{"gene":"CPSF6","run_date":"2026-06-09T22:57:19","timeline":{"discoveries":[{"year":2012,"finding":"CPSF6 binds to a novel protein-protein interface in the N-terminal domain of HIV-1 capsid (CA), defined by X-ray crystallography; this interface is conserved across lentiviruses and is accessible in the hexameric lattice. A truncated cytosolic form, CPSF6-358, restricts HIV-1 by binding this interface, and mutations that abolish CPSF6 binding also relieve dependence on nuclear entry cofactors TNPO3 and RanBP2.","method":"X-ray crystallography, mutagenesis, infectivity assays, binding assays","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus mutagenesis plus functional infectivity assays; replicated in multiple subsequent studies","pmids":["22956906"],"is_preprint":false},{"year":2014,"finding":"CPSF6 binds the assembled HIV-1 CA hexamer at the NTD-CTD interface pocket with at least 10-fold higher affinity than non-assembled CA or isolated domains; crystal structure of PF74 in complex with the hexamer shows CPSF6 and the drug bind the same preformed pocket, indicating the assembled capsid lattice is the principal binding target.","method":"Biochemical binding assays, X-ray crystallography of CA hexamer complexes","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstitution of hexameric complexes, crystal structure, quantitative binding measurements; independent from earlier structural paper","pmids":["25518861"],"is_preprint":false},{"year":2013,"finding":"TNPO3 promotes HIV-1 infectivity indirectly by importing CPSF6 into the nucleus; when TNPO3 is knocked down, CPSF6 accumulates in the cytoplasm and abnormally stabilizes the HIV-1 CA core, blocking infection. Mislocalization of CPSF6 to the cytoplasm (via NLS deletion or nuclear export signal fusion) phenocopies TNPO3 knockdown, while targeting CPSF6 to the nucleus with a heterologous NLS rescues infection. Sensitivity of 27 CA mutants to TNPO3 knockdown correlates strongly with sensitivity to CPSF6-358 inhibition (R²=0.883).","method":"TNPO3 knockdown, CPSF6 localization mutants, fate-of-capsid assays, 2-LTR circle quantification, correlation of CA mutant panels","journal":"Retrovirology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (genetic, cell biology, biochemistry), large CA mutant panel correlation, replicated by independent lab (PMID 23622145)","pmids":["23414560"],"is_preprint":false},{"year":2013,"finding":"Cytoplasmic full-length CPSF6 (overexpressed without NLS) blocks HIV-1 nuclear import and enhances stability of the HIV-1 core; simultaneous depletion of both TNPO3 and CPSF6 rescues HIV-1 infection that is blocked by TNPO3 depletion alone, establishing CPSF6 as the effector of TNPO3-dependent restriction.","method":"siRNA depletion, cytoplasmic CPSF6 overexpression, fate-of-capsid assay, infectivity rescue","journal":"Retrovirology","confidence":"High","confidence_rationale":"Tier 2 / Strong — epistatic rescue experiment, capsid stability assay, multiple conditions; corroborates PMID 23414560","pmids":["23622145"],"is_preprint":false},{"year":2013,"finding":"A carboxy-terminally truncated CPSF6 variant (hCPSF6-375, lacking exon 6) aberrantly accelerates HIV-1 capsid disassembly in target cells and inhibits viral cDNA synthesis; residues encoded by exon 6 are responsible for the cDNA synthesis block. This is mechanistically distinct from CPSF6-358, which does not accelerate uncoating.","method":"cDNA expression cloning, ganciclovir-mediated selection, mutational analysis, capsid disassembly assay, viral cDNA quantification","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain mapping by mutagenesis plus mechanistic phenotype readout; single lab","pmids":["23658440"],"is_preprint":false},{"year":2016,"finding":"CPSF6 knockout preferentially decreases HIV-1 integration into transcriptionally active genes, spliced genes, and euchromatic regions; capsid-binding-deficient CPSF6 fails to rescue integration site distribution. Dual knockout of CPSF6 and LEDGF/p75 showed CPSF6 plays a more dominant role in directing integration to euchromatin, while LEDGF/p75 mainly directs positional targeting within gene bodies, establishing two mechanistically distinct pathways.","method":"CPSF6 knockout, LEDGF/p75 depletion, integration site sequencing, CPSF6 complementation with capsid-binding mutant","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — KO with rescue (including binding-deficient mutant), integration site deep sequencing, epistasis with LEDGF/p75","pmids":["26858452"],"is_preprint":false},{"year":2016,"finding":"The majority of cellular CPSF6 is incorporated into the CFIm complex (with CPSF5/CFIm25 and CPSF7); HIV-1 capsid recruits the CFIm complex in a CPSF6-dependent manner. However, CPSF6 incorporation into CFIm is not required for its ability to direct HIV-1 integration into genes; CPSF6 alone, independent of its CFIm partners CPSF5 and CPSF7, controls the key molecular interactions for PIC trafficking to active chromatin.","method":"Co-immunoprecipitation, CFIm-disrupting CPSF6 mutants, integration site analysis, virological assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP plus mutagenesis plus integration site sequencing; dissects complex subunit requirements","pmids":["26994143"],"is_preprint":false},{"year":2017,"finding":"CFIm (CPSF6/CFIm68 and CPSF5/CFIm59 subunits) functions as an enhancer-dependent activator of mRNA 3' processing; CFIm regulates global alternative polyadenylation by binding and activating enhancer-containing poly(A) sites. The RS domains of CFIm68/59 bind specifically to an RS-like region in CPSF/Fip1, and this interaction is inhibited by hyper-phosphorylation of CFIm68/59.","method":"Biochemical binding assays, APA profiling, RS-domain mutagenesis, phosphorylation analysis","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution of RS-domain interaction, mutagenesis, global APA profiling; multiple orthogonal methods","pmids":["29276085"],"is_preprint":false},{"year":2018,"finding":"Capsid-CPSF6 interaction licenses HIV-1 trafficking throughout the nuclear interior; loss of CPSF6 interaction dramatically shifts virus localization to the nuclear periphery and redirects integration into transcriptionally repressed lamina-associated heterochromatin, while loss of LEDGF/p75 does not significantly affect intranuclear HIV-1 localization. CPSF6 serves as a master regulator of HIV-1 intranuclear localization.","method":"Live-cell and fixed imaging of HIV-1 nuclear localization, CPSF6 knockout/complementation, integration site sequencing","journal":"Cell host & microbe","confidence":"High","confidence_rationale":"Tier 2 / Strong — quantitative imaging plus KO/rescue plus integration site analysis; multiple orthogonal methods","pmids":["30173955"],"is_preprint":false},{"year":2018,"finding":"Truncated CPSF6-358 forms higher-order oligomeric complexes that bind assembled wild-type HIV-1 CA tubes but not CA tubes bearing a CPSF6 binding-site mutation; binding physically disrupts the tubular capsid assemblies. In cells, CPSF6-358 forms cytoplasmic puncta upon HIV-1 infection, leading to capsid permeabilization in a capsid-binding-dependent manner.","method":"In vitro binding with purified CPSF6-358 oligomers and CA tubes, transmission electron microscopy, live- and fixed-cell imaging, capsid permeabilization assay","journal":"Journal of virology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with EM plus in cellulo imaging; single lab but multiple orthogonal methods","pmids":["29643241"],"is_preprint":false},{"year":2019,"finding":"CPSF6 is strongly recruited to nuclear HIV-1 replication complexes (but absent from cytoplasmic RTC/PIC) in primary human macrophages. Depletion of CPSF6 or lack of CPSF6 binding causes accumulation of HIV-1 subviral complexes at the nuclear envelope. STED microscopy showed that CPSF6-binding-deficient complexes are retained inside the nuclear pore in a CA-multimer-dependent manner, with CPSF6 clustering adjacent to the nuclear basket, suggesting consecutive Nup153/CPSF6 binding to the hexameric lattice mediates nuclear entry.","method":"Quantitative fluorescence microscopy, CPSF6 depletion, STED super-resolution microscopy, primary macrophage infection","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — super-resolution microscopy plus depletion plus primary cells; multiple imaging modalities","pmids":["30672737"],"is_preprint":false},{"year":2019,"finding":"The arginine/serine-like domain (RSLD) of CPSF6 mediates TNPO3 binding and is critical for CPSF6 nuclear import; the crystal structure of the RSLD-TNPO3 complex identified specific interaction residues confirmed by mutagenesis. RSLD phosphorylation is not required for TNPO3 binding or nuclear import, but a hyperphosphorylated mimetic mutant fails to bind TNPO3 and mislocalizes to the cytoplasm. Hypophosphorylated CPSF6 extends 3' UTRs similarly to depletion of CFIIm components.","method":"Crystal structure of RSLD-TNPO3 complex, mutagenesis of interaction residues, nuclear import assays, APA profiling","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus mutagenesis plus functional import assays plus APA profiling","pmids":["30916345"],"is_preprint":false},{"year":2020,"finding":"CPSF6 is post-transcriptionally regulated by the cellular microRNA miR-125b, which binds the 3'UTR of CPSF6 mRNA; miR-125b and CPSF6 levels are inversely correlated. Pulldown experiments show miR-125b physically interacts with CPSF6 3'UTR. HIV-1 infection down-regulates miR-125b (dependent on reverse transcription but not integration), concurrently upregulating CPSF6.","method":"miRNA knockdown/overexpression, luciferase reporter with CPSF6 3'UTR, seed-sequence mutagenesis, RNA pulldown","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple methods (reporter, pulldown, mutagenesis) but single lab; mechanism is post-transcriptional regulation of CPSF6 expression","pmids":["32152226"],"is_preprint":false},{"year":2020,"finding":"Primate lentiviral capsid proteins have evolved to interact with CPSF6 to target speckle-associated domains (SPADs) for integration; CPSF6 depletion specifically counteracts SPAD integration targeting by primate lentiviruses but not nonprimate lentiviruses, which also fail to appreciably interact with CPSF6. This demonstrates that CPSF6-capsid interaction is a primate lentivirus-specific evolutionary adaptation for integration into gene-dense, transcriptionally active chromatin.","method":"Integration site mapping (>5 million sites), CPSF6 KO/KD, LEDGF/p75 KO, Co-IP of CPSF6 with lentiviral capsids","journal":"mBio","confidence":"High","confidence_rationale":"Tier 2 / Strong — large-scale integration site mapping, comparative lentiviral analysis, KO/KD, binding assays; multiple orthogonal methods","pmids":["32994325"],"is_preprint":false},{"year":2021,"finding":"HIV-1 infection induces higher-order CPSF6 formation in cells, and capsid-CPSF6 complexes co-traffic on microtubules. Higher-order CPSF6 complexes bind and physically disrupt HIV-1 capsid assemblies in vitro. Disruption of CypA binding to capsid leads to increased CPSF6 binding and altered capsid trafficking; CypA prevents HIV-1 capsid from prematurely engaging cytoplasmic CPSF6.","method":"Live-cell imaging of capsid-CPSF6 co-trafficking, in vitro capsid binding/disruption assays, CypA inhibition, infectivity assays","journal":"mBio","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vitro reconstitution plus live imaging plus genetic perturbation; multiple orthogonal methods","pmids":["33758083"],"is_preprint":false},{"year":2023,"finding":"CPSF6 undergoes liquid-liquid phase separation (LLPS) in vitro; its arginine/serine-like domain (RSLD) controls LLPS activity. CLK2 kinase phosphorylates the RSLD to disrupt CPSF6 LLPS, reducing CPSF6 condensates and leading to preferential proximal poly(A) site usage (3' UTR shortening) and accelerated cell proliferation. CPSF6 LLPS, rather than expression level per se, determines APA regulation in cancer cells.","method":"In vitro LLPS assay, CLK2 kinase assay, RSLD mutagenesis, APA profiling, cell proliferation assays","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro LLPS reconstitution, kinase assay with mutagenesis, APA profiling; single lab but multiple orthogonal methods","pmids":["37777964"],"is_preprint":false},{"year":2023,"finding":"Upon HIV-1 nuclear entry, CPSF6 and CPSF5 (but not CPSF7) translocate from paraspeckles to nuclear speckles, forming biomolecular condensates. Neither HIV-1 integration nor reverse transcription is required for condensate formation; condensates are disrupted by osmotic stress and 1,6-hexanediol. Preventing condensate formation inhibits WT HIV-1 but not capsid mutants (N74D, A77V) that do not engage CPSF6, establishing that CPSF6 condensate formation is important for productive WT HIV-1 infection.","method":"Fluorescence microscopy of CPSF6 puncta, osmotic stress/hexanediol condensate disruption, integration-deficient and genome-free virus controls","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic and pharmacological perturbations, multiple capsid mutants, primary cells (T cells, macrophages)","pmids":["37414787"],"is_preprint":false},{"year":2024,"finding":"CPSF6 mixed-charge domain (MCD) is required for LLPS-dependent higher-order capsid binding and co-aggregation in vitro and in cells; MCD-deleted CPSF6 supports normal capsid binding affinity but fails to promote post-nuclear entry virus