{"gene":"CPSF1","run_date":"2026-06-09T22:57:19","timeline":{"discoveries":[{"year":2012,"finding":"CPSF1 binds a consensus polyadenylation signal (AAUAAA) in intron 6 of IL7R pre-mRNA directly downstream of the exon 6 5' splice site, and this interaction interferes with spliceosome binding, promoting exon 6 skipping. CPSF1 knockdown increased exon 6 inclusion, and mutations to the intronic AAUAAA also increased inclusion, while no evidence was found that the site produces cleaved/polyadenylated mRNAs, indicating a competition between splicing and polyadenylation machineries.","method":"RNA affinity chromatography followed by mass spectrometry to identify CPSF1 as an exon 6-binding factor; CPSF1 siRNA knockdown; mutagenesis of the intronic AAUAAA signal; minigene splicing assays","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal binding identified by RNA affinity chromatography+MS, validated by knockdown and site-directed mutagenesis with clear functional readout, multiple orthogonal methods in one study","pmids":["23151878"],"is_preprint":false},{"year":2011,"finding":"Loss-of-function mutation in zebrafish cpsf1 (grechetto mutant) causes defective polyadenylation of snrnp70 mRNA and subsequent apoptotic death of definitive HSCs in the caudal hematopoietic tissue, establishing that cpsf1-dependent 3' UTR processing of specific pre-mRNAs (including snrnp70) is required for HSC survival and differentiation.","method":"ENU mutagenesis screen in zebrafish; positional cloning; in situ hybridization; TUNEL apoptosis assay; c-myb:EGFP transgenic reporter; polyadenylation assay for snrnp70","journal":"Blood","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic loss-of-function with defined molecular substrate (snrnp70 polyadenylation defect) and specific cellular phenotype (HSC apoptosis), multiple orthogonal methods","pmids":["21330472"],"is_preprint":false},{"year":2022,"finding":"SIAH1 E3 ubiquitin ligase directly interacts with CPSF1 and promotes its ubiquitination and proteasomal degradation. Loss of SIAH1 (driven by m6A methylation) stabilizes CPSF1, which then binds the AAUAAA polyadenylation signal in androgen receptor cryptic exon CE3 to promote alternative splicing/polyadenylation generating the AR-v7 oncogenic isoform in prostate cancer.","method":"Co-immunoprecipitation (SIAH1-CPSF1 interaction); ubiquitination assay; CPSF1 RNA-binding to AR CE3 AAUAAA demonstrated by knockdown/overexpression with RT-PCR readout; m6A methylation analysis","journal":"Molecular therapy. Nucleic acids","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP for protein interaction, ubiquitination assay, and functional splicing readout, single lab","pmids":["35402071"],"is_preprint":false},{"year":2023,"finding":"CPSF1 functions as an E3 ubiquitin ligase that targets HIF-1α and MYC for proteasomal degradation. ABL kinases phosphorylate and interact with CUL4A (a cullin ring ligase adaptor) and compete with CPSF1 for CUL4A binding, thereby protecting HIF-1α and MYC from CPSF1-mediated degradation under hypoxia.","method":"FACS-based CRISPR/Cas9 screen identifying CPSF1 as HIF-1α regulator; co-immunoprecipitation of ABL kinases with CUL4A; competition binding assay between CPSF1 and ABL for CUL4A; proteasome inhibitor rescue experiments; CPSF1 knockdown with HIF-1α/MYC protein level readout","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR screen plus Co-IP plus competition assay, single lab, multiple methods but abstract-level detail limits full tier 1 assignment","pmids":["37040401"],"is_preprint":false},{"year":2025,"finding":"CPSF1 knockdown in prostate cancer cells causes widespread usage of intergenic poly(A) sites distal to annotated 3' UTRs, leading to 3' UTR lengthening and decreased levels of thousands of mRNAs including key glycolysis genes, thereby reducing glycolytic output. This establishes CPSF1 as a suppressor of intergenic polyadenylation sites.","method":"CPSF1 siRNA knockdown; global poly(A) site usage profiling (3' end sequencing); Seahorse glycolysis assay; RNA-seq","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genome-wide poly(A) site mapping plus functional metabolic readout, single lab, multiple orthogonal methods","pmids":["39847481"],"is_preprint":false},{"year":2022,"finding":"CPSF1 promotes NSDHL expression in gastric cancer via alternative polyadenylation, causing 3' UTR shortening of NSDHL mRNA; rescue assays demonstrated that NSDHL mediates the pro-tumorigenic effects of CPSF1.","method":"CPSF1 knockdown followed by RNA sequencing with 3' UTR length analysis; rescue overexpression of NSDHL; proliferation and migration assays","journal":"American journal of cancer