Affinage

U2AF2

Splicing factor U2AF 65 kDa subunit · UniProt P26368

Length
475 aa
Mass
53.5 kDa
Annotated
2026-06-10
100 papers in source corpus 45 papers cited in narrative 45 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 11/11 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

U2AF2 (U2AF65) is an essential pre-mRNA splicing factor that defines the 3' splice site by recognizing the intronic polypyrimidine tract and directing the spliceosome to the adjacent branch point (PMID:8781232, PMID:16818232). Its tandem RRM1–RRM2 domains contact uracil bases through a network of hydrogen bonds, flexible side chains, and ordered waters that adapt to varied pyrimidine sequences, with local RNA flexibility accommodating non-uridine nucleotides at central tract positions (PMID:16818232, PMID:35524551). These tandem RRMs sample a broad conformational ensemble dominated by transient interdomain contacts, and a strong polypyrimidine tract selects an open, RNA-bound arrangement from this pre-existing distribution—a conformational selection mechanism that underlies universal 3' splice site recognition (PMID:23376934, PMID:24734879, PMID:22702716). An intrinsically disordered inter-RRM linker imposes autoinhibition that suppresses nonproductive binding to weak tracts and preserves splicing fidelity, while the partner subunit U2AF1 (U2AF35) stabilizes a closed conformation in the absence of RNA (PMID:32188783, PMID:32343311). U2AF65 functions as a heterodimer with U2AF35, which docks onto a U2AF65 proline-rich region via reciprocal tryptophan contacts, folding the otherwise disordered U2AF35 RRM (PMID:11551507, PMID:12297299). Beyond RNA contact, the RS domain of U2AF65 directly contacts the branch point to promote U2 snRNA–branch point base pairing and is required for recruitment to sites of active splicing (PMID:8781232, PMID:9166400). A noncanonical third RRM (UHM) engages tryptophan-containing ULM motifs in successive partners—first SF1/mBBP for cooperative initial branch point recognition, then SF3B1 (SF3b155) during spliceosome maturation, an exchange driven by the lower stability of the SF3b155 complex—and the same UHM is read by additional ULM-bearing proteins including RBM39 (PMID:9512519, PMID:12718882, PMID:16376933, PMID:35780835, PMID:27050129). U2AF65 nucleates downstream assembly by recruiting the DEAD-box ATPase UAP56 required for stable U2 snRNP–branch point interaction and, through direct binding to the phosphorylated CTD of RNA Pol II, the Prp19 complex to activate co-transcriptional splicing (PMID:9242493, PMID:21536736). Its access to splice sites is gated competitively by trans-acting RBPs—MBNL1, PTB, hnRNP C, and HNRNPA1 either block or redirect U2AF65 binding, while FUBP1, CELF6, and PCBP1 enhance its recruitment—coupling exon choice to a competitive regulatory landscape (PMID:19470458, PMID:23374342, PMID:16982681, PMID:29643205, PMID:29650551). U2AF2 activity is further tuned by post-translational modification, including Jmjd6-catalyzed lysyl hydroxylation and SIRT4-mediated lysyl deacetylation, and by ubiquitin-dependent control of its abundance through OTUB2 stabilization and CD82-induced degradation (PMID:19574390, PMID:27899633, PMID:39495216, PMID:30662561, PMID:27041584). U2AF2 also associates with chromatin in gene bodies in an H3K36me3-dependent, RNA-independent manner, enhancing the accuracy of co-transcriptional exon selection (PMID:40315850).

Mechanistic history

Synthesis pass · year-by-year structured walk · 15 steps
  1. 1992 High

    Established that 3' splice site recognition by U2AF65 is not autonomous but coupled to downstream 5' splice site recognition, defining exon-bridging communication across the spliceosome.

    Evidence UV cross-linking and co-purification showing U1 snRNP-dependent enhancement of U2AF65 binding to an upstream 3' splice site

    PMID:1285125

    Open questions at the time
    • Did not identify the molecular bridge mediating cross-exon communication
    • Mechanism of U1 snRNP-to-U2AF65 signaling unresolved
  2. 1996 High

    Resolved how U2AF65 actively promotes branch point usage, showing the RS domain directly contacts the branch point to drive U2 snRNA pairing rather than acting only as a polypyrimidine anchor.

    Evidence In vitro splicing assays with RS-domain mutagenesis and UV cross-linking

    PMID:8781232

    Open questions at the time
    • Structural basis of RS-domain–RNA contact not defined
    • Did not address RS-domain phosphorylation state
  3. 1997 High

    Identified the ATP-dependent step downstream of U2AF65 binding by showing it recruits the DEAD-box helicase UAP56 required for stable U2 snRNP–branch point engagement.

    Evidence Affinity purification, cloning, and in vitro splicing complementation

    PMID:9242493

    Open questions at the time
    • Precise RNA/protein substrate of UAP56 ATPase unresolved
    • Structural interface with U2AF65 not mapped
  4. 1998 High

    Defined the protein-protein logic of initial branch point recognition, showing the U2AF65 UHM recruits SF1/mBBP for cooperative RNA binding.

    Evidence In vitro binding, cooperative RNA-binding assays, and deletion mutagenesis

    PMID:9512519

    Open questions at the time
    • Did not yet provide atomic structure of the UHM–ULM interface
    • In vivo consequence of cooperative binding not measured
  5. 2003 High

    Provided atomic and topological detail of the U2AF heterodimer and the UHM–ULM recognition mode, establishing how U2AF65 reads tryptophan-containing peptides and how it bends pre-mRNA at the 3' splice site.

    Evidence X-ray crystallography of the U2AF heterodimer, NMR/crystal structure of UHM–SF1 peptide, and directed hydroxyl radical probing

    PMID:11551507 PMID:12718882 PMID:14506271

    Open questions at the time
    • RNA-bending model derived from probing, not a co-complex structure
    • Dynamics of UHM partner exchange not addressed
  6. 2006 High

    Explained how a single factor recognizes degenerate polypyrimidine tracts, showing adaptable RRM1–RRM2 contacts and ordered waters accommodate sequence variation.