localization (PICs arrest at nuclear rim). Heterologous MCDs, but not Arg-Ser domains from SR proteins, can substitute for CPSF6 MCD in HIV-1 infection, and appending MCD to a heterologous capsid-binding protein partially restores nuclear penetration and integration targeting in CPSF6 KO cells.","method":"In vitro LLPS assay, capsid co-aggregation, domain-swap rescue experiments, imaging of intranuclear localization, integration site analysis in KO cells","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution, domain mutagenesis, heterologous rescue, integration site analysis; multiple orthogonal methods","pmids":["39258548"],"is_preprint":false},{"year":2024,"finding":"SYVN1 E3 ligase, whose nuclear import is triggered by MAVS signaling upon vesicular stomatitis virus infection (via NUP153), catalyzes K48-linked polyubiquitination of CPSF6, leading to proteasomal degradation of CPSF6, transcriptome-wide APA changes, and antiviral effects in macrophages.","method":"Co-IP, ubiquitination assay, proteasome inhibitor experiments, MAVS pathway perturbation, APA sequencing","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — biochemical identification of E3 ligase, K48-linkage specificity, pathway epistasis with MAVS/NUP153, APA readout","pmids":["39951376"],"is_preprint":false},{"year":2025,"finding":"Sequential binding of CypA (cytoplasm) then CPSF6 (nucleus) to HIV-1 capsid is required for optimal nuclear entry and integration targeting; a capsid mutant with increased CypA affinity shows reduced nuclear entry and mislocalized integration, but disrupting CypA binding restores these in a CPSF6-dependent manner. Nuclear relocation of CypA fails to rescue mutant HIV-1, confirming spatial separation of CypA and CPSF6 binding is mechanistically critical.","method":"CypA binding affinity mutants, CPSF6-dependent rescue assays, nuclear entry quantification, integration site analysis, CypA nuclear relocalization","journal":"mBio","confidence":"High","confidence_rationale":"Tier 2 / Strong — epistasis between CypA and CPSF6 binding mutants, spatial localization control, integration site sequencing; peer-reviewed with multiple orthogonal approaches","pmids":["40013779"],"is_preprint":false},{"year":2025,"finding":"CPSF6-RARG fusion protein (from t(1;12) chromosomal rearrangement in AML) interacts with histone deacetylase 3 (HDAC3) to suppress myeloid differentiation genes including PU.1; disrupting the CR-HDAC3 interaction restores PU.1 expression and myeloid differentiation, and HDAC inhibitors suppress CR-driven leukemia in vitro and in vivo.","method":"Co-IP of CPSF6-RARG with HDAC3, domain-disruption mutants, gene expression analysis, HDAC inhibitor treatment, mouse leukemia model","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP, domain disruption rescue, in vivo model; multiple methods establishing mechanism of oncogenic fusion","pmids":["39805830"],"is_preprint":false},{"year":2025,"finding":"CPSF6 directly promotes HIV-1 preintegration complex (PIC) activity; PICs extracted from CPSF6-depleted or capsid-binding-deficient CPSF6 mutant cells show significantly lower viral DNA integration activity in vitro. Adding purified recombinant CPSF6 restores integration activity of PICs from CPSF6-mutant cells. Disruption of CPSF6-CA binding in cells reduces viral DNA integration and redirects integration away from gene-dense chromatin, independent of effects on reverse transcription or nuclear entry.","method":"PIC extraction and in vitro integration assay, recombinant CPSF6 add-back, integration site sequencing, reverse transcription/nuclear entry controls","journal":"Journal of virology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with recombinant protein add-back, multiple independent controls, integration site sequencing; single lab","pmids":["40202316"],"is_preprint":false},{"year":2025,"finding":"The NLS of CPSF6 governs post-nuclear import steps of HIV-1 infection; some NLS chimeras drive CPSF6-358 into the nucleus but fail to support efficient HIV-1 infection. HIV-1 still enters the nucleus in these cells but fails to traffic to speckle-associated domains (SPADs) and fails to integrate efficiently, demonstrating that CPSF6's NLS facilitates intranuclear trafficking and SPAD targeting rather than merely nuclear import per se.","method":"Heterologous NLS rescue of CPSF6-358, HIV-1 nuclear entry quantification, integration site analysis, SPAD localization imaging","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 / Strong — panel of heterologous NLS chimeras, nuclear entry decoupled from integration targeting, integration site sequencing","pmids":["39823525"],"is_preprint":false},{"year":2008,"finding":"CPSF6 is fused to FGFR1 in the t(8;12)(p11;q15) rearrangement in an 8p11 myeloproliferative syndrome patient; the predicted CPSF6-FGFR1 fusion encodes the N-terminal domain of CPSF6 linked to the entire tyrosine kinase domain and C-terminal sequences of FGFR1. CPSF6 thus acts as a dimerization/oligomerization partner that constitutively activates FGFR1 kinase.","method":"Cytogenetics, genomic breakpoint PCR, RT-PCR confirming in-frame fusion","journal":"Genes, chromosomes & cancer","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — molecular cloning of fusion, in-frame confirmation; no in vitro kinase assay but structural inference of mechanism is supported","pmids":["18205209"],"is_preprint":false},{"year":2007,"finding":"CPSF6 and CPSF5 (CFIm subunits) are highly enriched in mouse male germ cells and both subunits are expressed from shorter spermatogenic mRNAs generated by alternative polyadenylation using proximal poly(A) signals; CFIm binding sites were identified near the 3' ends of numerous male germ cell transcripts utilizing noncanonical poly(A) signals, suggesting CPSF6-containing CFIm complexes direct APA at noncanonical signals during spermatogenesis.","method":"Northern blotting, cDNA sequencing, RT-PCR, CFIm binding site analysis, Western blot during spermatogenesis","journal":"Biology of reproduction","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — multiple detection methods establishing localization and APA role; no direct functional reconstitution assay","pmids":["18032416"],"is_preprint":false},{"year":2019,"finding":"NP1 protein of minute virus of canines (MVC) physically interacts with CPSF6 in transfected cells, and CPSF6 participates with NP1 to modulate suppression of proximal polyadenylation and splicing enhancement at the MVC capsid gene, demonstrating CPSF6 can be co-opted by viral non-retroviral proteins to modulate alternative RNA processing.","method":"Co-immunoprecipitation, functional RNA processing assays in transfected cells","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP plus functional RNA processing assay; single lab","pmids":["30355695"],"is_preprint":false},{"year":2017,"finding":"CPSF6 interacts with components of the A-to-I RNA editing machinery and paraspeckles, including ADAR1, and is required for their physical integrity; prolactin suppresses CPSF6 and RNA editing activity, placing CPSF6 in a paraspeckle-regulatory pathway.","method":"Co-immunoprecipitation, paraspeckle integrity assays (CPSF6 depletion), prolactin treatment","journal":"EBioMedicine","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP and functional integrity assay; single lab, limited mechanistic detail in abstract","pmids":["28673861"],"is_preprint":false},{"year":2023,"finding":"CPSF6 regulates temperature compensation of the mammalian circadian clock; CPSF6 knockdown significantly alters circadian temperature compensation in U-2 OS cells. Global 3' UTR length changes and temperature-dependent gene expression changes in CPSF6 KD cells identify candidate genes including EIF2S1 as underlying circadian temperature compensation.","method":"CPSF6 knockdown, 3'-end RNA-seq, mass spectrometry proteomics, circadian period analysis","journal":"PLoS biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — KD with defined phenotype and multi-omics profiling, but single lab and no direct mechanistic reconstitution","pmids":["37379316"],"is_preprint":false},{"year":2021,"finding":"CPSF6 knockdown in HCC cells induces widespread 3'UTR lengthening; specifically, CPSF6 drives proximal poly(A) site usage at NQO1, producing a short 3'UTR NQO1 isoform that is more stable and mediates CPSF6-dependent metabolic alterations and tumorigenic activity, establishing a molecular mechanism linking CPSF6-regulated APA to oncogenic phenotype.","method":"CPSF6 knockdown, APA profiling (3T-seq), NQO1 isoform functional assays, metabolic assays","journal":"Journal of experimental & clinical cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — APA profiling plus specific target validation; single lab","pmids":["33648552"],"is_preprint":false},{"year":2023,"finding":"CPSF6 mediates 3'UTR shortening of XBP1 by promoting proximal PAS usage; BRCA1-disrupted R-loop accumulation at the CPSF6 5' end causes CPSF6 elevation, and nuclear LINC00221 facilitates CPSF6-induced proximal PAS choice at pre-XBP1, producing a more stable XBP1-S isoform that contributes to cisplatin resistance in lung adenocarcinoma.","method":"CPSF6 manipulation, poly(A) site sequencing, R-loop analysis, luciferase reporter, cisplatin resistance assays","journal":"Drug resistance updates","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — mechanistic chain demonstrated with multiple assays but all in single study/lab","pmids":["36821972"],"is_preprint":false},{"year":2024,"finding":"Downregulation of CPSF6 upon viral infection (reduced protein abundance) promotes proximal poly(A) site usage of immune-related genes in macrophages and fibroblasts, shortening their 3' UTRs, which improves mRNA stability and translation efficiency to enhance type I IFN antiviral signaling.","method":"CPSF6 knockdown/overexpression, APA sequencing, mRNA stability assays, IFN signaling measurement","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — APA profiling combined with functional immune readout; multiple cell types tested","pmids":["38416782"],"is_preprint":false},{"year":2022,"finding":"FXR1 forms a complex with CFIm25 and CFIm68 (CPSF6) acting as a platform for sequence-specific poly(A) site recognition; this FXR1-CFIm complex affects 3' processing of TRAF1 mRNA, leading to nuclear mRNA stabilization and enhanced cell proliferation in urothelial carcinoma.","method":"Co-immunoprecipitation of FXR1-CPSF6/CFIm25 complex, APA analysis, mRNA stability assays","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP identifying novel complex, functional APA readout; single lab","pmids":["35194031"],"is_preprint":false},{"year":2025,"finding":"CPSF6 KO in primary CD4+ T cells leads to global 3' UTR shortening via APA, downregulation of innate immune genes and restriction factors (including TRIM5α), and upregulation of HIV-1 co-receptors, increasing permissivity to HIV-1 infection. HIV-1 recruitment of CPSF6 to incoming cores is sufficient to perturb CPSF6 function and cause similar APA-driven transcriptional reprogramming.","method":"CPSF6 KO in primary CD4+ T cells, APA sequencing, transcriptome analysis, HIV-1 infectivity assays, co-receptor expression measurement","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 / Strong — primary cell KO, APA sequencing, functional infectivity assays, mechanistic link between APA and immune gene regulation established","pmids":["41385587"],"is_preprint":false},{"year":2024,"finding":"The CPSF6 FG domain is essential for both HIV-induced nuclear puncta formation and binding to the viral core, which serves as the scaffold for CPSF6 condensates; low-complexity regions and mixed-charge domains modulate CPSF6 binding to capsid but do not contribute to puncta formation. SRRM2's intrinsically disordered region is required for enlarging nuclear speckles in the presence of HIV capsid, and puncta form individually then fuse with nuclear speckles.","method":"CPSF6 domain deletion mutants, live imaging, SRRM2 depletion, viral replication assays","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — systematic domain mapping, multiple genetic perturbations, functional viral replication readout; peer-reviewed","pmids":["41493399"],"is_preprint":false}],"current_model":"CPSF6 is a component of the cleavage factor Im (CFIm) complex that regulates mRNA alternative polyadenylation by binding UGUA-containing enhancer elements and activating distal poly(A) sites via its RS-like domain interacting with Fip1; its nuclear import is mediated by TNPO3 binding to the RS-like domain. During HIV-1 infection, nuclear CPSF6 binds the FG-binding pocket of assembled HIV-1 CA hexamers (competed by cytoplasmic CypA), undergoes MCD-dependent liquid-liquid phase separation/condensation with incoming capsids at nuclear speckles, promotes PIC integration activity, and directs viral DNA integration into gene-dense, transcriptionally active speckle-associated chromatin domains; cytoplasmic mislocalization of CPSF6 aberrantly stabilizes the capsid and blocks nuclear entry, while SYVN1-mediated K48-polyubiquitination degrades CPSF6 during antiviral responses to enhance innate immune gene expression via APA."