{"gene":"HNRNPF","run_date":"2026-06-10T01:55:22","timeline":{"discoveries":[{"year":2017,"finding":"RNA G-quadruplex secondary structures promote exon inclusion by serving as binding sites for hnRNPF; destroying G-quadruplex-forming capacity while keeping G tracts intact abrogates exon inclusion. hnRNPF binds G-quadruplex-forming RNA elements and regulates an EMT-associated CD44 isoform switch in a G-quadruplex-dependent manner.","method":"RNA-binding protein footprint analysis (CLIP-seq), mutational analysis of G-quadruplex-forming sequences, alternative splicing reporter assays, knockdown experiments","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (CLIP-seq, mutational disruption of G-quadruplex, splicing assays), replicated across multiple exons and a functionally important isoform switch","pmids":["29269483"],"is_preprint":false},{"year":2019,"finding":"hnRNP-F directly binds the 3' UTR of Snail1 mRNA (validated by RNA immunoprecipitation and Snail1 mRNA truncation/mutation constructs) and stabilizes Snail1 mRNA, thereby promoting EMT in bladder cancer.","method":"RNA immunoprecipitation (RIP), actinomycin D mRNA stability assay, Snail1 mRNA truncation and mutant constructs","journal":"EBioMedicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RIP and functional mRNA stability assay with domain-mapping mutants, single lab","pmids":["31221586"],"is_preprint":false},{"year":2018,"finding":"FOXP3 physically associates with hnRNPF through the exon 2-encoded region of FOXP3 and the second quasi-RNA recognition motif (qRRM2) of hnRNPF, and represses hnRNPF's ability to bind target pre-mRNAs, thereby modulating alternative splicing and suppressive function of regulatory T cells.","method":"Co-immunoprecipitation, domain-mapping experiments (FOXP3 exon 2 and hnRNPF qRRM2 mutants), alternative splicing assays, Treg suppression functional assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal interaction domain mapping and functional splicing assays, single lab","pmids":["29773655"],"is_preprint":false},{"year":2019,"finding":"hnRNP-F physically interacts with TPX2 protein (identified by mass spectrometry and co-immunoprecipitation); hnRNP-F knockdown reduces TPX2 protein levels, which decreases cyclin D1 and increases p21, leading to cell cycle arrest. Overexpression of TPX2 rescues the proliferation defect caused by hnRNP-F knockdown.","method":"Mass spectrometry, co-immunoprecipitation, western blotting, rescue experiments with TPX2 overexpression, flow cytometry","journal":"American journal of translational research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS identification plus Co-IP plus genetic rescue, single lab","pmids":["31814907"],"is_preprint":false},{"year":2021,"finding":"hnRNP-F expression is regulated downstream of the PI3K/AKT signaling pathway; FOXO1, a downstream target of PI3K/AKT, binds to the hnRNPF promoter and transcriptionally represses hnRNPF expression (shown by ChIP and luciferase reporter assays). PI3K/AKT inhibition (LY294002) decreases hnRNP-F levels, while hnRNP-F knockdown does not affect PI3K or AKT expression.","method":"Chromatin immunoprecipitation (ChIP), luciferase reporter assay, western blotting with PI3K/AKT inhibitor LY294002, siRNA knockdown","journal":"Journal of Cancer","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and luciferase reporter for direct promoter binding, single lab with two orthogonal methods","pmids":["33391425"],"is_preprint":false},{"year":2024,"finding":"circCacna1c directly interacts with Hnrnpf in the cytoplasm, preventing its nuclear translocation; this reduces nuclear Hnrnpf levels and suppresses Hnrnpf-dependent RIPK1 expression, thereby inhibiting necroptosis in cardiomyocytes. FTO-mediated m6A demethylation of circCacna1c promotes its degradation and releases this inhibition.","method":"RNA pull-down assay, western blotting (nuclear/cytoplasmic fractionation), MeRIP-qPCR, overexpression in H9c2 cells and MI mouse model","journal":"Cellular & molecular biology letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNA pull-down plus fractionation plus in vivo MI model, single lab","pmids":["39533214"],"is_preprint":false},{"year":2024,"finding":"LINC03047 physically binds hnRNPF and inhibits its nuclear translocation; this cytoplasmic sequestration of hnRNPF enhances CTGF mRNA stability, promoting mitophagy and proliferation of pulmonary artery smooth muscle cells under hypoxia. Targeted inhibition of hnRNPF mitigates hypoxia-induced pulmonary hypertension in vivo.","method":"RNA pull-down, nuclear/cytoplasmic fractionation, mRNA stability assays, siRNA knockdown of hnRNPF, in vivo hypoxia-induced PH model","journal":"Free radical biology & medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pull-down plus fractionation plus in vivo model, single lab","pmids":["41232621"],"is_preprint":false},{"year":2025,"finding":"In the cytoplasm, the lncRNA USP30-AS1 interacts with HnRNPF and disrupts its binding to the p21 (CDKN1A) 3' UTR, destabilizing p21 mRNA and reducing p21 expression to promote breast cancer cell proliferation.","method":"RNA immunoprecipitation, mRNA stability assay, knockdown/overexpression experiments","journal":"Genes & diseases","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, limited methodological detail in abstract for hnRNPF-specific binding experiments","pmids":["41492473"],"is_preprint":false},{"year":2025,"finding":"hnRNPF binds to the lncRNA LINC01189, which promotes hnRNPF degradation through ubiquitination, thereby modulating gastric cancer cell invasion and migration.","method":"Co-immunoprecipitation/pull-down, ubiquitination assay, knockdown/overexpression functional assays","journal":"Cell death discovery","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, abstract lacks detail on ubiquitination mechanism for hnRNPF specifically","pmids":["37865686"],"is_preprint":false},{"year":2025,"finding":"hnRNP-F overexpression suppresses the TNFα/NFκB signaling pathway in renal tubular epithelial cells under high-glucose conditions; integrative CLIP-seq/RNA-seq analysis suggests hnRNPF binds lncRNA SNHG1 to negatively regulate inflammatory gene transcription, and also regulates alternative splicing by interacting with ZFP36 to form a complex.","method":"RNA-seq, CLIP-seq (downloaded GEO dataset), western blotting, overexpression in HK-2 and MPC5 cells","journal":"Frontiers in physiology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — integrative bioinformatic analysis plus overexpression/WB, CLIP-seq data from external source, single lab","pmids":["40995516"],"is_preprint":false},{"year":2026,"finding":"ERK2 directly phosphorylates HNRNPF on Ser346 and Tyr356; phospho-mimetic HNRNPF more potently rescues ESC proliferation and suppresses differentiation than unphospho-mimetic mutant. HNRNPF binds Cdk1, Ccnb1, and Eed mRNAs and enhances their translation; phosphorylation of HNRNPF increases its binding to these mRNAs and promotes their translation. Hnrnpf knockout reduces ESC proliferation by downregulating CDK1 and CCNB1 and promotes differentiation by reducing EED.","method":"In vitro kinase assay (ERK2 phosphorylation), phospho-mimetic and unphospho-mimetic mutagenesis, RNA immunoprecipitation, ribosome/translation assays, Hnrnpf knockout ESCs","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro kinase assay with site-specific mutagenesis, RIP, KO rescue experiments, multiple orthogonal methods in one study","pmids":["41495911"],"is_preprint":false},{"year":2026,"finding":"hnRNPF is recruited by the PFV Tas protein to nascent viral RNA; hnRNPF specifically recognizes a G-cluster II cis-acting element (GC-II) in the tas/bet pre-mRNA and promotes its splicing into bet mRNA (reducing unspliced tas transcript), thereby shifting viral expression from Tas to Bet and inhibiting PFV replication.","method":"Yeast two-hybrid screen, co-immunoprecipitation, splicing assays, cis-element mutation analysis, viral replication assays","journal":"Cell & bioscience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — yeast two-hybrid plus Co-IP plus functional splicing assay with cis-element mutation, single lab","pmids":["41935299"],"is_preprint":false}],"current_model":"HNRNPF is an RNA-binding protein that recognizes G-rich sequences and G-quadruplex RNA structures to regulate alternative splicing (promoting exon inclusion), mRNA stability (e.g., Snail1, CTGF, p21/CDKN1A), and mRNA translation (Cdk1, Ccnb1, Eed); it is phosphorylated by ERK2 on Ser346/Tyr356 to enhance mRNA binding and translation in embryonic stem cells, transcriptionally repressed by FOXO1 downstream of PI3K/AKT, and its nuclear localization is inhibited by cytoplasmic lncRNA/circRNA interactions (circCacna1c, LINC03047), with its splicing activity modulated by interaction with FOXP3 through hnRNPF's second qRRM domain."},"narrative":{"mechanistic_narrative":"HNRNPF is an RNA-binding protein that recognizes G-rich sequences and RNA G-quadruplex structures to control alternative splicing, mRNA stability, and translation across diverse cellular programs [PMID:29269483, PMID:41495911]. In splicing, HNRNPF binds G-quadruplex-forming RNA elements to promote exon inclusion, governing an EMT-associated CD44 isoform switch in a manner that depends specifically on G-quadruplex formation rather than on G-tract sequence alone [PMID:29269483]. Beyond splicing, HNRNPF binds target 3' UTRs to modulate transcript stability — stabilizing Snail1 mRNA to drive EMT [PMID:31221586] and, through cytoplasmic lncRNA interactions, governing CTGF and p21/CDKN1A mRNA stability [PMID:41232621, PMID:41492473]. In embryonic stem cells, ERK2 directly phosphorylates HNRNPF on Ser346 and Tyr356, which increases its binding to Cdk1, Ccnb1, and Eed mRNAs and enhances their translation; this phospho-regulated activity sustains proliferation and suppresses differentiation, and Hnrnpf loss reduces CDK1/CCNB1 and EED to impair proliferation [PMID:41495911]. HNRNPF activity is constrained at multiple levels: FOXP3 binds its second quasi-RNA recognition motif (qRRM2) to block pre-mRNA binding [PMID:29773655], FOXO1 downstream of PI3K/AKT transcriptionally represses HNRNPF [PMID:33391425], and cytoplasmic noncoding RNAs (circCacna1c) sequester it to prevent nuclear translocation [PMID:39533214, PMID:41232621]. HNRNPF also acts in viral pre-mRNA processing, where it is recruited by the foamy virus Tas protein to a G-cluster cis-element