{"gene":"RNPS1","run_date":"2026-06-10T06:43:37","timeline":{"discoveries":[{"year":1999,"finding":"RNPS1 was biochemically purified from HeLa cells as a general activator of pre-mRNA splicing; recombinant RNPS1 expressed in baculovirus functionally synergizes with SR proteins and strongly activates splicing of both constitutively and alternatively spliced pre-mRNAs. RNPS1 contains an RNA-recognition motif (RRM) preceded by a serine-rich domain.","method":"Biochemical purification from HeLa cells, baculovirus-expressed recombinant protein in splicing assays, in vitro splicing activation assay","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1 / Strong — direct biochemical purification and reconstituted in vitro splicing assay with recombinant protein","pmids":["10449421"],"is_preprint":false},{"year":1998,"finding":"RNPS1 specifically interacts in vitro and in vivo with the 110 kDa isoforms (p110) of the PITSLRE protein kinase family (CDC2L). Both RNPS1 and PITSLRE p110 localize to nuclear speckles; overexpression of RNPS1 disrupts normal nuclear speckle organization, causing aggregation into ~6 'mega' speckles.","method":"In vitro binding assay, co-immunoprecipitation in vivo, immunofluorescence/subcellular localization","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal in vitro and in vivo interaction confirmed, localization phenotype documented, single lab","pmids":["9580558"],"is_preprint":false},{"year":2001,"finding":"RNPS1, as a component of the post-splicing complex deposited 5' to exon-exon junctions, interacts with the human Upf complex (UPF1/UPF2/UPF3), a central component of NMD. Tethering RNPS1 to the 3' UTR of beta-globin mRNA triggers NMD, demonstrating its direct role in mRNA surveillance.","method":"Co-immunoprecipitation, tethering assay (MS2 coat protein fusion), NMD reporter assay","journal":"Science (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP plus functional tethering assay demonstrating NMD activation, replicated by subsequent studies","pmids":["11546874"],"is_preprint":false},{"year":2001,"finding":"SART3 (a tumor-rejection antigen/RNA-binding protein) interacts with RNPS1 through the N-terminal domains of RNPS1, as shown by yeast two-hybrid, in vitro pull-down, and co-immunoprecipitation. Co-transfection of SART3 with RNPS1 relocalized SART3 from diffuse nucleoplasmic to nuclear speckled domains. SART3 cooperates with RNPS1 to stimulate proximal alternative 3' splicing.","method":"Yeast two-hybrid, in vitro pull-down, co-immunoprecipitation, immunofluorescence, in vitro splicing assay","journal":"International journal of cancer","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (Y2H, pulldown, co-IP, functional splicing assay), single lab","pmids":["11477570"],"is_preprint":false},{"year":2003,"finding":"Pnn/DRS protein directly interacts with RNPS1; overexpression of the N-terminal fragment of Pnn that binds RNPS1 blocks pre-mRNA splicing. Pnn binds spliced mRNAs immediately upstream of the splice junction. Suppression of Pnn leads to nuclear accumulation of poly(A)+ RNA, suggesting Pnn participates in mRNA export via its interaction with RNPS1.","method":"Co-immunoprecipitation, in vitro splicing assay, oligonucleotide-directed RNase H mapping, heterokaryon export assay, siRNA knockdown","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal biochemical methods in one study, single lab","pmids":["14517304"],"is_preprint":false},{"year":2004,"finding":"Yeast two-hybrid screening identified four RNPS1-interacting factors: p54/SRp54, hTra2β, hLucA, and pinin. Domain mapping showed the S domain interacts with p54, the RRM interacts with pinin, and the C-terminal RS/P domain interacts with hTra2β. Interaction was verified in vitro and in vivo. Overexpression of RNPS1 induced exon skipping in beta-globin and tra-2β pre-mRNAs; co-expression with p54 cooperatively stimulated exon inclusion in ATP synthase γ-subunit pre-mRNA. The RS/P domain and RRM are required for exon-skipping activity; the S domain mediates cooperative effect with p54.","method":"Yeast two-hybrid, in vitro