},"narrative":{"mechanistic_narrative":"CPSF6 is a subunit of the cleavage factor Im (CFIm) complex that governs mRNA alternative polyadenylation (APA) genome-wide by activating enhancer-containing poly(A) sites, with its arginine/serine-like domain (RSLD) docking onto an RS-like region of the CPSF/Fip1 3'-processing machinery in a phosphorylation-sensitive manner [PMID:29276085]. Most cellular CPSF6 resides in CFIm with CPSF5 and CPSF7 [PMID:26994143], and its APA output is set not merely by abundance but by RSLD-dependent liquid-liquid phase separation, which CLK2 phosphorylation dissolves to shift usage toward proximal poly(A) sites and promote proliferation [PMID:37777964]. Nuclear import of CPSF6 is mediated by TNPO3 binding to the RSLD, an interaction resolved structurally and dispensable for, yet inhibited by, RSLD hyperphosphorylation [PMID:30916345]. Through this APA activity CPSF6 shapes diverse programs including innate antiviral gene expression, where reduced CPSF6 shortens 3' UTRs of immune transcripts to enhance type I IFN signaling [PMID:38416782, PMID:41385587], and is itself a degradation target of the MAVS-activated E3 ligase SYVN1, which K48-polyubiquitinates CPSF6 to remodel the APA transcriptome during antiviral responses [PMID:39951376]. CPSF6 is a central host cofactor for HIV-1: nuclear CPSF6 binds a conserved pocket in assembled HIV-1 capsid (CA) hexamers at the NTD-CTD interface [PMID:22956906, PMID:25518861], and this engagement is spatially gated by cytoplasmic cyclophilin A, whose prior binding prevents premature capsid-CPSF6 association [PMID:33758083, PMID:40013779]. CPSF6 licenses capsid trafficking through the nuclear pore and interior, undergoes capsid-scaffolded condensation at nuclear speckles via its FG and mixed-charge domains [PMID:39258548, PMID:41493399], directs viral DNA integration into gene-dense, transcriptionally active speckle-associated chromatin domains, and directly stimulates preintegration complex integration activity [PMID:26858452, PMID:30173955, PMID:40202316]. Cytoplasmic mislocalization or truncation of CPSF6 instead aberrantly stabilizes or disrupts the incoming capsid and blocks infection [PMID:23622145, PMID:29643241]. Chromosomal rearrangements fusing CPSF6 to FGFR1 or RARG drive myeloproliferative and acute myeloid leukemias, the latter through recruitment of HDAC3 to repress myeloid differentiation genes [PMID:39805830, PMID:18205209].","teleology":[{"year":2007,"claim":"Established that CPSF6, as a CFIm subunit, directs tissue-specific alternative polyadenylation, providing the first functional context for the protein in RNA 3'-end processing.","evidence":"Expression and CFIm binding-site analysis in mouse male germ cells","pmids":["18032416"],"confidence":"Medium","gaps":["No reconstitution of CFIm-directed APA in vitro","Causal role in spermatogenesis not tested by loss-of-function"]},{"year":2008,"claim":"Identified CPSF6 as a fusion partner in a myeloproliferative rearrangement, framing its N-terminal domain as an oligomerization module that can constitutively activate a partner kinase.","evidence":"Cytogenetics and breakpoint cloning of CPSF6-FGFR1 in an 8p11 syndrome patient","pmids":["18205209"],"confidence":"Medium","gaps":["No in vitro kinase activation assay","Oligomerization mechanism inferred, not measured"]},{"year":2012,"claim":"Defined the structural basis of CPSF6 recognition of HIV-1, revealing a conserved capsid interface and linking capsid binding to dependence on nuclear-entry cofactors.","evidence":"X-ray crystallography, mutagenesis, and infectivity assays with truncated CPSF6-358","pmids":["22956906"],"confidence":"High","gaps":["Did not establish whether assembled lattice versus monomeric CA is the target","Physiological role of full-length CPSF6 in infection unaddressed"]},{"year":2013,"claim":"Resolved the cell-biological logic of CPSF6 in HIV-1 by showing TNPO3 acts through CPSF6 nuclear import and that cytoplasmic CPSF6 is the effector that stabilizes the capsid and blocks nuclear entry.","evidence":"TNPO3/CPSF6 knockdown, localization mutants, epistatic rescue, and fate-of-capsid assays in two independent labs","pmids":["23414560","23622145","23658440"],"confidence":"High","gaps":["Mechanism by which cytoplasmic CPSF6 stabilizes the core unresolved","Distinct truncation phenotypes (uncoating acceleration vs. stabilization) not unified"]},{"year":2014,"claim":"Demonstrated that the assembled capsid hexamer lattice, not isolated CA, is the high-affinity CPSF6 target, defining a preformed druggable pocket shared with PF74.","evidence":"Quantitative binding and crystallography of CPSF6/PF74-CA hexamer complexes","pmids":["25518861"],"confidence":"High","gaps":["Stoichiometry of CPSF6 on intact cores in cells not determined","Link between lattice binding and downstream trafficking not yet established"]},{"year":2016,"claim":"Established CPSF6 as the dominant determinant of HIV-1 integration into euchromatin, mechanistically separable from LEDGF/p75 and independent of its CFIm partners.","evidence":"CPSF6/LEDGF knockouts with binding-deficient complementation, CFIm-disrupting mutants, and integration site sequencing","pmids":["26858452","26994143"],"confidence":"High","gaps":["How capsid-bound CPSF6 selects active chromatin not defined","Role of speckle association not yet identified"]},{"year":2017,"claim":"Defined CFIm/CPSF6 as an enhancer-dependent activator of 3' processing and identified the RSLD-Fip1 interaction as the phosphorylation-regulated molecular contact driving distal poly(A) site activation.","evidence":"In vitro RS-domain binding assays, RSLD mutagenesis, phosphorylation analysis, and global APA profiling","pmids":["29276085"],"confidence":"High","gaps":["Kinases controlling RSLD phosphorylation in vivo not identified here","Connection to phase behavior not yet appreciated"]},{"year":2018,"claim":"Showed CPSF6 is a master regulator of HIV-1 intranuclear localization, routing complexes to the nuclear interior and away from heterochromatin at the lamina.","evidence":"Live-cell and fixed imaging with CPSF6 knockout/complementation and integration site sequencing","pmids":["30173955"],"confidence":"High","gaps":["Molecular basis of interior targeting not defined","Relationship to nuclear speckles not yet shown"]},{"year":2019,"claim":"Provided structural and spatial detail for CPSF6 in nuclear entry, defining RSLD-TNPO3 recognition and showing CPSF6 acts at the nuclear basket after Nup153 to license pore passage.","evidence":"Crystal structure of RSLD-TNPO3, mutagenesis, STED microscopy, and primary macrophage infection","pmids":["30916345","30672737"],"confidence":"High","gaps":["Whether CPSF6 condensation participates in pore passage not addressed","Ordering of Nup153/CPSF6 handoff inferred"]},{"year":2020,"claim":"Established that capsid-CPSF6 interaction is a primate lentivirus-specific adaptation for targeting speckle-associated chromatin domains, and identified post-transcriptional control of CPSF6 by miR-125b during infection.","evidence":"Large-scale comparative integration mapping with KO/KD and binding assays; luciferase reporter, RNA pulldown, and seed mutagenesis for miR-125b","pmids":["32994325","32152226"],"confidence":"High","gaps":["How SPAD targeting is physically achieved still open","miR-125b regulation single-lab"]},{"year":2021,"claim":"Showed HIV-1 induces higher-order CPSF6 assemblies that bind and disrupt capsids, and that CypA binding gates premature cytoplasmic engagement of CPSF6.","evidence":"Live-cell co-trafficking imaging, in vitro capsid disruption, and CypA inhibition; plus APA/NQO1 oncogenic profiling in HCC","pmids":["33758083","33648552"],"confidence":"High","gaps":["Physical nature of higher-order CPSF6 not defined here","Spatial separation of CypA/CPSF6 not yet tested directly"]},{"year":2023,"claim":"Unified CPSF6 function around liquid-liquid phase separation: RSLD-driven LLPS sets APA output and CLK2 phosphorylation dissolves it, while capsid-scaffolded CPSF6/CPSF5 condensates at nuclear speckles are required for productive HIV-1 infection.","evidence":"In vitro LLPS and CLK2 kinase assays with APA profiling; hexanediol/osmotic disruption of CPSF6 condensates with capsid mutant controls; circadian temperature-compensation KD","pmids":["37777964","37414787","37379316"],"confidence":"High","gaps":["Whether the same condensates serve APA and HIV-1 integration unresolved","In vivo regulation of CLK2-CPSF6 axis untested"]},{"year":2024,"claim":"Dissected the domain requirements for CPSF6 condensation in HIV-1 (FG domain for puncta/core binding, MCD for LLPS-dependent intranuclear penetration) and placed CPSF6 in antiviral circuits via SYVN1-mediated K48 degradation and APA-driven IFN enhancement.","evidence":"Domain-deletion and heterologous-MCD rescue with integration analysis; FG/SRRM2 imaging; SYVN1 ubiquitination assays with MAVS/NUP153 epistasis; immune-gene APA profiling","pmids":["39258548","41493399","39951376","38416782"],"confidence":"High","gaps":["How condensation mechanically promotes pore-to-interior trafficking unresolved","Generality of SYVN1 regulation across cell types not established"]},{"year":2025,"claim":"Established that CPSF6 directly stimulates PIC integration activity, that its NLS governs intranuclear SPAD trafficking beyond import, and that CPSF6 loss reprograms immune APA to alter HIV-1 permissivity; also defined the CPSF6-RARG/HDAC3 leukemic mechanism.","evidence":"PIC in vitro integration with recombinant add-back; heterologous NLS chimeras with SPAD imaging; CypA/CPSF6 sequential-binding epistasis; primary CD4+ T-cell KO APA/infectivity; Co-IP and HDAC inhibitor leukemia model","pmids":["40202316","39823525","40013779","41385587","39805830"],"confidence":"High","gaps":["Biochemical mechanism by which CPSF6 stimulates integration unknown","Whether SPAD-targeting and PIC stimulation are separable activities unclear"]},{"year":null,"claim":"It remains unresolved whether CPSF6's APA-regulatory phase-separation activity and its HIV-1 integration-targeting condensate function share a common biophysical mechanism, and how the same condensate properties are partitioned between physiological 3'-processing and capsid-driven chromatin targeting.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structure of capsid-CPSF6 condensates at chromatin","Direct biochemical activity of CPSF6 on PIC integration undefined","Interplay between phosphorylation, LLPS, and APA versus HIV-1 functions not integrated"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[7,24,31]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[7,15,30]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[7,15]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[5,6,8]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[2,11,10]},{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[16,33]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[3,14,19]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[7,15,11]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[7,28,29]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[0,5,20,23]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[18,30,32]}],"complexes":["CFIm (cleavage factor Im)"],"partners":["CPSF5","CPSF7","TNPO3","FIP1L1","CLK2","SYVN1","HDAC3","FXR1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q16630","full_name":"Cleavage and polyadenylation specificity factor subunit 6","aliases":["Cleavage and polyadenylation specificity factor 68 kDa subunit","CPSF 68 kDa subunit","Cleavage factor Im complex 68 kDa subunit","CFIm68","Pre-mRNA cleavage factor Im 68 kDa subunit","Protein HPBRII-4/7"],"length_aa":551,"mass_kda":59.2,"function":"Component of the cleavage factor Im (CFIm) complex that functions as an activator of the pre-mRNA 3'-end cleavage and polyadenylation processing required for the maturation of pre-mRNA into functional mRNAs (PubMed:14690600, PubMed:29276085, PubMed:8626397, PubMed:9659921). CFIm contributes to the recruitment of multiprotein complexes on specific sequences on the pre-mRNA 3'-end, so called cleavage and polyadenylation signals (pA signals) (PubMed:14690600, PubMed:8626397, PubMed:9659921). Most pre-mRNAs contain multiple pA signals, resulting in alternative cleavage and polyadenylation (APA) producing mRNAs with variable 3'-end formation (PubMed:23187700, PubMed:29276085). The CFIm complex acts as a key regulator of cleavage and polyadenylation site choice during APA through its binding to 5'-UGUA-3' elements localized in the 3'-untranslated region (UTR) for a huge number of pre-mRNAs (PubMed:20695905, PubMed:29276085). CPSF6 enhances NUDT21/CPSF5 binding to 5'-UGUA-3' elements localized upstream of pA signals and promotes RNA looping, and hence activates directly the mRNA 3'-processing machinery (PubMed:15169763, PubMed:21295486, PubMed:29276085). Plays a role in mRNA export (PubMed:19864460) (Microbial infection) Binds HIV-1 capsid-nucleocapsid (HIV-1 CA-NC) complexes and might thereby promote the integration of the virus in the nucleus of dividing cells (in vitro)","subcellular_location":"Nucleus; Nucleus, nucleoplasm; Nucleus speckle; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q16630/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/CPSF6","classification":"Common Essential","n_dependent_lines":1110,"n_total_lines":1208,"dependency_fraction":0.9188741721854304},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000111605","cell_line_id":"CID000951","localizations":[{"compartment":"nucleoplasm","grade":3},{"compartment":"nuclear_punctae","grade":1}],"interactors":[{"gene":"TRA2B","stoichiometry":10.0},{"gene":"LEPRE1","stoichiometry":10.0},{"gene":"CPSF7","stoichiometry":10.0},{"gene":"NUDT21","stoichiometry":10.0},{"gene":"CRTAP","stoichiometry":10.0},{"gene":"PLOD1","stoichiometry":4.0},{"gene":"ERH","stoichiometry":4.0},{"gene":"TRA2A","stoichiometry":4.0},{"gene":"ZCCHC8","stoichiometry":4.0},{"gene":"ALYREF","stoichiometry":4.0}],"url":"https://opencell.sf.czbiohub.org/target/CID000951","total_profiled":1310},"omim":[{"mim_id":"621458","title":"WD REPEAT-CONTAINING PROTEIN 89; WDR89","url":"https://www.omim.org/entry/621458"},{"mim_id":"621247","title":"CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 7; CPSF7","url":"https://www.omim.org/entry/621247"},{"mim_id":"618608","title":"INTELLECTUAL DEVELOPMENTAL DISORDER WITH NASAL SPEECH, DYSMORPHIC FACIES, AND VARIABLE SKELETAL ANOMALIES; IDNADFS","url":"https://www.omim.org/entry/618608"},{"mim_id":"607992","title":"SURP AND G-PATCH DOMAINS-CONTAINING PROTEIN 1; SUGP1","url":"https://www.omim.org/entry/607992"},{"mim_id":"604979","title":"CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 6; CPSF6","url":"https://www.omim.org/entry/604979"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"},{"location":"Nuclear speckles","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CPSF6"},"hgnc":{"alias_symbol":["CFIM","HPBRII-4","HPBRII-7","CFIM68","CFIM72"],"prev_symbol":[]},"alphafold":{"accession":"Q16630","domains":[{"cath_id":"3.30.70.330","chopping":"80-159","consensus_level":"high","plddt":91.6606,"start":80,"end":159},{"cath_id":"1.20.58","chopping":"411-495","consensus_level":"medium","plddt":86.2152,"start":411,"end":495}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q16630","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q16630-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q16630-F1-predicted_aligned_error_v6.png","plddt_mean":64.