research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, indirect RNA-seq-based mechanism with rescue assay but no direct binding demonstrated between CPSF1 and NSDHL 3' UTR","pmids":["36381317"],"is_preprint":false},{"year":2019,"finding":"Knockdown of zebrafish cpsf1 by morpholino oligonucleotide results in small eye size and abnormal projection of retinal ganglion cell axons toward the tectum, establishing a role for cpsf1 in RGC axon projection and eye development; phenotype was rescued by co-injection of cpsf1 mRNA.","method":"Morpholino knockdown in zebrafish; rescue with cpsf1 mRNA co-injection; live imaging of RGC axon projection","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — morpholino knockdown with mRNA rescue (two orthogonal manipulations), specific cellular phenotype (RGC axon projection), single lab","pmids":["30689892"],"is_preprint":false},{"year":2020,"finding":"CPSF1 suppresses phosphorylation in the MAPK/ERK pathway in human retinal vascular endothelial cells under high-glucose conditions; adeno-associated viral delivery of CPSF1 attenuated histological retinal abnormalities in a streptozotocin-induced diabetic rat model.","method":"Adeno-associated viral CPSF1 overexpression in vivo (STZ rat model); CPSF1 knockdown/overexpression in HRVECs; Western blotting for p-ERK/ERK; apoptosis and migration assays","journal":"Archives of physiology and biochemistry","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, pathway placement based on phospho-western without direct binding or epistasis evidence","pmids":["32046510"],"is_preprint":false},{"year":2025,"finding":"HSF1 binds to the promoter region of CPSF1 to regulate its transcription; CPSF1 in turn modulates expression of SREBP1, influencing milk fat synthesis; both HSF1 and CPSF1 affect milk fat and protein synthesis through the AKT/mTOR signaling pathway in MAC-T cells.","method":"ChIP or promoter binding assay (HSF1 at CPSF1 promoter); CPSF1 knockdown/overexpression; SREBP1 expression readout; AKT/mTOR pathway western blotting in MAC-T cells","journal":"Journal of animal science","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, abstract does not specify ChIP methodology rigorously, indirect pathway placement","pmids":["39932399"],"is_preprint":false}],"current_model":"CPSF1 (CPSF160) is the largest subunit of the cleavage and polyadenylation specificity factor complex; it binds AAUAAA polyadenylation signals on pre-mRNAs to direct 3' end cleavage and polyadenylation, and can also compete with spliceosome assembly at adjacent 5' splice sites to regulate alternative splicing (e.g., IL7R exon 6 and AR-v7); it suppresses intergenic poly(A) site usage genome-wide; it is subject to ubiquitin-mediated degradation by SIAH1, and itself acts as an E3 ligase component (through CUL4A) targeting HIF-1α and MYC for proteasomal degradation in a manner antagonized by ABL kinase phosphorylation of CUL4A; loss of cpsf1 in zebrafish causes defective polyadenylation of snrnp70, HSC apoptosis, and aberrant retinal ganglion cell axon projection."},"narrative":{"mechanistic_narrative":"CPSF1 is a sequence-specific recognition factor for the AAUAAA polyadenylation signal that governs pre-mRNA 3' end formation and, through this activity, shapes alternative splicing and isoform choice [PMID:23151878, PMID:35402071]. By binding intronic AAUAAA signals positioned near 5' splice sites, CPSF1 competes with spliceosome assembly to drive exon skipping (IL7R exon 6) and cryptic-exon polyadenylation (AR-v7 in prostate cancer), coupling 3' end processing to splice-site selection [PMID:23151878, PMID:35402071]. Genome-wide, CPSF1 acts as a suppressor of intergenic poly(A) site usage; its loss causes use of distal poly(A) sites, 3' UTR lengthening, and reduced mRNA levels for glycolysis genes, lowering glycolytic output [PMID:39847481]. Beyond RNA processing, CPSF1 participates in protein degradation: it is itself ubiquitinated and degraded by the SIAH1 E3 ligase [PMID:35402071], and it functions as a CUL4A-associated E3 ligase component that targets HIF-1α and MYC for proteasomal degradation, an activity antagonized by ABL-mediated phosphorylation of CUL4A [PMID:37040401]. In vivo, loss of cpsf1 in zebrafish causes defective polyadenylation of snrnp70, apoptotic loss of hematopoietic stem cells, and aberrant retinal ganglion cell axon projection with reduced eye size [PMID:21330472, PMID:30689892].","teleology":[{"year":2011,"claim":"Whether CPSF1-dependent 3' end processing is required for a specific developmental program was unknown; a zebrafish loss-of-function mutant linked cpsf1 to defined substrate processing and cell survival.","evidence":"ENU mutagenesis, positional cloning, TUNEL and reporter assays, and