binding, co-immunoprecipitation, domain-deletion/mutation analysis, in vivo splicing reporter assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods, domain-mapping by mutagenesis, functional assays in vivo and in vitro","pmids":["14729963"],"is_preprint":false},{"year":2005,"finding":"RNPS1 incorporates into active spliceosomes and enhances formation of the ATP-dependent A complex, promoting generation of both splicing intermediates and final products. RNPS1 is phosphorylated in vivo by CK2 (casein kinase II), with Ser-53 identified as the major CK2 phosphorylation site in vitro and in vivo. The phosphorylation status of Ser-53 significantly affects splicing activation in vitro and influences splicing and translation efficiencies in vivo, but does not affect nuclear localization.","method":"In vitro spliceosome assembly assay, co-immunoprecipitation with CK2, in vitro kinase assay, site-directed mutagenesis (S53A/S53D), in vivo splicing and translation reporter assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro kinase assay with mutagenesis plus in vivo functional validation, multiple orthogonal methods","pmids":["15684395"],"is_preprint":false},{"year":2007,"finding":"Cellular RNPS1 protein abundance directly modulates NMD efficiency: a HeLa cell strain with low NMD efficiency has reduced RNPS1 levels, and restoration of functional RNPS1 (but not NMD-inactive mutant proteins) rescues efficient NMD.","method":"Quantitative NMD reporter assay, RNPS1 knockdown/rescue, NMD-inactive mutant rescue experiment","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional rescue with wild-type vs. inactive mutant, single lab, two orthogonal methods","pmids":["17586820"],"is_preprint":false},{"year":2007,"finding":"Overexpression of RNPS1 suppresses high-molecular-weight DNA fragmentation, hypermutation, and G2 cell cycle arrest caused by ASF/SF2 depletion. Knockdown of RNPS1 alone leads to accumulation of HMW DNA fragments. RNPS1 does not compensate for ASF/SF2 in splicing, suggesting RNPS1 prevents transcriptional R-loop formation by forming RNP complexes on nascent transcripts.","method":"RNAi knockdown of ASF/SF2 and RNPS1, overexpression rescue assay, DNA fragmentation assay, cell cycle analysis","journal":"RNA (New York, N.Y.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KD and OE with defined phenotypic readouts, single lab","pmids":["17959926"],"is_preprint":false},{"year":2017,"finding":"USP4 (ubiquitin-specific protease 4) is a binding partner of RNPS1 and specifically deubiquitinates K63-linked (but not K48-linked) polyubiquitin chains on RNPS1. SART3 elevates the catalytic activity of USP4 on ubiquitinated RNPS1.","method":"Co-immunoprecipitation, ubiquitination assay, deubiquitinase assay with K48/K63 linkage-specific analysis","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct enzymatic deubiquitinase assay with linkage specificity, single lab","pmids":["27990632"],"is_preprint":false},{"year":2018,"finding":"Knockdown of RNPS1 induces aberrant splicing of AURKB pre-mRNA at upstream pseudo 5' and 3' splice sites in intron 5, reducing wild-type AURKB protein and causing multinucleation. Rescue by ectopic AURKB expression confirmed AURKB as a key functional target. RNPS1 (not as an EJC component) directly binds a specific exonic element upstream of the authentic 5' splice site in AURKB. RNPS1 knockdown also causes parallel aberrant splicing of MDM2 pre-mRNA, indicating a global role in splicing fidelity.","method":"siRNA knockdown, RT-PCR splicing analysis, ectopic rescue experiment, RNA binding/pulldown to identify RNPS1 binding element, cell division phenotype assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KD with rescue, direct RNA binding, multiple phenotypic readouts, single lab","pmids":["29366779"],"is_preprint":false},{"year":2022,"finding":"The main function of RNPS1 is splicing regulation (suppressing cryptic/mis-splicing), with a moderate but non-essential contribution to NMD. RNPS1 core interactome (defined by complementary co-immunoprecipitations and proximity labeling) includes splicing-regulatory factors