to redirect splicing [PMID:41935299].","teleology":[{"year":2017,"claim":"Established that HNRNPF reads RNA structure, not merely sequence — it binds G-quadruplex-forming elements to promote exon inclusion, explaining how it controls a functionally important CD44 isoform switch in EMT.","evidence":"CLIP-seq, mutational disruption of G-quadruplex while preserving G-tracts, and splicing reporter assays with knockdown","pmids":["29269483"],"confidence":"High","gaps":["Does not define the full repertoire of G-quadruplex targets genome-wide","Structural basis of qRRM-G-quadruplex recognition not resolved"]},{"year":2018,"claim":"Revealed a protein-based brake on HNRNPF splicing activity: FOXP3 docks on the qRRM2 domain to block pre-mRNA binding, linking HNRNPF to regulatory T cell function.","evidence":"Co-IP with reciprocal domain mapping (FOXP3 exon 2, hnRNPF qRRM2 mutants) and Treg splicing/suppression assays","pmids":["29773655"],"confidence":"Medium","gaps":["Which endogenous splicing targets are affected in Tregs not enumerated","Single lab; interaction not validated by orthogonal structural methods"]},{"year":2019,"claim":"Extended HNRNPF function beyond splicing to mRNA stabilization, showing direct 3' UTR binding to Snail1 transcript stabilizes it and promotes EMT in bladder cancer.","evidence":"RIP, actinomycin D stability assay, and Snail1 truncation/mutant constructs","pmids":["31221586"],"confidence":"Medium","gaps":["Precise binding motif within the Snail1 3' UTR not defined","Whether stabilization requires G-quadruplex unknown"]},{"year":2019,"claim":"Connected HNRNPF to cell cycle control via a protein partner, TPX2, whose levels depend on HNRNPF and whose restoration rescues the proliferation defect of HNRNPF loss.","evidence":"Mass spectrometry, Co-IP, western blot, and TPX2 overexpression rescue with flow cytometry","pmids":["31814907"],"confidence":"Medium","gaps":["Whether HNRNPF regulates TPX2 at the RNA level vs. protein level not resolved","Direct RNA target underlying cyclin D1/p21 changes not identified"]},{"year":2021,"claim":"Placed HNRNPF in a signaling hierarchy, showing FOXO1 downstream of PI3K/AKT directly represses HNRNPF transcription, establishing it as an output rather than a regulator of this pathway.","evidence":"ChIP and luciferase promoter assays, plus LY294002 inhibition and knockdown epistasis","pmids":["33391425"],"confidence":"Medium","gaps":["FOXO1 binding site on the HNRNPF promoter not mapped to a specific element","Single lab"]},{"year":2024,"claim":"Defined a cytoplasmic sequestration mechanism: noncoding RNAs control HNRNPF by blocking its nuclear entry, with circCacna1c suppressing nuclear HNRNPF and its target RIPK1 to inhibit cardiomyocyte necroptosis, itself tuned by FTO-mediated m6A demethylation.","evidence":"RNA pull-down, nuclear/cytoplasmic fractionation, MeRIP-qPCR, and an in vivo MI model","pmids":["39533214"],"confidence":"Medium","gaps":["How HNRNPF activates RIPK1 expression mechanistically not detailed","Generality of circRNA sequestration across cell types untested"]},{"year":2024,"claim":"Generalized the cytoplasmic sequestration paradigm, showing LINC03047 binds HNRNPF and retains it in the cytoplasm where it stabilizes CTGF mRNA to drive smooth muscle mitophagy and proliferation in pulmonary hypertension.","evidence":"RNA pull-down, fractionation, mRNA stability assays, knockdown, and in vivo hypoxia PH model","pmids":["41232621"],"confidence":"Medium","gaps":["Whether cytoplasmic HNRNPF stabilizes CTGF directly via 3' UTR binding not fully mapped","Single lab"]},{"year":2025,"claim":"Added further noncoding-RNA control points — USP30-AS1 disrupting HNRNPF binding to the p21 3' UTR to destabilize it, and LINC01189 promoting HNRNPF ubiquitination/degradation — linking HNRNPF turnover and target binding to cancer proliferation and invasion.","evidence":"RIP, mRNA stability and ubiquitination assays, knockdown/overexpression functional assays","pmids":["41492473","37865686"],"confidence":"Low","gaps":["Limited methodological detail for HNRNPF-specific binding/ubiquitination in abstracts","E3 ligase mediating LINC01189-dependent degradation not identified"]},{"year":2026,"claim":"Established post-translational control of HNRNPF activity, showing ERK2 phosphorylates Ser346/Tyr356 to enhance binding and translation of Cdk1, Ccnb1, and Eed mRNAs, coupling HNRNPF to ESC proliferation and self-renewal.","evidence":"In vitro kinase assay, phospho-mimetic/unphospho-mimetic mutagenesis, RIP, translation/ribosome assays, and Hnrnpf knockout ESC rescue","pmids":["41495911"],"confidence":"High","gaps":["Whether phosphorylation alters G-quadruplex recognition specifically not addressed","Upstream signals activating ERK2 toward HNRNPF in ESCs not defined"]},{"year":2026,"claim":"Demonstrated HNRNPF participates in viral RNA processing, being recruited by foamy virus Tas to a G-cluster cis-element to promote tas/bet splicing and restrict replication.","evidence":"Yeast two-hybrid, Co-IP, splicing assays with cis-element mutation, and viral replication assays","pmids":["41935299"],"confidence":"Medium","gaps":["Whether the GC-II element forms a G-quadruplex recognized by HNRNPF not tested","Single