    Evidence Crystal structure of RRM1–RRM2 bound to poly-U7 RNA with SPR validation of mutants

    PMID:16818232

    Open questions at the time
    • Did not capture the full conformational range of tandem RRMs
    • Non-uridine accommodation not yet structurally tested
  7. 2006 High

    Established the UHM exchange and regulation logic during early assembly: SF3b155 presents multiple competing ULM sites, and SF1 phosphorylation by KIS/UHMK1 enhances the SF1–U2AF65 interaction.

    Evidence Thermodynamic/spectroscopic ULM mapping and in vitro kinase assays with domain mutagenesis

    PMID:16376933 PMID:16420481

    Open questions at the time
    • Cellular trigger for SF1-to-SF3b155 exchange timing not defined
    • Whether KIS phosphorylation operates in vivo on endogenous transcripts not shown
  8. 2009 High

    Revealed post-translational and competitive regulation of U2AF65 activity through Jmjd6-catalyzed lysyl hydroxylation and MBNL1 structure-based competition at shared RNA elements.

    Evidence Mass spectrometry, in vitro hydroxylation, knockdown with minigene reporters, and RNA-binding competition assays

    PMID:19470458 PMID:19574390

    Open questions at the time
    • Functional consequence of specific hydroxylated residues not pinpointed
    • Genome-wide scope of MBNL1 competition not yet mapped
  9. 2011 High

    Connected U2AF65 to co-transcriptional splicing by demonstrating direct binding to the Pol II phospho-CTD to recruit the Prp19 complex.

    Evidence Biochemical purification, in vitro phospho-CTD binding, in vivo Co-IP, and in vitro splicing complementation

    PMID:21536736

    Open questions at the time
    • Structural basis of the CTD–U2AF65 contact not resolved
    • Dependence on CTD phosphorylation pattern not dissected
  10. 2013 High

    Generalized the conformational-selection model and showed genome-wide competitive gating, with hnRNP C acting as a sentinel preventing U2AF65 binding at cryptic Alu polypyrimidine sites.

    Evidence Six crystal structures plus SAXS and mutagenesis for tandem-RRM spacing, and quantitative iCLIP with knockdown/minigene validation

    PMID:23374342 PMID:23376934

    Open questions at the time
    • Did not quantify the equilibrium populations of each RRM spacing in cells
    • Other genome-wide competitors not yet catalogued
  11. 2014 Medium

    Detailed the solution dynamics of multidomain U2AF65, showing transient electrostatic interdomain contacts and a minority pre-formed RNA-competent state.

    Evidence NMR paramagnetic relaxation enhancement and SAXS with stochastic conformational sampling

    PMID:22702716 PMID:24734879

    Open questions at the time
    • Single-lab conformational interpretation
    • Functional readout of altered interdomain contacts not directly tested
  12. 2018 High

    Showed that U2AF2's intrinsic specificity is low and is sharpened or redirected by trans-acting RBPs, defining a combinatorial code for 3' splice site selection.

    Evidence In vitro iCLIP with machine learning identifying FUBP1/CELF6/PCBP1 enhancers, and iCLIP in HNRNPA1-overexpression cells showing decoy-site redirection

    PMID:29643205 PMID:29650551

    Open questions at the time
    • Mechanism by which each cofactor alters U2AF2 binding kinetics not resolved
    • Generality across cell types not established
  13. 2020 High

    Resolved the autoinhibition and partner-driven conformational switching that govern fidelity, showing the disordered linker suppresses weak-tract binding and U2AF1 stabilizes a closed RRM state switched open by strong tracts.

    Evidence NMR with iCLIP and mutagenesis (linker autoinhibition) and single-molecule FRET with structure-guided mutants (U2AF1-modulated conformation)

    PMID:32188783 PMID:32343311

    Open questions at the time
    • How disease U2AF1 mutations reshape the equilibrium mechanistically not fully resolved
    • Linkage between conformation and downstream assembly kinetics not measured
  14. 2022 High

    Distinguished U2AF2 partner-specific UHM trajectories and the structural basis for promiscuous central-nucleotide tolerance, linking distinct partner complexes to distinct regulated splice sites.

    Evidence High-resolution crystal structures of U2AF2–SF3B1 and of U2AF2 bound to non-U central positions, with ITC, Co-IP, MD, and eCLIP/splicing validation

    PMID:35524551 PMID:35780835

    Open questions at the time
    • In vivo timing of SF1- versus SF3B1-directed splicing programs not established
    • Did not resolve full ternary assembly intermediates
  15. 2025 High

    Extended U2AF2 function beyond soluble spliceosome assembly to a chromatin-tethered, H3K36me3-dependent role that improves co-transcriptional exon selection accuracy.

    Evidence CUT&RUN with RNase control, knockdown RNA-seq, and histone-modification dependence assays

    PMID:40315850

    Open questions at the time
    • Reader/adaptor linking U2AF2 to H3K36me3 not identified
    • Relationship between chromatin pool and soluble assembly pool unresolved

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the many regulatory layers — conformational selection, UHM partner exchange, competing RBPs, post-translational modifications, ubiquitin-dependent turnover, and chromatin tethering — are integrated in real time at a single splice site remains unresolved.
  • No unified kinetic model coupling conformation, partner exchange, and chromatin context
  • Causal hierarchy among PTMs and turnover signals not established
  • Reader linking chromatin-bound U2AF2 to H3K36me3 unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 6 GO:0060090 molecular adaptor activity 6
Localization
GO:0005634 nucleus 2 GO:0000228 nuclear chromosome 1 GO:0005654 nucleoplasm 1
Pathway
R-HSA-8953854 Metabolism of RNA 5 R-HSA-74160 Gene expression (Transcription) 2
Partners
JMJD6PRPF19RBM39SF1SF3B1U2AF1UAP56UHMK1
Complex memberships
U2AF heterodimer (U2AF65/U2AF35)