whose interaction depends on either the C-terminal domain or the RRM domain of RNPS1. Both RRM and C-terminal domain partially contribute to RNPS1-dependent splicing regulation.","method":"Transcriptome-wide RNA-seq after RNPS1/EJC knockdown, complementary co-immunoprecipitation, proximity labeling (BioID), domain-deletion rescue analysis","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (interactome by co-IP and proximity labeling, transcriptome-wide splicing analysis, domain rescue), two human cell lines","pmids":["35640609"],"is_preprint":false},{"year":2022,"finding":"A missense allele (F181I) of mouse Rnps1 causes defective hematopoiesis via stem cell-intrinsic excessive apoptosis driven by TNF-dependent death signaling. Numerous splice variants with retained introns and skipped exons accumulate in Rnps1F181I/F181I cells, but NMD appeared normal. TNF knockout rescued hematopoietic cells to near-normal levels and dramatically reduced intron retention, placing RNPS1 upstream of TNF signaling in the hematopoietic context.","method":"ENU mutagenesis screen, homozygous mouse model, transcriptome analysis (RNA-seq), genetic epistasis (Tnf knockout rescue), flow cytometry of hematopoietic cells","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis with Tnf KO rescue, transcriptome-wide splicing analysis in vivo, well-controlled mouse model","pmids":["35482923"],"is_preprint":false},{"year":2022,"finding":"RNPS1 regulates the alternative splicing of Rac1 pre-mRNA to promote the tumorigenic splice variant Rac1b, and knockdown of RNPS1 in cervical cancer cells causes exon skipping of the RAS domain-encoding exons of RhoA, decreasing RhoA expression. RNPS1-mediated alternative splicing of key targets including MDM4 and WDR1 was also identified.","method":"siRNA knockdown, genome-wide RNA-seq isoform analysis, RT-PCR splicing validation","journal":"IUBMB life","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — transcriptome-wide analysis with RT-PCR validation, single lab, no mutagenesis","pmids":["36300671"],"is_preprint":false},{"year":2023,"finding":"Tethering RNPS1 or its isolated S (serine-rich) domain alone causes exon inclusion of an HIV-1 splicing substrate. Overexpression of the isolated RRM domain acts in a dominant negative manner and causes exon skipping of endogenous apoptotic pre-mRNAs (Bcl-X, MCL-1). Tethering of core EJC proteins (eIF4A3, MAGOH, Y14) does not produce exon inclusion, indicating the splicing activity is RNPS1-specific and not attributable to EJC core components.","method":"Tethering assay, domain overexpression, splicing reporter assay, RT-PCR of endogenous targets","journal":"Genes to cells","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain dissection with tethering and dominant-negative experiments, functional splicing readouts, single lab","pmids":["37204171"],"is_preprint":false},{"year":2024,"finding":"RNPS1 forms the PSAP complex with PNN and SAP18 (distinct from the ASAP complex containing ACIN1 and SAP18), and this PSAP complex is required for precise splicing of AURKB intron 5 and a subset of other introns. RNPS1 protein level oscillates periodically through the cell cycle, coordinating with cyclical splicing of PSAP-controlled introns including AURKB; this periodic decrease in RNPS1 protein is mediated by the ubiquitin-proteasome pathway.","method":"Co-immunoprecipitation (defining PSAP vs ASAP complexes), siRNA knockdown of RNPS1 and PNN, whole-transcriptome RNA-seq, cell-cycle synchronization and protein level analysis, proteasome inhibitor treatment","journal":"iScience","confidence":"High","confidence_rationale":"Tier 2 / Strong — complex composition defined by co-IP, transcriptome-wide splicing analysis, cell-cycle functional linkage with proteasome inhibitor confirmation, multiple orthogonal methods","pmids":["39687031"],"is_preprint":false},{"year":2024,"finding":"RNPS1 directly interacts with NAT10 and inhibits its ubiquitination-mediated degradation by the E3 ubiquitin ligase ZSWIM6, thereby stabilizing NAT10 protein. Elevated NAT10 stability promotes tRNA ac4C modification, which