{"gene":"HNRNPU","run_date":"2026-06-10T01:55:22","timeline":{"discoveries":[{"year":1992,"finding":"SAF-A (HNRNPU) was identified as a novel nuclear DNA-binding protein and constituent of the nuclear matrix/scaffold. The purified 120 kDa protein binds at multiple sites to human SAR (scaffold attachment region) elements, with binding sites residing in A/T-stretches. The protein forms large aggregates and mediates formation of looped DNA structures, suggesting a structural role in organizing chromatin loop domains.","method":"Protein purification, competition binding assays with synthetic polynucleotides, electron microscopy","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 / Strong — purified protein reconstitution with direct binding and EM structural visualization; foundational paper replicated by multiple subsequent studies","pmids":["1324173"],"is_preprint":false},{"year":1994,"finding":"SAF-A is identical to hnRNP-U. UV cross-linking demonstrated the protein is bound to chromosomal DNA in vivo. In vitro, the protein binds both double-stranded and single-stranded DNA and RNA, likely at different binding sites, indicating dual roles in chromatin organization and hnRNA metabolism.","method":"UV cross-linking, filter-binding experiments with diverse nucleic acid substrates","journal":"European journal of biochemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct biochemical demonstration in vivo and in vitro with multiple substrates; identity of SAF-A and hnRNP-U confirmed across multiple labs","pmids":["8174554"],"is_preprint":false},{"year":1994,"finding":"Two isoforms of hnRNP-U (form 1 and form 2) were purified and shown to differ in primary structure. Both isoforms bind double- and single-stranded DNA and RNA, form higher-ordered nucleic acid/protein complexes, and specifically bind and aggregate the human SAR element. The two isoforms differ morphologically: form 1 forms long unbranched filamentous DNA complexes while form 2 forms spherical aggregates (~35 nm diameter).","method":"Chromatographic purification, electron microscopy, nucleic acid binding assays","journal":"Biochemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — purified protein reconstitution with EM and biochemical characterization in one study","pmids":["8068679"],"is_preprint":false},{"year":1997,"finding":"SAF-A possesses a novel bipartite SAR-specific DNA-binding domain that is independent of its C-terminal RGG RNA-binding domain. During apoptosis, caspase-dependent cleavage occurs within this bipartite DNA-binding domain, causing loss of DNA-binding activity and detachment from nuclear structural sites without affecting hnRNP complex association, indicating the two functional domains are separable.","method":"Domain deletion/mutation analysis, apoptosis induction, subcellular fractionation","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 / Strong — domain mutagenesis with functional consequence, replicated by subsequent caspase cleavage study","pmids":["9405365"],"is_preprint":false},{"year":1997,"finding":"hnRNP-U/SAF-A is directly bound to chromosomal DNA in vivo, as demonstrated by formaldehyde cross-linking followed by CsCl density gradient purification. Dimethylsulfate cross-linking and limited protease digestion established that hnRNP-U contacts DNA directly rather than through bridging to other proteins.","method":"Formaldehyde cross-linking, CsCl density gradient centrifugation, dimethylsulfate cross-linking, limited protease digestion, western blotting","journal":"Biochemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — multiple orthogonal in vivo and in vitro methods in one study establishing direct DNA contact","pmids":["9204873"],"is_preprint":false},{"year":2000,"finding":"Caspase-3 cleaves SAF-A at Asp-100 within the non-canonical sequence SALD (rather than the canonical DEXD motif) in vitro and in vivo during apoptosis. A D100A point mutation abrogates cleavage by recombinant caspase-3 in vitro and during apoptosis in vivo, confirming SALD as a novel caspase-3 cleavage site.","method":"Recombinant caspase-3 in vitro cleavage assay, MALDI-TOF mass spectrometry, Edman sequencing, site-directed mutagenesis (D100A), in vivo apoptosis assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstitution with recombinant enzyme, mutagenesis validation both in vitro and in vivo","pmids":["10671544"],"is_preprint":false},{"year":2001,"finding":"hnRNP-U/SAF-A represses glucocorticoid receptor (GR)-dependent transcription. A construct lacking the GR-binding domain of hnRNP-U acts as a dominant negative factor that enhances GR-driven transcription. The repressive effect depends on relative concentrations of GR, hnRNP-U and GR DNA-binding sites, suggesting hnRNP-U acts as a storage site for intranuclear GR.","method":"Transient transfection of hnRNP-U deletion constructs, reporter gene assays in Ltk(-) cells","journal":"The Journal of steroid biochemistry and molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — functional reporter assays with domain deletion constructs in a single study","pmids":["11530285"],"is_preprint":false},{"year":2002,"finding":"hnRNP-U is the major nuclear binding partner of the SCF(β-TrCP) ubiquitin ligase subunit β-TrCP/E3RS. hnRNP-U occupies E3RS stoichiometrically, stabilizes the E3 component, and is responsible for its nuclear localization. hnRNP-U acts as a pseudosubstrate—binding via the WD region in an E3-substrate-type interaction but not being targeted for degradation—and dissociates from E3RS upon competition by high-affinity substrate, enabling substrate ubiquitination.","method":"Affinity purification, Co-IP, competition with pIκBα peptide, point mutation in WD region","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, stoichiometric interaction, mutagenesis, functional ubiquitination assay, multiple orthogonal methods","pmids":["11850407"],"is_preprint":false},{"year":2002,"finding":"An episomally replicating plasmid (pEPI-1) containing a S/MAR element binds exclusively to hnRNP-U/SAF-A in the nuclear matrix, as demonstrated by cis-diamminedichloroplatinum II cross-linking and southwestern analysis. Immunoprecipitation of the cross-linked DNA-protein complex confirmed that pEPI-1 is bound to hnRNP-U/SAF-A in vivo, providing the basis for episome mitotic stability.","method":"Cross-linking with cis-diamminedichloroplatinum II, nuclear matrix co-purification, southwestern analysis, immunoprecipitation","journal":"EMBO reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct in vivo cross-linking with orthogonal biochemical confirmation in a single study","pmids":["11897664"],"is_preprint":false},{"year":2003,"finding":"SAF-A is enriched at the inactive X chromosome (Xi) territory through its RGG RNA-binding domain. After removal of DNA and chromatin proteins, SAF-A remains with the nuclear matrix at the Xi. The enrichment depends on the RGG domain, raising the possibility that SAF-A interaction with XIST RNA contributes to Xi silencing through local changes in nuclear architecture.","method":"Immunofluorescence, nuclear matrix extraction, domain-deletion constructs, XIST RNA co-localization","journal":"Chromosoma","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiment with domain-deletion functional follow-up, single lab","pmids":["14608463"],"is_preprint":false},{"year":2006,"finding":"hnRNP-U directly interacts with the Wilms' tumour protein WT1 without requiring other proteins or nucleic acids; the interaction involves the zinc-fingers of WT1 and the middle domain of hnRNP-U. hnRNP-U modulates WT1 transcriptional activation of a bona fide WT1 target gene.","method":"Co-IP of endogenous proteins, domain deletion/interaction mapping, transcriptional reporter assay","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — endogenous co-IP plus domain mapping and functional transcriptional assay, single lab","pmids":["16924231"],"is_preprint":false},{"year":2006,"finding":"hnRNP-U enhances expression of specific genes including TNF-α, GADD45A, HEXIM1, HOXA2, IER3, NHLH2, and ZFY by binding to and stabilizing their mRNAs, likely through binding to 3' UTR sequences.","method":"RNAi knockdown, mRNA stability assays, 3' UTR binding","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — functional knockdown with mRNA stability readout, single lab, single study","pmids":["17174306"],"is_preprint":false},{"year":2008,"finding":"SAF-A binds to the 3'-flanking region of the Bmal1 promoter with circadian timing in vivo (detected by in vivo footprinting), and this rhythmic binding correlates with circadian Bmal1 transcription. The RORE region of the Bmal1 promoter resides in GC-rich open chromatin, and the 3'-flanking region inhibits rhythmic transcription in reporter assays.","method":"In vivo DNase I footprinting, in vitro reporter gene assay","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo footprinting and reporter assay with functional correlation, single lab","pmids":["18332112"],"is_preprint":false},{"year":2009,"finding":"hnRNP-U/SAF-A is phosphorylated at Ser59 specifically by DNA-PK in vitro and in cells in response to DNA double-strand breaks. This was identified using a cell-free system for dissecting DNA damage kinase substrates.","method":"Cell-free kinase assay, in vitro phosphorylation, in vivo phosphorylation after DNA damage induction, site identification","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution plus in vivo validation, replicated by a second independent study (PMID:19844162)","pmids":["19351595"],"is_preprint":false},{"year":2009,"finding":"SAF-A is phosphorylated at Ser59 in a sequence context matching a 'S-hydrophobic' consensus exclusively by DNA-PK in response to DSB-inducing agents. The extent and duration of phosphorylation inversely correlates with the capacity of cells to repair DSBs by NHEJ, linking SAF-A phosphorylation status to DSB repair efficacy.","method":"Phospho-specific antibody, kinase inhibitor experiments, NHEJ-deficient cell lines, mass spectrometry-based site mapping","journal":"Cell cycle (Georgetown, Tex.)","confidence":"High","confidence_rationale":"Tier 2 / Strong — phospho-site mapped, validated in multiple cell lines with defined NHEJ status, replicated phospho-Ser59 finding","pmids":["19844162"],"is_preprint":false},{"year":2011,"finding":"SAF-A localizes to mitotic spindles, spindle midzone, and cytoplasmic bridge. SAF-A depletion causes mitotic delay, chromosome misalignment, and spindle assembly defects. SAF-A co-immunoprecipitates with nucleolin, Aurora-A, and TPX2; co-localizes with TPX2 and Aurora-A at spindle poles and microtubules. SAF-A can bind microtubules directly and contributes to Aurora-A targeting to mitotic spindle microtubules. Elimination of TPX2 or Aurora-A abolishes SAF-A association with the mitotic spindle.","method":"RNAi, immunofluorescence, co-immunoprecipitation, direct microtubule binding assay","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct localization with functional loss-of-function, co-IP of endogenous proteins, direct microtubule binding assay, epistasis by depletion experiments","pmids":["21242313"],"is_preprint":false},{"year":2011,"finding":"SAF-A binds the Oct4 proximal promoter in ES cells and dissociates upon early differentiation. SAF-A depletion decreases Oct4 expression even with LIF. SAF-A interacts with the CTD of RNA polymerase II independently of CTD phosphorylation and mRNA. SAF-A exists in complexes with Sox2, Oct4, and STAT3 in ES cells, with complex numbers decreasing upon LIF withdrawal.","method":"ChIP, RNAi, co-immunoprecipitation of endogenous proteins, reporter assay","journal":"Cellular reprogramming","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and co-IP of endogenous proteins plus functional knockdown, single lab","pmids":["21235343"],"is_preprint":false},{"year":2011,"finding":"SAF-A interacts with BRG1 (the ATPase subunit of the SWI/SNF chromatin remodeling complex) in mouse ES cells. Dual depletion of SAF-A and BRG1 abolishes global RNA Pol II transcription while leaving RNA Pol I transcription unaffected, establishing that both are jointly required for RNA Pol II-mediated transcription.","method":"Co-immunoprecipitation, in situ proximity ligation assay, co-localization, RNAi double knockdown, transcription assay","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP confirmed by PLA, functional double-knockdown with global transcription readout, single lab","pmids":["22162999"],"is_preprint":false},{"year":2012,"finding":"hnRNP U regulates U2 snRNP maturation and Cajal body morphology. CLIP-seq reveals that hnRNP-U binds virtually all classes of regulatory noncoding RNAs including all snRNAs required for splicing of both major and minor intron classes. hnRNP-U depletion causes global alternative splicing changes, establishing it as a regulator of the core splicing machinery.","method":"RNAi screen, CLIP-seq (genome-wide), RNA-seq (genome-wide), Cajal body morphology assay","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — genome-wide CLIP-seq plus RNA-seq with mechanistic follow-up on snRNP maturation, multiple orthogonal methods","pmids":["22325991"],"is_preprint":false},{"year":2012,"finding":"hnRNP-U directly interacts with NEIL1 DNA glycosylase via NEIL1's C-terminal domain (dispensable for enzymatic activity). hnRNP-U stimulates NEIL1 base excision activity for oxidized bases primarily by enhancing product release. hnRNP-U and NEIL1 epistatically protect cells from low-level oxidative damage. The interacting regions in hnRNP-U map to both N and C termini. In-cell association increases after oxidative stress.","method":"Co-immunoprecipitation, in vitro base excision repair assay, domain mapping, FLAG-IP from human cells, epistasis analysis (hnRNP-U and NEIL1 double depletion), Kd measurement","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct in vitro biochemical reconstitution, Kd measurement, domain mapping, epistasis experiment, multiple orthogonal methods","pmids":["22902625"],"is_preprint":false},{"year":2014,"finding":"SAF-A exhibits biphasic dynamics at DNA damage sites: rapid transient recruitment via