3/CypB axis.","date":"2022","source":"Molecular carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/35384084","citation_count":10,"is_preprint":false},{"pmid":"23537237","id":"PMC_23537237","title":"Spatial and temporal aspects of occurrence of Mogera species in the Japanese islands inferred from mitochondrial and nuclear gene sequences.","date":"2013","source":"Zoological science","url":"https://pubmed.ncbi.nlm.nih.gov/23537237","citation_count":10,"is_preprint":false},{"pmid":"40169231","id":"PMC_40169231","title":"The ribosome-associated quality control factor TCF25 imposes K48 specificity on Listerin-mediated ubiquitination of nascent chains by binding and specifically orienting the acceptor ubiquitin.","date":"2025","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/40169231","citation_count":7,"is_preprint":false},{"pmid":"38038215","id":"PMC_38038215","title":"Chromosome 10q24.32 Variants Associate With Brain Arterial Diameters in Diverse Populations: A Genome-Wide Association Study.","date":"2023","source":"Journal of the American Heart Association","url":"https://pubmed.ncbi.nlm.nih.gov/38038215","citation_count":7,"is_preprint":false},{"pmid":"38228636","id":"PMC_38228636","title":"Transcriptional profile of ribosome-associated quality control components and their associated phenotypes in mammalian cells.","date":"2024","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/38228636","citation_count":6,"is_preprint":false},{"pmid":"38970134","id":"PMC_38970134","title":"A systematic review on the contribution of DNA methylation to hearing loss.","date":"2024","source":"Clinical epigenetics","url":"https://pubmed.ncbi.nlm.nih.gov/38970134","citation_count":5,"is_preprint":false},{"pmid":"39682459","id":"PMC_39682459","title":"Genome-Wide Association Study of Birth Wool Length, Birth Weight, and Head Color in Chinese Tan Sheep Through Whole-Genome Re-Sequencing.","date":"2024","source":"Animals : an open access journal from MDPI","url":"https://pubmed.ncbi.nlm.nih.gov/39682459","citation_count":5,"is_preprint":false},{"pmid":"39464025","id":"PMC_39464025","title":"The ribosome-associated quality control factor TCF25 imposes K48 specificity on Listerin-mediated ubiquitination of nascent chains by binding and specifically orienting the acceptor ubiquitin.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/39464025","citation_count":3,"is_preprint":false},{"pmid":"36778463","id":"PMC_36778463","title":"Chromosome 10q24.32 Variants Associate with Brain Arterial Diameters in Diverse Populations: A Genome-Wide Association Study.","date":"2023","source":"medRxiv : the preprint server for health sciences","url":"https://pubmed.ncbi.nlm.nih.gov/36778463","citation_count":3,"is_preprint":false},{"pmid":"41210950","id":"PMC_41210950","title":"Transcription factor 25 modulates gametocytogenesis and ribosome biogenesis in the malaria parasite Plasmodium falciparum.","date":"2025","source":"Frontiers in cellular and infection microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/41210950","citation_count":2,"is_preprint":false},{"pmid":"39113615","id":"PMC_39113615","title":"Identification of potential therapeutic targets for skin cutaneous melanoma on the basic of transcriptomics.","date":"2024","source":"Skin research and technology : official journal of International Society for Bioengineering and the Skin (ISBS) [and] International Society for Digital Imaging of Skin (ISDIS) [and] International Society for Skin Imaging (ISSI)","url":"https://pubmed.ncbi.nlm.nih.gov/39113615","citation_count":2,"is_preprint":false},{"pmid":"29437009","id":"PMC_29437009","title":"The bHLH Protein Nulp1 is Essential for Femur Development Via Acting as a Cofactor in Wnt Signaling in Drosophila.","date":"2018","source":"Current molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/29437009","citation_count":1,"is_preprint":false},{"pmid":"36222339","id":"PMC_36222339","title":"The role and mechanism of NDST1/NULP1 regulating right ventricular hypertrophy in hypoxic pulmonary hypertension.","date":"2022","source":"General physiology and biophysics","url":"https://pubmed.ncbi.nlm.nih.gov/36222339","citation_count":1,"is_preprint":false},{"pmid":"40428348","id":"PMC_40428348","title":"Whole-Genome DNA Methylation Analysis in Age-Related Hearing Loss.","date":"2025","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/40428348","citation_count":1,"is_preprint":false},{"pmid":"40840286","id":"PMC_40840286","title":"Whole genome resequencing uncovers candidate genes related to plumage color in Yuexi frizzled feather chicken.","date":"2025","source":"Poultry science","url":"https://pubmed.ncbi.nlm.nih.gov/40840286","citation_count":1,"is_preprint":false},{"pmid":"40844875","id":"PMC_40844875","title":"TCF25 serves as a nutrient sensor to orchestrate metabolic adaptation and cell death by enhancing lysosomal acidification under glucose starvation.","date":"2025","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/40844875","citation_count":0,"is_preprint":false},{"pmid":"41385958","id":"PMC_41385958","title":"Unraveling the population genetic structure and identifying candidate genes for dorsal plumage color in Liangshan Yanying chickens.","date":"2025","source":"Poultry science","url":"https://pubmed.ncbi.nlm.nih.gov/41385958","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":19771,"output_tokens":2481,"usd":0.048264},"stage2":{"model":"claude-opus-4-6","input_tokens":5791,"output_tokens":2576,"usd":0.140033},"total_usd":0.188297,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2018,\n      \"finding\": \"TCF25 is a component of the ribosome-associated quality control (RQC) pathway and ensures preferential formation of K48-ubiquitin linkage on nascent chains ubiquitinated by Listerin on stalled 60S ribosomal complexes.