enhances translation of genes in IL-6, IL-8, and PTEN signaling pathways.","method":"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, tRNA ac4C sequencing (TRMC-seq), translation analysis","journal":"International journal of oral science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus ubiquitination assay establishing the protein-protein interaction and stabilization mechanism, single lab","pmids":["38246918"],"is_preprint":false},{"year":2026,"finding":"RNPS1 stabilizes ETV4 mRNA in NSCLC cells; knockdown of RNPS1 destabilizes ETV4 mRNA, and blocking ETV4 expression partially reverses RNPS1-mediated suppression of erastin-triggered ferroptosis (lipid ROS accumulation, malondialdehyde, glutathione depletion).","method":"Lentiviral overexpression/knockdown, erastin-induced ferroptosis assay, lipid ROS/MDA/GSH measurement, ETV4 mRNA stability assay, ETV4 siRNA epistasis","journal":"DNA and cell biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, mRNA stabilization mechanism not deeply characterized at molecular level, epistasis by knockdown only","pmids":["41371758"],"is_preprint":false}],"current_model":"RNPS1 is a multifunctional RNA-binding protein that acts as a general activator and fidelity guardian of pre-mRNA splicing by binding directly to specific exonic elements and nucleating splicing-regulatory complexes (including the PSAP complex with PNN and SAP18), suppresses cryptic splice site usage transcriptome-wide, contributes to nonsense-mediated mRNA decay by bridging the exon junction complex to the UPF surveillance machinery, prevents transcriptional R-loop formation on nascent transcripts, is regulated by CK2-mediated phosphorylation at Ser-53 and by K63-linked deubiquitination via USP4/SART3, undergoes periodic proteasomal degradation to coordinate cell-cycle-dependent splicing of targets like AURKB, and additionally stabilizes the NAT10 protein by blocking its E3 ligase (ZSWIM6)-mediated ubiquitination."},"narrative":{"mechanistic_narrative":"RNPS1 is a multifunctional nuclear RNA-binding protein that acts as a general activator and fidelity guardian of pre-mRNA splicing, originally purified from HeLa cells as a factor that synergizes with SR proteins to activate both constitutive and alternative splicing through an RRM preceded by a serine-rich domain [PMID:10449421]. It incorporates into active spliceosomes and promotes ATP-dependent A-complex formation [PMID:15684395], and works combinatorially with multiple splicing regulators (SART3, pinin/PNN, p54/SRp54, hTra2β) via distinct domains — the S domain, RRM, and C-terminal RS/P domain each engaging different partners to direct exon inclusion or skipping [PMID:11477570, PMID:14729963, PMID:37204171]. Genome-wide, RNPS1 suppresses cryptic and aberrant splicing: it binds a specific exonic element upstream of the authentic 5' splice site of AURKB to enforce correct splicing, with loss causing pseudo-splice-site usage and multinucleation, and it similarly governs splicing fidelity of MDM2, Rac1, RhoA, and other targets [PMID:29366779, PMID:36300671]. This precise splicing function is executed through the PSAP complex (RNPS1–PNN–SAP18), which is required for accurate splicing of AURKB intron 5 and a subset of other introns; RNPS1 protein abundance oscillates through the cell cycle via ubiquitin-proteasome–mediated degradation, coordinating cyclical splicing of PSAP-controlled targets [PMID:39687031]. Independent of splicing, RNPS1 functions in nonsense-mediated mRNA decay as a post-splicing complex component deposited 5' to exon junctions that bridges to the UPF1/UPF2/UPF3 surveillance machinery, and its cellular level directly tunes NMD efficiency [PMID:11546874, PMID:17586820]. RNPS1 activity is post-translationally regulated by CK2-mediated phosphorylation at Ser-53, which modulates splicing activation [PMID:15684395], and by USP4-mediated removal of K63-linked polyubiquitin chains, stimulated by SART3 [PMID:27990632]. A missense Rnps1 allele in mouse causes intron-retention–driven defective hematopoiesis through TNF-dependent apoptosis, establishing RNPS1 