binding to Poly(ADP-ribose) (PAR), followed by prolonged exclusion dependent on ATM, ATR, and DNA-PK activity. Exclusion reflects dissociation of transcription-associated SAF-A from chromatin. The RNA-binding domain of SAF-A recapitulates this biphasic behavior. SAF-A exclusion is part of an anti-R-loop mechanism at damaged transcribed sites.","method":"Laser micro-irradiation, live-cell imaging, PAR binding assay, kinase inhibitor experiments, R-loop reporter (live imaging of DNA:RNA hybrids)","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — live imaging combined with biochemical binding assay and kinase inhibitor epistasis, multiple orthogonal approaches","pmids":["25030905"],"is_preprint":false},{"year":2015,"finding":"SAF-A Ser59 is phosphorylated by PLK1 (not DNA-PKcs) during mitosis. SAF-A interacts with PLK1 in nocodazole-arrested cells. Ser59 is dephosphorylated by PP2A during mitosis. Cells expressing S59A SAF-A show misaligned chromosomes, lagging chromosomes, polylobed nuclei, and delayed mitotic exit, demonstrating that both phosphorylation by PLK1 and dephosphorylation by PP2A at Ser59 are required for accurate mitosis.","method":"Phospho-specific antibody, kinase inhibitors, Co-IP with PLK1, phosphatase identification, S59A point mutation cell lines, mitotic phenotype analysis","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — site-directed mutagenesis with cellular phenotype, kinase/phosphatase identification, Co-IP, multiple orthogonal methods","pmids":["25986610"],"is_preprint":false},{"year":2016,"finding":"SAF-A phosphorylated at Ser59 by DNA-PK early after ionizing radiation is linked to transient release of chromatin-bound NEIL1, preventing base excision repair (BER) from proceeding prematurely. Dephosphorylated SAF-A relieves Ku-mediated inhibition of DNA glycosylases in vitro, but the phosphomimetic D59 mutant does not. This establishes a temporal coordination mechanism where SAF-A and Ku cooperate to prioritize NHEJ over BER at clustered genome lesions.","method":"In vitro DNA glycosylase inhibition assay, phosphomimetic mutant (D59), DNA-PK phosphorylation, chromatin fractionation after IR","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with phosphomimetic mutant and chromatin fractionation, single lab","pmids":["27303920"],"is_preprint":false},{"year":2017,"finding":"SAF-A oligomerizes with chromatin-associated RNAs (caRNAs) via its RGG domain to regulate interphase chromatin structure in a transcription-dependent manner. The AAA+ ATPase domain of SAF-A mediates cycles of oligomerization in response to ATP binding and hydrolysis. SAF-A oligomerization decompacts large-scale chromatin structure, while SAF-A loss or monomerization promotes aberrant chromosome folding and genome damage accumulation.","method":"Domain mutagenesis (RGG, ATPase), Hi-C, live-cell imaging, biochemical oligomerization assays, ATP hydrolysis assays, genome damage readouts","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — domain-level mutagenesis combined with Hi-C and biochemical reconstitution; multiple orthogonal methods in one rigorous study","pmids":["28622508"],"is_preprint":false},{"year":2017,"finding":"HNRNPU is required for maintaining 3D genome architecture in mouse hepatocytes. HNRNPU depletion increases LAD (lamina-associated domain) coverage, causes global chromatin condensation, compartment switching (7.5% of genome), decreased TAD boundary strengths at A/B compartment borders, and reduced chromatin loop intensities. HNRNPU mainly associates with active chromatin, and 80% of HNRNPU ChIP peaks coincide with CTCF or RAD21 binding.","method":"In situ Hi-C, DamID, ChIP-seq, RNA-seq, conditional knockout in hepatocytes","journal":"Genome research","confidence":"High","confidence_rationale":"Tier 1 / Strong — multiple genome-wide orthogonal assays (Hi-C, DamID, ChIP-seq) combined with genetic depletion; rigorous 3D genome phenotyping","pmids":["29273625"],"is_preprint":false},{"year":2018,"finding":"HPSE eRNA binds hnRNPU to facilitate its interaction with p300, promoting their enrichment on a super enhancer, resulting in chromatin looping between the super enhancer and HPSE promoter, p300-mediated transactivation of EGR1, and subsequent HPSE upregulation.","method":"Co-immunoprecipitation, ChIP, chromatin conformation capture, gain/loss-of-function experiments","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and ChIP with functional rescue experiments, single lab","pmids":["29511351"],"is_preprint":false},{"year":2020,"finding":"hnRNPU retains miR-30c-5p in the nucleus and prevents its export into large extracellular vesicles. Binding of miR-30c-5p to hnRNPU was confirmed by RNA-immunoprecipitation, EMSA, and miR-pulldown. Nuclear binding stabilizes miR-30c-5p, reducing cytoplasmic availability for vesicular export. hnRNPU-dependent miR-30c-5p export reduced cellular migration and pro-angiogenic gene expression in recipient cells.","method":"Gain/loss-of-function, RNA-immunoprecipitation, EMSA, miR-pulldown, nanoparticle tracking analysis, electron microscopy","journal":"Journal of extracellular vesicles","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct RNA-protein binding confirmed by three orthogonal methods (RIP, EMSA, pulldown), functional consequence assessed, single lab","pmids":["32944175"],"is_preprint":false},{"year":2020,"finding":"hnRNPU deficiency in mouse hepatocytes disrupts liver chromatin accessibility and stimulates expression of a truncated TrkB isoform (TRKB-T1) that promotes inflammatory signaling and stress-induced cell death. BDNF treatment reduced membrane TRKB-T1 and protected mice from diet-induced NASH, linking hnRNPU-chromatin regulation to disease-specific signaling.","method":"Hepatocyte-specific conditional knockout, RNA-seq, ChIP-seq, BDNF treatment rescue experiment","journal":"Hepatology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional KO with mechanistic follow-up (ChIP-seq and RNA-seq) and rescue experiment, single lab","pmids":["31469911"],"is_preprint":false},{"year":2020,"finding":"In HeLa cells, hnRNPU directly binds the 3'-UTR of IL-6 mRNA, and this interaction occurs specifically in the cytoplasmic fraction, suggesting a role for cytoplasmic hnRNPU in mRNA stability control distinct from its nuclear functions.","method":"Optimized HITS-CLIP (BrdU-CLIP), subcellular fractionation, CLIP validation","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct CLIP identification of target in fractionated cells, single lab, single method","pmids":["32302342"],"is_preprint":false},{"year":2021,"finding":"hnRNPU interacts with WT1 and SOX9 in Sertoli cells and enhances expression of Sox8 and Sox9 by directly binding to their promoter regions. Conditional knockout of hnRNPU in murine Sertoli cells causes rapid depletion of both Sertoli and germ cells and failure of spermatogonia proliferation and migration, leading to male sterility.","method":"Conditional knockout (Cre/loxP), luciferase reporter assay, ChIP-qPCR, RNA-seq, co-immunoprecipitation","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional KO phenotype with ChIP and reporter assay to establish promoter binding mechanism, single lab","pmids":["34815802"],"is_preprint":false},{"year":2022,"finding":"HNRNPU loss of function leads to rapid cell death of both postmitotic neurons and neural progenitors in the developing mouse cortex, with neural progenitors being more sensitive. HNRNPU truncation causes dysregulation of gene expression and alternative splicing of genes involved in cell survival, cell motility, and synapse formation. Pharmaceutical and genetic agents partially rescued loss of cortical structures, radial migration defects, and neural progenitor cell death.","method":"Conditional truncation in mouse cortex, RNA-seq, alternative splicing analysis, pharmacological rescue, cell death assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo conditional truncation with transcriptomic analysis and rescue experiments; multi-orthogonal approach","pmids":["35864088"],"is_preprint":false},{"year":2022,"finding":"HNRNPU promotes antibody class-switch recombination (CSR) by facilitating C-NHEJ-mediated S-S joining through the 53BP1-shieldin complex. HNRNPU binds switch region RNA/DNA G-quadruplexes and regulates R-loop and ssDNA accumulation. HNRNPU interacts with both C-NHEJ and R-loop complexes in an RNA-dependent manner. Recruitment of HNRNPU and C-NHEJ factors is sensitive to liquid-liquid phase separation inhibitors, suggesting DNA-repair condensate formation.","method":"Conditional knockout in B cells, CSR assay, Co-IP, G-quadruplex binding assay, LLPS inhibitor treatment, ssDNA/R-loop detection","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO with mechanistic Co-IP and binding assays, single lab","pmids":["36943867"],"is_preprint":false},{"year":2022,"finding":"CDC20-mediated ubiquitination of hnRNPU promotes its interaction with the CTCF-cohesin complex, modulating chromatin condensation. The molecular domain on hnRNPU required for CDC20 interaction was mapped to amino acid residues 461–653. Dysregulation of the CDC20-hnRNPU axis contributes to altered chromatin condensation, tumor progression, and drug resistance.","method":"Affinity purification/mass spectrometry, Co-IP, immunostaining, domain mapping, DAPI/H2B-mCherry chromatin condensation assay","journal":"Cancers","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with domain mapping and functional chromatin readout, single lab","pmids":["35954396"],"is_preprint":false},{"year":2022,"finding":"SAF-A promotes origin licensing in G1 phase, origin activation frequency in S phase, and consistent replication fork progression. SAF-A depletion causes reduced MCM loading, decreased origin activation, inconsistent fork progression, blurred replication timing domain boundaries, and elevated γ-H2AX formation leading to cellular quiescence.","method":"DNA fiber assay, origin licensing assay (MCM loading), single-cell replication timing, γ-H2AX immunostaining, siRNA depletion","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple replication assays with genetic depletion, mechanistic focus on origin licensing and fork progression, single lab","pmids":["34888666"],"is_preprint":false},{"year":2022,"finding":"hnRNPU promotes TNBC cell proliferation and migration via association with DDX5. The HNRNPU-DDX5 complex prevents intron retention of MCM10 pre-mRNA (reducing nonsense-mediated decay) and activates Wnt/β-catenin signaling. Additionally, the HNRNPU-DDX5 complex promotes transcription of LMO4 from its transcriptional start site, activating PI3K-Akt-mTOR signaling.","method":"CRISPR screen, RNAi, Co-IP of endogenous proteins, splicing analysis, transcriptional reporter, Western blot","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP of endogenous proteins plus splicing and transcriptional mechanistic analysis, single lab","pmids":["36347834"],"is_preprint":false},{"year":2023,"finding":"SAF-A/hnRNPU directly interacts with polyphosphoinositides (PPIn) via a lysine-rich polybasic motif located at amino acids 9–24 within its SAP DNA-binding domain. Deletion of this polybasic motif prevents PPIn interaction, suggesting the SAP domain has dual functions in DNA and PPIn binding.","method":"Quantitative interactomics, direct PPIn binding assay, deletion mutagenesis","journal":"microPublication biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — direct binding assay with deletion mutagenesis, single lab, single study","pmids":["37038481"],"is_preprint":false},{"year":2024,"finding":"hnRNPU is required for establishing the spermatogonial stem cell (SSC) pool. Conditional loss of hnRNPU in prospermatogonia arrests spermatogenesis and sterility. hnRNPU-deficient ProSG fails to differentiate and migrate to the basement membrane. hnRNPU binds Vrk1, Slx4, and Dazl transcripts, which show aberrant alternative splicing in hnRNPU-deficient testes.","method":"Conditional knockout (Cre/loxP), single-cell transcriptomics, RNA binding analysis, alternative splicing assays","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional KO with defined cellular phenotype and RNA-binding/splicing mechanistic analysis, single lab","pmids":["38625792"],"is_preprint":false},{"year":2024,"finding":"circMYO9B promotes translocation of hnRNPU from nucleus to cytoplasm, which destabilizes CBL and reduces ubiquitination/degradation of KDM1A, thereby promoting VEGFA expression in endothelial cells and angiogenesis in diabetic wound healing.","method":"Co-IP, subcellular fractionation, protein stability assay, ubiquitination assay, in vivo diabetic wound healing model","journal":"Communications biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mechanistic pathway defined by Co-IP and ubiquitination assay with in vivo validation, single lab","pmids":["39725699"],"is_preprint":false},{"year":2025,"finding":"α-Satellite RNAs bind SAF-A and are required for recruitment of SAF-A back to chromatin upon mitotic exit. Both α-satellite RNA and SAF-A are required for chromosome segregation fidelity; depletion of either causes chromosome missegregation. SAF-A is globally excluded from chromatin during mitosis and α-satellite RNAs are required for its reestablishment, with both also aiding nuclear lamina reassembly.","method":"SAF-A RNA binding identification, RNAi depletion of α-satellite RNA or SAF-A, chromosome missegregation assays, live-cell imaging, nuclear lamina reassembly assay","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding identification plus epistatic depletion experiments with functional chromosome segregation readout, single lab","pmids":["40219970"],"is_preprint":false},{"year":2025,"finding":"The SAF-A SAP domain (N-terminal DNA-binding domain) and its serines S14 and S26 are required for: XIST RNA localization and XIST-dependent histone modifications on the inactive X chromosome; normal protein nuclear dynamics; and cell proliferation. The SAP domain is not required for global gene expression but plays only a minor role in mRNA splicing. A Xi localization signal resides in the SAP domain. SAF-A is highly dynamic, interacting