Evidence

Reading pass · 45 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1996 U2AF65 binds the polypyrimidine tract via its RNA binding domain, and its RS domain directly contacts the branch point sequence to promote U2 snRNA–branch point base pairing, even in the absence of other splicing factors; RS domain mutants that lose branch point contact also lose splicing activity. In vitro splicing assays, RS domain mutagenesis, UV cross-linking Science High 8781232
1992 U1 snRNP binding at a downstream 5' splice site facilitates U2AF65 binding to the upstream 3' splice site through exon-bridging interactions, as demonstrated by UV cross-linking showing that p61/U2AF65 binding to the 3' splice site of alternative exon E4 is enhanced by the downstream 5' splice site in a U1 snRNP-dependent manner. UV cross-linking, co-purification, selective polypyrimidine tract binding assays Genes & development High 1285125
1997 U2AF65 recruits the DEAD-box helicase UAP56 (a 56-kDa U2AF65-associated protein) to the pre-mRNA branch point region; UAP56 is required for stable U2 snRNP–branch point interaction and constitutes an essential ATP-hydrolyzing activity for this step. Affinity purification, cloning, in vitro splicing complementation, Co-IP Genes & development High 9242493
1998 WT1 (+KTS isoform) interacts with U2AF65 in vitro and in vivo; the DDS-associated WT1 mutation enhances this interaction; WT1 co-localizes with splicing factors and can be incorporated into spliceosomes. In vitro binding, co-immunoprecipitation, immunofluorescence co-localization, spliceosome fractionation Genes & development Medium 9784496
1998 mBBP/SF1 interacts directly with U2AF65 via the third RBD (UHM) of U2AF65, and this interaction promotes cooperative binding of both proteins to a branchpoint sequence–polypyrimidine tract RNA, facilitating initial branch point recognition. In vitro binding assays, cooperative RNA-binding assays, deletion mutagenesis Genes & development High 9512519
2001 X-ray crystal structure of the core U2AF heterodimer shows that an atypical RRM of U2AF35 and a proline-rich region of U2AF65 interact via reciprocal 'tongue-in-groove' tryptophan residues; mutagenesis of these tryptophans abolishes dimerization; the heterodimer binds RNA. X-ray crystallography at 2.2 Å, site-directed mutagenesis, biochemical RNA-binding assays Cell High 11551507
2003 NMR/crystal structure of U2AF65 RRM3 (UHM domain) complexed with N-terminal SF1 peptide reveals SF1 inserts a conserved tryptophan into a hydrophobic pocket on the helical face of UHM, establishing a paradigm for protein–protein recognition by noncanonical RRMs distinct from RNA binding. NMR spectroscopy, X-ray crystallography Molecular cell High 12718882
2006 X-ray crystal structure of U2AF65 RNA binding domain (RRM1–RRM2) bound to a poly-U7 RNA at 2.5 Å reveals specific hydrogen bonds between U2AF65 and uracil bases; flexible side chains and bound water molecules allow adaptation to varied pyrimidine sequences. X-ray crystallography at 2.5 Å, surface plasmon resonance with site-directed mutants Molecular cell High 16818232
2009 Jmjd6, an Fe(II)- and 2-oxoglutarate-dependent dioxygenase, catalyzes lysyl-5-hydroxylation of U2AF65; Jmjd6 is nuclear and alters alternative RNA splicing of a subset of endogenous and reporter genes, supporting a functional role in splicing regulation. Mass spectrometry identification of hydroxylated lysine, in vitro hydroxylation assay, siRNA knockdown, minigene splicing reporters Science High 19574390
2009 MBNL1 controls splicing of cardiac troponin T exon 5 by competing directly with U2AF65 for binding to the 3' end of intron 4; MBNL1 binds a stem-loop structure while U2AF65 requires single-stranded RNA at the same region, and stabilizing the stem-loop decreases U2AF65 affinity and represses exon inclusion. In vitro RNA-binding competition assays, UV cross-linking, structure-stabilizing mutations, splicing assays PNAS High 19470458
2011 U2AF65 binds directly to the phosphorylated CTD of RNA Pol II, and this interaction recruits U2AF65 and the Prp19 complex (PRP19C) to the pre-mRNA to activate CTD-dependent splicing; the U2AF65–PRP19C interaction is required for this activation. Biochemical purification, in vitro binding to phospho-CTD, Co-IP in vivo, in vitro splicing complementation assay Genes & development High 21536736
2013 hnRNP C competes with U2AF65 for binding at polypyrimidine-like sequences within Alu elements; loss of hnRNP C allows U2AF65 to bind these cryptic sites and drive aberrant Alu exon inclusion, demonstrating that hnRNP C acts as a genome-wide sentinel by preventing U2AF65 access. Quantitative iCLIP (individual-nucleotide resolution CLIP), siRNA knockdown, minigene splicing experiments Cell High 23374342
1997 U2AF65 is diffusely distributed in the nucleoplasm with additional concentration in nuclear speckles; the RS domain is specifically required for recruitment of U2AF65 to sites of active splicing (demonstrated by adenovirus-infected nuclei), whereas other domains (RNA binding domain, U2AF35-interaction region) are not required for speckle localization. Immunofluorescence with monoclonal antibody, transient expression of deletion mutants, adenovirus infection model, live-cell imaging The Journal of cell biology High 9166400
2005 SF3b155 contains multiple tryptophan-containing ULM sites that are recognized by the U2AF65 UHM domain similarly to SF1; five of seven sites bind U2AF65; the SF1–U2AF65 complex is 3.3 kcal/mol more stable than the SF3b155–U2AF65 complex, consistent with ATP-driven exchange during spliceosome assembly. Intrinsic tryptophan fluorescence spectroscopy, isothermal titration calorimetry, circular dichroism Journal of molecular biology High 16376933
2006 PTB directly competes with U2AF65 for binding to the polypyrimidine tract of the beta-tropomyosin exon 6B; PTB prevents U2 snRNA association at the branch point by displacing U2AF65, as shown by competition experiments and correlation of PTB depletion with increased U2AF65 cross-linking. UV cross-linking, immunoprecipitation, psoralen cross-linking, PTB siRNA knockdown, in vitro splicing assays Molecular and cellular biology High 16982681