\",\n      \"method\": \"In vitro reconstitution of RQC pathway with mammalian components; ubiquitin linkage analysis\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution with defined components, replicated and extended by subsequent studies\",\n      \"pmids\": [\"30244831\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TCF25 imposes K48 ubiquitin-linkage specificity on Listerin-mediated ubiquitination by directly interacting with both the RING domain of Listerin and the acceptor ubiquitin (UbA), orienting UbA so that its K48 is positioned to attack the thioester bond of the Ube2D1~Ub conjugate. TCF25 itself is also subject to K48-specific ubiquitination by Listerin, leading to its proteasomal degradation in vivo.\",\n      \"method\": \"Functional biochemical reconstitution, AlphaFold3 structural modeling, site-directed mutagenesis, ubiquitin linkage assays\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution with mutagenesis plus structural modeling, mechanistic detail rigorously established\",\n      \"pmids\": [\"40169231\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TCF25 (preprint version of the same study as PMID 40169231): TCF25 specifically interacts with the RING domain of Listerin and acceptor ubiquitin to impose K48-linkage specificity; TCF25 itself undergoes K48-specific ubiquitination by Listerin and is degraded by the proteasome.\",\n      \"method\": \"Functional biochemical reconstitution, AlphaFold3 modeling, ubiquitin linkage assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — same data as peer-reviewed version; preprint precedes publication\",\n      \"pmids\": [\"39464025\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TCF25 protein levels are substantially lower than its mRNA levels in mammalian cells due to post-translational degradation by the proteasome, confirming that TCF25 itself is a proteasome substrate in vivo.\",\n      \"method\": \"Proteasome inhibitor treatment, immunoblot, comparison of mRNA and protein levels across cell lines\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct pharmacological inhibition experiment with clear functional readout, single lab\",\n      \"pmids\": [\"38228636\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Human NULP1 (TCF25) contains a bHLH domain and a C-terminal DUF654 domain; it functions as a transcriptional repressor, with the DUF654 motif mediating basal repressive activity via histone deacetylase activity. Overexpression of NULP1 inhibits the transcriptional activity of serum response factor (SRF).\",\n      \"method\": \"GAL4-fusion transcriptional reporter assays, co-transfection with VP-16, trichostatin A treatment, SRF reporter assay in COS-7 cells\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple reporter assays with pharmacological validation, single lab\",\n      \"pmids\": [\"16574069\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Mouse Nulp1 (ortholog of TCF25) localizes to the nucleus when expressed as an EGFP fusion in human embryonic kidney cells, consistent with its function as a transcription factor.\",\n      \"method\": \"Transfection of Nulp1-EGFP fusion into HEK cells, fluorescence microscopy\",\n      \"journal\": \"Cell and tissue research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — direct localization experiment, single lab, foundational characterization\",\n      \"pmids\": [\"12107429\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"NULP1 (TCF25) localizes predominantly to the cell nucleus, induces cell death with DNA fragmentation upon overexpression in human osteosarcoma Saos2 cells, and physically binds XIAP (X-linked inhibitor of apoptosis protein); this interaction is enhanced during cell death.\",\n      \"method\": \"Immunostaining with novel antibody, overexpression assays, co-immunoprecipitation with XIAP\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — Co-IP plus localization and functional overexpression, single lab\",\n      \"pmids\": [\"18068114\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"NULP1 (TCF25) directly interacts with the topologically associating domain (TAD) of NFAT3 via its C-terminal region, suppressing NFAT3 transcriptional activity; Nulp1 knockout exacerbates aortic banding-induced cardiac hypertrophy, and NFAT pathway inactivation rescues this phenotype in vivo.\",\n      \"method\": \"Co-immunoprecipitation, domain mapping, Nulp1 knockout and transgenic mouse models, aortic banding surgery, VIVIT peptide treatment, NFAT reporter assays\",\n      \"journal\": \"Journal of the American Heart Association\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP with domain mapping, KO and transgenic rescue in vivo, epistasis via VIVIT peptide, multiple orthogonal methods\",\n      \"pmids\": [\"32805187\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Drosophila Nulp1 (dNulp1, ortholog of TCF25) is required for femur development and survival; dNulp1 mutants generated by CRISPR/Cas9 targeting the DUF654 domain show bent femurs, and dNulp1 acts as a positive cofactor in the Wnt/Wingless signaling pathway, activating Wg target genes and the TopFlash reporter.