with nascent transcripts as part of this dynamic movement rather than as a static nuclear scaffold component.","method":"Allelic reconstitution, FRAP/protein dynamics assays, XIST RNA FISH, histone modification ChIP, splicing analysis, proliferation assays","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 1 / Moderate — allelic reconstitution strategy with multiple orthogonal functional readouts including FRAP, ChIP, and FISH, single lab","pmids":["40493679"],"is_preprint":false},{"year":2025,"finding":"The SAF-A ATPase domain and RGG repeats both control SAF-A nuclear dynamics. The RGG repeats mediate interaction with nascent transcripts. Both the ATPase domain and RGG repeats are required for maintaining XIST RNA and facultative heterochromatin marks on the Xi, for proper mRNA splicing, and for cell proliferation. Mutations blocking ATP binding vs. ATP hydrolysis have distinct effects on Xi maintenance.","method":"Allelic reconstitution, FRAP, XIST FISH, ChIP for heterochromatin marks, splicing analysis (RNA-seq), proliferation assays","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — allelic reconstitution with mechanistic mutagenesis; preprint, not yet peer-reviewed","pmids":["41473319"],"is_preprint":true},{"year":2025,"finding":"HNRNPU is required for long-range Polycomb recruitment by the lncRNAs Airn, Kcnq1ot1, and Xist. RNA immunoprecipitation showed enriched and correlated HNRNPU association with all three lncRNAs. HNRNPU depletion impaired PRC-directed histone modifications induced by all three lncRNAs without being necessary for proper localization of Airn or Kcnq1ot1.","method":"RNA-immunoprecipitation from formaldehyde-crosslinked cells, HNRNPU knockdown, PRC-directed histone modification assays (ChIP), lncRNA localization assays","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RIP with functional epistasis (KD + PRC modification readout), preprint, multiple lncRNA systems tested","pmids":["40791421"],"is_preprint":true}],"current_model":"HNRNPU/SAF-A is a multifunctional nuclear scaffold protein that directly binds both DNA (via its N-terminal SAP bipartite domain) and RNA (via its C-terminal RGG domain), oligomerizes in an ATP-dependent manner through its AAA+ ATPase domain to form a dynamic RNA-chromatin mesh that maintains 3D genome organization (TADs, compartments, chromatin loops), regulates alternative splicing by binding snRNAs and controlling U2 snRNP maturation, stabilizes specific mRNAs through 3'-UTR binding, is phosphorylated at Ser59 by DNA-PK in response to DNA double-strand breaks and by PLK1 during mitosis (with PP2A-mediated dephosphorylation required for mitotic exit), acts as a pseudosubstrate for SCF(β-TrCP) ubiquitin ligase controlling its nuclear localization and substrate threshold, stimulates NEIL1-mediated oxidized base repair, localizes to the inactive X chromosome via its RGG domain to interact with XIST RNA and maintain Xi chromatin structure, and undergoes caspase-3-mediated cleavage at a non-canonical SALD site during apoptosis to release it from chromatin."},"narrative":{"mechanistic_narrative":"HNRNPU (SAF-A/hnRNP-U) is a multifunctional nuclear scaffold protein that organizes 3D genome architecture by directly contacting both chromosomal DNA and RNA and oligomerizing into a dynamic RNA-chromatin mesh [PMID:1324173, PMID:9204873, PMID:28622508]. It binds scaffold/matrix attachment region (SAR/S/MAR) DNA elements through a bipartite SAR-specific domain that is structurally and functionally separable from its C-terminal RGG RNA-binding domain [PMID:1324173, PMID:8068679, PMID:9405365], and is bound directly to chromosomal DNA in vivo rather than through protein bridges [PMID:8174554, PMID:9204873]. Genome-scale studies establish that HNRNPU maintains TAD boundaries, A/B compartments, chromatin loops, and lamina-associated domains, associating mainly with active chromatin and co-occupying sites with CTCF/RAD21 [PMID:29273625]; this scaffolding activity depends on RGG-mediated binding to chromatin-associated RNAs and on cycles of oligomerization driven by its AAA+ ATPase domain, with oligomerization decompacting chromatin and loss or monomerization causing aberrant folding and genome damage [PMID:28622508]. Through its RGG domain HNRNPU binds noncoding RNAs to control chromatin states, localizing to the inactive X via XIST RNA to maintain Xi heterochromatin [PMID:14608463, PMID:40493679] and mediating long-range Polycomb recruitment by the lncRNAs Airn, Kcnq1ot1, and Xist [PMID:40791421]. As an RNA-binding regulator it binds essentially all spliceosomal snRNAs, governs U2 snRNP maturation and Cajal body morphology, and shapes global alternative splicing [PMID:22325991], while also stabilizing specific target mRNAs through 3'-UTR binding [PMID:17174306, PMID:32302342]. HNRNPU function is regulated by phosphorylation of Ser59 — by DNA-PK in response to DNA double-strand breaks, where its phosphorylation status tracks NHEJ repair capacity [PMID:19351595, PMID:19844162], and by PLK1 during mitosis with PP2A-mediated dephosphorylation required for accurate chromosome segregation and mitotic exit [PMID:25986610]. At sites of damage it is transiently recruited via poly(ADP-ribose) and then excluded in an ATM/ATR/DNA-PK-dependent manner as part of an anti-R-loop response [PMID:25030905], and it directly stimulates NEIL1-mediated excision of oxidized bases [PMID:22902625]. In vivo conditional loss causes cell death of cortical neurons and progenitors with dysregulated splicing of survival and synaptic genes [PMID:35864088], and failures in spermatogenesis [PMID:34815802, PMID:38625792], reflecting its essential roles in genome organization and RNA processing.","teleology":[{"year":1992,"claim":"Established HNRNPU's founding identity: it was unknown what proteins anchor chromatin loops to the nuclear scaffold; SAF-A was purified as a SAR/MAR-binding protein that mediates looped DNA structures, defining a structural role in chromatin loop organization.","evidence":"Protein purification, competition binding assays, and electron microscopy of SAR-element complexes","pmids":["1324173"],"confidence":"High","gaps":["Sequence-specificity of SAR recognition and in vivo loop topology not resolved","Relationship to hnRNA metabolism unaddressed at this stage"]},{"year":1994,"claim":"Unified two protein identities and demonstrated dual nucleic-acid binding: it was unclear whether the scaffold protein and hnRNP-U were the same; UV cross-linking showed SAF-A=hnRNP-U is bound to chromosomal DNA in vivo and binds ds/ssDNA and RNA, predicting dual chromatin/hnRNA roles.","evidence":"UV cross-linking and filter-binding with diverse nucleic acid substrates; isoform purification with EM","pmids":["8174554","8068679"],"confidence":"High","gaps":["Distinct DNA vs RNA binding sites inferred but not mapped","Functional consequence of isoform differences unknown"]},{"year":1997,"claim":"Defined separable DNA- and RNA-binding modules and direct DNA contact: it was unknown whether scaffold attachment and hnRNP functions reside in one domain; mutagenesis localized a bipartite SAR-specific DNA-binding domain independent of the RGG domain, and orthogonal cross-linking proved direct DNA contact.","evidence":"Domain deletion/mutation, apoptosis fractionation, formaldehyde/DMS cross-linking with protease digestion","pmids":["9405365","9204873"],"confidence":"High","gaps":["Structural basis of bipartite domain not solved","How the two domains are coordinated on chromatin not addressed"]},{"year":2000,"claim":"Resolved how HNRNPU is dismantled during apoptosis: the protease and site were unknown; caspase-3 was shown to cleave at a non-canonical SALD motif (Asp-100), with D100A abolishing cleavage, defining a regulated detachment from chromatin during cell death.","evidence":"Recombinant caspase-3 assay, MS/Edman sequencing, D100A mutagenesis in vitro and in vivo","pmids":["10671544"],"confidence":"High","gaps":["Functional consequence of cleavage for apoptotic chromatin disassembly not directly tested"]},{"year":2002,"claim":"Identified a non-degradative regulatory partnership: it was unknown how HNRNPU controls ubiquitin ligase activity; HNRNPU was shown to be the major nuclear partner of SCF(beta-TrCP), acting as a pseudosubstrate that stabilizes and nuclear-localizes the E3 and sets a substrate threshold.","evidence":"Affinity purification, reciprocal Co-IP, peptide competition, WD-region point mutation, ubiquitination assay","pmids":["11850407","11897664"],"confidence":"High","gaps":["Physiological substrates whose threshold is set by HNRNPU not enumerated","Link between scaffolding and E3 sequestration unclear"]},{"year":2003,"claim":"Connected HNRNPU to facultative heterochromatin via RNA: the basis of its Xi enrichment was unknown; the RGG domain was shown to retain SAF-A at the Xi nuclear matrix and co-localize with XIST RNA, implicating it in Xi architecture.","evidence":"Immunofluorescence, nuclear matrix extraction, RGG-deletion constructs, XIST co-localization","pmids":["14608463"],"confidence":"Medium","gaps":["Direct XIST-HNRNPU binding not biochemically demonstrated here","Causal contribution to silencing not tested"]},{"year":2006,"claim":"Extended HNRNPU into transcriptional and post-transcriptional regulation: it was unknown whether it modulates specific transcription factors and mRNAs; direct WT1 binding modulated WT1 target transcription, and 3'-UTR binding stabilized a defined panel of mRNAs.","evidence":"Endogenous Co-IP and domain mapping (WT1); RNAi with mRNA stability and 3'-UTR binding (TNF-alpha, GADD45A et al.)","pmids":["16924231","17174306"],"confidence":"Medium","gaps":["Whether mRNA stabilization is direct vs scaffold-mediated not separated","Generality of 3'-UTR target set untested"]},{"year":2009,"claim":"Placed HNRNPU in the DNA-damage signaling network: the relevant kinase and site were unknown; Ser59 was identified as a DNA-PK phosphosite induced by double-strand breaks, with phosphorylation extent inversely tracking NHEJ repair capacity.","evidence":"Cell-free kinase assays, phospho-specific antibody, kinase inhibitors, NHEJ-deficient lines, MS site mapping","pmids":["19351595","19844162"],"confidence":"High","gaps":["Direct effect of Ser59 phosphorylation on HNRNPU chromatin binding not yet defined","Downstream repair effectors unspecified at this stage"]},{"year":2011,"claim":"Revealed a mitotic, cytoplasmic role and key partners: it was unclear whether HNRNPU acts outside interphase chromatin; it was shown to localize to spindles, bind microtubules directly, co-IP with nucleolin, Aurora-A and TPX2, and be required for spindle assembly and chromosome alignment.","evidence":"RNAi, immunofluorescence, endogenous Co-IP, direct microtubule binding, depletion epistasis","pmids":["21242313"],"confidence":"High","gaps":["How a chromatin scaffold protein is repurposed to spindles mechanistically unresolved","Relationship to its mitotic exclusion from chromatin not yet linked"]},{"year":2011,"claim":"Linked HNRNPU to the core transcription/remodeling machinery: it was unknown how it supports Pol II output; it bound the Pol II CTD and BRG1, with HNRNPU/BRG1 co-depletion abolishing global Pol II (not Pol I) transcription, and bound the Oct4 promoter in ES cells.","evidence":"ChIP, RNAi double knockdown, Co-IP, PLA, transcription assays","pmids":["22162999","21235343"],"confidence":"Medium","gaps":["Whether the BRG1 interaction is direct not established","Mechanistic basis of joint requirement for Pol II transcription unresolved"]},{"year":2012,"claim":"Defined HNRNPU as a regulator of the splicing machinery and oxidative repair: it was unknown how broadly it controls RNA processing; CLIP-seq showed binding to all spliceosomal snRNAs with control of U2 snRNP maturation and global splicing, while direct NEIL1 binding stimulated oxidized-base excision via enhanced product release.","evidence":"CLIP-seq/RNA-seq with Cajal body assays; in vitro BER reconstitution, Kd, domain mapping, epistasis","pmids":["22325991","22902625"],"confidence":"High","gaps":["How snRNA binding mechanistically drives U2 maturation not fully resolved","Connection between splicing role and chromatin scaffolding not bridged here"]},{"year":2014,"claim":"Resolved HNRNPU dynamics at damage sites: it was unknown how it behaves at lesions; live imaging revealed biphasic PAR-dependent recruitment then ATM/ATR/DNA-PK-dependent exclusion of transcription-associated SAF-A, functioning in an anti-R-loop mechanism.","evidence":"Laser micro-irradiation, live imaging, PAR-binding, kinase inhibitors, DNA:RNA hybrid reporter","pmids":["25030905"],"confidence":"High","gaps":["Direct link between Ser59 phosphorylation and the exclusion phase not established here","Which RNA species mediate R-loop suppression unspecified"]},{"year":2015,"claim":"Distinguished mitotic from damage-related Ser59 control: it was unclear what regulates Ser59 in mitosis; PLK1 (not DNA-PK) phosphorylates Ser59 and PP2A dephosphorylates it, with both required for accurate segregation and mitotic exit.","evidence":"Phospho-antibody, kinase inhibitors, PLK1 Co-IP, phosphatase identification, S59A phenotypes","pmids":["25986610"],"confidence":"High","gaps":["Substrate(s) downstream of Ser59 phospho-cycling in mitosis unknown","How the same site integrates damage vs mitotic inputs unresolved"]},{"year":2016,"claim":"Connected Ser59 phosphorylation to repair pathway choice: it was unknown how HNRNPU coordinates competing repair pathways; DNA-PK-phosphorylated SAF-A transiently releases NEIL1 from chromatin, relieving Ku-mediated glycosylase inhibition only when dephosphorylated, prioritizing NHEJ over BER at clustered lesions.","evidence":"In vitro glycosylase inhibition assays, D59 phosphomimetic, chromatin fractionation after IR","pmids":["27303920"],"confidence":"Medium","gaps":["In vitro reconstitution not confirmed at endogenous chromatin in cells","Single-lab finding awaiting independent replication"]},{"year":2017,"claim":"Provided the unifying mechanistic model for genome organization: it was unknown how HNRNPU physically shapes the genome; RGG-mediated