2006 Phosphorylation of SF1 on the SPSP motif by the kinase KIS (UHMK1, which contains a UHM domain) enhances SF1 binding to U2AF65 and enhances formation of the ternary SF1–U2AF65–RNA complex; KIS requires its UHM domain to interact with SF1 and efficiently phosphorylate it. In vitro kinase assay, pull-down, fluorescence binding assays, domain mutagenesis The FEBS journal High 16420481
1999 The solution structures of U2AF65 RBD1 and RBD2 were determined by NMR; RBD2 has a canonical beta1-alpha1-beta2-beta3-alpha2-beta4 topology and its four beta-strands interact with RNA; RBD1 has unique structural features including an elongated α1 helix and an unusually long α1/β2 loop that does not contact RNA and may interact with UAP56. NMR spectroscopy, chemical shift perturbation The EMBO journal High 10449418
2012 The SF1–U2AF65 complex undergoes a large conformational change (contraction of ~15 Å in maximum dimension) upon binding splice-site RNA, whereas isolated SF1 or U2AF65 alone show no detectable conformational change with RNA. Small-angle X-ray scattering (SAXS), ab initio shape restoration Journal of molecular biology Medium 21146534
2013 U2AF65 tandem RRMs adopt distinct inter-RRM spacings selected by Py tract sequence variations; RRM1 is more promiscuous for cytosine-containing Py tracts than RRM2; conformational selection from a pre-existing ensemble underlies universal 3' splice site recognition. X-ray crystallography (six structures), SAXS, site-directed mutagenesis, RNA-binding assays Nucleic acids research High 23376934
2019 OTUB2 directly binds U2AF2 (U2AF65) and acts as a deubiquitinase to stabilize U2AF2 protein by removing its ubiquitin modifications, preventing U2AF2 degradation, which in turn promotes the Warburg effect and AKT/mTOR signaling in NSCLC. Co-immunoprecipitation, mass spectrometry, ubiquitination assay, siRNA knockdown, xenograft tumor model Theranostics Medium 30662561
2011 U2AF65 binds specifically to expanded CAG repeat RNA via its RRM3 domain; U2AF65 forms an RNA/protein complex with the nuclear export receptor NXF1, serving as an adaptor to link expanded CAG RNA to NXF1 for nuclear export; reduction of U2AF65/U2AF50 function increases nuclear accumulation of expanded CAG RNA and exacerbates CAG RNA toxicity in vivo. Co-immunoprecipitation, domain deletion analysis (RRM3), Drosophila genetics, RNA-binding assays Human molecular genetics Medium 21725067
2016 CD82 suppresses U2AF2-mediated alternative splicing of CD44 by inducing U2AF2 ubiquitination and degradation; U2AF2-mediated CD44v8-10 splicing is required for melanoma cell migration and metastasis. In vivo and in vitro ubiquitination assays, Co-IP, knockdown/overexpression, in vivo metastasis assay Oncogene Medium 27041584
2014 NMR and SAXS analyses show that multidomain U2AF65 samples a highly anisotropic conformational space dominated by transient, electrostatic interdomain contacts; these contacts are reduced at higher salt concentration; the RNA-bound domain arrangement represents a minority pre-formed state selected by conformational selection. NMR paramagnetic relaxation enhancement, SAXS, stochastic conformational sampling Journal of the American Chemical Society Medium 24734879
2005 FRET microscopy in live cells identifies direct interaction sites between U2AF35 and U2AF65 in the cell nucleus; additionally reveals a novel U2AF35 self-interaction confirmed in vitro, suggesting that the U2AF complex stoichiometry in vivo may differ from the expected heterodimer. FRET microscopy (two approaches), biochemical in vitro binding assays RNA Medium 16043505
2019 RS domain of U2AF65 drives liquid-liquid phase separation amplified by intronic RNA with repeated pyrimidine tracts; U2AF65 and CAPERα cooperatively bind the multi-ULM domain of SF3b155 and knockdown of either factor promotes inclusion of cassette exons preceded by repeated pyrimidine-rich motifs. Phase separation assay, Co-IP, isoform-specific knockdown with splicing readout, interaction domain mapping EMBO reports Medium 31271494
2020 An autoinhibitory intramolecular interaction mediated by the intrinsically disordered linker between RRM1 and RRM2 of U2AF2 reduces nonproductive binding to weak Py-tract RNAs; mutations that impair linker autoinhibition enhance affinity for weak Py-tracts, promote promiscuous binding, and impair splicing fidelity. NMR structural biology, iCLIP, mutagenesis, in vitro RNA-binding assays PNAS High 32188783
2020 Single-molecule FRET shows that U2AF1 stabilizes a high-FRET closed conformation of U2AF2 RRMs in the absence of RNA; a strong Py tract switches U2AF2 to an open conformation; weak Py tracts produce a mixture; the MDS-associated S34F mutation of U2AF1 modulates this conformational equilibrium. Single-molecule FRET, structure-guided mutagenesis Nucleic acids research High 32343311
2022 Crystal structures of U2AF2 bound to central Py tract positions containing cytidine, guanosine, or adenosine show that local RNA flexibility accommodates different nucleotides with little change in the polypeptide backbone; structure-guided mutants confirm tolerance of nucleotide substitutions at the central position, and eCLIP confirms lower sequence conservation at central nucleotide positions in vivo. X-ray crystallography (multiple structures), molecular dynamics, mutagenesis, RNA-binding assays, eCLIP Nucleic acids research High 35524551
2020 Cancer-associated U2AF2 mutations N196K and G301D alter RNA binding affinity (N196K increases, G301D decreases) through distinct structural mechanisms; G301D reduces splicing of a prototypical minigene; both mutations subtly alter endogenous splicing patterns in cells. X-ray crystallography at 1.4–1.7 Å, surface plasmon resonance, minigene splicing assay, endogenous splicing analysis The Journal of biological chemistry High 33020180
2021 A small molecule (NSC-194308) specifically enhances RNA binding by the U2AF2 subunit by bridging its tandem RRMs via hydrophobic and electrostatic moieties; this inhibits spliceosome progression by stalling assembly at the U2AF2 stage; cancer cells expressing mutant U2AF1 are preferentially killed. Compound screen, biochemical RNA-binding assay, in vitro splicing assay, computational docking, structure-guided mutagenesis, cell viability assays Cell chemical biology High 33689684