\",\n      \"method\": \"CRISPR/Cas9 knockout, overexpression rescue, qRT-PCR of Wg target genes, TopFlash luciferase reporter assay in Drosophila\",\n      \"journal\": \"Current molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic KO with rescue, reporter assay, epistasis with sgg/GSK3β; Drosophila ortholog\",\n      \"pmids\": [\"29437009\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TCF25 acts as a nutrient sensor that enhances lysosomal acidification by targeting V-ATPase, promoting autophagy and ATP generation under glucose starvation. Prolonged glucose starvation leads TCF25 to constitutively activate ferritinophagy, increasing lysosomal membrane permeability and causing lysosome-dependent cell death (LDCD). TCF25 or V-ATPase KO prevents this cell death, and TCF25 deficiency protects mice from hepatic ischemia-reperfusion injury.\",\n      \"method\": \"Genome-wide CRISPR-Cas9 screen, TCF25 knockout in cell lines and mice, lysosomal acidification assays, V-ATPase interaction studies, autophagy flux assays, hepatic ischemia-reperfusion injury mouse model\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genome-wide screen followed by mechanistic KO studies in vitro and in vivo with multiple orthogonal readouts\",\n      \"pmids\": [\"40844875\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TCF25 (also known as NULP1) is a multifunctional nuclear protein: in the ribosome-associated quality control (RQC) pathway, it imposes K48-specific ubiquitin-linkage on stalled nascent chains by binding the RING domain of the E3 ligase Listerin and the acceptor ubiquitin to orient K48 for attack on the E2~Ub thioester, while also serving as a Listerin substrate itself; independently, it acts as a transcriptional repressor (via its DUF654/bHLH domains) that suppresses SRF and NFAT3 signaling and interacts with XIAP to modulate apoptosis; and it functions as a lysosomal nutrient sensor that targets V-ATPase to regulate lysosomal acidification, autophagy, and glucose-starvation-induced lysosome-dependent cell death.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TCF25 (NULP1) is a multifunctional protein that operates in ribosome-associated quality control (RQC), transcriptional regulation, and lysosomal nutrient sensing. In the RQC pathway, TCF25 imposes K48-ubiquitin linkage specificity on nascent chains ubiquitinated by the E3 ligase Listerin by directly binding the Listerin RING domain and the acceptor ubiquitin to orient K48 for nucleophilic attack on the E2~Ub thioester; TCF25 itself is a K48-ubiquitinated Listerin substrate subject to proteasomal degradation [PMID:30244831, PMID:40169231, PMID:38228636]. As a nuclear bHLH/DUF654-containing transcriptional repressor, TCF25 suppresses SRF transcriptional activity through HDAC-dependent mechanisms and inhibits NFAT3 signaling via direct interaction with the NFAT3 transactivation domain, with Nulp1 knockout exacerbating pressure-overload cardiac hypertrophy in mice [PMID:16574069, PMID:32805187]. TCF25 also functions as a lysosomal nutrient sensor that targets V-ATPase to enhance lysosomal acidification and autophagy under glucose starvation, and its sustained activation drives ferritinophagy and lysosome-dependent cell death, with TCF25 deficiency protecting against hepatic ischemia-reperfusion injury in vivo [PMID:40844875].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Establishing TCF25 as a nuclear protein resolved its likely compartment of action and was consistent with a transcriptional role for this uncharacterized bHLH-containing factor.\",\n      \"evidence\": \"EGFP-fusion of mouse Nulp1 expressed in HEK cells, fluorescence microscopy\",\n      \"pmids\": [\"12107429\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Overexpression of fusion protein; endogenous localization not confirmed\", \"No functional assay beyond localization\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Demonstrating that the DUF654 domain mediates transcriptional repression through HDAC activity and that TCF25 inhibits SRF signaling established its first mechanistic role as a transcriptional repressor.\",\n      \"evidence\": \"GAL4-fusion reporter assays, trichostatin A derepression, SRF reporter co-transfection in COS-7 cells\",\n      \"pmids\": [\"16574069\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No direct HDAC binding or recruitment shown\", \"Endogenous target genes not identified\", \"Reporter-based assays only\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Identifying a physical interaction between TCF25 and the anti-apoptotic protein XIAP, enhanced during cell death, linked TCF25 to apoptotic regulation beyond transcription.