a snrnp70 polyadenylation assay in the grechetto mutant","pmids":["21330472"],"confidence":"High","gaps":["Did not define how broadly cpsf1 processes substrates beyond snrnp70","Mechanism of substrate selectivity not established"]},{"year":2012,"claim":"It was unclear how polyadenylation machinery could affect splicing; CPSF1 was shown to bind an intronic AAUAAA near a 5' splice site and block spliceosome binding, establishing competition between the two machineries.","evidence":"RNA affinity chromatography with MS, siRNA knockdown, AAUAAA mutagenesis, and minigene splicing assays on IL7R exon 6","pmids":["23151878"],"confidence":"High","gaps":["Did not resolve structural basis of spliceosome exclusion","Generality of splice-competition across transcripts not tested"]},{"year":2019,"claim":"Whether cpsf1 contributes to neural development was unaddressed; knockdown linked it to retinal ganglion cell axon guidance and eye size.","evidence":"Morpholino knockdown with mRNA rescue and live imaging of RGC axons in zebrafish","pmids":["30689892"],"confidence":"Medium","gaps":["Molecular substrate underlying the axon phenotype not identified","Morpholino specificity supported only by mRNA rescue"]},{"year":2020,"claim":"A possible signaling role was raised by data placing CPSF1 upstream of MAPK/ERK in retinal endothelial cells under high glucose.","evidence":"AAV overexpression in an STZ diabetic rat model plus knockdown/overexpression with p-ERK western blotting in HRVECs","pmids":["32046510"],"confidence":"Low","gaps":["Pathway placement rests on phospho-western without direct binding or epistasis","Single lab, no mechanistic link to RNA processing"]},{"year":2022,"claim":"How CPSF1 abundance is controlled and how it drives an oncogenic isoform was addressed by identifying SIAH1-mediated degradation and CPSF1 binding to the AR-v7 cryptic-exon AAUAAA.","evidence":"Co-IP, ubiquitination assay, m6A analysis, and CPSF1 manipulation with RT-PCR readout of AR CE3 in prostate cancer","pmids":["35402071"],"confidence":"Medium","gaps":["SIAH1-CPSF1 interaction from Co-IP without reciprocal structural validation","Direct CPSF1 occupancy on CE3 inferred from functional readouts"]},{"year":2022,"claim":"A pro-tumorigenic APA function in gastric cancer was proposed via CPSF1-driven 3' UTR shortening of NSDHL.","evidence":"Knockdown with RNA-seq 3' UTR length analysis and NSDHL rescue in proliferation/migration assays","pmids":["36381317"],"confidence":"Low","gaps":["No direct binding shown between CPSF1 and the NSDHL 3' UTR","Mechanism inferred from RNA-seq rather than direct measurement"]},{"year":2023,"claim":"An unexpected protein-degradation activity was uncovered: CPSF1 acts as a CUL4A-associated E3 ligase targeting HIF-1α and MYC, with ABL kinase antagonism providing hypoxic regulation.","evidence":"FACS-based CRISPR screen, Co-IP of ABL with CUL4A, CPSF1/ABL competition binding, proteasome rescue, and protein-level readouts","pmids":["37040401"],"confidence":"Medium","gaps":["Direct ubiquitin transfer by a CPSF1-CUL4A complex not biochemically reconstituted","Relationship between this ligase role and CPSF1's RNA-processing function unresolved"]},{"year":2025,"claim":"The genome-wide consequence of CPSF1 loss was defined as derepression of intergenic poly(A) sites, linking 3' UTR lengthening to suppressed glycolysis.","evidence":"siRNA knockdown with 3' end sequencing, RNA-seq, and Seahorse glycolysis assays in prostate cancer cells","pmids":["39847481"],"confidence":"Medium","gaps":["Direct CPSF1 occupancy at suppressed intergenic sites not mapped","Single cancer model"]},{"year":2025,"claim":"Transcriptional and metabolic context was extended by placing CPSF1 downstream of HSF1 and upstream of SREBP1 and AKT/mTOR in milk fat synthesis.","evidence":"Promoter-binding/ChIP for HSF1 at CPSF1, CPSF1 manipulation, and AKT/mTOR westerns in MAC-T cells","pmids":["39932399"],"confidence":"Low","gaps":["ChIP rigor unspecified and pathway placement indirect","No direct CPSF1 RNA-processing target tied to SREBP1"]},{"year":null,"claim":"How CPSF1's canonical role in poly(A) signal recognition is mechanistically reconciled with its reported CUL4A-dependent E3 ligase activity, and what determines substrate selection in each role, remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model integrating RNA-binding and ubiquitin-ligase functions","Substrate selectivity rules for both activities undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,1,2,4]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[1,4]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[3]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[3]}],"localization":[],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1,4]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[3]}],"complexes":["CPSF"],"partners":["SIAH1","CUL4A"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q10570","full_name":"Cleavage