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CPSF6","jax_strain_url":"https://www.jax.org/strain/search?query=CPSF6"},"sequence":{"accession":"Q16630","fasta_url":"https://rest.uniprot.org/uniprotkb/Q16630.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q16630/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q16630"}},"corpus_meta":[{"pmid":"22956906","id":"PMC_22956906","title":"CPSF6 defines a conserved capsid interface that modulates HIV-1 replication.","date":"2012","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/22956906","citation_count":238,"is_preprint":false},{"pmid":"25518861","id":"PMC_25518861","title":"Structural basis of HIV-1 capsid recognition by PF74 and CPSF6.","date":"2014","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/25518861","citation_count":232,"is_preprint":false},{"pmid":"26858452","id":"PMC_26858452","title":"A critical role for alternative polyadenylation factor CPSF6 in targeting HIV-1 integration to transcriptionally active chromatin.","date":"2016","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/26858452","citation_count":210,"is_preprint":false},{"pmid":"29276085","id":"PMC_29276085","title":"Molecular Mechanisms for CFIm-Mediated Regulation of mRNA Alternative Polyadenylation.","date":"2017","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/29276085","citation_count":179,"is_preprint":false},{"pmid":"30173955","id":"PMC_30173955","title":"Capsid-CPSF6 Interaction Licenses Nuclear HIV-1 Trafficking to Sites of Viral DNA Integration.","date":"2018","source":"Cell host & microbe","url":"https://pubmed.ncbi.nlm.nih.gov/30173955","citation_count":176,"is_preprint":false},{"pmid":"30672737","id":"PMC_30672737","title":"HIV-1 nuclear import in macrophages is regulated by CPSF6-capsid interactions at the nuclear pore complex.","date":"2019","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/30672737","citation_count":164,"is_preprint":false},{"pmid":"26586435","id":"PMC_26586435","title":"Direct Visualization of HIV-1 Replication Intermediates Shows that Capsid and CPSF6 Modulate HIV-1 Intra-nuclear Invasion and Integration.","date":"2015","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/26586435","citation_count":144,"is_preprint":false},{"pmid":"23414560","id":"PMC_23414560","title":"TNPO3 protects HIV-1 replication from CPSF6-mediated capsid stabilization in the host cell cytoplasm.","date":"2013","source":"Retrovirology","url":"https://pubmed.ncbi.nlm.nih.gov/23414560","citation_count":122,"is_preprint":false},{"pmid":"23622145","id":"PMC_23622145","title":"The ability of TNPO3-depleted cells to inhibit HIV-1 infection requires CPSF6.","date":"2013","source":"Retrovirology","url":"https://pubmed.ncbi.nlm.nih.gov/23622145","citation_count":81,"is_preprint":false},{"pmid":"27307565","id":"PMC_27307565","title":"Capsid-CPSF6 Interaction Is Dispensable for HIV-1 Replication in Primary Cells but Is Selected during Virus Passage In Vivo.","date":"2016","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/27307565","citation_count":58,"is_preprint":false},{"pmid":"36821972","id":"PMC_36821972","title":"CPSF6-mediated XBP1 3'UTR shortening attenuates cisplatin-induced ER stress and elevates chemo-resistance in lung adenocarcinoma.","date":"2023","source":"Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/36821972","citation_count":57,"is_preprint":false},{"pmid":"32994325","id":"PMC_32994325","title":"CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration.","date":"2020","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/32994325","citation_count":56,"is_preprint":false},{"pmid":"33758083","id":"PMC_33758083","title":"Cytoplasmic CPSF6 Regulates HIV-1 Capsid Trafficking and Infection in a Cyclophilin A-Dependent Manner.","date":"2021","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/33758083","citation_count":54,"is_preprint":false},{"pmid":"26994143","id":"PMC_26994143","title":"The Cleavage and Polyadenylation Specificity Factor 6 (CPSF6) Subunit of the Capsid-recruited Pre-messenger RNA Cleavage Factor I (CFIm) Complex Mediates HIV-1 Integration into Genes.","date":"2016","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/26994143","citation_count":53,"is_preprint":false},{"pmid":"33706811","id":"PMC_33706811","title":"SRSF3 and SRSF7 modulate 3'UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels.","date":"2021","source":"Genome biology","url":"https://pubmed.ncbi.nlm.nih.gov/33706811","citation_count":53,"is_preprint":false},{"pmid":"33648552","id":"PMC_33648552","title":"CPSF6 links alternative polyadenylation to metabolism adaption in hepatocellular carcinoma progression.","date":"2021","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/33648552","citation_count":51,"is_preprint":false},{"pmid":"27528751","id":"PMC_27528751","title":"Cleavage factor Im (CFIm) as a regulator of alternative polyadenylation.","date":"2016","source":"Biochemical Society transactions","url":"https://pubmed.ncbi.nlm.nih.gov/27528751","citation_count":48,"is_preprint":false},{"pmid":"18032416","id":"PMC_18032416","title":"Pre-messenger RNA cleavage factor I (CFIm): potential role in alternative polyadenylation during spermatogenesis.","date":"2007","source":"Biology of reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/18032416","citation_count":48,"is_preprint":false},{"pmid":"30916345","id":"PMC_30916345","title":"Differential role for phosphorylation in alternative polyadenylation function versus nuclear import of SR-like protein CPSF6.","date":"2019","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/30916345","citation_count":48,"is_preprint":false},{"pmid":"28673861","id":"PMC_28673861","title":"CPSF6 is a Clinically Relevant Breast Cancer Vulnerability Target: Role of CPSF6 in Breast Cancer.","date":"2017","source":"EBioMedicine","url":"https://pubmed.ncbi.nlm.nih.gov/28673861","citation_count":45,"is_preprint":false},{"pmid":"23658440","id":"PMC_23658440","title":"A carboxy-terminally truncated human CPSF6 lacking residues encoded by exon 6 inhibits HIV-1 cDNA synthesis and promotes capsid disassembly.","date":"2013","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/23658440","citation_count":45,"is_preprint":false},{"pmid":"18205209","id":"PMC_18205209","title":"The t(1;9)(p34;q34) and t(8;12)(p11;q15) fuse pre-mRNA processing proteins SFPQ (PSF) and CPSF6 to ABL and FGFR1.","date":"2008","source":"Genes, chromosomes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/18205209","citation_count":44,"is_preprint":false},{"pmid":"24415937","id":"PMC_24415937","title":"In vivo functions of CPSF6 for HIV-1 as revealed by HIV-1 capsid evolution in HLA-B27-positive subjects.","date":"2014","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/24415937","citation_count":43,"is_preprint":false},{"pmid":"37777964","id":"PMC_37777964","title":"CPSF6 regulates alternative polyadenylation and proliferation of cancer cells through phase separation.","date":"2023","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/37777964","citation_count":40,"is_preprint":false},{"pmid":"29643241","id":"PMC_29643241","title":"Truncated CPSF6 Forms Higher-Order Complexes That Bind and Disrupt HIV-1 Capsid.","date":"2018","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/29643241","citation_count":39,"is_preprint":false},{"pmid":"31690677","id":"PMC_31690677","title":"Analysis of CA Content and CPSF6 Dependence of Early HIV-1 Replication Complexes in SupT1-R5 Cells.","date":"2019","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/31690677","citation_count":39,"is_preprint":false},{"pmid":"29891591","id":"PMC_29891591","title":"A case of acute myeloid leukemia with promyelocytic features characterized by expression of a novel RARG-CPSF6 fusion.","date":"2018","source":"Blood advances","url":"https://pubmed.ncbi.nlm.nih.gov/29891591","citation_count":30,"is_preprint":false},{"pmid":"26355392","id":"PMC_26355392","title":"Fusion of PDGFRB to MPRIP, CPSF6, and GOLGB1 in three patients with eosinophilia-associated myeloproliferative neoplasms.","date":"2015","source":"Genes, chromosomes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/26355392","citation_count":29,"is_preprint":false},{"pmid":"35234914","id":"PMC_35234914","title":"CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis.","date":"2022","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/35234914","citation_count":27,"is_preprint":false},{"pmid":"38993554","id":"PMC_38993554","title":"Negative Regulation of CPSF6 Suppresses the Warburg Effect and Angiogenesis Leading to Tumor Progression Via c-Myc Signaling Network: Potential Therapeutic Target for Liver Cancer Therapy.","date":"2024","source":"International journal of biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/38993554","citation_count":24,"is_preprint":false},{"pmid":"37414787","id":"PMC_37414787","title":"Formation of nuclear CPSF6/CPSF5 biomolecular condensates upon HIV-1 entry into the nucleus is important for productive infection.","date":"2023","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/37414787","citation_count":23,"is_preprint":false},{"pmid":"32600399","id":"PMC_32600399","title":"MxB impedes the NUP358-mediated HIV-1 pre-integration complex nuclear import and viral replication cooperatively with CPSF6.","date":"2020","source":"Retrovirology","url":"https://pubmed.ncbi.nlm.nih.gov/32600399","citation_count":23,"is_preprint":false},{"pmid":"38416782","id":"PMC_38416782","title":"Downregulation of CPSF6 leads to global mRNA 3' UTR shortening and enhanced antiviral immune responses.","date":"2024","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/38416782","citation_count":22,"is_preprint":false},{"pmid":"35194031","id":"PMC_35194031","title":"FXR1 can bind with the CFIm25/CFIm68 complex and promote the progression of urothelial carcinoma of the bladder by stabilizing TRAF1 mRNA.","date":"2022","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/35194031","citation_count":20,"is_preprint":false},{"pmid":"39258548","id":"PMC_39258548","title":"HIV-1 usurps mixed-charge domain-dependent CPSF6 phase separation for higher-order capsid binding, nuclear entry and viral DNA integration.","date":"2024","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/39258548","citation_count":19,"is_preprint":false},{"pmid":"34594359","id":"PMC_34594359","title":"Suppression of CPSF6 Enhances Apoptosis Through Alternative Polyadenylation-Mediated Shortening of the VHL 3'UTR in Gastric Cancer Cells.","date":"2021","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/34594359","citation_count":19,"is_preprint":false},{"pmid":"31448372","id":"PMC_31448372","title":"Capsid-CPSF6 interaction: Master regulator of nuclear HIV-1 positioning and integration.","date":"2019","source":"Journal of life sciences (Westlake Village, Calif.)","url":"https://pubmed.ncbi.nlm.nih.gov/31448372","citation_count":19,"is_preprint":false},{"pmid":"30355695","id":"PMC_30355695","title":"Minute Virus of Canines NP1 Protein Interacts with the Cellular Factor CPSF6 To Regulate Viral Alternative RNA Processing.","date":"2019","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/30355695","citation_count":16,"is_preprint":false},{"pmid":"37061085","id":"PMC_37061085","title":"HIV-Induced CPSF6 Condensates.","date":"2023","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/37061085","citation_count":15,"is_preprint":false},{"pmid":"32152226","id":"PMC_32152226","title":"The HIV-1 capsid-binding host factor CPSF6 is post-transcriptionally regulated by the cellular microRNA miR-125b.","date":"2020","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32152226","citation_count":15,"is_preprint":false},{"pmid":"32431549","id":"PMC_32431549","title":"NUDT21 