upstream of TNF death signaling in vivo [PMID:35482923].","teleology":[{"year":1999,"claim":"Established RNPS1 as a bona fide splicing activator, answering whether it had intrinsic biochemical activity rather than merely associating with the splicing machinery.","evidence":"Biochemical purification from HeLa and reconstituted in vitro splicing assays with baculovirus-expressed recombinant protein","pmids":["10449421"],"confidence":"High","gaps":["Did not define the RNA sequence elements bound","Mechanism of SR-protein synergy not resolved"]},{"year":1998,"claim":"Linked RNPS1 to nuclear speckle architecture and the PITSLRE/CDC2L kinase, situating it within nuclear RNA-processing compartments.","evidence":"In vitro binding, in vivo co-IP, and immunofluorescence localization in human cells","pmids":["9580558"],"confidence":"Medium","gaps":["Functional consequence of PITSLRE interaction unknown","Speckle disruption phenotype mechanism unclear"]},{"year":2001,"claim":"Defined a splicing-independent role for RNPS1 in mRNA surveillance, showing it bridges the post-splicing exon-junction complex to the UPF NMD machinery.","evidence":"Co-IP with UPF1/UPF2/UPF3 and MS2 tethering NMD reporter assays","pmids":["11546874"],"confidence":"High","gaps":["Direct vs. indirect UPF contacts not mapped","Quantitative contribution to global NMD not measured"]},{"year":2001,"claim":"Identified SART3 as a domain-specific partner that cooperates with RNPS1 in alternative 3' splice site selection, beginning the dissection of its combinatorial partnerships.","evidence":"Yeast two-hybrid, pull-down, co-IP, immunofluorescence, and in vitro splicing assay","pmids":["11477570"],"confidence":"Medium","gaps":["Single lab","Endogenous SART3-RNPS1 stoichiometry undefined"]},{"year":2003,"claim":"Established Pnn/PNN as a direct RNPS1 partner coupling splicing to mRNA export.","evidence":"Co-IP, in vitro splicing, RNase H mapping, heterokaryon export assay, and siRNA knockdown","pmids":["14517304"],"confidence":"Medium","gaps":["Direct export role vs. indirect effect not separated","Single lab"]},{"year":2004,"claim":"Mapped RNPS1 domains to specific partners and splicing outcomes, showing it can drive either exon skipping or inclusion depending on cofactor and domain engaged.","evidence":"Yeast two-hybrid, in vitro/in vivo binding, domain-deletion mutagenesis, and splicing reporters","pmids":["14729963"],"confidence":"High","gaps":["Structural basis of domain-specific contacts unknown","Target-element specificity not defined transcriptome-wide"]},{"year":2005,"claim":"Connected RNPS1 to spliceosome assembly and identified CK2 phosphorylation of Ser-53 as a regulatory switch on its splicing activity.","evidence":"In vitro spliceosome assembly assay, CK2 kinase assay, S53A/S53D mutagenesis, and in vivo reporters","pmids":["15684395"],"confidence":"High","gaps":["Upstream signals controlling CK2 phosphorylation unknown","Effect on endogenous targets not surveyed"]},{"year":2007,"claim":"Showed RNPS1 abundance is rate-limiting for NMD efficiency, distinguishing functional from inactive forms.","evidence":"Quantitative NMD reporter with knockdown/rescue using wild-type vs. NMD-inactive mutants","pmids":["17586820"],"confidence":"Medium","gaps":["Which NMD targets are most sensitive not defined","Single cell-line system"]},{"year":2007,"claim":"Revealed a genome-protective role: RNPS1 suppresses DNA fragmentation and is proposed to prevent R-loop formation on nascent transcripts.","evidence":"RNAi of ASF/SF2 and RNPS1, overexpression rescue, DNA fragmentation, and cell-cycle assays","pmids":["17959926"],"confidence":"Medium","gaps":["Direct R-loop detection not performed","Mechanistic link to genome integrity inferred"]},{"year":2018,"claim":"Demonstrated RNPS1 enforces splicing fidelity at specific targets by direct exonic binding, with AURKB mis-splicing causing multinucleation.","evidence":"siRNA knockdown, RT-PCR splicing analysis, RNA binding/pulldown, ectopic AURKB rescue, and division phenotype","pmids":["29366779"],"confidence":"Medium","gaps":["Binding-element consensus not