lab"]},{"year":null,"claim":"How HNRNPF integrates its dual nuclear (splicing) and cytoplasmic (stability/translation) roles, and what determines target selection across these compartments, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model of how phosphorylation and noncoding-RNA sequestration jointly partition HNRNPF between splicing and cytoplasmic functions","No structural model of qRRM-G-quadruplex engagement","Genome-wide direct target catalog across cell types incomplete"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,1,10,11]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[10]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0,11]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[5,6]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[5,6,7]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1,10]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0]}],"complexes":[],"partners":["FOXP3","TPX2","ERK2","FOXO1","ZFP36"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P52597","full_name":"Heterogeneous nuclear ribonucleoprotein F","aliases":["Nucleolin-like protein mcs94-1"],"length_aa":415,"mass_kda":45.7,"function":"Component of the heterogeneous nuclear ribonucleoprotein (hnRNP) complexes which provide the substrate for the processing events that pre-mRNAs undergo before becoming functional, translatable mRNAs in the cytoplasm. Plays a role in the regulation of alternative splicing events. Binds G-rich sequences in pre-mRNAs and keeps target RNA in an unfolded state","subcellular_location":"Nucleus, nucleoplasm","url":"https://www.uniprot.org/uniprotkb/P52597/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/HNRNPF","classification":"Not Classified","n_dependent_lines":163,"n_total_lines":1208,"dependency_fraction":0.13493377483443708},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CAPZB","stoichiometry":0.2},{"gene":"DHX9","stoichiometry":0.2},{"gene":"HNRNPH1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/HNRNPF","total_profiled":1310},"omim":[{"mim_id":"618033","title":"ZINC FINGER PROTEIN 689; ZNF689","url":"https://www.omim.org/entry/618033"},{"mim_id":"617544","title":"LONG INTERGENIC NONCODING RNA 672; LINC00672","url":"https://www.omim.org/entry/617544"},{"mim_id":"608537","title":"VON HIPPEL-LINDAU TUMOR SUPPRESSOR; VHL","url":"https://www.omim.org/entry/608537"},{"mim_id":"608004","title":"NUCLEAR FACTOR KAPPA-B INHIBITOR, ZETA; NFKBIZ","url":"https://www.omim.org/entry/608004"},{"mim_id":"603445","title":"KH-TYPE SPLICING REGULATORY PROTEIN; KHSRP","url":"https://www.omim.org/entry/603445"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/HNRNPF"},"hgnc":{"alias_symbol":[],"prev_symbol":["HNRPF"]},"alphafold":{"accession":"P52597","domains":[{"cath_id":"3.30.70.330","chopping":"10-99","consensus_level":"high","plddt":81.9313,"start":10,"end":99},{"cath_id":"3.30.70.330","chopping":"111-194","consensus_level":"high","plddt":77.9025,"start":111,"end":194},{"cath_id":"3.30.70.330","chopping":"288-362","consensus_level":"high","plddt":83.32,"start":288,"end":362}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P52597","model_url":"https://alphafold.ebi.ac.uk/files/AF-P52597-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P52597-F1-predicted_aligned_error_v6.png","plddt_mean":64.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=HNRNPF","jax_strain_url":"https://www.jax.org/strain/search?query=HNRNPF"},"sequence":{"accession":"P52597","fasta_url":"https://rest.uniprot.org/uniprotkb/P52597.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P52597/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P52597"}},"corpus_meta":[{"pmid":"29269483","id":"PMC_29269483","title":"RNA G-quadruplex secondary structure promotes alternative splicing via the RNA-binding protein hnRNPF.","date":"2017","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/29269483","citation_count":151,"is_preprint":false},{"pmid":"31221586","id":"PMC_31221586","title":"HnRNP-F regulates EMT in bladder cancer by mediating the stabilization of Snail1 mRNA by binding to its 3' UTR.","date":"2019","source":"EBioMedicine","url":"https://pubmed.ncbi.nlm.nih.gov/31221586","citation_count":51,"is_preprint":false},{"pmid":"37042074","id":"PMC_37042074","title":"The HNRNPF/H RNA binding proteins and disease.","date":"2023","source":"Wiley interdisciplinary reviews. RNA","url":"https://pubmed.ncbi.nlm.nih.gov/37042074","citation_count":32,"is_preprint":false},{"pmid":"33391425","id":"PMC_33391425","title":"HnRNP-F promotes the proliferation of bladder cancer cells mediated by PI3K/AKT/FOXO1.","date":"2021","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/33391425","citation_count":24,"is_preprint":false},{"pmid":"29773655","id":"PMC_29773655","title":"FOXP3 interacts with hnRNPF to modulate pre-mRNA alternative splicing.","date":"2018","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/29773655","citation_count":20,"is_preprint":false},{"pmid":"31814907","id":"PMC_31814907","title":"HnRNP-F promotes cell proliferation by regulating TPX2 in bladder cancer.","date":"2019","source":"American journal of translational research","url":"https://pubmed.ncbi.nlm.nih.gov/31814907","citation_count":19,"is_preprint":false},{"pmid":"37865686","id":"PMC_37865686","title":"The