2022 The U2AF2 UHM binds a SF3B1 ULM site in a distinctive trajectory (resolved by crystal structure at 1.8 Å) that differs from prior UHM/ULM complexes; key interface residues contribute to co-immunoprecipitation of U2AF2–SF3B1; disruption of the interface alters splicing of representative transcripts; splice sites coregulated by U2AF2–SF3B1 differ from those coregulated by U2AF2–SF1. X-ray crystallography at 1.8 Å, isothermal titration calorimetry, Co-IP, splicing analysis of endogenous transcripts The Journal of biological chemistry High 35780835
2012 U2AF65 solution ensemble characterized by SAXS shows a broad range of inter-RRM conformations, with a majority having few RRM–RRM contacts and a subpopulation showing tight interdomain contacts; this diversity allows pre-existing conformational selection by diverse splice sites. Small-angle X-ray scattering, solution conformational analysis Biochemistry Medium 22702716
2013 U2AF65 interacts with and stabilizes TRF1 protein by inhibiting its ubiquitin-dependent proteolysis; U2AF65 competes with Fbx4 E3 ubiquitin ligase for TRF1 binding; siRNA-mediated depletion of U2AF65 reduces TRF1 stability. In vitro pull-down, Co-IP, ubiquitination assay, siRNA knockdown, protein half-life measurement Biochemical and biophysical research communications Medium 24389012
2018 In vitro iCLIP experiments show that U2AF2 alone has lower binding specificity for 3' splice sites; trans-acting RBPs (including FUBP1, CELF6, and PCBP1) enhance U2AF2 recruitment to 3' splice sites and promote clearance of introns; machine learning identified and validated these novel regulators of U2AF2 binding and splicing outcomes. In vitro iCLIP, mathematical modeling, machine learning, siRNA knockdown with splicing readout Genome research High 29643205
2018 HNRNPA1 overexpression shifts U2AF2 crosslinking from bona fide 3' splice sites to distal intronic 'decoy' sites (including Alu-derived sequences) for alternative cassette exons, as measured by iCLIP; HNRNPA1 directly interacts with the U2AF heterodimer. iCLIP in control and HNRNPA1-overexpression cells, direct interaction assay Genome research High 29650551
2017 JMJD6 co-regulates a large set of alternative splicing events with U2AF65 through RNA-dependent interaction; JMJD6 enzymatic activity (lysine hydroxylation of U2AF65) is required for a subset of co-regulated splicing events; both enzymatic activity-dependent and -independent mechanisms contribute to splicing regulation. RASL-seq, JMJD6 knockout mice, enzymatic activity-dead mutants, co-IP/RNA interaction assays Nucleic acids research High 27899633
2016 Crystal and NMR structures of the RBM39 UHM bound to U2AF65 ULM reveal common and discriminating recognition elements compared to U2AF35–U2AF65; the interaction was confirmed by Co-IP from human cell extracts and ITC with purified proteins. X-ray crystallography, NMR, Co-IP, isothermal titration calorimetry Acta crystallographica Section D High 27050129
2012 NMR shows that isolated U2AF35 RRM is intrinsically disordered in solution but adopts a folded tertiary structure upon binding to the N-terminal proline-rich region of U2AF65; the RNA binding domains of U2AF65 are not involved in this interaction. NMR spectroscopy, protein co-purification FEBS letters Medium 12297299
2015 MBNL1 activates insulin receptor exon 11 inclusion by binding a downstream intronic enhancer and enhancing U2AF65 binding to the upstream intron 3' splice site, which promotes early spliceosome (complex A) formation; neither the 5' splice site nor exon 11 is required for MBNL1-activated U2AF65 binding. In vitro splicing assay, complex A formation, UV cross-linking for U2AF65 binding, deletion mutagenesis Nucleic acids research High 24185704
2003 Hydroxyl radical probing using Fe-EDTA-modified U2AF65 deletion mutants shows that U2AF65 bends the pre-mRNA at the 3' splice site; structural model suggests U2AF65 juxtaposes reactive RNA functionalities to organize the pre-mRNA for spliceosome assembly. Directed hydroxyl radical probing, Fe-EDTA modification of U2AF65 N-terminus, RNA structural analysis The Journal of biological chemistry Medium 14506271
2021 U2AF2 binds an ectopic polypyrimidine tract within IL7R exon 6 (adjacent to an exonic branchpoint-like sequence) and recruits U2 snRNP components to the exon, thereby repressing exon 6 inclusion; this binding is enhanced by the MS-risk allele (C at rs6897932) and competes with PTBP1 at the upstream intron 5 PPT. RNA immunoprecipitation, minigene reporter, siRNA knockdown, cross-linking experiments, evolutionary conservation analysis RNA Medium 33568552
2024 SIRT4 translocates from mitochondria to nucleus under TGF-β stimulation (via BAX/BAK pore and ERK-mediated phosphorylation at Ser36 enabling importin α1 interaction); nuclear SIRT4 deacetylates U2AF2 at K413, facilitating CCN2 pre-mRNA splicing and promoting renal fibrosis. Co-IP, subcellular fractionation, deacetylation assay, site-directed mutagenesis, siRNA/knockout mouse models, splicing reporter assay eLife Medium 39495216
2025 Chromatin-bound U2AF2 accumulates in gene bodies of intron-containing genes in a histone H3K36me3-dependent, RNA-independent manner; this chromatin association preferentially targets exons of highly expressed exon-dense genes; chromatin-bound U2AF2 enhances exon selection accuracy and is required for efficient co-transcriptional splicing. CUT&RUN chromatin profiling, RNase A treatment, knockdown with RNA-seq, histone modification dependence assays Molecular cell High 40315850
2021 AKT-phosphorylated IWS1 regulates U2AF2 exon 2 inclusion via LEDGF/SRSF1 splicing complexes assembled through H3K36me3 deposition; the exon 2-deficient U2AF65 isoform (lacking the RS domain) is defective in CDCA5 pre-mRNA processing, leading to reduced Sororin, impaired ERK phosphorylation, G2/M arrest, and reduced tumor growth. RNA-seq, RT-PCR, siRNA knockdown, histone modification analysis, cell cycle analysis, xenograft model Nature communications Medium 34330897
2012 NMR structure of SF1 N-terminal domain reveals a helix-hairpin that forms a secondary hydrophobic interface with U2AF65 UHM in addition to the known ULM interaction; this helix-hairpin is essential for cooperative ternary SF1–U2AF65–RNA complex formation; SPSP phosphorylation rigidifies the unstructured linker and slightly enhances RNA binding. NMR spectroscopy, SAXS, mutagenesis, RNA-binding assays Nucleic acids research High 23175611