generalized","EJC-independence asserted but not exhaustively tested here"]},{"year":2022,"claim":"Defined RNPS1's primary function transcriptome-wide as suppression of cryptic splicing with a moderate, non-essential NMD contribution, and mapped its core interactome to RRM- and C-terminal-dependent partnerships.","evidence":"RNA-seq after RNPS1/EJC knockdown, co-IP, BioID proximity labeling, and domain-deletion rescue in two human cell lines","pmids":["35640609"],"confidence":"High","gaps":["Individual interactor contributions not deconvolved","Direct vs. proximity-only partners not separated"]},{"year":2022,"claim":"Provided in vivo physiological evidence: a missense Rnps1 allele causes intron-retention-driven hematopoietic failure through TNF-dependent apoptosis.","evidence":"ENU mutagenesis mouse model, RNA-seq, Tnf-knockout genetic epistasis, and flow cytometry","pmids":["35482923"],"confidence":"High","gaps":["How aberrant splicing triggers TNF signaling not resolved","Allele is hypomorphic, not null"]},{"year":2022,"claim":"Extended RNPS1's splicing regulation to oncogenic isoform choices including Rac1b, RhoA, MDM4, and WDR1.","evidence":"siRNA knockdown, genome-wide RNA-seq isoform analysis, and RT-PCR validation","pmids":["36300671"],"confidence":"Medium","gaps":["Direct binding to these targets not shown","Tumor relevance correlative"]},{"year":2023,"claim":"Dissected RNPS1 domain functions in splicing direction, showing the S domain drives exon inclusion while an isolated RRM acts dominant-negative, and confirmed activity is RNPS1-specific rather than EJC-core-derived.","evidence":"Tethering assays with isolated domains, dominant-negative overexpression, and RT-PCR of endogenous apoptotic targets","pmids":["37204171"],"confidence":"Medium","gaps":["Endogenous domain cooperation not reconstituted","Single lab"]},{"year":2024,"claim":"Defined the PSAP complex (RNPS1-PNN-SAP18) as the effector for precise intron splicing and linked cell-cycle-periodic, proteasome-mediated RNPS1 turnover to cyclical splicing of targets like AURKB.","evidence":"Co-IP defining PSAP vs ASAP, siRNA knockdown, whole-transcriptome RNA-seq, cell-cycle synchronization, and proteasome-inhibitor treatment","pmids":["39687031"],"confidence":"High","gaps":["E3 ligase driving cyclical degradation not identified","Structural organization of PSAP not resolved"]},{"year":2024,"claim":"Uncovered a non-RNA role: RNPS1 stabilizes NAT10 by blocking its ZSWIM6-mediated ubiquitination, downstream affecting tRNA ac4C modification and translation.","evidence":"Co-IP, ubiquitination assay, siRNA knockdown, TRMC-seq, and translation analysis","pmids":["38246918"],"confidence":"Medium","gaps":["Mechanism by which RNPS1 shields NAT10 not defined","Single lab"]},{"year":2026,"claim":"Reported RNPS1 stabilization of ETV4 mRNA suppressing erastin-induced ferroptosis in NSCLC.","evidence":"Lentiviral overexpression/knockdown, ferroptosis and lipid-ROS assays, mRNA stability, and ETV4 siRNA epistasis","pmids":["41371758"],"confidence":"Low","gaps":["mRNA stabilization mechanism not characterized molecularly","Epistasis by knockdown only","Single lab, not independently confirmed"]},{"year":null,"claim":"How RNPS1 distinguishes authentic from cryptic splice sites at the level of RNA recognition, and which E3 ligase and signals drive its cell-cycle-periodic degradation, remain unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No structural model of RNPS1 bound to a target exonic element","E3 ligase for periodic RNPS1 turnover unidentified","Mechanistic basis of EJC-independent vs. EJC-associated functions not separated"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,10,11]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,5,14]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,15]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[9,16]}],"localization":[{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[1,3]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,6]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,2,11,15]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,5,10]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[10,15]}],"complexes":["PSAP