caRNA binding plus AAA+ ATPase-driven oligomerization cycles form a chromatin mesh that decompacts chromatin, while loss/monomerization causes aberrant folding and damage, and genome-wide assays confirmed maintenance of TADs, compartments, loops and LADs.","evidence":"Domain mutagenesis, Hi-C, live imaging, oligomerization/ATP assays; conditional KO with Hi-C/DamID/ChIP-seq in hepatocytes","pmids":["28622508","29273625"],"confidence":"High","gaps":["Structure of the oligomeric mesh not determined","How ATPase cycling is regulated in vivo unclear"]},{"year":2018,"claim":"Showed enhancer-RNA-guided coactivator recruitment: it was unknown whether HNRNPU bridges eRNAs to coactivators; HPSE eRNA binding facilitated HNRNPU-p300 super-enhancer enrichment and chromatin looping to activate target genes.","evidence":"Co-IP, ChIP, chromatin conformation capture, gain/loss-of-function","pmids":["29511351"],"confidence":"Medium","gaps":["Direct eRNA-HNRNPU binding mode not mapped","Generality beyond the HPSE locus untested"]},{"year":2020,"claim":"Expanded cytoplasmic and RNA-trafficking roles: it was unclear whether HNRNPU acts in the cytoplasm; it directly binds IL-6 3'-UTR in the cytoplasmic fraction and retains/stabilizes miR-30c-5p in the nucleus to limit its vesicular export, while hepatic loss disrupted chromatin accessibility and TrkB isoform expression.","evidence":"HITS-CLIP with fractionation; RIP/EMSA/miR-pulldown; conditional KO RNA-seq/ChIP-seq with rescue","pmids":["32302342","32944175","31469911"],"confidence":"Medium","gaps":["Nucleocytoplasmic partitioning control not defined","Single-lab disease-context findings"]},{"year":2022,"claim":"Linked HNRNPU to replication, ubiquitin-dependent chromatin condensation, repair condensates, and tissue development: its roles in S-phase, CTCF-cohesin modulation, class-switch recombination and neurodevelopment were unknown; studies showed it promotes origin licensing/fork progression, that CDC20 ubiquitination drives CTCF-cohesin association, that it facilitates C-NHEJ S-S joining via G-quadruplex/R-loop control in LLPS-sensitive condensates, and that its loss kills cortical neurons/progenitors with splicing dysregulation.","evidence":"DNA fiber/MCM loading assays; AP-MS, Co-IP, domain mapping, condensation assays; conditional KO CSR with G4/R-loop and LLPS-inhibitor assays; in vivo cortical truncation with RNA-seq and rescue","pmids":["34888666","35954396","36943867","35864088"],"confidence":"High","gaps":["Mechanistic integration of these roles with the oligomeric mesh model not established","Several findings single-lab and context-specific"]},{"year":2023,"claim":"Identified a lipid-binding capacity within the SAP domain: it was unknown that HNRNPU contacts phosphoinositides; a lysine-rich polybasic motif (aa 9–24) directly bound polyphosphoinositides, implying dual DNA/PPIn functions for the SAP domain.","evidence":"Quantitative interactomics, direct PPIn binding assay, deletion mutagenesis","pmids":["37038481"],"confidence":"Medium","gaps":["Functional role of PPIn binding undefined","Single-study, single-lab observation"]},{"year":2024,"claim":"Defined RNA-binding requirements in germline development and a cytoplasmic disease axis: it was unknown which transcripts HNRNPU regulates in spermatogenesis; conditional loss in prospermatogonia caused splicing defects in Vrk1/Slx4/Dazl and SSC-pool failure, while circMYO9B-driven cytoplasmic translocation stabilized KDM1A to promote VEGFA/angiogenesis.","evidence":"Conditional KO, single-cell transcriptomics, RNA-binding/splicing assays; Co-IP, fractionation, ubiquitination assay, in vivo wound model","pmids":["38625792","39725699"],"confidence":"Medium","gaps":["Direct vs indirect splicing targets not fully separated","Disease-context mechanism single-lab"]},{"year":2025,"claim":"Dissected domain-specific contributions to Xi maintenance, dynamics, and lncRNA-directed Polycomb recruitment: it was unclear which domains and residues drive each activity; allelic reconstitution showed the SAP domain (with S14/S26) and a Xi-localization signal control XIST localization and dynamics, while the ATPase and RGG domains maintain XIST/heterochromatin and splicing, α-satellite RNA reestablishes chromatin association after mitosis, and HNRNPU is required for Airn/Kcnq1ot1/Xist-directed Polycomb modifications.","evidence":"Allelic reconstitution, FRAP, XIST FISH, heterochromatin ChIP, splicing analysis; α-satellite RNA depletion with segregation assays; RIP and PRC modification assays (two preprints)","pmids":["40219970","40493679","40791421","41473319"],"confidence":"High","gaps":["ATP-binding vs hydrolysis effects on Xi only partially resolved","Two of the lncRNA/ATPase findings are preprints awaiting peer review"]},{"year":null,"claim":"How the distinct activities — ATPase-driven oligomeric chromatin mesh, snRNA/splicing regulation, lncRNA-directed heterochromatin, DNA-repair condensates, and Ser59 phospho-switching — are integrated into a single regulated protein remains the central open question.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No high-resolution structure of the oligomeric RNA-chromatin mesh","Mechanism coupling phosphorylation/ubiquitination state to scaffold assembly unresolved","Whether cytoplasmic and nuclear functions are coordinated or independent unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0,1,4,3]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[1,18,23,26,28]},{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[23]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,23,24]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[35]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[15]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[6,10,16]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,4,9]},{"term_id":"GO:0000228","term_label":"nuclear chromosome","supporting_discovery_ids":[1,4,24]},{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[9,23]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[28,37]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[15]}],"pathway":[{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[23,24,39,41]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[18,11,28]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[16,17,25]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[13,19,20,22,31]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[15,21,33,38]},{"term_id":"R-HSA-69306","term_label":"DNA Replication","supporting_discovery_ids":[33]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[3,5]}],"complexes":["SCF(beta-TrCP) ubiquitin ligase (pseudosubstrate partner)","53BP1-shieldin/C-NHEJ complex","SWI/SNF (BRG1-associated)"],"partners":["BTRC","WT1","NEIL1","AURKA","TPX2","BRG1/SMARCA4","DDX5","CDC20"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q00839","full_name":"Heterogeneous nuclear ribonucleoprotein U","aliases":["GRIP120","Nuclear p120 ribonucleoprotein","Scaffold-attachment factor A","SAF-A","p120","pp120"],"length_aa":825,"mass_kda":90.6,"function":"DNA- and RNA-binding protein involved in several cellular processes such as nuclear chromatin organization, telomere-length regulation, transcription, mRNA alternative splicing and stability, Xist-mediated transcriptional silencing and mitotic cell progression (PubMed:10490622, PubMed:18082603, PubMed:19029303, PubMed:22325991, PubMed:25986610, PubMed:28622508). Plays a role in the regulation of interphase large-scale gene-rich chromatin organization through chromatin-associated RNAs (caRNAs) in a transcription-dependent manner, and thereby maintains genomic stability (PubMed:1324173, PubMed:28622508, PubMed:8174554). Required for the localization of the long non-coding Xist RNA on the inactive chromosome X (Xi) and the subsequent initiation and maintenance of X-linked transcriptional gene silencing during X-inactivation (By similarity). Plays a role as a RNA polymerase II (Pol II) holoenzyme transcription regulator (PubMed:10490622, PubMed:15711563, PubMed:19617346, PubMed:23811339, PubMed:8174554, PubMed:9353307). Promotes transcription initiation by direct association with the core-TFIIH basal transcription factor complex for the assembly of a functional pre-initiation complex with Pol II in a actin-dependent manner (PubMed:10490622, PubMed:15711563). Blocks Pol II transcription elongation activity by inhibiting the C-terminal domain (CTD) phosphorylation of Pol II and dissociates from Pol II pre-initiation complex prior to productive transcription elongation (PubMed:10490622). Positively regulates CBX5-induced transcriptional gene silencing and retention of CBX5 in the nucleus (PubMed:19617346). Negatively regulates glucocorticoid-mediated transcriptional activation (PubMed:9353307). Key regulator of transcription initiation and elongation in embryonic stem cells upon leukemia inhibitory factor (LIF) signaling (By similarity). Involved in the long non-coding RNA H19-mediated Pol II transcriptional repression (PubMed:23811339). Participates in the circadian regulation of the core clock component BMAL1 transcription (By similarity). Plays a role in the regulation of telomere length (PubMed:18082603). Plays a role as a global pre-mRNA alternative splicing modulator by regulating U2 small nuclear ribonucleoprotein (snRNP) biogenesis (PubMed:22325991). Plays a role in mRNA stability (PubMed:17174306, PubMed:17289661, PubMed:19029303). Component of the CRD-mediated complex that promotes MYC mRNA stabilization (PubMed:19029303). Enhances the expression of specific genes, such as tumor necrosis factor TNFA, by regulating mRNA stability, possibly through binding to the 3'-untranslated region (UTR) (PubMed:17174306). Plays a role in mitotic cell cycle regulation (PubMed:21242313, PubMed:25986610). Involved in the formation of stable mitotic spindle microtubules (MTs) attachment to kinetochore, spindle organization and chromosome congression (PubMed:21242313). Phosphorylation at Ser-59 by PLK1 is required for chromosome alignement and segregation and progression through mitosis (PubMed:25986610). Also contributes to the targeting of AURKA to mitotic spindle MTs (PubMed:21242313). Binds to double- and single-stranded DNA and RNA, poly(A), poly(C) and poly(G) oligoribonucleotides (PubMed:1628625, PubMed:8068679, PubMed:8174554, PubMed:9204873, PubMed:9405365). Binds to chromatin-associated RNAs (caRNAs) (PubMed:28622508). Associates with chromatin to scaffold/matrix attachment region (S/MAR) elements in a chromatin-associated RNAs (caRNAs)-dependent manner (PubMed:10671544, PubMed:11003645, PubMed:11909954, PubMed:1324173, PubMed:28622508, PubMed:7509195, PubMed:9204873, PubMed:9405365). Binds to the Xist RNA (PubMed:26244333). Binds the long non-coding H19 RNA (PubMed:23811339). Binds to SMN1/2 pre-mRNAs at G/U-rich regions (PubMed:22325991). Binds to small nuclear RNAs (snRNAs) (PubMed:22325991). Binds to the 3'-UTR of TNFA mRNA (PubMed:17174306). Binds (via RNA-binding RGG-box region) to the long non-coding Xist RNA; this binding is direct and bridges the Xist RNA and the inactive chromosome X (Xi) (By similarity). Also negatively regulates embryonic stem cell differentiation upon LIF signaling (By similarity). Required for embryonic development (By similarity). Binds to brown fat long non-coding RNA 1 (Blnc1); facilitates the recruitment of Blnc1 by ZBTB7B required to drive brown and beige fat development and thermogenesis (By similarity) (Microbial infection) Negatively regulates immunodeficiency virus type 1 (HIV-1) replication by preventing the accumulation of viral mRNA transcripts in the cytoplasm","subcellular_location":"Nucleus; Nucleus matrix; Chromosome; Nucleus speckle; Cytoplasm, cytoskeleton, microtubule organizing center, centrosome; Chromosome, centromere, kinetochore; Cytoplasm, cytoskeleton, spindle; Cytoplasm, cytoskeleton, spindle pole; Midbody; Cytoplasm; Cell surface; Cytoplasmic granule","url":"https://www.uniprot.org/uniprotkb/Q00839/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/HNRNPU","classification":"Common Essential","n_dependent_lines":1173,"n_total_lines":1208,"dependency_fraction":0.9710264900662252},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000153187","cell_line_id":"CID001837","localizations":[{"compartment":"nucleoplasm","grade":3},{"compartment":"chromatin","grade":2}],"interactors":[{"gene":"HNRNPD","stoichiometry":10.0},{"gene":"HNRNPDL","stoichiometry":10.0},{"gene":"HNRNPAB","stoichiometry":10.0},{"gene":"KPNB1","stoichiometry":10.0},{"gene":"KPNA2","stoichiometry":10.0},{"gene":"DDX21","stoichiometry":4.0},{"gene":"HNRNPL","stoichiometry":4.0},{"gene":"SSRP1","stoichiometry":4.0},{"gene":"TOP1","stoichiometry":4.0},{"gene":"CAPZB","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001837","total_profiled":1310},"omim":[{"mim_id":"618172","title":"LONG NONCODING RNA UPREGULATOR OF ANTIVIRAL RESPONSE INTERFERON SIGNALING; LUARIS","url":"https://www.omim.org/entry/618172"},{"mim_id":"618033","title":"ZINC FINGER PROTEIN 689; ZNF689","url":"https://www.omim.org/entry/618033"},{"mim_id":"617391","title":"DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 54; DEE54","url":"https://www.omim.org/entry/617391"},{"mim_id":"612337","title":"INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL DOMINANT 22; MRD22","url":"https://www.omim.org/entry/612337"},{"mim_id":"610677","title":"LSM14A mRNA PROCESSING BODY ASSEMBLY FACTOR; LSM14A","url":"https://www.omim.org/entry/610677"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/HNRNPU"},"hgnc":{"alias_symbol":["SAF-A","FLJ37978","FLJ30202"],"prev_symbol":["HNRPU","HNRNPU-AS1","C1orf199","NCRNA00201"]},"alphafold":{"accession":"Q00839","domains":[{"cath_id":"-","chopping":"7-40","consensus_level":"high","plddt":92.6865,"start":7,"end":40},{"cath_id":"2.60.120.920","chopping":"289-485","consensus_level":"high","plddt":93.6207,"start":289,"end":485},{"cath_id":"3.40.50.300","chopping":"493-525_576-675","consensus_level":"high","plddt":89.9001,"start":493,"end":675}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q00839","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q00839-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q00839-F1-predicted_aligned_error_v6.png","plddt_mean":64.