and polyadenylation specificity factor subunit 1","aliases":["Cleavage and polyadenylation specificity factor 160 kDa subunit","CPSF 160 kDa subunit"],"length_aa":1443,"mass_kda":160.9,"function":"Component of the cleavage and polyadenylation specificity factor (CPSF) complex that plays a key role in pre-mRNA 3'-end formation, recognizing the AAUAAA signal sequence and interacting with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition. This subunit is involved in the RNA recognition step of the polyadenylation reaction (PubMed:14749727). May play a role in eye morphogenesis and the development of retinal ganglion cell projections to the midbrain (By similarity)","subcellular_location":"Nucleus, nucleoplasm","url":"https://www.uniprot.org/uniprotkb/Q10570/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/CPSF1","classification":"Common Essential","n_dependent_lines":1194,"n_total_lines":1208,"dependency_fraction":0.9884105960264901},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CPSF6","stoichiometry":0.2},{"gene":"FKBP5","stoichiometry":0.2},{"gene":"RBM14","stoichiometry":0.2},{"gene":"SNRPA","stoichiometry":0.2},{"gene":"SNRPB","stoichiometry":0.2},{"gene":"SNRPC","stoichiometry":0.2},{"gene":"SSRP1","stoichiometry":0.2},{"gene":"TOP1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/CPSF1","total_profiled":1310},"omim":[{"mim_id":"618827","title":"MYOPIA 27, AUTOSOMAL DOMINANT; MYP27","url":"https://www.omim.org/entry/618827"},{"mim_id":"618082","title":"WD REPEAT-CONTAINING PROTEIN 33; WDR33","url":"https://www.omim.org/entry/618082"},{"mim_id":"606028","title":"CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 2; CPSF2","url":"https://www.omim.org/entry/606028"},{"mim_id":"606027","title":"CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 1; CPSF1","url":"https://www.omim.org/entry/606027"},{"mim_id":"602388","title":"SYMPLEKIN; SYMPK","url":"https://www.omim.org/entry/602388"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CPSF1"},"hgnc":{"alias_symbol":["CPSF160"],"prev_symbol":[]},"alphafold":{"accession":"Q10570","domains":[{"cath_id":"-","chopping":"473-521_1003-1020","consensus_level":"medium","plddt":90.5555,"start":473,"end":1020},{"cath_id":"-","chopping":"693-713_779-824_845-897","consensus_level":"medium","plddt":89.9147,"start":693,"end":897},{"cath_id":"2.130.10.10","chopping":"1024-1185","consensus_level":"medium","plddt":92.861,"start":1024,"end":1185},{"cath_id":"2.130.10.10","chopping":"1209-1343","consensus_level":"medium","plddt":91.0641,"start":1209,"end":1343}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q10570","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q10570-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q10570-F1-predicted_aligned_error_v6.png","plddt_mean":82.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CPSF1","jax_strain_url":"https://www.jax.org/strain/search?query=CPSF1"},"sequence":{"accession":"Q10570","fasta_url":"https://rest.uniprot.org/uniprotkb/Q10570.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q10570/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q10570"}},"corpus_meta":[{"pmid":"23151878","id":"PMC_23151878","title":"Cleavage and polyadenylation specificity factor 1 (CPSF1) regulates alternative splicing of interleukin 7 receptor (IL7R) exon 6.","date":"2012","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/23151878","citation_count":37,"is_preprint":false},{"pmid":"30689892","id":"PMC_30689892","title":"CPSF1 mutations are associated with early-onset high myopia and involved in retinal ganglion cell axon projection.","date":"2019","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30689892","citation_count":35,"is_preprint":false},{"pmid":"21330472","id":"PMC_21330472","title":"cpsf1 is required for definitive HSC survival in zebrafish.","date":"2011","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/21330472","citation_count":30,"is_preprint":false},{"pmid":"11369601","id":"PMC_11369601","title":"Overexpression of the CstF-64 and CPSF-160 polyadenylation protein messenger RNAs in mouse male germ cells.","date":"2001","source":"Biology of reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/11369601","citation_count":28,"is_preprint":false},{"pmid":"32437477","id":"PMC_32437477","title":"Aberrant expression of CPSF1 promotes head and neck squamous cell carcinoma via regulating alternative