Source papers

Stage 0 corpus · 100 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2013 Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell 382 23374342
2009 Jmjd6 catalyses lysyl-hydroxylation of U2AF65, a protein associated with RNA splicing. Science (New York, N.Y.) 326 19574390
1996 Interaction of U2AF65 RS region with pre-mRNA branch point and promotion of base pairing with U2 snRNA [corrected]. Science (New York, N.Y.) 248 8781232
1997 U2AF65 recruits a novel human DEAD box protein required for the U2 snRNP-branchpoint interaction. Genes & development 228 9242493
1998 WT1 interacts with the splicing factor U2AF65 in an isoform-dependent manner and can be incorporated into spliceosomes. Genes & development 216 9784496
1998 A cooperative interaction between U2AF65 and mBBP/SF1 facilitates branchpoint region recognition. Genes & development 213 9512519
1992 U1 snRNP targets an essential splicing factor, U2AF65, to the 3' splice site by a network of interactions spanning the exon. Genes & development 192 1285125
2003 Structural basis for the molecular recognition between human splicing factors U2AF65 and SF1/mBBP. Molecular cell 184 12718882
2001 A novel peptide recognition mode revealed by the X-ray structure of a core U2AF35/U2AF65 heterodimer. Cell 184 11551507
2005 Steroid hormone receptor coactivation and alternative RNA splicing by U2AF65-related proteins CAPERalpha and CAPERbeta. Molecular cell 168 15694343
2006 Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65. Molecular cell 162 16818232
2011 The RNA polymerase II C-terminal domain promotes splicing activation through recruitment of a U2AF65-Prp19 complex. Genes & development 154 21536736
2019 OTUB2 stabilizes U2AF2 to promote the Warburg effect and tumorigenesis via the AKT/mTOR signaling pathway in non-small cell lung cancer. Theranostics 128 30662561
1999 PUF60: a novel U2AF65-related splicing activity. RNA (New York, N.Y.) 121 10606266
2009 The protein factors MBNL1 and U2AF65 bind alternative RNA structures to regulate splicing. Proceedings of the National Academy of Sciences of the United States of America 119 19470458
1997 Targeting of U2AF65 to sites of active splicing in the nucleus. The Journal of cell biology 117 9166400
2007 Control of pre-mRNA splicing by the general splicing factors PUF60 and U2AF(65). PloS one 116 17579712
2001 The role of U2AF35 and U2AF65 in enhancer-dependent splicing. RNA (New York, N.Y.) 114 11421359
2020 The U2AF2 /circRNA ARF1/miR-342-3p/ISL2 feedback loop regulates angiogenesis in glioma stem cells. Journal of experimental & clinical cancer research : CR 95 32894165
1997 A protein related to splicing factor U2AF35 that interacts with U2AF65 and SR proteins in splicing of pre-mRNA. Nature 92 9237760
1999 Evidence for substrate-specific requirement of the splicing factor U2AF(35) and for its function after polypyrimidine tract recognition by U2AF(65). Molecular and cellular biology 79 10567551
2006 The polypyrimidine tract binding protein (PTB) represses splicing of exon 6B from the beta-tropomyosin pre-mRNA by directly interfering with the binding of the U2AF65 subunit. Molecular and cellular biology 75 16982681
2014 Transient electrostatic interactions dominate the conformational equilibrium sampled by multidomain splicing factor U2AF65: a combined NMR and SAXS study. Journal of the American Chemical Society 68 24734879
2018 In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors. Genome research 65 29643205
2005 Multiple U2AF65 binding sites within SF3b155: thermodynamic and spectroscopic characterization of protein-protein interactions among pre-mRNA splicing factors. Journal of molecular biology 61 16376933
2003 Human immunodeficiency virus type 1 hnRNP A/B-dependent exonic splicing silencer ESSV antagonizes binding of U2AF65 to viral polypyrimidine tracts. Molecular and cellular biology 58 14612416
2010 A flexible RNA backbone within the polypyrimidine tract is required for U2AF65 binding and pre-mRNA splicing in vivo. Molecular and cellular biology 52 20606010
2000 Differential recognition of the polypyrimidine-tract by the general splicing factor U2AF65 and the splicing repressor sex-lethal. RNA (New York, N.Y.) 49 10864047
2006 Major phosphorylation of SF1 on adjacent Ser-Pro motifs enhances interaction with U2AF65. The FEBS journal 48 16420481
2012 Structure, phosphorylation and U2AF65 binding of the N-terminal domain of splicing factor 1 during 3'-splice site recognition. Nucleic acids research 47 23175611
2003 Sex lethal and U2 small nuclear ribonucleoprotein auxiliary factor (U2AF65) recognize polypyrimidine tracts using multiple modes of binding. RNA (New York, N.Y.) 45 12554879
2016 UHM-ULM interactions in the RBM39-U2AF65 splicing-factor complex. Acta crystallographica. Section D, Structural biology 44 27050129
2015 Nuclear retention of full-length HTT RNA is mediated by splicing factors MBNL1 and U2AF65. Scientific reports 44 26218986
2005 FRET analyses of the U2AF complex localize the U2AF35/U2AF65 interaction in vivo and reveal a novel self-interaction of U2AF35. RNA (New York, N.Y.) 44 16043505