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=HNRNPU","jax_strain_url":"https://www.jax.org/strain/search?query=HNRNPU"},"sequence":{"accession":"Q00839","fasta_url":"https://rest.uniprot.org/uniprotkb/Q00839.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q00839/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q00839"}},"corpus_meta":[{"pmid":"1324173","id":"PMC_1324173","title":"Characterization 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genetics","url":"https://pubmed.ncbi.nlm.nih.gov/40493679","citation_count":3,"is_preprint":false},{"pmid":"38797891","id":"PMC_38797891","title":"Loss of HNRNPU in Skeletal Muscle Increases Intramuscular Infiltration of Ly6C Positive Cells, leading to Muscle Atrophy through Activation of NF-κB Signaling.","date":"2024","source":"Advanced biology","url":"https://pubmed.ncbi.nlm.nih.gov/38797891","citation_count":3,"is_preprint":false},{"pmid":"39011773","id":"PMC_39011773","title":"The nuclear matrix protein HNRNPU restricts hepatitis B virus transcription by promoting OAS3-based activation of host innate immunity.","date":"2024","source":"Journal of medical virology","url":"https://pubmed.ncbi.nlm.nih.gov/39011773","citation_count":3,"is_preprint":false},{"pmid":"40640337","id":"PMC_40640337","title":"The molecular axis hnRNPU/circKCNK2/EDC4/IL-11 aggravates osteolytic bone metastasis of RCC.","date":"2025","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/40640337","citation_count":2,"is_preprint":false},{"pmid":"41310105","id":"PMC_41310105","title":"RNA-binding protein HnRNPU regulates proliferation and ferroptosis in colon adenocarcinoma by stabilizing the mRNA of system xc.","date":"2025","source":"Experimental & molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/41310105","citation_count":2,"is_preprint":false},{"pmid":"38279497","id":"PMC_38279497","title":"ITGA9-AS1 up-regulates ITGA9 by targeting miR-4765 and recruiting HNRNPU to affect the proliferation and apoptosis of non-small cell lung cancer cells.","date":"2023","source":"Cellular and molecular biology (Noisy-le-Grand, France)","url":"https://pubmed.ncbi.nlm.nih.gov/38279497","citation_count":2,"is_preprint":false},{"pmid":"38665420","id":"PMC_38665420","title":"Biological functions and clinic significance of SAF‑A (Review).","date":"2024","source":"Biomedical reports","url":"https://pubmed.ncbi.nlm.nih.gov/38665420","citation_count":1,"is_preprint":false},{"pmid":"37038481","id":"PMC_37038481","title":"SAF-A/hnRNP U binds polyphosphoinositides via a lysine rich polybasic motif located in the SAP domain.","date":"2023","source":"microPublication biology","url":"https://pubmed.ncbi.nlm.nih.gov/37038481","citation_count":1,"is_preprint":false},{"pmid":"40926024","id":"PMC_40926024","title":"Long non-coding RNA STMN1P2 promotes breast cancer doxorubicin resistance by inhibiting pyroptosis through the hnRNPU-EZH2-TARF6-MALT1-caspase-1 pathway.","date":"2025","source":"Acta pharmacologica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/40926024","citation_count":1,"is_preprint":false},{"pmid":"41473319","id":"PMC_41473319","title":"Role of the SAF-A/HNRNPU ATPase and RGG domains in X chromosome inactivation, nuclear dynamics, transcription, splicing, and cell proliferation.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/41473319","citation_count":1,"is_preprint":false},{"pmid":"39664183","id":"PMC_39664183","title":"circUBE2G1 interacts with hnRNPU to promote VEGF-C-mediated lymph node metastasis of lung adenocarcinoma.","date":"2024","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/39664183","citation_count":1,"is_preprint":false},{"pmid":"40791421","id":"PMC_40791421","title":"Correlated protein-RNA associations reveal a requirement for HNRNPU in long-range Polycomb recruitment by the lncRNAs Airn , Kcnq1ot1 , and Xist.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/40791421","citation_count":1,"is_preprint":false},{"pmid":"38846959","id":"PMC_38846959","title":"Case report: Early use of whole exome sequencing unveils HNRNPU-related neurodevelopmental disorder and answers additional clinical questions through reanalysis.","date":"2024","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/38846959","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":47597,"output_tokens":10544,"usd":0.150476,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":21425,"output_tokens":8138,"usd":0.155287,"stage2_stop_reason":"end_turn"},"total_usd":0.305763,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1992,\n      \"finding\": \"SAF-A (HNRNPU) was identified as a novel nuclear DNA-binding protein and constituent of the nuclear matrix/scaffold. The purified 120 kDa protein binds at multiple sites to human SAR (scaffold attachment region) elements, with binding sites residing in A/T-stretches. The protein forms large aggregates and mediates formation of looped DNA structures, suggesting a structural role in organizing chromatin loop domains.\",\n      \"method\": \"Protein purification, competition binding assays with synthetic polynucleotides, electron microscopy\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — purified protein reconstitution with direct binding and EM structural visualization; foundational paper replicated by multiple subsequent studies\",\n      \"pmids\": [\"1324173\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"SAF-A is identical to hnRNP-U. UV cross-linking demonstrated the protein is bound to chromosomal DNA in vivo. In vitro, the protein binds both double-stranded and single-stranded DNA and RNA, likely at different binding sites, indicating dual roles in chromatin organization and hnRNA metabolism.\",\n      \"method\": \"UV cross-linking, filter-binding experiments with diverse nucleic acid substrates\",\n      \"journal\": \"European journal of biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct biochemical demonstration in vivo and in vitro with multiple substrates; identity of SAF-A and hnRNP-U confirmed across multiple labs\",\n      \"pmids\": [\"8174554\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"Two isoforms of hnRNP-U (form 1 and form 2) were purified and shown to differ in primary structure. Both isoforms bind double- and single-stranded DNA and RNA, form higher-ordered nucleic acid/protein complexes, and specifically bind and aggregate the human SAR element. The two isoforms differ morphologically: form 1 forms long unbranched filamentous DNA complexes while form 2 forms spherical aggregates (~35 nm diameter).\",\n      \"method\": \"Chromatographic purification, electron microscopy, nucleic acid binding assays\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — purified protein reconstitution with EM and biochemical characterization in one study\",\n      \"pmids\": [\"8068679\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"SAF-A possesses a novel bipartite SAR-specific DNA-binding domain that is independent of its C-terminal RGG RNA-binding domain. During apoptosis, caspase-dependent cleavage occurs within this bipartite DNA-binding domain, causing loss of DNA-binding activity and detachment from nuclear structural sites without affecting hnRNP complex association, indicating the two functional domains are separable.\",\n      \"method\": \"Domain deletion/mutation analysis, apoptosis induction, subcellular fractionation\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — domain mutagenesis with functional consequence, replicated by subsequent caspase cleavage study\",\n      \"pmids\": [\"9405365\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"hnRNP-U/SAF-A is directly bound to chromosomal DNA in vivo, as demonstrated by formaldehyde cross-linking followed by CsCl density gradient purification. Dimethylsulfate cross-linking and limited protease digestion established that hnRNP-U contacts DNA directly rather than through bridging to other proteins.\",\n      \"method\": \"Formaldehyde cross-linking, CsCl density gradient centrifugation, dimethylsulfate cross-linking, limited protease digestion, western blotting\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — multiple orthogonal in vivo and in vitro methods in one study establishing direct DNA contact\",\n      \"pmids\": [\"9204873\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Caspase-3 cleaves SAF-A at Asp-100 within the non-canonical sequence SALD (rather than the canonical DEXD motif) in vitro and in vivo during apoptosis. A D100A point mutation abrogates cleavage by recombinant caspase-3 in vitro and during apoptosis in vivo, confirming SALD as a novel caspase-3 cleavage site.\",\n      \"method\": \"Recombinant caspase-3 in vitro cleavage assay, MALDI-TOF mass spectrometry, Edman sequencing, site-directed mutagenesis (D100A), in vivo apoptosis assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstitution with recombinant enzyme, mutagenesis validation both in vitro and in vivo\",\n      \"pmids\": [\"10671544\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"hnRNP-U/SAF-A represses glucocorticoid receptor (GR)-dependent transcription. A construct lacking the GR-binding domain of hnRNP-U acts as a dominant negative factor that enhances GR-driven transcription. The repressive effect depends on relative concentrations of GR, hnRNP-U and GR DNA-binding sites, suggesting hnRNP-U acts as a storage site for intranuclear GR.\",\n      \"method\": \"Transient transfection of hnRNP-U deletion constructs, reporter gene assays in Ltk(-) cells\",\n      \"journal\": \"The Journal of steroid biochemistry and molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — functional reporter assays with domain deletion constructs in a single study\",\n      \"pmids\": [\"11530285\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"hnRNP-U is the major nuclear binding partner of the SCF(β-TrCP) ubiquitin ligase subunit β-TrCP/E3RS. hnRNP-U occupies E3RS stoichiometrically, stabilizes the E3 component, and is responsible for its nuclear localization. hnRNP-U acts as a pseudosubstrate—binding via the WD region in an E3-substrate-type interaction but not being targeted for degradation—and dissociates from E3RS upon competition by high-affinity substrate, enabling substrate ubiquitination.\",\n      \"method\": \"Affinity purification, Co-IP, competition with pIκBα peptide, point mutation in WD region\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, stoichiometric interaction, mutagenesis, functional ubiquitination assay, multiple orthogonal methods\",\n      \"pmids\": [\"11850407\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"An episomally replicating plasmid (pEPI-1) containing a S/MAR element binds exclusively to hnRNP-U/SAF-A in the nuclear matrix, as demonstrated by cis-diamminedichloroplatinum II cross-linking and southwestern analysis. Immunoprecipitation of the cross-linked DNA-protein complex confirmed that pEPI-1 is bound to hnRNP-U/SAF-A in vivo, providing the basis for episome mitotic stability.\",\n      \"method\": \"Cross-linking with cis-diamminedichloroplatinum II, nuclear matrix co-purification, southwestern analysis, immunoprecipitation\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct in vivo cross-linking with orthogonal biochemical confirmation in a single study\",\n      \"pmids\": [\"11897664\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"SAF-A is enriched at the inactive X chromosome (Xi) territory through its RGG RNA-binding domain. After removal of DNA and chromatin proteins, SAF-A remains with the nuclear matrix at the Xi. The enrichment depends on the RGG domain, raising the possibility that SAF-A interaction with XIST RNA contributes to Xi silencing through local changes in nuclear architecture.\",\n      \"method\": \"Immunofluorescence, nuclear matrix extraction, domain-deletion constructs, XIST RNA co-localization\",\n      \"journal\": \"Chromosoma\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment with domain-deletion functional follow-up, single lab\",\n      \"pmids\": [\"14608463\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"hnRNP-U directly interacts with the Wilms' tumour protein WT1 without requiring other proteins or nucleic acids; the interaction involves the zinc-fingers of WT1 and the middle domain of hnRNP-U. hnRNP-U modulates WT1 transcriptional activation of a bona fide WT1 target gene.\",\n      \"method\": \"Co-IP of endogenous proteins, domain deletion/interaction mapping, transcriptional reporter assay\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — endogenous co-IP plus domain mapping and functional transcriptional assay, single lab\",\n      \"pmids\": [\"16924231\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"hnRNP-U enhances expression of specific genes including TNF-α, GADD45A, HEXIM1, HOXA2, IER3, NHLH2, and ZFY by binding to and stabilizing their mRNAs, likely through binding to 3' UTR sequences.\",\n      \"method\": \"RNAi knockdown, mRNA stability assays, 3' UTR binding\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — functional knockdown with mRNA stability readout, single lab, single study\",\n      \"pmids\": [\"17174306\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"SAF-A binds to the 3'-flanking region of the Bmal1 promoter with circadian timing in vivo (detected by in vivo footprinting), and this rhythmic binding correlates with circadian Bmal1 transcription. The RORE region of the Bmal1 promoter resides in GC-rich open chromatin, and the 3'-flanking region inhibits rhythmic transcription in reporter assays.\",\n      \"method\": \"In vivo DNase I footprinting, in vitro reporter gene assay\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo footprinting and reporter assay with functional correlation, single lab\",\n      \"pmids\": [\"18332112\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"hnRNP-U/SAF-A is phosphorylated at Ser59 specifically by DNA-PK in vitro and in cells in response to DNA double-strand breaks. This was identified using a cell-free system for dissecting DNA damage kinase substrates.