complex (RNPS1-PNN-SAP18)","exon junction complex (post-splicing complex)"],"partners":["PNN","SAP18","SART3","USP4","UPF2","UPF3","NAT10","CDC2L"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q15287","full_name":"RNA-binding protein with serine-rich domain 1","aliases":["SR-related protein LDC2"],"length_aa":305,"mass_kda":34.2,"function":"Part of pre- and post-splicing multiprotein mRNP complexes. Auxiliary component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junction on mRNAs. The EJC is a dynamic structure consisting of core proteins and several peripheral nuclear and cytoplasmic associated factors that join the complex only transiently either during EJC assembly or during subsequent mRNA metabolism. Component of the ASAP and PSAP complexes which bind RNA in a sequence-independent manner and are proposed to be recruited to the EJC prior to or during the splicing process and to regulate specific excision of introns in specific transcription subsets. The ASAP complex can inhibit RNA processing during in vitro splicing reactions. The ASAP complex promotes apoptosis and is disassembled after induction of apoptosis. Enhances the formation of the ATP-dependent A complex of the spliceosome. Involved in both constitutive splicing and, in association with SRP54 and TRA2B/SFRS10, in distinctive modulation of alternative splicing in a substrate-dependent manner. Involved in the splicing modulation of BCL2L1/Bcl-X (and probably other apoptotic genes); specifically inhibits formation of proapoptotic isoforms such as Bcl-X(S); the activity is different from the established EJC assembly and function. Participates in mRNA 3'-end cleavage. Involved in UPF2-dependent nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. Also mediates increase of mRNA abundance and translational efficiency. Binds spliced mRNA 20-25 nt upstream of exon-exon junctions","subcellular_location":"Nucleus; Nucleus speckle; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q15287/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RNPS1","classification":"Common Essential","n_dependent_lines":1186,"n_total_lines":1208,"dependency_fraction":0.9817880794701986},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"SNRPB","stoichiometry":4.0},{"gene":"SSRP1","stoichiometry":4.0},{"gene":"TOP1","stoichiometry":4.0},{"gene":"CPSF6","stoichiometry":0.2},{"gene":"PRPF4B","stoichiometry":0.2},{"gene":"RBM33","stoichiometry":0.2},{"gene":"RBM39","stoichiometry":0.2},{"gene":"RBM8A","stoichiometry":0.2},{"gene":"RNF40","stoichiometry":0.2},{"gene":"SF3A1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/RNPS1","total_profiled":1310},"omim":[{"mim_id":"617031","title":"PRE-mRNA-PROCESSING FACTOR 38A; PRPF38A","url":"https://www.omim.org/entry/617031"},{"mim_id":"606447","title":"RNA-BINDING PROTEIN S1; RNPS1","url":"https://www.omim.org/entry/606447"}],"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/RNPS1"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q15287","domains":[{"cath_id":"3.30.70.330","chopping":"161-237","consensus_level":"high","plddt":90.7825,"start":161,"end":237}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q15287","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q15287-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q15287-F1-predicted_aligned_error_v6.png","plddt_mean":61.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RNPS1","jax_strain_url":"https://www.jax.org/strain/search?query=RNPS1"},"sequence":{"accession":"Q15287","fasta_url":"https://rest.uniprot.org/uniprotkb/Q15287.