Suppresses Breast Cancer Tumorigenesis Through Regulating CPSF6 Expression.","date":"2020","source":"Cancer management and research","url":"https://pubmed.ncbi.nlm.nih.gov/32431549","citation_count":15,"is_preprint":false},{"pmid":"40013779","id":"PMC_40013779","title":"Spatiotemporal binding of cyclophilin A and CPSF6 to capsid regulates HIV-1 nuclear entry and integration.","date":"2025","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/40013779","citation_count":14,"is_preprint":false},{"pmid":"33473264","id":"PMC_33473264","title":"Acute myeloid leukemia with CPSF6-RARG fusion resembling acute promyelocytic leukemia with extramedullary infiltration.","date":"2021","source":"Therapeutic advances in hematology","url":"https://pubmed.ncbi.nlm.nih.gov/33473264","citation_count":14,"is_preprint":false},{"pmid":"35993810","id":"PMC_35993810","title":"Distinct, opposing functions for CFIm59 and CFIm68 in mRNA alternative polyadenylation of Pten and in the PI3K/Akt signalling cascade.","date":"2022","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/35993810","citation_count":12,"is_preprint":false},{"pmid":"35355934","id":"PMC_35355934","title":"Deregulated expression and subcellular localization of CPSF6, a circRNA-binding protein, promote malignant development of esophageal squamous cell carcinoma.","date":"2022","source":"Chinese journal of cancer research = Chung-kuo yen cheng yen chiu","url":"https://pubmed.ncbi.nlm.nih.gov/35355934","citation_count":10,"is_preprint":false},{"pmid":"38267295","id":"PMC_38267295","title":"HIV-1-induced translocation of CPSF6 to biomolecular condensates.","date":"2024","source":"Trends in microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/38267295","citation_count":9,"is_preprint":false},{"pmid":"36563685","id":"PMC_36563685","title":"CFIm-mediated alternative polyadenylation safeguards the development of mammalian pre-implantation embryos.","date":"2022","source":"Stem cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/36563685","citation_count":9,"is_preprint":false},{"pmid":"34217312","id":"PMC_34217312","title":"Ribonucleic acid-binding protein CPSF6 promotes glycolysis and suppresses apoptosis in hepatocellular carcinoma cells by inhibiting the BTG2 expression.","date":"2021","source":"Biomedical engineering online","url":"https://pubmed.ncbi.nlm.nih.gov/34217312","citation_count":9,"is_preprint":false},{"pmid":"36446361","id":"PMC_36446361","title":"The roles of CPSF6 in proliferation, apoptosis and tumorigenicity of lung adenocarcinoma.","date":"2022","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/36446361","citation_count":8,"is_preprint":false},{"pmid":"38645162","id":"PMC_38645162","title":"Spatiotemporal binding of cyclophilin A and CPSF6 to capsid regulates HIV-1 nuclear entry and integration.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38645162","citation_count":8,"is_preprint":false},{"pmid":"39823525","id":"PMC_39823525","title":"The nuclear localization signal of CPSF6 governs post-nuclear import steps of HIV-1 infection.","date":"2025","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/39823525","citation_count":7,"is_preprint":false},{"pmid":"39805830","id":"PMC_39805830","title":"CPSF6-RARγ interacts with histone deacetylase 3 to promote myeloid transformation in RARG-fusion acute myeloid leukemia.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/39805830","citation_count":7,"is_preprint":false},{"pmid":"38793552","id":"PMC_38793552","title":"HIV-1 Capsid Rapidly Induces Long-Lived CPSF6 Puncta in Non-Dividing Cells, but Similar Puncta Already Exist in Uninfected T-Cells.","date":"2024","source":"Viruses","url":"https://pubmed.ncbi.nlm.nih.gov/38793552","citation_count":7,"is_preprint":false},{"pmid":"40010558","id":"PMC_40010558","title":"m6A-mediated regulation of CPSF6 by METTL3 promotes oxaliplatin resistance in colorectal cancer through enhanced glycolysis.","date":"2025","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/40010558","citation_count":5,"is_preprint":false},{"pmid":"37665675","id":"PMC_37665675","title":"A twin UGUA motif directs the balance between gene isoforms through CFIm and the mTORC1 signaling pathway.","date":"2023","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/37665675","citation_count":4,"is_preprint":false},{"pmid":"37379316","id":"PMC_37379316","title":"Alternative polyadenylation factor CPSF6 regulates temperature compensation of the mammalian circadian clock.","date":"2023","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/37379316","citation_count":4,"is_preprint":false},{"pmid":"39951376","id":"PMC_39951376","title":"E3 ligase SYVN1-mediated polyubiquitination of CPSF6 promotes alternative polyadenylation and antivirus effects of macrophages.","date":"2025","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/39951376","citation_count":4,"is_preprint":false},{"pmid":"40202316","id":"PMC_40202316","title":"CPSF6 promotes HIV-1 preintegration complex function.","date":"2025","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/40202316","citation_count":3,"is_preprint":false},{"pmid":"37746647","id":"PMC_37746647","title":"RNA-binding protein CPSF6 regulates IBSP to affect pyroptosis in gastric cancer.","date":"2023","source":"World journal of gastrointestinal oncology","url":"https://pubmed.ncbi.nlm.nih.gov/37746647","citation_count":3,"is_preprint":false},{"pmid":"40629911","id":"PMC_40629911","title":"IGF2BP2 binding to CPSF6 facilitates m6A-mediated alternative polyadenylation of PUM2 and promotes malignant progression in ovarian cancer.","date":"2025","source":"Clinical and translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/40629911","citation_count":3,"is_preprint":false},{"pmid":"31477156","id":"PMC_31477156","title":"Effect of CFIm68 knockdown on RNA polymerase II transcription.","date":"2019","source":"BMC research notes","url":"https://pubmed.ncbi.nlm.nih.gov/31477156","citation_count":3,"is_preprint":false},{"pmid":"27596537","id":"PMC_27596537","title":"Evidence that a threshold of serine/arginine-rich (SR) proteins recruits CFIm to promote rous sarcoma virus mRNA 3' end formation.","date":"2016","source":"Virology","url":"https://pubmed.ncbi.nlm.nih.gov/27596537","citation_count":3,"is_preprint":false},{"pmid":"36185228","id":"PMC_36185228","title":"Case report: A rare case of acute myeloid leukemia with CPSF6-RARG fusion resembling acute promyelocytic leukemia.","date":"2022","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/36185228","citation_count":3,"is_preprint":false},{"pmid":"38743225","id":"PMC_38743225","title":"Detection of CPSF6 in Biomolecular Condensates as a Reporter of HIV-1 Nuclear Import.","date":"2024","source":"Methods in molecular biology (Clifton, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/38743225","citation_count":2,"is_preprint":false},{"pmid":"41493399","id":"PMC_41493399","title":"Decoding the biogenesis of HIV-induced CPSF6 puncta and their fusion with nuclear speckles.","date":"2026","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/41493399","citation_count":2,"is_preprint":false},{"pmid":"38979149","id":"PMC_38979149","title":"The nuclear localization signal of CPSF6 governs post-nuclear import steps of HIV-1 infection.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38979149","citation_count":2,"is_preprint":false},{"pmid":"31941344","id":"PMC_31941344","title":"The 4th and 112th Residues of Viral Capsid Cooperatively Modulate Capsid-CPSF6 Interactions of HIV-1.","date":"2020","source":"AIDS research and human retroviruses","url":"https://pubmed.ncbi.nlm.nih.gov/31941344","citation_count":2,"is_preprint":false},{"pmid":"39678349","id":"PMC_39678349","title":"Disruption of CPSF6 enhances cellular permissivity to HIV-1 infection through alternative polyadenylation.","date":"2024","source":"Research square","url":"https://pubmed.ncbi.nlm.nih.gov/39678349","citation_count":1,"is_preprint":false},{"pmid":"41385587","id":"PMC_41385587","title":"Alternative polyadenylation upon CPSF6 knock-out enhances HIV-1 infection in primary T cells.","date":"2025","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/41385587","citation_count":1,"is_preprint":false},{"pmid":"32330562","id":"PMC_32330562","title":"Expression of zebrafish cpsf6 in embryogenesis and role of protein domains on subcellular localization.","date":"2020","source":"Gene expression patterns : GEP","url":"https://pubmed.ncbi.nlm.nih.gov/32330562","citation_count":1,"is_preprint":false},{"pmid":"41076169","id":"PMC_41076169","title":"CPSF6 loss mediates LDHA 3'UTR shortening to promote fibroblast glycolysis and pulmonary fibrosis.","date":"2025","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/41076169","citation_count":1,"is_preprint":false},{"pmid":"35356883","id":"PMC_35356883","title":"[The nuclear translocation of circRNA CPSF6 promotes apoptosis of trophoblast cells induced by homocysteine].","date":"2022","source":"Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/35356883","citation_count":1,"is_preprint":false},{"pmid":"39662264","id":"PMC_39662264","title":"CircSugp1 interacts with CPSF6 to modulate intestinal mucosa repair by regulating alternative polyadenylation-mediated shortening of the Wdr89 3'UTR.","date":"2024","source":"International immunopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/39662264","citation_count":1,"is_preprint":false},{"pmid":"41278918","id":"PMC_41278918","title":"Loss of CFIm activates YAP/TAZ and connects mRNA cleavage and polyadenylation inhibition to BRCAness.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/41278918","citation_count":0,"is_preprint":false},{"pmid":"42074139","id":"PMC_42074139","title":"Block-and-Lock Approaches for HIV Cure: Mechanistic Insights, Challenges, and Emerging Role of CPSF6.","date":"2026","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/42074139","citation_count":0,"is_preprint":false},{"pmid":"41540455","id":"PMC_41540455","title":"CPSF6-mediated alternative polyadenylation of RUNX1 to regulate silica-induced pulmonary fibrosis progression.","date":"2026","source":"Respiratory research","url":"https://pubmed.ncbi.nlm.nih.gov/41540455","citation_count":0,"is_preprint":false},{"pmid":"38994163","id":"PMC_38994163","title":"Retraction note to: RNA-binding protein CPSF6 regulates IBSP to affect pyroptosis in gastric cancer.","date":"2024","source":"World journal of gastrointestinal oncology","url":"https://pubmed.ncbi.nlm.nih.gov/38994163","citation_count":0,"is_preprint":false},{"pmid":"41708579","id":"PMC_41708579","title":"Apoptosis and Metabolic Reprogramming by RHART in Hepatocellular Carcinoma Through the CPSF6/MCT4/c-Myc Signaling In Vitro and In Vivo.","date":"2026","source":"Phytotherapy research : PTR","url":"https://pubmed.ncbi.nlm.nih.gov/41708579","citation_count":0,"is_preprint":false},{"pmid":"39225594","id":"PMC_39225594","title":"Inhibiting circ_0000673 blocks the progression of colorectal cancer through downregulating CPSF6 via targeting miR-548b-3p.","date":"2025","source":"Advances in clinical and experimental medicine : official organ Wroclaw Medical University","url":"https://pubmed.ncbi.nlm.nih.gov/39225594","citation_count":0,"is_preprint":false},{"pmid":"41606827","id":"PMC_41606827","title":"A stress-dependent postembryonic role for the core CPA factor CFIM-1 in germline integrity.","date":"2026","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/41606827","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.08.11.669633","title":"Competitive binding and geometric changes allow fast, complete translocation of intact HIV-1 capsids through the nuclear pore complex","date":"2025-08-13","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.11.669633","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.02.27.640555","title":"Construction and characterization of coronavirus nonstructural protein 3-host protein interaction networks unravel an important role of cleavage and polyadenylation specificity factor 6 in regulation of viral RNA replication","date":"2025-02-28","source":"bioRxiv","url":"https://doi.org/10.1101/2025.02.27.640555","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.06.19.660645","title":"Alternative Polyadenylation Releases PCBP1-Mediated Suppression of CFIm25 During Macrophage Differentiation","date":"2025-06-22","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.19.660645","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.03.04.641496","title":"Correlative In Situ Cryo-ET Reveals Cellular and Viral Remodeling Associated with Selective HIV-1 Core Nuclear Import","date":"2025-03-04","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.04.641496","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.03.13.643050","title":"Governed by surface amino acid composition: HIV capsid passage through the NPC barrier","date":"2025-03-13","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.13.643050","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.10.06.616889","title":"Decoding the biogenesis of HIV-induced CPSF6 puncta and their fusion with the nuclear speckle","date":"2024-10-07","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.06.616889","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.10.09.617312","title":"Structural insights into HIV-2 CA lattice formation and FG-pocket binding revealed by single particle cryo-EM","date":"2024-10-09","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.09.617312","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.11.25.625199","title":"Structural and Mechanistic Bases for Resistance of the M66I Capsid Variant to Lenacapavir","date":"2024-11-25","source":"bioRxiv","url":"https://doi.org/10.1101/2024.11.25.625199","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":46434,"output_tokens":9128,"usd":0.138111,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":19048,"output_tokens":5181,"usd":0.112382,"stage2_stop_reason":"end_turn"},"total_usd":0.250493,"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\": \"CPSF6 binds to a novel protein-protein interface in the N-terminal domain of HIV-1 capsid (CA), defined by X-ray crystallography; this interface is conserved across lentiviruses and is accessible in the hexameric lattice. A truncated cytosolic form, CPSF6-358, restricts HIV-1 by binding this interface, and mutations that abolish CPSF6 binding also relieve dependence on nuclear entry cofactors TNPO3 and RanBP2.