VAX2-LINC01189-hnRNPF signaling axis regulates cell invasion and migration in gastric cancer.","date":"2023","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/37865686","citation_count":10,"is_preprint":false},{"pmid":"39533214","id":"PMC_39533214","title":"m6A-modified circCacna1c regulates necroptosis and ischemic myocardial injury by inhibiting Hnrnpf entry into the nucleus.","date":"2024","source":"Cellular & molecular biology letters","url":"https://pubmed.ncbi.nlm.nih.gov/39533214","citation_count":8,"is_preprint":false},{"pmid":"39092172","id":"PMC_39092172","title":"The role of HnrnpF/H as a driver of oligoteratozoospermia.","date":"2024","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/39092172","citation_count":2,"is_preprint":false},{"pmid":"41492473","id":"PMC_41492473","title":"Nuclear and cytoplasmic USP30-AS1 coordinately regulate breast cancer progression through HnRNPF/p21 and EZH2/c-Myc/p21 axes.","date":"2025","source":"Genes & diseases","url":"https://pubmed.ncbi.nlm.nih.gov/41492473","citation_count":1,"is_preprint":false},{"pmid":"41241017","id":"PMC_41241017","title":"Circ_0057582 inhibits breast cancer progression via hnRNPF/YAP/SOX9 axis and M2 polarization in TAMs by autophagic degradation of ISG15.","date":"2025","source":"Biochemical pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/41241017","citation_count":1,"is_preprint":false},{"pmid":"41136556","id":"PMC_41136556","title":"Super-enhancer-associated long noncoding RNA lnc-SPI1U mediates SPI1 feedback regulation by interacting with HNRNPH1 and HNRNPF.","date":"2025","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/41136556","citation_count":0,"is_preprint":false},{"pmid":"41495911","id":"PMC_41495911","title":"ERK phosphorylates HNRNPF to promote the proliferation and suppress the differentiation of embryonic stem cells.","date":"2026","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/41495911","citation_count":0,"is_preprint":false},{"pmid":"40995516","id":"PMC_40995516","title":"Integrative RNA-seq and CLIP-seq analysis reveals hnRNP-F regulation of TNFα/NFκB signaling in high-glucose conditions.","date":"2025","source":"Frontiers in physiology","url":"https://pubmed.ncbi.nlm.nih.gov/40995516","citation_count":0,"is_preprint":false},{"pmid":"41232621","id":"PMC_41232621","title":"LINC03047 promotes mitophagy by recruiting hnRNPF to enhance CTGF mRNA stability in hypoxic pulmonary hypertension.","date":"2025","source":"Free radical biology & medicine","url":"https://pubmed.ncbi.nlm.nih.gov/41232621","citation_count":0,"is_preprint":false},{"pmid":"41935299","id":"PMC_41935299","title":"PFV Tas protein recruits hnRNPF to promote the splicing of tas/bet pre-mRNA.","date":"2026","source":"Cell & bioscience","url":"https://pubmed.ncbi.nlm.nih.gov/41935299","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10568,"output_tokens":3132,"usd":0.039342,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10537,"output_tokens":3690,"usd":0.072468,"stage2_stop_reason":"end_turn"},"total_usd":0.11181,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2017,\n      \"finding\": \"RNA G-quadruplex secondary structures promote exon inclusion by serving as binding sites for hnRNPF; destroying G-quadruplex-forming capacity while keeping G tracts intact abrogates exon inclusion. hnRNPF binds G-quadruplex-forming RNA elements and regulates an EMT-associated CD44 isoform switch in a G-quadruplex-dependent manner.\",\n      \"method\": \"RNA-binding protein footprint analysis (CLIP-seq), mutational analysis of G-quadruplex-forming sequences, alternative splicing reporter assays, knockdown experiments\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (CLIP-seq, mutational disruption of G-quadruplex, splicing assays), replicated across multiple exons and a functionally important isoform switch\",\n      \"pmids\": [\"29269483\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"hnRNP-F directly binds the 3' UTR of Snail1 mRNA (validated by RNA immunoprecipitation and Snail1 mRNA truncation/mutation constructs) and stabilizes Snail1 mRNA, thereby promoting EMT in bladder cancer.\",\n      \"method\": \"RNA immunoprecipitation (RIP), actinomycin D mRNA stability assay, Snail1 mRNA truncation and mutant constructs\",\n      \"journal\": \"EBioMedicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RIP and functional mRNA stability assay with domain-mapping mutants, single lab\",\n      \"pmids\": [\"31221586\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"FOXP3 physically associates with hnRNPF through the exon 2-encoded region of FOXP3 and the second quasi-RNA recognition motif (qRRM2) of hnRNPF, and represses hnRNPF's ability to bind target pre-mRNAs, thereby modulating alternative splicing and suppressive function of regulatory T cells.\",\n      \"method\": \"Co-immunoprecipitation, domain-mapping experiments (FOXP3 exon 2 and hnRNPF qRRM2 mutants), alternative splicing assays, Treg suppression functional assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal interaction domain mapping and functional splicing assays, single lab\",\n      \"pmids\": [\"29773655\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"hnRNP-F physically interacts with TPX2 protein (identified by mass spectrometry and co-immunoprecipitation); hnRNP-F knockdown reduces TPX2 protein levels, which decreases cyclin D1 and increases p21, leading to cell cycle arrest. Overexpression of TPX2 rescues the proliferation defect caused by hnRNP-F knockdown.