\",\n      \"method\": \"Cell-free kinase assay, in vitro phosphorylation, in vivo phosphorylation after DNA damage induction, site identification\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution plus in vivo validation, replicated by a second independent study (PMID:19844162)\",\n      \"pmids\": [\"19351595\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"SAF-A is phosphorylated at Ser59 in a sequence context matching a 'S-hydrophobic' consensus exclusively by DNA-PK in response to DSB-inducing agents. The extent and duration of phosphorylation inversely correlates with the capacity of cells to repair DSBs by NHEJ, linking SAF-A phosphorylation status to DSB repair efficacy.\",\n      \"method\": \"Phospho-specific antibody, kinase inhibitor experiments, NHEJ-deficient cell lines, mass spectrometry-based site mapping\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — phospho-site mapped, validated in multiple cell lines with defined NHEJ status, replicated phospho-Ser59 finding\",\n      \"pmids\": [\"19844162\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"SAF-A localizes to mitotic spindles, spindle midzone, and cytoplasmic bridge. SAF-A depletion causes mitotic delay, chromosome misalignment, and spindle assembly defects. SAF-A co-immunoprecipitates with nucleolin, Aurora-A, and TPX2; co-localizes with TPX2 and Aurora-A at spindle poles and microtubules. SAF-A can bind microtubules directly and contributes to Aurora-A targeting to mitotic spindle microtubules. Elimination of TPX2 or Aurora-A abolishes SAF-A association with the mitotic spindle.\",\n      \"method\": \"RNAi, immunofluorescence, co-immunoprecipitation, direct microtubule binding assay\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct localization with functional loss-of-function, co-IP of endogenous proteins, direct microtubule binding assay, epistasis by depletion experiments\",\n      \"pmids\": [\"21242313\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"SAF-A binds the Oct4 proximal promoter in ES cells and dissociates upon early differentiation. SAF-A depletion decreases Oct4 expression even with LIF. SAF-A interacts with the CTD of RNA polymerase II independently of CTD phosphorylation and mRNA. SAF-A exists in complexes with Sox2, Oct4, and STAT3 in ES cells, with complex numbers decreasing upon LIF withdrawal.\",\n      \"method\": \"ChIP, RNAi, co-immunoprecipitation of endogenous proteins, reporter assay\",\n      \"journal\": \"Cellular reprogramming\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and co-IP of endogenous proteins plus functional knockdown, single lab\",\n      \"pmids\": [\"21235343\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"SAF-A interacts with BRG1 (the ATPase subunit of the SWI/SNF chromatin remodeling complex) in mouse ES cells. Dual depletion of SAF-A and BRG1 abolishes global RNA Pol II transcription while leaving RNA Pol I transcription unaffected, establishing that both are jointly required for RNA Pol II-mediated transcription.\",\n      \"method\": \"Co-immunoprecipitation, in situ proximity ligation assay, co-localization, RNAi double knockdown, transcription assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP confirmed by PLA, functional double-knockdown with global transcription readout, single lab\",\n      \"pmids\": [\"22162999\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"hnRNP U regulates U2 snRNP maturation and Cajal body morphology. CLIP-seq reveals that hnRNP-U binds virtually all classes of regulatory noncoding RNAs including all snRNAs required for splicing of both major and minor intron classes. hnRNP-U depletion causes global alternative splicing changes, establishing it as a regulator of the core splicing machinery.\",\n      \"method\": \"RNAi screen, CLIP-seq (genome-wide), RNA-seq (genome-wide), Cajal body morphology assay\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — genome-wide CLIP-seq plus RNA-seq with mechanistic follow-up on snRNP maturation, multiple orthogonal methods\",\n      \"pmids\": [\"22325991\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"hnRNP-U directly interacts with NEIL1 DNA glycosylase via NEIL1's C-terminal domain (dispensable for enzymatic activity). hnRNP-U stimulates NEIL1 base excision activity for oxidized bases primarily by enhancing product release. hnRNP-U and NEIL1 epistatically protect cells from low-level oxidative damage. The interacting regions in hnRNP-U map to both N and C termini. In-cell association increases after oxidative stress.\",\n      \"method\": \"Co-immunoprecipitation, in vitro base excision repair assay, domain mapping, FLAG-IP from human cells, epistasis analysis (hnRNP-U and NEIL1 double depletion), Kd measurement\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct in vitro biochemical reconstitution, Kd measurement, domain mapping, epistasis experiment, multiple orthogonal methods\",\n      \"pmids\": [\"22902625\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"SAF-A exhibits biphasic dynamics at DNA damage sites: rapid transient recruitment via binding to Poly(ADP-ribose) (PAR), followed by prolonged exclusion dependent on ATM, ATR, and DNA-PK activity. Exclusion reflects dissociation of transcription-associated SAF-A from chromatin. The RNA-binding domain of SAF-A recapitulates this biphasic behavior. SAF-A exclusion is part of an anti-R-loop mechanism at damaged transcribed sites.\",\n      \"method\": \"Laser micro-irradiation, live-cell imaging, PAR binding assay, kinase inhibitor experiments, R-loop reporter (live imaging of DNA:RNA hybrids)\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — live imaging combined with biochemical binding assay and kinase inhibitor epistasis, multiple orthogonal approaches\",\n      \"pmids\": [\"25030905\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"SAF-A Ser59 is phosphorylated by PLK1 (not DNA-PKcs) during mitosis. SAF-A interacts with PLK1 in nocodazole-arrested cells. Ser59 is dephosphorylated by PP2A during mitosis. Cells expressing S59A SAF-A show misaligned chromosomes, lagging chromosomes, polylobed nuclei, and delayed mitotic exit, demonstrating that both phosphorylation by PLK1 and dephosphorylation by PP2A at Ser59 are required for accurate mitosis.\",\n      \"method\": \"Phospho-specific antibody, kinase inhibitors, Co-IP with PLK1, phosphatase identification, S59A point mutation cell lines, mitotic phenotype analysis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — site-directed mutagenesis with cellular phenotype, kinase/phosphatase identification, Co-IP, multiple orthogonal methods\",\n      \"pmids\": [\"25986610\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"SAF-A phosphorylated at Ser59 by DNA-PK early after ionizing radiation is linked to transient release of chromatin-bound NEIL1, preventing base excision repair (BER) from proceeding prematurely. Dephosphorylated SAF-A relieves Ku-mediated inhibition of DNA glycosylases in vitro, but the phosphomimetic D59 mutant does not. This establishes a temporal coordination mechanism where SAF-A and Ku cooperate to prioritize NHEJ over BER at clustered genome lesions.\",\n      \"method\": \"In vitro DNA glycosylase inhibition assay, phosphomimetic mutant (D59), DNA-PK phosphorylation, chromatin fractionation after IR\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with phosphomimetic mutant and chromatin fractionation, single lab\",\n      \"pmids\": [\"27303920\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"SAF-A oligomerizes with chromatin-associated RNAs (caRNAs) via its RGG domain to regulate interphase chromatin structure in a transcription-dependent manner. The AAA+ ATPase domain of SAF-A mediates cycles of oligomerization in response to ATP binding and hydrolysis. SAF-A oligomerization decompacts large-scale chromatin structure, while SAF-A loss or monomerization promotes aberrant chromosome folding and genome damage accumulation.\",\n      \"method\": \"Domain mutagenesis (RGG, ATPase), Hi-C, live-cell imaging, biochemical oligomerization assays, ATP hydrolysis assays, genome damage readouts\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — domain-level mutagenesis combined with Hi-C and biochemical reconstitution; multiple orthogonal methods in one rigorous study\",\n      \"pmids\": [\"28622508\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"HNRNPU is required for maintaining 3D genome architecture in mouse hepatocytes. HNRNPU depletion increases LAD (lamina-associated domain) coverage, causes global chromatin condensation, compartment switching (7.5% of genome), decreased TAD boundary strengths at A/B compartment borders, and reduced chromatin loop intensities. HNRNPU mainly associates with active chromatin, and 80% of HNRNPU ChIP peaks coincide with CTCF or RAD21 binding.\",\n      \"method\": \"In situ Hi-C, DamID, ChIP-seq, RNA-seq, conditional knockout in hepatocytes\",\n      \"journal\": \"Genome research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — multiple genome-wide orthogonal assays (Hi-C, DamID, ChIP-seq) combined with genetic depletion; rigorous 3D genome phenotyping\",\n      \"pmids\": [\"29273625\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"HPSE eRNA binds hnRNPU to facilitate its interaction with p300, promoting their enrichment on a super enhancer, resulting in chromatin looping between the super enhancer and HPSE promoter, p300-mediated transactivation of EGR1, and subsequent HPSE upregulation.\",\n      \"method\": \"Co-immunoprecipitation, ChIP, chromatin conformation capture, gain/loss-of-function experiments\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and ChIP with functional rescue experiments, single lab\",\n      \"pmids\": [\"29511351\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"hnRNPU retains miR-30c-5p in the nucleus and prevents its export into large extracellular vesicles. Binding of miR-30c-5p to hnRNPU was confirmed by RNA-immunoprecipitation, EMSA, and miR-pulldown. Nuclear binding stabilizes miR-30c-5p, reducing cytoplasmic availability for vesicular export. hnRNPU-dependent miR-30c-5p export reduced cellular migration and pro-angiogenic gene expression in recipient cells.\",\n      \"method\": \"Gain/loss-of-function, RNA-immunoprecipitation, EMSA, miR-pulldown, nanoparticle tracking analysis, electron microscopy\",\n      \"journal\": \"Journal of extracellular vesicles\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct RNA-protein binding confirmed by three orthogonal methods (RIP, EMSA, pulldown), functional consequence assessed, single lab\",\n      \"pmids\": [\"32944175\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"hnRNPU deficiency in mouse hepatocytes disrupts liver chromatin accessibility and stimulates expression of a truncated TrkB isoform (TRKB-T1) that promotes inflammatory signaling and stress-induced cell death. BDNF treatment reduced membrane TRKB-T1 and protected mice from diet-induced NASH, linking hnRNPU-chromatin regulation to disease-specific signaling.\",\n      \"method\": \"Hepatocyte-specific conditional knockout, RNA-seq, ChIP-seq, BDNF treatment rescue experiment\",\n      \"journal\": \"Hepatology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional KO with mechanistic follow-up (ChIP-seq and RNA-seq) and rescue experiment, single lab\",\n      \"pmids\": [\"31469911\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"In HeLa cells, hnRNPU directly binds the 3'-UTR of IL-6 mRNA, and this interaction occurs specifically in the cytoplasmic fraction, suggesting a role for cytoplasmic hnRNPU in mRNA stability control distinct from its nuclear functions.\",\n      \"method\": \"Optimized HITS-CLIP (BrdU-CLIP), subcellular fractionation, CLIP validation\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct CLIP identification of target in fractionated cells, single lab, single method\",\n      \"pmids\": [\"32302342\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"hnRNPU interacts with WT1 and SOX9 in Sertoli cells and enhances expression of Sox8 and Sox9 by directly binding to their promoter regions. Conditional knockout of hnRNPU in murine Sertoli cells causes rapid depletion of both Sertoli and germ cells and failure of spermatogonia proliferation and migration, leading to male sterility.\",\n      \"method\": \"Conditional knockout (Cre/loxP), luciferase reporter assay, ChIP-qPCR, RNA-seq, co-immunoprecipitation\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional KO phenotype with ChIP and reporter assay to establish promoter binding mechanism, single lab\",\n      \"pmids\": [\"34815802\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"HNRNPU loss of function leads to rapid cell death of both postmitotic neurons and neural progenitors in the developing mouse cortex, with neural progenitors being more sensitive. HNRNPU truncation causes dysregulation of gene expression and alternative splicing of genes involved in cell survival, cell motility, and synapse formation. Pharmaceutical and genetic agents partially rescued loss of cortical structures, radial migration defects, and neural progenitor cell death.\",\n      \"method\": \"Conditional truncation in mouse cortex, RNA-seq, alternative splicing analysis, pharmacological rescue, cell death assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo conditional truncation with transcriptomic analysis and rescue experiments; multi-orthogonal approach\",\n      \"pmids\": [\"35864088\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"HNRNPU promotes antibody class-switch recombination (CSR) by facilitating C-NHEJ-mediated S-S joining through the 53BP1-shieldin complex. HNRNPU binds switch region RNA/DNA G-quadruplexes and regulates R-loop and ssDNA accumulation. HNRNPU interacts with both C-NHEJ and R-loop complexes in an RNA-dependent manner. Recruitment of HNRNPU and C-NHEJ factors is sensitive to liquid-liquid phase separation inhibitors, suggesting DNA-repair condensate formation.