\",\n      \"method\": \"X-ray crystallography, mutagenesis, infectivity assays, binding assays\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus mutagenesis plus functional infectivity assays; replicated in multiple subsequent studies\",\n      \"pmids\": [\"22956906\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"CPSF6 binds the assembled HIV-1 CA hexamer at the NTD-CTD interface pocket with at least 10-fold higher affinity than non-assembled CA or isolated domains; crystal structure of PF74 in complex with the hexamer shows CPSF6 and the drug bind the same preformed pocket, indicating the assembled capsid lattice is the principal binding target.\",\n      \"method\": \"Biochemical binding assays, X-ray crystallography of CA hexamer complexes\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstitution of hexameric complexes, crystal structure, quantitative binding measurements; independent from earlier structural paper\",\n      \"pmids\": [\"25518861\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"TNPO3 promotes HIV-1 infectivity indirectly by importing CPSF6 into the nucleus; when TNPO3 is knocked down, CPSF6 accumulates in the cytoplasm and abnormally stabilizes the HIV-1 CA core, blocking infection. Mislocalization of CPSF6 to the cytoplasm (via NLS deletion or nuclear export signal fusion) phenocopies TNPO3 knockdown, while targeting CPSF6 to the nucleus with a heterologous NLS rescues infection. Sensitivity of 27 CA mutants to TNPO3 knockdown correlates strongly with sensitivity to CPSF6-358 inhibition (R²=0.883).\",\n      \"method\": \"TNPO3 knockdown, CPSF6 localization mutants, fate-of-capsid assays, 2-LTR circle quantification, correlation of CA mutant panels\",\n      \"journal\": \"Retrovirology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (genetic, cell biology, biochemistry), large CA mutant panel correlation, replicated by independent lab (PMID 23622145)\",\n      \"pmids\": [\"23414560\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Cytoplasmic full-length CPSF6 (overexpressed without NLS) blocks HIV-1 nuclear import and enhances stability of the HIV-1 core; simultaneous depletion of both TNPO3 and CPSF6 rescues HIV-1 infection that is blocked by TNPO3 depletion alone, establishing CPSF6 as the effector of TNPO3-dependent restriction.\",\n      \"method\": \"siRNA depletion, cytoplasmic CPSF6 overexpression, fate-of-capsid assay, infectivity rescue\",\n      \"journal\": \"Retrovirology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — epistatic rescue experiment, capsid stability assay, multiple conditions; corroborates PMID 23414560\",\n      \"pmids\": [\"23622145\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"A carboxy-terminally truncated CPSF6 variant (hCPSF6-375, lacking exon 6) aberrantly accelerates HIV-1 capsid disassembly in target cells and inhibits viral cDNA synthesis; residues encoded by exon 6 are responsible for the cDNA synthesis block. This is mechanistically distinct from CPSF6-358, which does not accelerate uncoating.\",\n      \"method\": \"cDNA expression cloning, ganciclovir-mediated selection, mutational analysis, capsid disassembly assay, viral cDNA quantification\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain mapping by mutagenesis plus mechanistic phenotype readout; single lab\",\n      \"pmids\": [\"23658440\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"CPSF6 knockout preferentially decreases HIV-1 integration into transcriptionally active genes, spliced genes, and euchromatic regions; capsid-binding-deficient CPSF6 fails to rescue integration site distribution. Dual knockout of CPSF6 and LEDGF/p75 showed CPSF6 plays a more dominant role in directing integration to euchromatin, while LEDGF/p75 mainly directs positional targeting within gene bodies, establishing two mechanistically distinct pathways.\",\n      \"method\": \"CPSF6 knockout, LEDGF/p75 depletion, integration site sequencing, CPSF6 complementation with capsid-binding mutant\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — KO with rescue (including binding-deficient mutant), integration site deep sequencing, epistasis with LEDGF/p75\",\n      \"pmids\": [\"26858452\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"The majority of cellular CPSF6 is incorporated into the CFIm complex (with CPSF5/CFIm25 and CPSF7); HIV-1 capsid recruits the CFIm complex in a CPSF6-dependent manner. However, CPSF6 incorporation into CFIm is not required for its ability to direct HIV-1 integration into genes; CPSF6 alone, independent of its CFIm partners CPSF5 and CPSF7, controls the key molecular interactions for PIC trafficking to active chromatin.\",\n      \"method\": \"Co-immunoprecipitation, CFIm-disrupting CPSF6 mutants, integration site analysis, virological assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP plus mutagenesis plus integration site sequencing; dissects complex subunit requirements\",\n      \"pmids\": [\"26994143\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"CFIm (CPSF6/CFIm68 and CPSF5/CFIm59 subunits) functions as an enhancer-dependent activator of mRNA 3' processing; CFIm regulates global alternative polyadenylation by binding and activating enhancer-containing poly(A) sites. The RS domains of CFIm68/59 bind specifically to an RS-like region in CPSF/Fip1, and this interaction is inhibited by hyper-phosphorylation of CFIm68/59.\",\n      \"method\": \"Biochemical binding assays, APA profiling, RS-domain mutagenesis, phosphorylation analysis\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution of RS-domain interaction, mutagenesis, global APA profiling; multiple orthogonal methods\",\n      \"pmids\": [\"29276085\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Capsid-CPSF6 interaction licenses HIV-1 trafficking throughout the nuclear interior; loss of CPSF6 interaction dramatically shifts virus localization to the nuclear periphery and redirects integration into transcriptionally repressed lamina-associated heterochromatin, while loss of LEDGF/p75 does not significantly affect intranuclear HIV-1 localization. CPSF6 serves as a master regulator of HIV-1 intranuclear localization.\",\n      \"method\": \"Live-cell and fixed imaging of HIV-1 nuclear localization, CPSF6 knockout/complementation, integration site sequencing\",\n      \"journal\": \"Cell host & microbe\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — quantitative imaging plus KO/rescue plus integration site analysis; multiple orthogonal methods\",\n      \"pmids\": [\"30173955\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Truncated CPSF6-358 forms higher-order oligomeric complexes that bind assembled wild-type HIV-1 CA tubes but not CA tubes bearing a CPSF6 binding-site mutation; binding physically disrupts the tubular capsid assemblies. In cells, CPSF6-358 forms cytoplasmic puncta upon HIV-1 infection, leading to capsid permeabilization in a capsid-binding-dependent manner.\",\n      \"method\": \"In vitro binding with purified CPSF6-358 oligomers and CA tubes, transmission electron microscopy, live- and fixed-cell imaging, capsid permeabilization assay\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with EM plus in cellulo imaging; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"29643241\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CPSF6 is strongly recruited to nuclear HIV-1 replication complexes (but absent from cytoplasmic RTC/PIC) in primary human macrophages. Depletion of CPSF6 or lack of CPSF6 binding causes accumulation of HIV-1 subviral complexes at the nuclear envelope. STED microscopy showed that CPSF6-binding-deficient complexes are retained inside the nuclear pore in a CA-multimer-dependent manner, with CPSF6 clustering adjacent to the nuclear basket, suggesting consecutive Nup153/CPSF6 binding to the hexameric lattice mediates nuclear entry.\",\n      \"method\": \"Quantitative fluorescence microscopy, CPSF6 depletion, STED super-resolution microscopy, primary macrophage infection\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — super-resolution microscopy plus depletion plus primary cells; multiple imaging modalities\",\n      \"pmids\": [\"30672737\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The arginine/serine-like domain (RSLD) of CPSF6 mediates TNPO3 binding and is critical for CPSF6 nuclear import; the crystal structure of the RSLD-TNPO3 complex identified specific interaction residues confirmed by mutagenesis. RSLD phosphorylation is not required for TNPO3 binding or nuclear import, but a hyperphosphorylated mimetic mutant fails to bind TNPO3 and mislocalizes to the cytoplasm. Hypophosphorylated CPSF6 extends 3' UTRs similarly to depletion of CFIIm components.\",\n      \"method\": \"Crystal structure of RSLD-TNPO3 complex, mutagenesis of interaction residues, nuclear import assays, APA profiling\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus mutagenesis plus functional import assays plus APA profiling\",\n      \"pmids\": [\"30916345\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"CPSF6 is post-transcriptionally regulated by the cellular microRNA miR-125b, which binds the 3'UTR of CPSF6 mRNA; miR-125b and CPSF6 levels are inversely correlated. Pulldown experiments show miR-125b physically interacts with CPSF6 3'UTR. HIV-1 infection down-regulates miR-125b (dependent on reverse transcription but not integration), concurrently upregulating CPSF6.\",\n      \"method\": \"miRNA knockdown/overexpression, luciferase reporter with CPSF6 3'UTR, seed-sequence mutagenesis, RNA pulldown\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple methods (reporter, pulldown, mutagenesis) but single lab; mechanism is post-transcriptional regulation of CPSF6 expression\",\n      \"pmids\": [\"32152226\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Primate lentiviral capsid proteins have evolved to interact with CPSF6 to target speckle-associated domains (SPADs) for integration; CPSF6 depletion specifically counteracts SPAD integration targeting by primate lentiviruses but not nonprimate lentiviruses, which also fail to appreciably interact with CPSF6. This demonstrates that CPSF6-capsid interaction is a primate lentivirus-specific evolutionary adaptation for integration into gene-dense, transcriptionally active chromatin.\",\n      \"method\": \"Integration site mapping (>5 million sites), CPSF6 KO/KD, LEDGF/p75 KO, Co-IP of CPSF6 with lentiviral capsids\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — large-scale integration site mapping, comparative lentiviral analysis, KO/KD, binding assays; multiple orthogonal methods\",\n      \"pmids\": [\"32994325\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"HIV-1 infection induces higher-order CPSF6 formation in cells, and capsid-CPSF6 complexes co-traffic on microtubules. Higher-order CPSF6 complexes bind and physically disrupt HIV-1 capsid assemblies in vitro. Disruption of CypA binding to capsid leads to increased CPSF6 binding and altered capsid trafficking; CypA prevents HIV-1 capsid from prematurely engaging cytoplasmic CPSF6.\",\n      \"method\": \"Live-cell imaging of capsid-CPSF6 co-trafficking, in vitro capsid binding/disruption assays, CypA inhibition, infectivity assays\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vitro reconstitution plus live imaging plus genetic perturbation; multiple orthogonal methods\",\n      \"pmids\": [\"33758083\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CPSF6 undergoes liquid-liquid phase separation (LLPS) in vitro; its arginine/serine-like domain (RSLD) controls LLPS activity. CLK2 kinase phosphorylates the RSLD to disrupt CPSF6 LLPS, reducing CPSF6 condensates and leading to preferential proximal poly(A) site usage (3' UTR shortening) and accelerated cell proliferation. CPSF6 LLPS, rather than expression level per se, determines APA regulation in cancer cells.\",\n      \"method\": \"In vitro LLPS assay, CLK2 kinase assay, RSLD mutagenesis, APA profiling, cell proliferation assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro LLPS reconstitution, kinase assay with mutagenesis, APA profiling; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"37777964\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Upon HIV-1 nuclear entry, CPSF6 and CPSF5 (but not CPSF7) translocate from paraspeckles to nuclear speckles, forming biomolecular condensates. Neither HIV-1 integration nor reverse transcription is required for condensate formation; condensates are disrupted by osmotic stress and 1,6-hexanediol. Preventing condensate formation inhibits WT HIV-1 but not capsid mutants (N74D, A77V) that do not engage CPSF6, establishing that CPSF6 condensate formation is important for productive WT HIV-1 infection.