\",\n      \"method\": \"Mass spectrometry, co-immunoprecipitation, western blotting, rescue experiments with TPX2 overexpression, flow cytometry\",\n      \"journal\": \"American journal of translational research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS identification plus Co-IP plus genetic rescue, single lab\",\n      \"pmids\": [\"31814907\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"hnRNP-F expression is regulated downstream of the PI3K/AKT signaling pathway; FOXO1, a downstream target of PI3K/AKT, binds to the hnRNPF promoter and transcriptionally represses hnRNPF expression (shown by ChIP and luciferase reporter assays). PI3K/AKT inhibition (LY294002) decreases hnRNP-F levels, while hnRNP-F knockdown does not affect PI3K or AKT expression.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP), luciferase reporter assay, western blotting with PI3K/AKT inhibitor LY294002, siRNA knockdown\",\n      \"journal\": \"Journal of Cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and luciferase reporter for direct promoter binding, single lab with two orthogonal methods\",\n      \"pmids\": [\"33391425\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"circCacna1c directly interacts with Hnrnpf in the cytoplasm, preventing its nuclear translocation; this reduces nuclear Hnrnpf levels and suppresses Hnrnpf-dependent RIPK1 expression, thereby inhibiting necroptosis in cardiomyocytes. FTO-mediated m6A demethylation of circCacna1c promotes its degradation and releases this inhibition.\",\n      \"method\": \"RNA pull-down assay, western blotting (nuclear/cytoplasmic fractionation), MeRIP-qPCR, overexpression in H9c2 cells and MI mouse model\",\n      \"journal\": \"Cellular & molecular biology letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNA pull-down plus fractionation plus in vivo MI model, single lab\",\n      \"pmids\": [\"39533214\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"LINC03047 physically binds hnRNPF and inhibits its nuclear translocation; this cytoplasmic sequestration of hnRNPF enhances CTGF mRNA stability, promoting mitophagy and proliferation of pulmonary artery smooth muscle cells under hypoxia. Targeted inhibition of hnRNPF mitigates hypoxia-induced pulmonary hypertension in vivo.\",\n      \"method\": \"RNA pull-down, nuclear/cytoplasmic fractionation, mRNA stability assays, siRNA knockdown of hnRNPF, in vivo hypoxia-induced PH model\",\n      \"journal\": \"Free radical biology & medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pull-down plus fractionation plus in vivo model, single lab\",\n      \"pmids\": [\"41232621\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In the cytoplasm, the lncRNA USP30-AS1 interacts with HnRNPF and disrupts its binding to the p21 (CDKN1A) 3' UTR, destabilizing p21 mRNA and reducing p21 expression to promote breast cancer cell proliferation.\",\n      \"method\": \"RNA immunoprecipitation, mRNA stability assay, knockdown/overexpression experiments\",\n      \"journal\": \"Genes & diseases\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, limited methodological detail in abstract for hnRNPF-specific binding experiments\",\n      \"pmids\": [\"41492473\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"hnRNPF binds to the lncRNA LINC01189, which promotes hnRNPF degradation through ubiquitination, thereby modulating gastric cancer cell invasion and migration.\",\n      \"method\": \"Co-immunoprecipitation/pull-down, ubiquitination assay, knockdown/overexpression functional assays\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, abstract lacks detail on ubiquitination mechanism for hnRNPF specifically\",\n      \"pmids\": [\"37865686\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"hnRNP-F overexpression suppresses the TNFα/NFκB signaling pathway in renal tubular epithelial cells under high-glucose conditions; integrative CLIP-seq/RNA-seq analysis suggests hnRNPF binds lncRNA SNHG1 to negatively regulate inflammatory gene transcription, and also regulates alternative splicing by interacting with ZFP36 to form a complex.\",\n      \"method\": \"RNA-seq, CLIP-seq (downloaded GEO dataset), western blotting, overexpression in HK-2 and MPC5 cells\",\n      \"journal\": \"Frontiers in physiology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — integrative bioinformatic analysis plus overexpression/WB, CLIP-seq data from external source, single lab\",\n      \"pmids\": [\"40995516\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"ERK2 directly phosphorylates HNRNPF on Ser346 and Tyr356; phospho-mimetic HNRNPF more potently rescues ESC proliferation and suppresses differentiation than unphospho-mimetic mutant. HNRNPF binds Cdk1, Ccnb1, and Eed mRNAs and enhances their translation; phosphorylation of HNRNPF increases its binding to these mRNAs and promotes their translation. Hnrnpf knockout reduces ESC proliferation by downregulating CDK1 and CCNB1 and promotes differentiation by reducing EED.