splicing.","date":"2020","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/32437477","citation_count":17,"is_preprint":false},{"pmid":"35402071","id":"PMC_35402071","title":"m6A-induced repression of SIAH1 facilitates alternative splicing of androgen receptor variant 7 by regulating CPSF1.","date":"2022","source":"Molecular therapy. Nucleic acids","url":"https://pubmed.ncbi.nlm.nih.gov/35402071","citation_count":14,"is_preprint":false},{"pmid":"32046510","id":"PMC_32046510","title":"CPSF1 mediates retinal vascular dysfunction in diabetes mellitus via the MAPK/ERK pathway.","date":"2020","source":"Archives of physiology and biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32046510","citation_count":11,"is_preprint":false},{"pmid":"37040401","id":"PMC_37040401","title":"ABL kinases regulate the stabilization of HIF-1α and MYC through CPSF1.","date":"2023","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/37040401","citation_count":9,"is_preprint":false},{"pmid":"35002215","id":"PMC_35002215","title":"Mutational screening of AGRN, SLC39A5, SCO2, P4HA2, BSG, ZNF644, and CPSF1 in a Chinese cohort of 103 patients with nonsyndromic high myopia.","date":"2021","source":"Molecular vision","url":"https://pubmed.ncbi.nlm.nih.gov/35002215","citation_count":8,"is_preprint":false},{"pmid":"36381317","id":"PMC_36381317","title":"CPSF1 positively regulates NSDHL by alternative polyadenylation and promotes gastric cancer progression.","date":"2022","source":"American journal of cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/36381317","citation_count":5,"is_preprint":false},{"pmid":"38174951","id":"PMC_38174951","title":"Integrated RNA expression and alternative polyadenylation analysis identified CPSF1-CCDC137 oncogenic axis in lung adenocarcinoma.","date":"2024","source":"Environmental toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/38174951","citation_count":3,"is_preprint":false},{"pmid":"36671487","id":"PMC_36671487","title":"Circ-CPSF1 Worsens Radiation-Induced Oxidative Stress Injury in Caenorhabditis elegans.","date":"2023","source":"Biomolecules","url":"https://pubmed.ncbi.nlm.nih.gov/36671487","citation_count":2,"is_preprint":false},{"pmid":"39847481","id":"PMC_39847481","title":"CPSF1 inhibition promotes widespread use of intergenic polyadenylation sites and impairs glycolysis in prostate cancer cells.","date":"2025","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/39847481","citation_count":1,"is_preprint":false},{"pmid":"39932399","id":"PMC_39932399","title":"HSF1 and CPSF1 affect milk fat and protein synthesis by regulating the AKT/mTOR signaling pathway.","date":"2025","source":"Journal of animal science","url":"https://pubmed.ncbi.nlm.nih.gov/39932399","citation_count":0,"is_preprint":false},{"pmid":"41463412","id":"PMC_41463412","title":"CPSF1 Is Co-Amplified with MYC but Is Independently Associated with Alternative Polyadenylation in Cancer.","date":"2025","source":"Biology","url":"https://pubmed.ncbi.nlm.nih.gov/41463412","citation_count":0,"is_preprint":false},{"pmid":"39838867","id":"PMC_39838867","title":"RETRACTION: Integrated RNA Expression and Alternative Polyadenylation Analysis Identified CPSF1-CCDC137 Oncogenic Axis in Lung Adenocarcinoma.","date":"2025","source":"Environmental toxicology","url":"https://pubmed.ncbi.nlm.nih.gov/39838867","citation_count":0,"is_preprint":false},{"pmid":"41498167","id":"PMC_41498167","title":"A Homozygous CPSF1 Variant Causes Congenital Cataract, Intellectual Disability and Hyperphagia.","date":"2026","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/41498167","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10061,"output_tokens":2722,"usd":0.035507,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9893,"output_tokens":3109,"usd":0.063595,"stage2_stop_reason":"end_turn"},"total_usd":0.099102,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2012,\n      \"finding\": \"CPSF1 binds a consensus polyadenylation signal (AAUAAA) in intron 6 of IL7R pre-mRNA directly downstream of the exon 6 5' splice site, and this interaction interferes with spliceosome binding, promoting exon 6 skipping. CPSF1 knockdown increased exon 6 inclusion, and mutations to the intronic AAUAAA also increased inclusion, while no evidence was found that the site produces cleaved/polyadenylated mRNAs, indicating a competition between splicing and polyadenylation machineries.