1999 Solution structures of the first and second RNA-binding domains of human U2 small nuclear ribonucleoprotein particle auxiliary factor (U2AF(65)). The EMBO journal 43 10449418
1995 Sequential recognition of the pre-mRNA branch point by U2AF65 and a novel spliceosome-associated 28-kDa protein. RNA (New York, N.Y.) 43 7493318
2013 U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs. Nucleic acids research 42 23376934
2017 JMJD6 and U2AF65 co-regulate alternative splicing in both JMJD6 enzymatic activity dependent and independent manner. Nucleic acids research 41 27899633
2015 Splicing inhibition of U2AF65 leads to alternative exon skipping. Proceedings of the National Academy of Sciences of the United States of America 41 26216990
2013 Muscleblind-like 1 activates insulin receptor exon 11 inclusion by enhancing U2AF65 binding and splicing of the upstream intron. Nucleic acids research 40 24185704
2011 Perturbation of U2AF65/NXF1-mediated RNA nuclear export enhances RNA toxicity in polyQ diseases. Human molecular genetics 39 21725067
2022 Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal. Nucleic acids research 38 35524551
2019 U2AF65 assemblies drive sequence-specific splice site recognition. EMBO reports 38 31271494
2016 CD82 suppresses CD44 alternative splicing-dependent melanoma metastasis by mediating U2AF2 ubiquitination and degradation. Oncogene 37 27041584
1997 Cloning of Caenorhabditis U2AF65: an alternatively spliced RNA containing a novel exon. Molecular and cellular biology 37 9001248
2003 Structuring of the 3' splice site by U2AF65. The Journal of biological chemistry 36 14506271
2021 A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex. Cell chemical biology 34 33689684
2020 Representative cancer-associated U2AF2 mutations alter RNA interactions and splicing. The Journal of biological chemistry 34 33020180
2013 Iron availability modulates aberrant splicing of ferrochelatase through the iron- and 2-oxoglutarate dependent dioxygenase Jmjd6 and U2AF(65.). Blood cells, molecules & diseases 31 23787363
2015 Prp40 pre-mRNA processing factor 40 homolog B (PRPF40B) associates with SF1 and U2AF65 and modulates alternative pre-mRNA splicing in vivo. RNA (New York, N.Y.) 30 25605964
2018 HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo. Genome research 29 29650551
2023 The U2AF65/circNCAPG/RREB1 feedback loop promotes malignant phenotypes of glioma stem cells through activating the TGF-β pathway. Cell death & disease 28 36635261
2008 Solution conformation and thermodynamic characteristics of RNA binding by the splicing factor U2AF65. The Journal of biological chemistry 28 18842594
2017 Cancer-Associated Mutations Mapped on High-Resolution Structures of the U2AF2 RNA Recognition Motifs. Biochemistry 27 28850223
1995 The U1 small nuclear ribonucleoprotein/5' splice site interaction affects U2AF65 binding to the downstream 3' splice site. The Journal of biological chemistry 27 7876151
2020 A splice site-sensing conformational switch in U2AF2 is modulated by U2AF1 and its recurrent myelodysplasia-associated mutation. Nucleic acids research 26 32343311
2015 RNA structure replaces the need for U2AF2 in splicing. Genome research 26 26566657
2020 An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2. Proceedings of the National Academy of Sciences of the United States of America 25 32188783
2017 Stoichiometries of U2AF35, U2AF65 and U2 snRNP reveal new early spliceosome assembly pathways. Nucleic acids research 24 27683217
2012 TEG-1 CD2BP2 regulates stem cell proliferation and sex determination in the C. elegans germ line and physically interacts with the UAF-1 U2AF65 splicing factor. Developmental dynamics : an official publication of the American Association of Anatomists 23 22275078
2021 Circular RNA FOXP1 Induced by ZNF263 Upregulates U2AF2 Expression to Accelerate Renal Cell Carcinoma Tumorigenesis and Warburg Effect through Sponging miR-423-5p. Journal of immunology research 21 34514002
2012 RBM5 promotes exon 4 skipping of AID pre-mRNA by competing with the binding of U2AF65 to the polypyrimidine tract. FEBS letters 20 23017209
2009 Functional characterization and protein-protein interactions of trypanosome splicing factors U2AF35, U2AF65 and SF1. Molecular and biochemical parasitology 20 19320097
2006 Alternative conformations at the RNA-binding surface of the N-terminal U2AF(65) RNA recognition motif. Journal of molecular biology 19 17188295
2002 Induced folding of the U2AF35 RRM upon binding to U2AF65. FEBS letters 19 12297299
2022 lncRNA ZFAS1 Promotes HMGCR mRNA Stabilization via Binding U2AF2 to Modulate Pancreatic Carcinoma Lipometabolism. Journal of immunology research 16 35846429
1998 Role of the constitutive splicing factors U2AF65 and SAP49 in suboptimal RNA splicing of novel retroviral mutants. The Journal of biological chemistry 16 9614130
2022 A UHM-ULM interface with unusual structural features contributes to U2AF2 and SF3B1 association for pre-mRNA splicing. The Journal of biological chemistry 15 35780835