\",\n      \"method\": \"Conditional knockout in B cells, CSR assay, Co-IP, G-quadruplex binding assay, LLPS inhibitor treatment, ssDNA/R-loop detection\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with mechanistic Co-IP and binding assays, single lab\",\n      \"pmids\": [\"36943867\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CDC20-mediated ubiquitination of hnRNPU promotes its interaction with the CTCF-cohesin complex, modulating chromatin condensation. The molecular domain on hnRNPU required for CDC20 interaction was mapped to amino acid residues 461–653. Dysregulation of the CDC20-hnRNPU axis contributes to altered chromatin condensation, tumor progression, and drug resistance.\",\n      \"method\": \"Affinity purification/mass spectrometry, Co-IP, immunostaining, domain mapping, DAPI/H2B-mCherry chromatin condensation assay\",\n      \"journal\": \"Cancers\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with domain mapping and functional chromatin readout, single lab\",\n      \"pmids\": [\"35954396\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SAF-A promotes origin licensing in G1 phase, origin activation frequency in S phase, and consistent replication fork progression. SAF-A depletion causes reduced MCM loading, decreased origin activation, inconsistent fork progression, blurred replication timing domain boundaries, and elevated γ-H2AX formation leading to cellular quiescence.\",\n      \"method\": \"DNA fiber assay, origin licensing assay (MCM loading), single-cell replication timing, γ-H2AX immunostaining, siRNA depletion\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple replication assays with genetic depletion, mechanistic focus on origin licensing and fork progression, single lab\",\n      \"pmids\": [\"34888666\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"hnRNPU promotes TNBC cell proliferation and migration via association with DDX5. The HNRNPU-DDX5 complex prevents intron retention of MCM10 pre-mRNA (reducing nonsense-mediated decay) and activates Wnt/β-catenin signaling. Additionally, the HNRNPU-DDX5 complex promotes transcription of LMO4 from its transcriptional start site, activating PI3K-Akt-mTOR signaling.\",\n      \"method\": \"CRISPR screen, RNAi, Co-IP of endogenous proteins, splicing analysis, transcriptional reporter, Western blot\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP of endogenous proteins plus splicing and transcriptional mechanistic analysis, single lab\",\n      \"pmids\": [\"36347834\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SAF-A/hnRNPU directly interacts with polyphosphoinositides (PPIn) via a lysine-rich polybasic motif located at amino acids 9–24 within its SAP DNA-binding domain. Deletion of this polybasic motif prevents PPIn interaction, suggesting the SAP domain has dual functions in DNA and PPIn binding.\",\n      \"method\": \"Quantitative interactomics, direct PPIn binding assay, deletion mutagenesis\",\n      \"journal\": \"microPublication biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — direct binding assay with deletion mutagenesis, single lab, single study\",\n      \"pmids\": [\"37038481\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"hnRNPU is required for establishing the spermatogonial stem cell (SSC) pool. Conditional loss of hnRNPU in prospermatogonia arrests spermatogenesis and sterility. hnRNPU-deficient ProSG fails to differentiate and migrate to the basement membrane. hnRNPU binds Vrk1, Slx4, and Dazl transcripts, which show aberrant alternative splicing in hnRNPU-deficient testes.\",\n      \"method\": \"Conditional knockout (Cre/loxP), single-cell transcriptomics, RNA binding analysis, alternative splicing assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional KO with defined cellular phenotype and RNA-binding/splicing mechanistic analysis, single lab\",\n      \"pmids\": [\"38625792\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"circMYO9B promotes translocation of hnRNPU from nucleus to cytoplasm, which destabilizes CBL and reduces ubiquitination/degradation of KDM1A, thereby promoting VEGFA expression in endothelial cells and angiogenesis in diabetic wound healing.\",\n      \"method\": \"Co-IP, subcellular fractionation, protein stability assay, ubiquitination assay, in vivo diabetic wound healing model\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mechanistic pathway defined by Co-IP and ubiquitination assay with in vivo validation, single lab\",\n      \"pmids\": [\"39725699\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"α-Satellite RNAs bind SAF-A and are required for recruitment of SAF-A back to chromatin upon mitotic exit. Both α-satellite RNA and SAF-A are required for chromosome segregation fidelity; depletion of either causes chromosome missegregation. SAF-A is globally excluded from chromatin during mitosis and α-satellite RNAs are required for its reestablishment, with both also aiding nuclear lamina reassembly.\",\n      \"method\": \"SAF-A RNA binding identification, RNAi depletion of α-satellite RNA or SAF-A, chromosome missegregation assays, live-cell imaging, nuclear lamina reassembly assay\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding identification plus epistatic depletion experiments with functional chromosome segregation readout, single lab\",\n      \"pmids\": [\"40219970\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The SAF-A SAP domain (N-terminal DNA-binding domain) and its serines S14 and S26 are required for: XIST RNA localization and XIST-dependent histone modifications on the inactive X chromosome; normal protein nuclear dynamics; and cell proliferation. The SAP domain is not required for global gene expression but plays only a minor role in mRNA splicing. A Xi localization signal resides in the SAP domain. SAF-A is highly dynamic, interacting with nascent transcripts as part of this dynamic movement rather than as a static nuclear scaffold component.\",\n      \"method\": \"Allelic reconstitution, FRAP/protein dynamics assays, XIST RNA FISH, histone modification ChIP, splicing analysis, proliferation assays\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — allelic reconstitution strategy with multiple orthogonal functional readouts including FRAP, ChIP, and FISH, single lab\",\n      \"pmids\": [\"40493679\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The SAF-A ATPase domain and RGG repeats both control SAF-A nuclear dynamics. The RGG repeats mediate interaction with nascent transcripts. Both the ATPase domain and RGG repeats are required for maintaining XIST RNA and facultative heterochromatin marks on the Xi, for proper mRNA splicing, and for cell proliferation. Mutations blocking ATP binding vs. ATP hydrolysis have distinct effects on Xi maintenance.\",\n      \"method\": \"Allelic reconstitution, FRAP, XIST FISH, ChIP for heterochromatin marks, splicing analysis (RNA-seq), proliferation assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — allelic reconstitution with mechanistic mutagenesis; preprint, not yet peer-reviewed\",\n      \"pmids\": [\"41473319\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"HNRNPU is required for long-range Polycomb recruitment by the lncRNAs Airn, Kcnq1ot1, and Xist. RNA immunoprecipitation showed enriched and correlated HNRNPU association with all three lncRNAs. HNRNPU depletion impaired PRC-directed histone modifications induced by all three lncRNAs without being necessary for proper localization of Airn or Kcnq1ot1.\",\n      \"method\": \"RNA-immunoprecipitation from formaldehyde-crosslinked cells, HNRNPU knockdown, PRC-directed histone modification assays (ChIP), lncRNA localization assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RIP with functional epistasis (KD + PRC modification readout), preprint, multiple lncRNA systems tested\",\n      \"pmids\": [\"40791421\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"HNRNPU/SAF-A is a multifunctional nuclear scaffold protein that directly binds both DNA (via its N-terminal SAP bipartite domain) and RNA (via its C-terminal RGG domain), oligomerizes in an ATP-dependent manner through its AAA+ ATPase domain to form a dynamic RNA-chromatin mesh that maintains 3D genome organization (TADs, compartments, chromatin loops), regulates alternative splicing by binding snRNAs and controlling U2 snRNP maturation, stabilizes specific mRNAs through 3'-UTR binding, is phosphorylated at Ser59 by DNA-PK in response to DNA double-strand breaks and by PLK1 during mitosis (with PP2A-mediated dephosphorylation required for mitotic exit), acts as a pseudosubstrate for SCF(β-TrCP) ubiquitin ligase controlling its nuclear localization and substrate threshold, stimulates NEIL1-mediated oxidized base repair, localizes to the inactive X chromosome via its RGG domain to interact with XIST RNA and maintain Xi chromatin structure, and undergoes caspase-3-mediated cleavage at a non-canonical SALD site during apoptosis to release it from chromatin.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"HNRNPU (SAF-A/hnRNP-U) is a multifunctional nuclear scaffold protein that organizes 3D genome architecture by directly contacting both chromosomal DNA and RNA and oligomerizing into a dynamic RNA-chromatin mesh [#0, #4, #23]. It binds scaffold/matrix attachment region (SAR/S/MAR) DNA elements through a bipartite SAR-specific domain that is structurally and functionally separable from its C-terminal RGG RNA-binding domain [#0, #2, #3], and is bound directly to chromosomal DNA in vivo rather than through protein bridges [#1, #4]. Genome-scale studies establish that HNRNPU maintains TAD boundaries, A/B compartments, chromatin loops, and lamina-associated domains, associating mainly with active chromatin and co-occupying sites with CTCF/RAD21 [#24]; this scaffolding activity depends on RGG-mediated binding to chromatin-associated RNAs and on cycles of oligomerization driven by its AAA+ ATPase domain, with oligomerization decompacting chromatin and loss or monomerization causing aberrant folding and genome damage [#23]. Through its RGG domain HNRNPU binds noncoding RNAs to control chromatin states, localizing to the inactive X via XIST RNA to maintain Xi heterochromatin [#9, #39] and mediating long-range Polycomb recruitment by the lncRNAs Airn, Kcnq1ot1, and Xist [#41]. As an RNA-binding regulator it binds essentially all spliceosomal snRNAs, governs U2 snRNP maturation and Cajal body morphology, and shapes global alternative splicing [#18], while also stabilizing specific target mRNAs through 3'-UTR binding [#11, #28]. HNRNPU function is regulated by phosphorylation of Ser59 — by DNA-PK in response to DNA double-strand breaks, where its phosphorylation status tracks NHEJ repair capacity [#13, #14], and by PLK1 during mitosis with PP2A-mediated dephosphorylation required for accurate chromosome segregation and mitotic exit [#21]. At sites of damage it is transiently recruited via poly(ADP-ribose) and then excluded in an ATM/ATR/DNA-PK-dependent manner as part of an anti-R-loop response [#20], and it directly stimulates NEIL1-mediated excision of oxidized bases [#19]. In vivo conditional loss causes cell death of cortical neurons and progenitors with dysregulated splicing of survival and synaptic genes [#30], and failures in spermatogenesis [#29, #36], reflecting its essential roles in genome organization and RNA processing.\",\n  \"teleology\": [\n    {\n      \"year\": 1992,\n      \"claim\": \"Established HNRNPU's founding identity: it was unknown what proteins anchor chromatin loops to the nuclear scaffold; SAF-A was purified as a SAR/MAR-binding protein that mediates looped DNA structures, defining a structural role in chromatin loop organization.\",\n      \"evidence\": \"Protein purification, competition binding assays, and electron microscopy of SAR-element complexes\",\n      \"pmids\": [\"1324173\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Sequence-specificity of SAR recognition and in vivo loop topology not resolved\", \"Relationship to hnRNA metabolism unaddressed at this stage\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"Unified two protein identities and demonstrated dual nucleic-acid binding: it was unclear whether the scaffold protein and hnRNP-U were the same; UV cross-linking showed SAF-A=hnRNP-U is bound to chromosomal DNA in vivo and binds ds/ssDNA and RNA, predicting dual chromatin/hnRNA roles.\",\n      \"evidence\": \"UV cross-linking and filter-binding with diverse nucleic acid substrates; isoform purification with EM\",\n      \"pmids\": [\"8174554\", \"8068679\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Distinct DNA vs RNA binding sites inferred but not mapped\", \"Functional consequence of isoform differences unknown\"]\n    },\n    {\n      \"year\": 1997,\n      \"claim\": \"Defined separable DNA- and RNA-binding modules and direct DNA contact: it was unknown whether scaffold attachment and hnRNP functions reside in one domain; mutagenesis localized a bipartite SAR-specific DNA-binding domain independent of the RGG domain, and orthogonal cross-linking proved direct DNA contact.\",\n      \"evidence\": \"Domain deletion/mutation, apoptosis fractionation, formaldehyde/DMS cross-linking with protease digestion\",\n      \"pmids\": [\"9405365\", \"9204873\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of bipartite domain not solved\", \"How the two domains are coordinated on chromatin not addressed\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Resolved how HNRNPU is dismantled during apoptosis: the protease and site were unknown; caspase-3 was shown to cleave at a non-canonical SALD motif (Asp-100), with D100A abolishing cleavage, defining a regulated detachment from chromatin during cell death.\",\n      \"evidence\": \"Recombinant caspase-3 assay, MS/Edman sequencing, D100A mutagenesis in vitro and in vivo\",\n      \"pmids\": [\"10671544\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of cleavage for apoptotic chromatin disassembly not directly tested\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Identified a non-degradative regulatory partnership: it was unknown how HNRNPU controls ubiquitin ligase activity; HNRNPU was shown to be the major nuclear partner of SCF(beta-TrCP), acting as a pseudosubstrate that stabilizes and nuclear-localizes the E3 and sets a substrate threshold.