\",\n      \"method\": \"RNA affinity chromatography followed by mass spectrometry to identify CPSF1 as an exon 6-binding factor; CPSF1 siRNA knockdown; mutagenesis of the intronic AAUAAA signal; minigene splicing assays\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal binding identified by RNA affinity chromatography+MS, validated by knockdown and site-directed mutagenesis with clear functional readout, multiple orthogonal methods in one study\",\n      \"pmids\": [\"23151878\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Loss-of-function mutation in zebrafish cpsf1 (grechetto mutant) causes defective polyadenylation of snrnp70 mRNA and subsequent apoptotic death of definitive HSCs in the caudal hematopoietic tissue, establishing that cpsf1-dependent 3' UTR processing of specific pre-mRNAs (including snrnp70) is required for HSC survival and differentiation.\",\n      \"method\": \"ENU mutagenesis screen in zebrafish; positional cloning; in situ hybridization; TUNEL apoptosis assay; c-myb:EGFP transgenic reporter; polyadenylation assay for snrnp70\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic loss-of-function with defined molecular substrate (snrnp70 polyadenylation defect) and specific cellular phenotype (HSC apoptosis), multiple orthogonal methods\",\n      \"pmids\": [\"21330472\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SIAH1 E3 ubiquitin ligase directly interacts with CPSF1 and promotes its ubiquitination and proteasomal degradation. Loss of SIAH1 (driven by m6A methylation) stabilizes CPSF1, which then binds the AAUAAA polyadenylation signal in androgen receptor cryptic exon CE3 to promote alternative splicing/polyadenylation generating the AR-v7 oncogenic isoform in prostate cancer.\",\n      \"method\": \"Co-immunoprecipitation (SIAH1-CPSF1 interaction); ubiquitination assay; CPSF1 RNA-binding to AR CE3 AAUAAA demonstrated by knockdown/overexpression with RT-PCR readout; m6A methylation analysis\",\n      \"journal\": \"Molecular therapy. Nucleic acids\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP for protein interaction, ubiquitination assay, and functional splicing readout, single lab\",\n      \"pmids\": [\"35402071\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CPSF1 functions as an E3 ubiquitin ligase that targets HIF-1α and MYC for proteasomal degradation. ABL kinases phosphorylate and interact with CUL4A (a cullin ring ligase adaptor) and compete with CPSF1 for CUL4A binding, thereby protecting HIF-1α and MYC from CPSF1-mediated degradation under hypoxia.\",\n      \"method\": \"FACS-based CRISPR/Cas9 screen identifying CPSF1 as HIF-1α regulator; co-immunoprecipitation of ABL kinases with CUL4A; competition binding assay between CPSF1 and ABL for CUL4A; proteasome inhibitor rescue experiments; CPSF1 knockdown with HIF-1α/MYC protein level readout\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR screen plus Co-IP plus competition assay, single lab, multiple methods but abstract-level detail limits full tier 1 assignment\",\n      \"pmids\": [\"37040401\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CPSF1 knockdown in prostate cancer cells causes widespread usage of intergenic poly(A) sites distal to annotated 3' UTRs, leading to 3' UTR lengthening and decreased levels of thousands of mRNAs including key glycolysis genes, thereby reducing glycolytic output. This establishes CPSF1 as a suppressor of intergenic polyadenylation sites.\",\n      \"method\": \"CPSF1 siRNA knockdown; global poly(A) site usage profiling (3' end sequencing); Seahorse glycolysis assay; RNA-seq\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genome-wide poly(A) site mapping plus functional metabolic readout, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"39847481\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CPSF1 promotes NSDHL expression in gastric cancer via alternative polyadenylation, causing 3' UTR shortening of NSDHL mRNA; rescue assays demonstrated that NSDHL mediates the pro-tumorigenic effects of CPSF1.\",\n      \"method\": \"CPSF1 knockdown followed by RNA sequencing with 3' UTR length analysis; rescue overexpression of NSDHL; proliferation and migration assays\",\n      \"journal\": \"American journal of cancer research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, indirect RNA-seq-based mechanism with rescue assay but no direct binding demonstrated between CPSF1 and NSDHL 3' UTR\",\n      \"pmids\": [\"36381317\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Knockdown of zebrafish cpsf1 by morpholino oligonucleotide results in small eye size and abnormal projection of retinal ganglion cell axons toward the tectum, establishing a role for cpsf1 in RGC axon projection and eye development; phenotype was rescued by co-injection of cpsf1 mRNA.