2014 Structure-guided U2AF65 variant improves recognition and splicing of a defective pre-mRNA. Proceedings of the National Academy of Sciences of the United States of America 15 25422459
2003 U2 small nuclear ribonucleoprotein particle (snRNP) auxiliary factor of 65 kDa, U2AF65, can promote U1 snRNP recruitment to 5' splice sites. The Biochemical journal 15 12558503
2016 SF1 Phosphorylation Enhances Specific Binding to U2AF65 and Reduces Binding to 3'-Splice-Site RNA. Biophysical journal 14 28002734
2012 A Broad range of conformations contribute to the solution ensemble of the essential splicing factor U2AF(65). Biochemistry 14 22702716
2024 U2AF2-SNORA68 promotes triple-negative breast cancer stemness through the translocation of RPL23 from nucleoplasm to nucleolus and c-Myc expression. Breast cancer research : BCR 13 38594783
2023 A presumed missense variant in the U2AF2 gene causes exon skipping in neurodevelopmental diseases. Journal of human genetics 13 36747105
2022 All-Atom Simulations Elucidate the Impact of U2AF2 Cancer-Associated Mutations on Pre-mRNA Recognition. Journal of chemical information and modeling 12 36040856
2020 Cancer-Associated Substitutions in RNA Recognition Motifs of PUF60 and U2AF65 Reveal Residues Required for Correct Folding and 3' Splice-Site Selection. Cancers 12 32664474
2019 U2AF65 enhances milk synthesis and growth of bovine mammary epithelial cells by positively regulating the mTOR-SREBP-1c signalling pathway. Cell biochemistry and function 12 30773658
2010 RNA induces conformational changes in the SF1/U2AF65 splicing factor complex. Journal of molecular biology 12 21146534
2024 Nuclear translocation of SIRT4 mediates deacetylation of U2AF2 to modulate renal fibrosis through alternative splicing-mediated upregulation of CCN2. eLife 11 39495216
2021 The role of JMJD6/U2AF65/AR-V7 axis in castration-resistant prostate cancer progression. Cancer cell international 11 33430885
2021 Global developmental delay, systemic dysmorphism and epilepsy in a patient with a de novo U2AF2 variant. Journal of human genetics 11 34112922
2020 Differential regulation of sFlt-1 splicing by U2AF65 and JMJD6 in placental-derived and endothelial cells. Bioscience reports 11 32039444
2011 Promiscuity in protein-RNA interactions: conformational ensembles facilitate molecular recognition in the spliceosome: conformational diversity in U2AF⁶⁵ facilitates binding to diverse RNA sequences. BioEssays : news and reviews in molecular, cellular and developmental biology 11 22144099
2006 Crystallization and preliminary X-ray analysis of a U2AF65 variant in complex with a polypyrimidine-tract analogue by use of protein engineering. Acta crystallographica. Section F, Structural biology and crystallization communications 11 16682775
2023 U2AF2 variant in a patient with developmental delay, dysmorphic features, and epilepsy. American journal of medical genetics. Part A 10 37092751
2021 U2AF2 binds IL7R exon 6 ectopically and represses its inclusion. RNA (New York, N.Y.) 10 33568552
2013 The splicing factor U2AF65 stabilizes TRF1 protein by inhibiting its ubiquitin-dependent proteolysis. Biochemical and biophysical research communications 10 24389012
2012 Binding of hnRNP H and U2AF65 to respective G-codes and a poly-uridine tract collaborate in the N50-5'ss selection of the REST N exon in H69 cells. PloS one 10 22792276
2005 The splicing factor U2AF65 is functionally conserved in the thermotolerant deep-sea worm Alvinella pompejana. Biochimica et biophysica acta 10 15777616
2022 LncRNA NEAT1 stabilized Wnt3a via U2AF2 and activated Wnt/β-catenin pathway to alleviate ischemia stroke induced injury. Brain research 9 35452660
2021 AKT3-mediated IWS1 phosphorylation promotes the proliferation of EGFR-mutant lung adenocarcinomas through cell cycle-regulated U2AF2 RNA splicing. Nature communications 9 34330897
2025 Super-Enhancer-Driven HCG20 Promotes Pulmonary Hypertension Through U2AF2 Splicing. Circulation research 8 40433695
2007 Alternative modes of binding by U2AF65 at the polypyrimidine tract. Biochemistry 8 18067274
2025 Chromatin-bound U2AF2 splicing factor ensures exon inclusion. Molecular cell 7 40315850
2023 Assessing the Binding Mode of a Splicing Modulator Stimulating Pre-mRNA Binding to the Plastic U2AF2 Splicing Factor. Journal of chemical information and modeling 7 37967032
2024 Exosomal U2AF2 derived from human bone marrow mesenchymal stem cells attenuates the intervertebral disc degeneration through circ_0036763/miR-583/ACAN axis. Regenerative therapy 6 38362337
2023 LncRNA CECR7 boosts hepatocellular carcinoma progression by recruiting RNA binding protein U2AF2 to enhance the stability of EXO1 mRNA. Heliyon 6 37809785
2020 U2AF65-Dependent SF3B1 Function in SMN Alternative Splicing. Cells 6 33317029
1996 Biochemical properties of a novel U2AF65 protein isoform generated by alternative RNA splicing. Biochemical and biophysical research communications 4 8713106
2025 HPGD induces ferroptosis and autophagy to suppress esophageal squamous cell carcinoma through the LXA4-ERK1/2-U2AF2-TFRC axis. Molecular cancer 3 41039452

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