\",\n      \"evidence\": \"Affinity purification, reciprocal Co-IP, peptide competition, WD-region point mutation, ubiquitination assay\",\n      \"pmids\": [\"11850407\", \"11897664\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological substrates whose threshold is set by HNRNPU not enumerated\", \"Link between scaffolding and E3 sequestration unclear\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Connected HNRNPU to facultative heterochromatin via RNA: the basis of its Xi enrichment was unknown; the RGG domain was shown to retain SAF-A at the Xi nuclear matrix and co-localize with XIST RNA, implicating it in Xi architecture.\",\n      \"evidence\": \"Immunofluorescence, nuclear matrix extraction, RGG-deletion constructs, XIST co-localization\",\n      \"pmids\": [\"14608463\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct XIST-HNRNPU binding not biochemically demonstrated here\", \"Causal contribution to silencing not tested\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Extended HNRNPU into transcriptional and post-transcriptional regulation: it was unknown whether it modulates specific transcription factors and mRNAs; direct WT1 binding modulated WT1 target transcription, and 3'-UTR binding stabilized a defined panel of mRNAs.\",\n      \"evidence\": \"Endogenous Co-IP and domain mapping (WT1); RNAi with mRNA stability and 3'-UTR binding (TNF-alpha, GADD45A et al.)\",\n      \"pmids\": [\"16924231\", \"17174306\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether mRNA stabilization is direct vs scaffold-mediated not separated\", \"Generality of 3'-UTR target set untested\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Placed HNRNPU in the DNA-damage signaling network: the relevant kinase and site were unknown; Ser59 was identified as a DNA-PK phosphosite induced by double-strand breaks, with phosphorylation extent inversely tracking NHEJ repair capacity.\",\n      \"evidence\": \"Cell-free kinase assays, phospho-specific antibody, kinase inhibitors, NHEJ-deficient lines, MS site mapping\",\n      \"pmids\": [\"19351595\", \"19844162\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct effect of Ser59 phosphorylation on HNRNPU chromatin binding not yet defined\", \"Downstream repair effectors unspecified at this stage\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Revealed a mitotic, cytoplasmic role and key partners: it was unclear whether HNRNPU acts outside interphase chromatin; it was shown to localize to spindles, bind microtubules directly, co-IP with nucleolin, Aurora-A and TPX2, and be required for spindle assembly and chromosome alignment.\",\n      \"evidence\": \"RNAi, immunofluorescence, endogenous Co-IP, direct microtubule binding, depletion epistasis\",\n      \"pmids\": [\"21242313\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How a chromatin scaffold protein is repurposed to spindles mechanistically unresolved\", \"Relationship to its mitotic exclusion from chromatin not yet linked\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Linked HNRNPU to the core transcription/remodeling machinery: it was unknown how it supports Pol II output; it bound the Pol II CTD and BRG1, with HNRNPU/BRG1 co-depletion abolishing global Pol II (not Pol I) transcription, and bound the Oct4 promoter in ES cells.\",\n      \"evidence\": \"ChIP, RNAi double knockdown, Co-IP, PLA, transcription assays\",\n      \"pmids\": [\"22162999\", \"21235343\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the BRG1 interaction is direct not established\", \"Mechanistic basis of joint requirement for Pol II transcription unresolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Defined HNRNPU as a regulator of the splicing machinery and oxidative repair: it was unknown how broadly it controls RNA processing; CLIP-seq showed binding to all spliceosomal snRNAs with control of U2 snRNP maturation and global splicing, while direct NEIL1 binding stimulated oxidized-base excision via enhanced product release.\",\n      \"evidence\": \"CLIP-seq/RNA-seq with Cajal body assays; in vitro BER reconstitution, Kd, domain mapping, epistasis\",\n      \"pmids\": [\"22325991\", \"22902625\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How snRNA binding mechanistically drives U2 maturation not fully resolved\", \"Connection between splicing role and chromatin scaffolding not bridged here\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Resolved HNRNPU dynamics at damage sites: it was unknown how it behaves at lesions; live imaging revealed biphasic PAR-dependent recruitment then ATM/ATR/DNA-PK-dependent exclusion of transcription-associated SAF-A, functioning in an anti-R-loop mechanism.\",\n      \"evidence\": \"Laser micro-irradiation, live imaging, PAR-binding, kinase inhibitors, DNA:RNA hybrid reporter\",\n      \"pmids\": [\"25030905\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct link between Ser59 phosphorylation and the exclusion phase not established here\", \"Which RNA species mediate R-loop suppression unspecified\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Distinguished mitotic from damage-related Ser59 control: it was unclear what regulates Ser59 in mitosis; PLK1 (not DNA-PK) phosphorylates Ser59 and PP2A dephosphorylates it, with both required for accurate segregation and mitotic exit.\",\n      \"evidence\": \"Phospho-antibody, kinase inhibitors, PLK1 Co-IP, phosphatase identification, S59A phenotypes\",\n      \"pmids\": [\"25986610\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Substrate(s) downstream of Ser59 phospho-cycling in mitosis unknown\", \"How the same site integrates damage vs mitotic inputs unresolved\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Connected Ser59 phosphorylation to repair pathway choice: it was unknown how HNRNPU coordinates competing repair pathways; DNA-PK-phosphorylated SAF-A transiently releases NEIL1 from chromatin, relieving Ku-mediated glycosylase inhibition only when dephosphorylated, prioritizing NHEJ over BER at clustered lesions.\",\n      \"evidence\": \"In vitro glycosylase inhibition assays, D59 phosphomimetic, chromatin fractionation after IR\",\n      \"pmids\": [\"27303920\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vitro reconstitution not confirmed at endogenous chromatin in cells\", \"Single-lab finding awaiting independent replication\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Provided the unifying mechanistic model for genome organization: it was unknown how HNRNPU physically shapes the genome; RGG-mediated caRNA binding plus AAA+ ATPase-driven oligomerization cycles form a chromatin mesh that decompacts chromatin, while loss/monomerization causes aberrant folding and damage, and genome-wide assays confirmed maintenance of TADs, compartments, loops and LADs.\",\n      \"evidence\": \"Domain mutagenesis, Hi-C, live imaging, oligomerization/ATP assays; conditional KO with Hi-C/DamID/ChIP-seq in hepatocytes\",\n      \"pmids\": [\"28622508\", \"29273625\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure of the oligomeric mesh not determined\", \"How ATPase cycling is regulated in vivo unclear\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Showed enhancer-RNA-guided coactivator recruitment: it was unknown whether HNRNPU bridges eRNAs to coactivators; HPSE eRNA binding facilitated HNRNPU-p300 super-enhancer enrichment and chromatin looping to activate target genes.\",\n      \"evidence\": \"Co-IP, ChIP, chromatin conformation capture, gain/loss-of-function\",\n      \"pmids\": [\"29511351\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct eRNA-HNRNPU binding mode not mapped\", \"Generality beyond the HPSE locus untested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Expanded cytoplasmic and RNA-trafficking roles: it was unclear whether HNRNPU acts in the cytoplasm; it directly binds IL-6 3'-UTR in the cytoplasmic fraction and retains/stabilizes miR-30c-5p in the nucleus to limit its vesicular export, while hepatic loss disrupted chromatin accessibility and TrkB isoform expression.\",\n      \"evidence\": \"HITS-CLIP with fractionation; RIP/EMSA/miR-pulldown; conditional KO RNA-seq/ChIP-seq with rescue\",\n      \"pmids\": [\"32302342\", \"32944175\", \"31469911\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Nucleocytoplasmic partitioning control not defined\", \"Single-lab disease-context findings\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Linked HNRNPU to replication, ubiquitin-dependent chromatin condensation, repair condensates, and tissue development: its roles in S-phase, CTCF-cohesin modulation, class-switch recombination and neurodevelopment were unknown; studies showed it promotes origin licensing/fork progression, that CDC20 ubiquitination drives CTCF-cohesin association, that it facilitates C-NHEJ S-S joining via G-quadruplex/R-loop control in LLPS-sensitive condensates, and that its loss kills cortical neurons/progenitors with splicing dysregulation.\",\n      \"evidence\": \"DNA fiber/MCM loading assays; AP-MS, Co-IP, domain mapping, condensation assays; conditional KO CSR with G4/R-loop and LLPS-inhibitor assays; in vivo cortical truncation with RNA-seq and rescue\",\n      \"pmids\": [\"34888666\", \"35954396\", \"36943867\", \"35864088\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanistic integration of these roles with the oligomeric mesh model not established\", \"Several findings single-lab and context-specific\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified a lipid-binding capacity within the SAP domain: it was unknown that HNRNPU contacts phosphoinositides; a lysine-rich polybasic motif (aa 9–24) directly bound polyphosphoinositides, implying dual DNA/PPIn functions for the SAP domain.\",\n      \"evidence\": \"Quantitative interactomics, direct PPIn binding assay, deletion mutagenesis\",\n      \"pmids\": [\"37038481\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional role of PPIn binding undefined\", \"Single-study, single-lab observation\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined RNA-binding requirements in germline development and a cytoplasmic disease axis: it was unknown which transcripts HNRNPU regulates in spermatogenesis; conditional loss in prospermatogonia caused splicing defects in Vrk1/Slx4/Dazl and SSC-pool failure, while circMYO9B-driven cytoplasmic translocation stabilized KDM1A to promote VEGFA/angiogenesis.\",\n      \"evidence\": \"Conditional KO, single-cell transcriptomics, RNA-binding/splicing assays; Co-IP, fractionation, ubiquitination assay, in vivo wound model\",\n      \"pmids\": [\"38625792\", \"39725699\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs indirect splicing targets not fully separated\", \"Disease-context mechanism single-lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Dissected domain-specific contributions to Xi maintenance, dynamics, and lncRNA-directed Polycomb recruitment: it was unclear which domains and residues drive each activity; allelic reconstitution showed the SAP domain (with S14/S26) and a Xi-localization signal control XIST localization and dynamics, while the ATPase and RGG domains maintain XIST/heterochromatin and splicing, α-satellite RNA reestablishes chromatin association after mitosis, and HNRNPU is required for Airn/Kcnq1ot1/Xist-directed Polycomb modifications.\",\n      \"evidence\": \"Allelic reconstitution, FRAP, XIST FISH, heterochromatin ChIP, splicing analysis; α-satellite RNA depletion with segregation assays; RIP and PRC modification assays (two preprints)\",\n      \"pmids\": [\"40219970\", \"40493679\", \"40791421\", \"41473319\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"ATP-binding vs hydrolysis effects on Xi only partially resolved\", \"Two of the lncRNA/ATPase findings are preprints awaiting peer review\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the distinct activities — ATPase-driven oligomeric chromatin mesh, snRNA/splicing regulation, lncRNA-directed heterochromatin, DNA-repair condensates, and Ser59 phospho-switching — are integrated into a single regulated protein remains the central open question.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No high-resolution structure of the oligomeric RNA-chromatin mesh\", \"Mechanism coupling phosphorylation/ubiquitination state to scaffold assembly unresolved\", \"Whether cytoplasmic and nuclear functions are coordinated or independent unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0, 1, 4, 3]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [1, 18, 23, 26, 28]},\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [23]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 23, 24]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [35]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [15]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [6, 10, 16]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 4, 9]},\n      {\"term_id\": \"GO:0000228\", \"supporting_discovery_ids\": [1, 4, 24]},\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [9, 23]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [28, 37]},\n      {\"term_id\": \"GO:0005819\", \"supporting_discovery_ids\": [15]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [15]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [23, 24, 39, 41]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [18, 11, 28]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [16, 17, 25]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [13, 19, 20, 22, 31]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [15, 21, 33, 38]},\n      {\"term_id\": \"R-HSA-69306\", \"supporting_discovery_ids\": [33]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [3, 5]}\n    ],\n    \"complexes\": [\"SCF(beta-TrCP) ubiquitin ligase (pseudosubstrate partner)\", \"53BP1-shieldin/C-NHEJ complex\", \"SWI/SNF (BRG1-associated)\"],\n    \"partners\": [\"BTRC\", \"WT1\", \"NEIL1\", \"AURKA\", \"TPX2\", \"BRG1/SMARCA4\", \"DDX5\", \"CDC20\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}