\",\n      \"method\": \"Morpholino knockdown in zebrafish; rescue with cpsf1 mRNA co-injection; live imaging of RGC axon projection\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — morpholino knockdown with mRNA rescue (two orthogonal manipulations), specific cellular phenotype (RGC axon projection), single lab\",\n      \"pmids\": [\"30689892\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"CPSF1 suppresses phosphorylation in the MAPK/ERK pathway in human retinal vascular endothelial cells under high-glucose conditions; adeno-associated viral delivery of CPSF1 attenuated histological retinal abnormalities in a streptozotocin-induced diabetic rat model.\",\n      \"method\": \"Adeno-associated viral CPSF1 overexpression in vivo (STZ rat model); CPSF1 knockdown/overexpression in HRVECs; Western blotting for p-ERK/ERK; apoptosis and migration assays\",\n      \"journal\": \"Archives of physiology and biochemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, pathway placement based on phospho-western without direct binding or epistasis evidence\",\n      \"pmids\": [\"32046510\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"HSF1 binds to the promoter region of CPSF1 to regulate its transcription; CPSF1 in turn modulates expression of SREBP1, influencing milk fat synthesis; both HSF1 and CPSF1 affect milk fat and protein synthesis through the AKT/mTOR signaling pathway in MAC-T cells.\",\n      \"method\": \"ChIP or promoter binding assay (HSF1 at CPSF1 promoter); CPSF1 knockdown/overexpression; SREBP1 expression readout; AKT/mTOR pathway western blotting in MAC-T cells\",\n      \"journal\": \"Journal of animal science\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, abstract does not specify ChIP methodology rigorously, indirect pathway placement\",\n      \"pmids\": [\"39932399\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CPSF1 (CPSF160) is the largest subunit of the cleavage and polyadenylation specificity factor complex; it binds AAUAAA polyadenylation signals on pre-mRNAs to direct 3' end cleavage and polyadenylation, and can also compete with spliceosome assembly at adjacent 5' splice sites to regulate alternative splicing (e.g., IL7R exon 6 and AR-v7); it suppresses intergenic poly(A) site usage genome-wide; it is subject to ubiquitin-mediated degradation by SIAH1, and itself acts as an E3 ligase component (through CUL4A) targeting HIF-1α and MYC for proteasomal degradation in a manner antagonized by ABL kinase phosphorylation of CUL4A; loss of cpsf1 in zebrafish causes defective polyadenylation of snrnp70, HSC apoptosis, and aberrant retinal ganglion cell axon projection.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CPSF1 is a sequence-specific recognition factor for the AAUAAA polyadenylation signal that governs pre-mRNA 3' end formation and, through this activity, shapes alternative splicing and isoform choice [#0, #2]. By binding intronic AAUAAA signals positioned near 5' splice sites, CPSF1 competes with spliceosome assembly to drive exon skipping (IL7R exon 6) and cryptic-exon polyadenylation (AR-v7 in prostate cancer), coupling 3' end processing to splice-site selection [#0, #2]. Genome-wide, CPSF1 acts as a suppressor of intergenic poly(A) site usage; its loss causes use of distal poly(A) sites, 3' UTR lengthening, and reduced mRNA levels for glycolysis genes, lowering glycolytic output [#4]. Beyond RNA processing, CPSF1 participates in protein degradation: it is itself ubiquitinated and degraded by the SIAH1 E3 ligase [#2], and it functions as a CUL4A-associated E3 ligase component that targets HIF-1\\u03b1 and MYC for proteasomal degradation, an activity antagonized by ABL-mediated phosphorylation of CUL4A [#3]. In vivo, loss of cpsf1 in zebrafish causes defective polyadenylation of snrnp70, apoptotic loss of hematopoietic stem cells, and aberrant retinal ganglion cell axon projection with reduced eye size [#1, #6].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"Whether CPSF1-dependent 3' end processing is required for a specific developmental program was unknown; a zebrafish loss-of-function mutant linked cpsf1 to defined substrate processing and cell survival.\",\n      \"evidence\": \"ENU mutagenesis, positional cloning, TUNEL and reporter assays, and a snrnp70 polyadenylation assay in the grechetto mutant\",\n      \"pmids\": [\"21330472\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define how broadly cpsf1 processes substrates beyond snrnp70\", \"Mechanism of substrate selectivity not established\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"It was unclear how polyadenylation machinery could affect splicing; CPSF1 was shown to bind an intronic AAUAAA near a 5' splice site and block spliceosome binding, establishing competition between the two machineries.