\",\n      \"evidence\": \"Co-immunoprecipitation, immunostaining, overexpression-induced DNA fragmentation in Saos2 cells\",\n      \"pmids\": [\"18068114\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single co-IP direction reported; no reciprocal validation described\", \"Mechanism by which XIAP binding modulates cell death not determined\", \"Overexpression artifacts not excluded\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Reconstitution of the mammalian RQC pathway revealed a completely unexpected role for TCF25 as the factor that ensures K48-linkage specificity on nascent chains ubiquitinated by Listerin on stalled 60S complexes, establishing TCF25 as a core RQC component.\",\n      \"evidence\": \"In vitro reconstitution with purified mammalian RQC components, ubiquitin linkage analysis\",\n      \"pmids\": [\"30244831\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis for K48 specificity not resolved\", \"In vivo relevance in mammalian cells not directly tested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Drosophila genetic studies showed that the TCF25 ortholog dNulp1 is required for limb development and acts as a Wnt/Wingless pathway cofactor, extending TCF25 function to developmental signaling.\",\n      \"evidence\": \"CRISPR/Cas9 knockout, overexpression rescue, qRT-PCR of Wg targets, TopFlash reporter in Drosophila\",\n      \"pmids\": [\"29437009\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Conservation of Wnt cofactor role in mammals not tested\", \"Direct binding partner in Wnt pathway not identified\", \"Mechanism of transcriptional activation versus known repressor activity unresolved\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Mapping the direct TCF25–NFAT3 interaction to the NFAT3 transactivation domain and demonstrating that Nulp1 knockout worsens cardiac hypertrophy (rescued by NFAT inhibition) established TCF25 as a physiologically relevant negative regulator of NFAT signaling in the heart.\",\n      \"evidence\": \"Reciprocal co-IP, domain mapping, Nulp1 KO and transgenic mice, aortic banding, VIVIT peptide rescue, NFAT reporter assays\",\n      \"pmids\": [\"32805187\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether TCF25 represses NFAT3 through HDAC recruitment or a distinct mechanism not resolved\", \"Cardiac-specific versus systemic functions not dissected\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Confirming that endogenous TCF25 protein is maintained at low levels by proteasomal degradation validated the in vitro finding that TCF25 is itself a ubiquitin-proteasome substrate.\",\n      \"evidence\": \"Proteasome inhibitor treatment, immunoblotting, mRNA-protein level comparison across cell lines\",\n      \"pmids\": [\"38228636\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Which E3 ligase(s) mediate endogenous TCF25 turnover not fully established in vivo\", \"Functional consequence of TCF25 stabilization not tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Structural and biochemical dissection revealed the precise mechanism by which TCF25 enforces K48 specificity: it simultaneously contacts the Listerin RING domain and the acceptor ubiquitin to position K48 for thioester attack, and TCF25 itself undergoes the same K48-specific modification by Listerin.\",\n      \"evidence\": \"In vitro reconstitution, AlphaFold3 structural modeling, site-directed mutagenesis, ubiquitin linkage assays\",\n      \"pmids\": [\"40169231\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No experimentally determined high-resolution structure yet\", \"Relative contributions of TCF25 auto-ubiquitination versus substrate ubiquitination to RQC flux unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"A genome-wide CRISPR screen uncovered TCF25 as a lysosomal nutrient sensor that targets V-ATPase to control lysosomal acidification, autophagy, and glucose-starvation-induced lysosome-dependent cell death, with in vivo validation in hepatic ischemia-reperfusion injury.\",\n      \"evidence\": \"Genome-wide CRISPR-Cas9 screen, TCF25 KO in cell lines and mice, lysosomal acidification assays, V-ATPase interaction studies, autophagy flux, hepatic I/R model\",\n      \"pmids\": [\"40844875\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How TCF25 senses glucose versus other nutrient signals not defined\", \"Molecular interface between TCF25 and V-ATPase subunits not mapped\", \"Relationship between lysosomal and RQC functions of TCF25 unexplored\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown how the three major functions of TCF25 — RQC ubiquitin-linkage specification, transcriptional repression, and lysosomal nutrient sensing — are coordinated in cells, and whether distinct pools or post-translational modifications partition TCF25 among these pathways.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No integrative study connecting RQC, transcriptional, and lysosomal roles\", \"No high-resolution experimental structure of TCF25 in any complex\", \"Tissue-specific and developmental functions in mammals remain largely uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [4, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [5, 6]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [4, 7]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [9]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [6, 9]}\n    ],\n    \"complexes\": [\n      \"Listerin-RQC complex\"\n    ],\n    \"partners\": [\n      \"LTN1\",\n      \"XIAP\",\n      \"NFAT3\",\n      \"UBE2D1\",\n      \"ATP6V1A\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}