\",\n      \"method\": \"In vitro kinase assay (ERK2 phosphorylation), phospho-mimetic and unphospho-mimetic mutagenesis, RNA immunoprecipitation, ribosome/translation assays, Hnrnpf knockout ESCs\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro kinase assay with site-specific mutagenesis, RIP, KO rescue experiments, multiple orthogonal methods in one study\",\n      \"pmids\": [\"41495911\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"hnRNPF is recruited by the PFV Tas protein to nascent viral RNA; hnRNPF specifically recognizes a G-cluster II cis-acting element (GC-II) in the tas/bet pre-mRNA and promotes its splicing into bet mRNA (reducing unspliced tas transcript), thereby shifting viral expression from Tas to Bet and inhibiting PFV replication.\",\n      \"method\": \"Yeast two-hybrid screen, co-immunoprecipitation, splicing assays, cis-element mutation analysis, viral replication assays\",\n      \"journal\": \"Cell & bioscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — yeast two-hybrid plus Co-IP plus functional splicing assay with cis-element mutation, single lab\",\n      \"pmids\": [\"41935299\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"HNRNPF is an RNA-binding protein that recognizes G-rich sequences and G-quadruplex RNA structures to regulate alternative splicing (promoting exon inclusion), mRNA stability (e.g., Snail1, CTGF, p21/CDKN1A), and mRNA translation (Cdk1, Ccnb1, Eed); it is phosphorylated by ERK2 on Ser346/Tyr356 to enhance mRNA binding and translation in embryonic stem cells, transcriptionally repressed by FOXO1 downstream of PI3K/AKT, and its nuclear localization is inhibited by cytoplasmic lncRNA/circRNA interactions (circCacna1c, LINC03047), with its splicing activity modulated by interaction with FOXP3 through hnRNPF's second qRRM domain.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"HNRNPF is an RNA-binding protein that recognizes G-rich sequences and RNA G-quadruplex structures to control alternative splicing, mRNA stability, and translation across diverse cellular programs [#0, #10]. In splicing, HNRNPF binds G-quadruplex-forming RNA elements to promote exon inclusion, governing an EMT-associated CD44 isoform switch in a manner that depends specifically on G-quadruplex formation rather than on G-tract sequence alone [#0]. Beyond splicing, HNRNPF binds target 3' UTRs to modulate transcript stability — stabilizing Snail1 mRNA to drive EMT [#1] and, through cytoplasmic lncRNA interactions, governing CTGF and p21/CDKN1A mRNA stability [#6, #7]. In embryonic stem cells, ERK2 directly phosphorylates HNRNPF on Ser346 and Tyr356, which increases its binding to Cdk1, Ccnb1, and Eed mRNAs and enhances their translation; this phospho-regulated activity sustains proliferation and suppresses differentiation, and Hnrnpf loss reduces CDK1/CCNB1 and EED to impair proliferation [#10]. HNRNPF activity is constrained at multiple levels: FOXP3 binds its second quasi-RNA recognition motif (qRRM2) to block pre-mRNA binding [#2], FOXO1 downstream of PI3K/AKT transcriptionally represses HNRNPF [#4], and cytoplasmic noncoding RNAs (circCacna1c) sequester it to prevent nuclear translocation [#5, #6]. HNRNPF also acts in viral pre-mRNA processing, where it is recruited by the foamy virus Tas protein to a G-cluster cis-element to redirect splicing [#11].\",\n  \"teleology\": [\n    {\n      \"year\": 2017,\n      \"claim\": \"Established that HNRNPF reads RNA structure, not merely sequence — it binds G-quadruplex-forming elements to promote exon inclusion, explaining how it controls a functionally important CD44 isoform switch in EMT.\",\n      \"evidence\": \"CLIP-seq, mutational disruption of G-quadruplex while preserving G-tracts, and splicing reporter assays with knockdown\",\n      \"pmids\": [\"29269483\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define the full repertoire of G-quadruplex targets genome-wide\", \"Structural basis of qRRM-G-quadruplex recognition not resolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Revealed a protein-based brake on HNRNPF splicing activity: FOXP3 docks on the qRRM2 domain to block pre-mRNA binding, linking HNRNPF to regulatory T cell function.\",\n      \"evidence\": \"Co-IP with reciprocal domain mapping (FOXP3 exon 2, hnRNPF qRRM2 mutants) and Treg splicing/suppression assays\",\n      \"pmids\": [\"29773655\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Which endogenous splicing targets are affected in Tregs not enumerated\", \"Single lab; interaction not validated by orthogonal structural methods\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Extended HNRNPF function beyond splicing to mRNA stabilization, showing direct 3' UTR binding to Snail1 transcript stabilizes it and promotes EMT in bladder cancer.\",\n      \"evidence\": \"RIP, actinomycin D stability assay, and Snail1 truncation/mutant constructs\",\n      \"pmids\": [\"31221586\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Precise binding motif within the Snail1 3' UTR not defined\", \"Whether stabilization requires G-quadruplex unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Connected HNRNPF to cell cycle control via a protein partner, TPX2, whose levels depend on HNRNPF and whose restoration rescues the proliferation defect of HNRNPF loss.