\",\n      \"evidence\": \"RNA affinity chromatography with MS, siRNA knockdown, AAUAAA mutagenesis, and minigene splicing assays on IL7R exon 6\",\n      \"pmids\": [\"23151878\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve structural basis of spliceosome exclusion\", \"Generality of splice-competition across transcripts not tested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Whether cpsf1 contributes to neural development was unaddressed; knockdown linked it to retinal ganglion cell axon guidance and eye size.\",\n      \"evidence\": \"Morpholino knockdown with mRNA rescue and live imaging of RGC axons in zebrafish\",\n      \"pmids\": [\"30689892\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular substrate underlying the axon phenotype not identified\", \"Morpholino specificity supported only by mRNA rescue\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"A possible signaling role was raised by data placing CPSF1 upstream of MAPK/ERK in retinal endothelial cells under high glucose.\",\n      \"evidence\": \"AAV overexpression in an STZ diabetic rat model plus knockdown/overexpression with p-ERK western blotting in HRVECs\",\n      \"pmids\": [\"32046510\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Pathway placement rests on phospho-western without direct binding or epistasis\", \"Single lab, no mechanistic link to RNA processing\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"How CPSF1 abundance is controlled and how it drives an oncogenic isoform was addressed by identifying SIAH1-mediated degradation and CPSF1 binding to the AR-v7 cryptic-exon AAUAAA.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, m6A analysis, and CPSF1 manipulation with RT-PCR readout of AR CE3 in prostate cancer\",\n      \"pmids\": [\"35402071\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"SIAH1-CPSF1 interaction from Co-IP without reciprocal structural validation\", \"Direct CPSF1 occupancy on CE3 inferred from functional readouts\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"A pro-tumorigenic APA function in gastric cancer was proposed via CPSF1-driven 3' UTR shortening of NSDHL.\",\n      \"evidence\": \"Knockdown with RNA-seq 3' UTR length analysis and NSDHL rescue in proliferation/migration assays\",\n      \"pmids\": [\"36381317\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct binding shown between CPSF1 and the NSDHL 3' UTR\", \"Mechanism inferred from RNA-seq rather than direct measurement\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"An unexpected protein-degradation activity was uncovered: CPSF1 acts as a CUL4A-associated E3 ligase targeting HIF-1\\u03b1 and MYC, with ABL kinase antagonism providing hypoxic regulation.\",\n      \"evidence\": \"FACS-based CRISPR screen, Co-IP of ABL with CUL4A, CPSF1/ABL competition binding, proteasome rescue, and protein-level readouts\",\n      \"pmids\": [\"37040401\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct ubiquitin transfer by a CPSF1-CUL4A complex not biochemically reconstituted\", \"Relationship between this ligase role and CPSF1's RNA-processing function unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"The genome-wide consequence of CPSF1 loss was defined as derepression of intergenic poly(A) sites, linking 3' UTR lengthening to suppressed glycolysis.\",\n      \"evidence\": \"siRNA knockdown with 3' end sequencing, RNA-seq, and Seahorse glycolysis assays in prostate cancer cells\",\n      \"pmids\": [\"39847481\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct CPSF1 occupancy at suppressed intergenic sites not mapped\", \"Single cancer model\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Transcriptional and metabolic context was extended by placing CPSF1 downstream of HSF1 and upstream of SREBP1 and AKT/mTOR in milk fat synthesis.\",\n      \"evidence\": \"Promoter-binding/ChIP for HSF1 at CPSF1, CPSF1 manipulation, and AKT/mTOR westerns in MAC-T cells\",\n      \"pmids\": [\"39932399\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"ChIP rigor unspecified and pathway placement indirect\", \"No direct CPSF1 RNA-processing target tied to SREBP1\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CPSF1's canonical role in poly(A) signal recognition is mechanistically reconciled with its reported CUL4A-dependent E3 ligase activity, and what determines substrate selection in each role, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model integrating RNA-binding and ubiquitin-ligase functions\", \"Substrate selectivity rules for both activities undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 1, 2, 4]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [1, 4]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1, 4]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\"CPSF\"],\n    \"partners\": [\"SIAH1\", \"CUL4A\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}