\",\n      \"method\": \"Fluorescence microscopy of CPSF6 puncta, osmotic stress/hexanediol condensate disruption, integration-deficient and genome-free virus controls\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic and pharmacological perturbations, multiple capsid mutants, primary cells (T cells, macrophages)\",\n      \"pmids\": [\"37414787\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CPSF6 mixed-charge domain (MCD) is required for LLPS-dependent higher-order capsid binding and co-aggregation in vitro and in cells; MCD-deleted CPSF6 supports normal capsid binding affinity but fails to promote post-nuclear entry virus localization (PICs arrest at nuclear rim). Heterologous MCDs, but not Arg-Ser domains from SR proteins, can substitute for CPSF6 MCD in HIV-1 infection, and appending MCD to a heterologous capsid-binding protein partially restores nuclear penetration and integration targeting in CPSF6 KO cells.\",\n      \"method\": \"In vitro LLPS assay, capsid co-aggregation, domain-swap rescue experiments, imaging of intranuclear localization, integration site analysis in KO cells\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution, domain mutagenesis, heterologous rescue, integration site analysis; multiple orthogonal methods\",\n      \"pmids\": [\"39258548\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SYVN1 E3 ligase, whose nuclear import is triggered by MAVS signaling upon vesicular stomatitis virus infection (via NUP153), catalyzes K48-linked polyubiquitination of CPSF6, leading to proteasomal degradation of CPSF6, transcriptome-wide APA changes, and antiviral effects in macrophages.\",\n      \"method\": \"Co-IP, ubiquitination assay, proteasome inhibitor experiments, MAVS pathway perturbation, APA sequencing\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — biochemical identification of E3 ligase, K48-linkage specificity, pathway epistasis with MAVS/NUP153, APA readout\",\n      \"pmids\": [\"39951376\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Sequential binding of CypA (cytoplasm) then CPSF6 (nucleus) to HIV-1 capsid is required for optimal nuclear entry and integration targeting; a capsid mutant with increased CypA affinity shows reduced nuclear entry and mislocalized integration, but disrupting CypA binding restores these in a CPSF6-dependent manner. Nuclear relocation of CypA fails to rescue mutant HIV-1, confirming spatial separation of CypA and CPSF6 binding is mechanistically critical.\",\n      \"method\": \"CypA binding affinity mutants, CPSF6-dependent rescue assays, nuclear entry quantification, integration site analysis, CypA nuclear relocalization\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — epistasis between CypA and CPSF6 binding mutants, spatial localization control, integration site sequencing; peer-reviewed with multiple orthogonal approaches\",\n      \"pmids\": [\"40013779\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CPSF6-RARG fusion protein (from t(1;12) chromosomal rearrangement in AML) interacts with histone deacetylase 3 (HDAC3) to suppress myeloid differentiation genes including PU.1; disrupting the CR-HDAC3 interaction restores PU.1 expression and myeloid differentiation, and HDAC inhibitors suppress CR-driven leukemia in vitro and in vivo.\",\n      \"method\": \"Co-IP of CPSF6-RARG with HDAC3, domain-disruption mutants, gene expression analysis, HDAC inhibitor treatment, mouse leukemia model\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP, domain disruption rescue, in vivo model; multiple methods establishing mechanism of oncogenic fusion\",\n      \"pmids\": [\"39805830\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CPSF6 directly promotes HIV-1 preintegration complex (PIC) activity; PICs extracted from CPSF6-depleted or capsid-binding-deficient CPSF6 mutant cells show significantly lower viral DNA integration activity in vitro. Adding purified recombinant CPSF6 restores integration activity of PICs from CPSF6-mutant cells. Disruption of CPSF6-CA binding in cells reduces viral DNA integration and redirects integration away from gene-dense chromatin, independent of effects on reverse transcription or nuclear entry.\",\n      \"method\": \"PIC extraction and in vitro integration assay, recombinant CPSF6 add-back, integration site sequencing, reverse transcription/nuclear entry controls\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with recombinant protein add-back, multiple independent controls, integration site sequencing; single lab\",\n      \"pmids\": [\"40202316\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The NLS of CPSF6 governs post-nuclear import steps of HIV-1 infection; some NLS chimeras drive CPSF6-358 into the nucleus but fail to support efficient HIV-1 infection. HIV-1 still enters the nucleus in these cells but fails to traffic to speckle-associated domains (SPADs) and fails to integrate efficiently, demonstrating that CPSF6's NLS facilitates intranuclear trafficking and SPAD targeting rather than merely nuclear import per se.\",\n      \"method\": \"Heterologous NLS rescue of CPSF6-358, HIV-1 nuclear entry quantification, integration site analysis, SPAD localization imaging\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — panel of heterologous NLS chimeras, nuclear entry decoupled from integration targeting, integration site sequencing\",\n      \"pmids\": [\"39823525\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"CPSF6 is fused to FGFR1 in the t(8;12)(p11;q15) rearrangement in an 8p11 myeloproliferative syndrome patient; the predicted CPSF6-FGFR1 fusion encodes the N-terminal domain of CPSF6 linked to the entire tyrosine kinase domain and C-terminal sequences of FGFR1. CPSF6 thus acts as a dimerization/oligomerization partner that constitutively activates FGFR1 kinase.\",\n      \"method\": \"Cytogenetics, genomic breakpoint PCR, RT-PCR confirming in-frame fusion\",\n      \"journal\": \"Genes, chromosomes & cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — molecular cloning of fusion, in-frame confirmation; no in vitro kinase assay but structural inference of mechanism is supported\",\n      \"pmids\": [\"18205209\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"CPSF6 and CPSF5 (CFIm subunits) are highly enriched in mouse male germ cells and both subunits are expressed from shorter spermatogenic mRNAs generated by alternative polyadenylation using proximal poly(A) signals; CFIm binding sites were identified near the 3' ends of numerous male germ cell transcripts utilizing noncanonical poly(A) signals, suggesting CPSF6-containing CFIm complexes direct APA at noncanonical signals during spermatogenesis.\",\n      \"method\": \"Northern blotting, cDNA sequencing, RT-PCR, CFIm binding site analysis, Western blot during spermatogenesis\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — multiple detection methods establishing localization and APA role; no direct functional reconstitution assay\",\n      \"pmids\": [\"18032416\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"NP1 protein of minute virus of canines (MVC) physically interacts with CPSF6 in transfected cells, and CPSF6 participates with NP1 to modulate suppression of proximal polyadenylation and splicing enhancement at the MVC capsid gene, demonstrating CPSF6 can be co-opted by viral non-retroviral proteins to modulate alternative RNA processing.\",\n      \"method\": \"Co-immunoprecipitation, functional RNA processing assays in transfected cells\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP plus functional RNA processing assay; single lab\",\n      \"pmids\": [\"30355695\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"CPSF6 interacts with components of the A-to-I RNA editing machinery and paraspeckles, including ADAR1, and is required for their physical integrity; prolactin suppresses CPSF6 and RNA editing activity, placing CPSF6 in a paraspeckle-regulatory pathway.\",\n      \"method\": \"Co-immunoprecipitation, paraspeckle integrity assays (CPSF6 depletion), prolactin treatment\",\n      \"journal\": \"EBioMedicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP and functional integrity assay; single lab, limited mechanistic detail in abstract\",\n      \"pmids\": [\"28673861\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CPSF6 regulates temperature compensation of the mammalian circadian clock; CPSF6 knockdown significantly alters circadian temperature compensation in U-2 OS cells. Global 3' UTR length changes and temperature-dependent gene expression changes in CPSF6 KD cells identify candidate genes including EIF2S1 as underlying circadian temperature compensation.\",\n      \"method\": \"CPSF6 knockdown, 3'-end RNA-seq, mass spectrometry proteomics, circadian period analysis\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — KD with defined phenotype and multi-omics profiling, but single lab and no direct mechanistic reconstitution\",\n      \"pmids\": [\"37379316\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CPSF6 knockdown in HCC cells induces widespread 3'UTR lengthening; specifically, CPSF6 drives proximal poly(A) site usage at NQO1, producing a short 3'UTR NQO1 isoform that is more stable and mediates CPSF6-dependent metabolic alterations and tumorigenic activity, establishing a molecular mechanism linking CPSF6-regulated APA to oncogenic phenotype.\",\n      \"method\": \"CPSF6 knockdown, APA profiling (3T-seq), NQO1 isoform functional assays, metabolic assays\",\n      \"journal\": \"Journal of experimental & clinical cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — APA profiling plus specific target validation; single lab\",\n      \"pmids\": [\"33648552\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CPSF6 mediates 3'UTR shortening of XBP1 by promoting proximal PAS usage; BRCA1-disrupted R-loop accumulation at the CPSF6 5' end causes CPSF6 elevation, and nuclear LINC00221 facilitates CPSF6-induced proximal PAS choice at pre-XBP1, producing a more stable XBP1-S isoform that contributes to cisplatin resistance in lung adenocarcinoma.\",\n      \"method\": \"CPSF6 manipulation, poly(A) site sequencing, R-loop analysis, luciferase reporter, cisplatin resistance assays\",\n      \"journal\": \"Drug resistance updates\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — mechanistic chain demonstrated with multiple assays but all in single study/lab\",\n      \"pmids\": [\"36821972\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Downregulation of CPSF6 upon viral infection (reduced protein abundance) promotes proximal poly(A) site usage of immune-related genes in macrophages and fibroblasts, shortening their 3' UTRs, which improves mRNA stability and translation efficiency to enhance type I IFN antiviral signaling.\",\n      \"method\": \"CPSF6 knockdown/overexpression, APA sequencing, mRNA stability assays, IFN signaling measurement\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — APA profiling combined with functional immune readout; multiple cell types tested\",\n      \"pmids\": [\"38416782\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"FXR1 forms a complex with CFIm25 and CFIm68 (CPSF6) acting as a platform for sequence-specific poly(A) site recognition; this FXR1-CFIm complex affects 3' processing of TRAF1 mRNA, leading to nuclear mRNA stabilization and enhanced cell proliferation in urothelial carcinoma.\",\n      \"method\": \"Co-immunoprecipitation of FXR1-CPSF6/CFIm25 complex, APA analysis, mRNA stability assays\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP identifying novel complex, functional APA readout; single lab\",\n      \"pmids\": [\"35194031\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CPSF6 KO in primary CD4+ T cells leads to global 3' UTR shortening via APA, downregulation of innate immune genes and restriction factors (including TRIM5α), and upregulation of HIV-1 co-receptors, increasing permissivity to HIV-1 infection. HIV-1 recruitment of CPSF6 to incoming cores is sufficient to perturb CPSF6 function and cause similar APA-driven transcriptional reprogramming.\",\n      \"method\": \"CPSF6 KO in primary CD4+ T cells, APA sequencing, transcriptome analysis, HIV-1 infectivity assays, co-receptor expression measurement\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — primary cell KO, APA sequencing, functional infectivity assays, mechanistic link between APA and immune gene regulation established\",\n      \"pmids\": [\"41385587\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"The CPSF6 FG domain is essential for both HIV-induced nuclear puncta formation and binding to the viral core, which serves as the scaffold for CPSF6 condensates; low-complexity regions and mixed-charge domains modulate CPSF6 binding to capsid but do not contribute to puncta formation. SRRM2's intrinsically disordered region is required for enlarging nuclear speckles in the presence of HIV capsid, and puncta form individually then fuse with nuclear speckles.