\",\n      \"evidence\": \"Mass spectrometry, Co-IP, western blot, and TPX2 overexpression rescue with flow cytometry\",\n      \"pmids\": [\"31814907\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether HNRNPF regulates TPX2 at the RNA level vs. protein level not resolved\", \"Direct RNA target underlying cyclin D1/p21 changes not identified\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Placed HNRNPF in a signaling hierarchy, showing FOXO1 downstream of PI3K/AKT directly represses HNRNPF transcription, establishing it as an output rather than a regulator of this pathway.\",\n      \"evidence\": \"ChIP and luciferase promoter assays, plus LY294002 inhibition and knockdown epistasis\",\n      \"pmids\": [\"33391425\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"FOXO1 binding site on the HNRNPF promoter not mapped to a specific element\", \"Single lab\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined a cytoplasmic sequestration mechanism: noncoding RNAs control HNRNPF by blocking its nuclear entry, with circCacna1c suppressing nuclear HNRNPF and its target RIPK1 to inhibit cardiomyocyte necroptosis, itself tuned by FTO-mediated m6A demethylation.\",\n      \"evidence\": \"RNA pull-down, nuclear/cytoplasmic fractionation, MeRIP-qPCR, and an in vivo MI model\",\n      \"pmids\": [\"39533214\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How HNRNPF activates RIPK1 expression mechanistically not detailed\", \"Generality of circRNA sequestration across cell types untested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Generalized the cytoplasmic sequestration paradigm, showing LINC03047 binds HNRNPF and retains it in the cytoplasm where it stabilizes CTGF mRNA to drive smooth muscle mitophagy and proliferation in pulmonary hypertension.\",\n      \"evidence\": \"RNA pull-down, fractionation, mRNA stability assays, knockdown, and in vivo hypoxia PH model\",\n      \"pmids\": [\"41232621\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether cytoplasmic HNRNPF stabilizes CTGF directly via 3' UTR binding not fully mapped\", \"Single lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Added further noncoding-RNA control points — USP30-AS1 disrupting HNRNPF binding to the p21 3' UTR to destabilize it, and LINC01189 promoting HNRNPF ubiquitination/degradation — linking HNRNPF turnover and target binding to cancer proliferation and invasion.\",\n      \"evidence\": \"RIP, mRNA stability and ubiquitination assays, knockdown/overexpression functional assays\",\n      \"pmids\": [\"41492473\", \"37865686\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Limited methodological detail for HNRNPF-specific binding/ubiquitination in abstracts\", \"E3 ligase mediating LINC01189-dependent degradation not identified\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Established post-translational control of HNRNPF activity, showing ERK2 phosphorylates Ser346/Tyr356 to enhance binding and translation of Cdk1, Ccnb1, and Eed mRNAs, coupling HNRNPF to ESC proliferation and self-renewal.\",\n      \"evidence\": \"In vitro kinase assay, phospho-mimetic/unphospho-mimetic mutagenesis, RIP, translation/ribosome assays, and Hnrnpf knockout ESC rescue\",\n      \"pmids\": [\"41495911\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether phosphorylation alters G-quadruplex recognition specifically not addressed\", \"Upstream signals activating ERK2 toward HNRNPF in ESCs not defined\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Demonstrated HNRNPF participates in viral RNA processing, being recruited by foamy virus Tas to a G-cluster cis-element to promote tas/bet splicing and restrict replication.\",\n      \"evidence\": \"Yeast two-hybrid, Co-IP, splicing assays with cis-element mutation, and viral replication assays\",\n      \"pmids\": [\"41935299\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the GC-II element forms a G-quadruplex recognized by HNRNPF not tested\", \"Single lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How HNRNPF integrates its dual nuclear (splicing) and cytoplasmic (stability/translation) roles, and what determines target selection across these compartments, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model of how phosphorylation and noncoding-RNA sequestration jointly partition HNRNPF between splicing and cytoplasmic functions\", \"No structural model of qRRM-G-quadruplex engagement\", \"Genome-wide direct target catalog across cell types incomplete\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 1, 10, 11]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [10]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 11]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [5, 6]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [5, 6, 7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1, 10]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"FOXP3\", \"TPX2\", \"ERK2\", \"FOXO1\", \"ZFP36\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":6,"faith_pct":66.66666666666667}}