\",\n      \"method\": \"CPSF6 domain deletion mutants, live imaging, SRRM2 depletion, viral replication assays\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — systematic domain mapping, multiple genetic perturbations, functional viral replication readout; peer-reviewed\",\n      \"pmids\": [\"41493399\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CPSF6 is a component of the cleavage factor Im (CFIm) complex that regulates mRNA alternative polyadenylation by binding UGUA-containing enhancer elements and activating distal poly(A) sites via its RS-like domain interacting with Fip1; its nuclear import is mediated by TNPO3 binding to the RS-like domain. During HIV-1 infection, nuclear CPSF6 binds the FG-binding pocket of assembled HIV-1 CA hexamers (competed by cytoplasmic CypA), undergoes MCD-dependent liquid-liquid phase separation/condensation with incoming capsids at nuclear speckles, promotes PIC integration activity, and directs viral DNA integration into gene-dense, transcriptionally active speckle-associated chromatin domains; cytoplasmic mislocalization of CPSF6 aberrantly stabilizes the capsid and blocks nuclear entry, while SYVN1-mediated K48-polyubiquitination degrades CPSF6 during antiviral responses to enhance innate immune gene expression via APA.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CPSF6 is a subunit of the cleavage factor Im (CFIm) complex that governs mRNA alternative polyadenylation (APA) genome-wide by activating enhancer-containing poly(A) sites, with its arginine/serine-like domain (RSLD) docking onto an RS-like region of the CPSF/Fip1 3'-processing machinery in a phosphorylation-sensitive manner [#7]. Most cellular CPSF6 resides in CFIm with CPSF5 and CPSF7 [#6], and its APA output is set not merely by abundance but by RSLD-dependent liquid-liquid phase separation, which CLK2 phosphorylation dissolves to shift usage toward proximal poly(A) sites and promote proliferation [#15]. Nuclear import of CPSF6 is mediated by TNPO3 binding to the RSLD, an interaction resolved structurally and dispensable for, yet inhibited by, RSLD hyperphosphorylation [#11]. Through this APA activity CPSF6 shapes diverse programs including innate antiviral gene expression, where reduced CPSF6 shortens 3' UTRs of immune transcripts to enhance type I IFN signaling [#30, #32], and is itself a degradation target of the MAVS-activated E3 ligase SYVN1, which K48-polyubiquitinates CPSF6 to remodel the APA transcriptome during antiviral responses [#18]. CPSF6 is a central host cofactor for HIV-1: nuclear CPSF6 binds a conserved pocket in assembled HIV-1 capsid (CA) hexamers at the NTD-CTD interface [#0, #1], and this engagement is spatially gated by cytoplasmic cyclophilin A, whose prior binding prevents premature capsid-CPSF6 association [#14, #19]. CPSF6 licenses capsid trafficking through the nuclear pore and interior, undergoes capsid-scaffolded condensation at nuclear speckles via its FG and mixed-charge domains [#17, #33], directs viral DNA integration into gene-dense, transcriptionally active speckle-associated chromatin domains, and directly stimulates preintegration complex integration activity [#5, #8, #21]. Cytoplasmic mislocalization or truncation of CPSF6 instead aberrantly stabilizes or disrupts the incoming capsid and blocks infection [#3, #9]. Chromosomal rearrangements fusing CPSF6 to FGFR1 or RARG drive myeloproliferative and acute myeloid leukemias, the latter through recruitment of HDAC3 to repress myeloid differentiation genes [#20, #23].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Established that CPSF6, as a CFIm subunit, directs tissue-specific alternative polyadenylation, providing the first functional context for the protein in RNA 3'-end processing.\",\n      \"evidence\": \"Expression and CFIm binding-site analysis in mouse male germ cells\",\n      \"pmids\": [\"18032416\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No reconstitution of CFIm-directed APA in vitro\", \"Causal role in spermatogenesis not tested by loss-of-function\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Identified CPSF6 as a fusion partner in a myeloproliferative rearrangement, framing its N-terminal domain as an oligomerization module that can constitutively activate a partner kinase.\",\n      \"evidence\": \"Cytogenetics and breakpoint cloning of CPSF6-FGFR1 in an 8p11 syndrome patient\",\n      \"pmids\": [\"18205209\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No in vitro kinase activation assay\", \"Oligomerization mechanism inferred, not measured\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Defined the structural basis of CPSF6 recognition of HIV-1, revealing a conserved capsid interface and linking capsid binding to dependence on nuclear-entry cofactors.\",\n      \"evidence\": \"X-ray crystallography, mutagenesis, and infectivity assays with truncated CPSF6-358\",\n      \"pmids\": [\"22956906\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish whether assembled lattice versus monomeric CA is the target\", \"Physiological role of full-length CPSF6 in infection unaddressed\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Resolved the cell-biological logic of CPSF6 in HIV-1 by showing TNPO3 acts through CPSF6 nuclear import and that cytoplasmic CPSF6 is the effector that stabilizes the capsid and blocks nuclear entry.\",\n      \"evidence\": \"TNPO3/CPSF6 knockdown, localization mutants, epistatic rescue, and fate-of-capsid assays in two independent labs\",\n      \"pmids\": [\"23414560\", \"23622145\", \"23658440\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which cytoplasmic CPSF6 stabilizes the core unresolved\", \"Distinct truncation phenotypes (uncoating acceleration vs. stabilization) not unified\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Demonstrated that the assembled capsid hexamer lattice, not isolated CA, is the high-affinity CPSF6 target, defining a preformed druggable pocket shared with PF74.\",\n      \"evidence\": \"Quantitative binding and crystallography of CPSF6/PF74-CA hexamer complexes\",\n      \"pmids\": [\"25518861\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry of CPSF6 on intact cores in cells not determined\", \"Link between lattice binding and downstream trafficking not yet established\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Established CPSF6 as the dominant determinant of HIV-1 integration into euchromatin, mechanistically separable from LEDGF/p75 and independent of its CFIm partners.\",\n      \"evidence\": \"CPSF6/LEDGF knockouts with binding-deficient complementation, CFIm-disrupting mutants, and integration site sequencing\",\n      \"pmids\": [\"26858452\", \"26994143\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How capsid-bound CPSF6 selects active chromatin not defined\", \"Role of speckle association not yet identified\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined CFIm/CPSF6 as an enhancer-dependent activator of 3' processing and identified the RSLD-Fip1 interaction as the phosphorylation-regulated molecular contact driving distal poly(A) site activation.\",\n      \"evidence\": \"In vitro RS-domain binding assays, RSLD mutagenesis, phosphorylation analysis, and global APA profiling\",\n      \"pmids\": [\"29276085\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Kinases controlling RSLD phosphorylation in vivo not identified here\", \"Connection to phase behavior not yet appreciated\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Showed CPSF6 is a master regulator of HIV-1 intranuclear localization, routing complexes to the nuclear interior and away from heterochromatin at the lamina.\",\n      \"evidence\": \"Live-cell and fixed imaging with CPSF6 knockout/complementation and integration site sequencing\",\n      \"pmids\": [\"30173955\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of interior targeting not defined\", \"Relationship to nuclear speckles not yet shown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Provided structural and spatial detail for CPSF6 in nuclear entry, defining RSLD-TNPO3 recognition and showing CPSF6 acts at the nuclear basket after Nup153 to license pore passage.\",\n      \"evidence\": \"Crystal structure of RSLD-TNPO3, mutagenesis, STED microscopy, and primary macrophage infection\",\n      \"pmids\": [\"30916345\", \"30672737\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether CPSF6 condensation participates in pore passage not addressed\", \"Ordering of Nup153/CPSF6 handoff inferred\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Established that capsid-CPSF6 interaction is a primate lentivirus-specific adaptation for targeting speckle-associated chromatin domains, and identified post-transcriptional control of CPSF6 by miR-125b during infection.\",\n      \"evidence\": \"Large-scale comparative integration mapping with KO/KD and binding assays; luciferase reporter, RNA pulldown, and seed mutagenesis for miR-125b\",\n      \"pmids\": [\"32994325\", \"32152226\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How SPAD targeting is physically achieved still open\", \"miR-125b regulation single-lab\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed HIV-1 induces higher-order CPSF6 assemblies that bind and disrupt capsids, and that CypA binding gates premature cytoplasmic engagement of CPSF6.\",\n      \"evidence\": \"Live-cell co-trafficking imaging, in vitro capsid disruption, and CypA inhibition; plus APA/NQO1 oncogenic profiling in HCC\",\n      \"pmids\": [\"33758083\", \"33648552\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physical nature of higher-order CPSF6 not defined here\", \"Spatial separation of CypA/CPSF6 not yet tested directly\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Unified CPSF6 function around liquid-liquid phase separation: RSLD-driven LLPS sets APA output and CLK2 phosphorylation dissolves it, while capsid-scaffolded CPSF6/CPSF5 condensates at nuclear speckles are required for productive HIV-1 infection.\",\n      \"evidence\": \"In vitro LLPS and CLK2 kinase assays with APA profiling; hexanediol/osmotic disruption of CPSF6 condensates with capsid mutant controls; circadian temperature-compensation KD\",\n      \"pmids\": [\"37777964\", \"37414787\", \"37379316\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the same condensates serve APA and HIV-1 integration unresolved\", \"In vivo regulation of CLK2-CPSF6 axis untested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Dissected the domain requirements for CPSF6 condensation in HIV-1 (FG domain for puncta/core binding, MCD for LLPS-dependent intranuclear penetration) and placed CPSF6 in antiviral circuits via SYVN1-mediated K48 degradation and APA-driven IFN enhancement.\",\n      \"evidence\": \"Domain-deletion and heterologous-MCD rescue with integration analysis; FG/SRRM2 imaging; SYVN1 ubiquitination assays with MAVS/NUP153 epistasis; immune-gene APA profiling\",\n      \"pmids\": [\"39258548\", \"41493399\", \"39951376\", \"38416782\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How condensation mechanically promotes pore-to-interior trafficking unresolved\", \"Generality of SYVN1 regulation across cell types not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Established that CPSF6 directly stimulates PIC integration activity, that its NLS governs intranuclear SPAD trafficking beyond import, and that CPSF6 loss reprograms immune APA to alter HIV-1 permissivity; also defined the CPSF6-RARG/HDAC3 leukemic mechanism.\",\n      \"evidence\": \"PIC in vitro integration with recombinant add-back; heterologous NLS chimeras with SPAD imaging; CypA/CPSF6 sequential-binding epistasis; primary CD4+ T-cell KO APA/infectivity; Co-IP and HDAC inhibitor leukemia model\",\n      \"pmids\": [\"40202316\", \"39823525\", \"40013779\", \"41385587\", \"39805830\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Biochemical mechanism by which CPSF6 stimulates integration unknown\", \"Whether SPAD-targeting and PIC stimulation are separable activities unclear\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved whether CPSF6's APA-regulatory phase-separation activity and its HIV-1 integration-targeting condensate function share a common biophysical mechanism, and how the same condensate properties are partitioned between physiological 3'-processing and capsid-driven chromatin targeting.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure of capsid-CPSF6 condensates at chromatin\", \"Direct biochemical activity of CPSF6 on PIC integration undefined\", \"Interplay between phosphorylation, LLPS, and APA versus HIV-1 functions not integrated\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [7, 24, 31]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [7, 15, 30]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [7, 15]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [5, 6, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2, 11, 10]},\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [16, 33]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [3, 14, 19]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [7, 15, 11]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [7, 28, 29]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [0, 5, 20, 23]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [18, 30, 32]}\n    ],\n    \"complexes\": [\"CFIm (cleavage factor Im)\"],\n    \"partners\": [\"CPSF5\", \"CPSF7\", \"TNPO3\", \"FIP1L1\", \"CLK2\", \"SYVN1\", \"HDAC3\", \"FXR1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":8,"faith_pct":87.5}}