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q15287/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q15287"}},"corpus_meta":[{"pmid":"11546874","id":"PMC_11546874","title":"Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1.","date":"2001","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/11546874","citation_count":330,"is_preprint":false},{"pmid":"10449421","id":"PMC_10449421","title":"Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing.","date":"1999","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/10449421","citation_count":128,"is_preprint":false},{"pmid":"17586820","id":"PMC_17586820","title":"The abundance of RNPS1, a protein component of the exon junction complex, can determine the variability in efficiency of the Nonsense Mediated Decay pathway.","date":"2007","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/17586820","citation_count":102,"is_preprint":false},{"pmid":"14729963","id":"PMC_14729963","title":"Human RNPS1 and its associated factors: a versatile alternative pre-mRNA splicing regulator in vivo.","date":"2004","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/14729963","citation_count":92,"is_preprint":false},{"pmid":"9580558","id":"PMC_9580558","title":"The RNP protein, RNPS1, associates with specific isoforms of the p34cdc2-related PITSLRE protein kinase in vivo.","date":"1998","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/9580558","citation_count":83,"is_preprint":false},{"pmid":"14517304","id":"PMC_14517304","title":"Nuclear Pnn/DRS protein binds to spliced mRNPs and participates in mRNA processing and export via interaction with RNPS1.","date":"2003","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/14517304","citation_count":61,"is_preprint":false},{"pmid":"17959926","id":"PMC_17959926","title":"The RNA binding protein RNPS1 alleviates ASF/SF2 depletion-induced genomic instability.","date":"2007","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/17959926","citation_count":53,"is_preprint":false},{"pmid":"15684395","id":"PMC_15684395","title":"Activation of pre-mRNA splicing by human RNPS1 is regulated by CK2 phosphorylation.","date":"2005","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/15684395","citation_count":43,"is_preprint":false},{"pmid":"11477570","id":"PMC_11477570","title":"Binding of a SART3 tumor-rejection antigen to a pre-mRNA splicing factor RNPS1: a possible regulation of splicing by a complex formation.","date":"2001","source":"International journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/11477570","citation_count":30,"is_preprint":false},{"pmid":"38246918","id":"PMC_38246918","title":"RNPS1 stabilizes NAT10 protein to facilitate translation in cancer via tRNA ac4C modification.","date":"2024","source":"International journal of oral science","url":"https://pubmed.ncbi.nlm.nih.gov/38246918","citation_count":16,"is_preprint":false},{"pmid":"35640609","id":"PMC_35640609","title":"Exon junction complex-associated multi-adapter RNPS1 nucleates splicing regulatory complexes to maintain transcriptome surveillance.","date":"2022","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/35640609","citation_count":16,"is_preprint":false},{"pmid":"36300671","id":"PMC_36300671","title":"RNPS1 functions as an oncogenic splicing factor in cervical cancer cells.","date":"2022","source":"IUBMB life","url":"https://pubmed.ncbi.nlm.nih.gov/36300671","citation_count":13,"is_preprint":false},{"pmid":"31831174","id":"PMC_31831174","title":"RNPS1 inhibition aggravates ischemic brain injury and promotes neuronal death.","date":"2019","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/31831174","citation_count":13,"is_preprint":false},{"pmid":"29366779","id":"PMC_29366779","title":"Splicing activator RNPS1 suppresses errors in pre-mRNA splicing: A key factor for mRNA quality control.","date":"2018","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/29366779","citation_count":13,"is_preprint":false},{"pmid":"27990632","id":"PMC_27990632","title":"RNPS1 is modulated by ubiquitin-specific protease 4.","date":"2017","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/27990632","citation_count":12,"is_preprint":false},{"pmid":"35482923","id":"PMC_35482923","title":"RNPS1 inhibits excessive tumor necrosis factor/tumor necrosis factor receptor signaling to support hematopoiesis in mice.","date":"2022","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/35482923","citation_count":11,"is_preprint":false},{"pmid":"39687031","id":"PMC_39687031","title":"RNPS1 in PSAP complex controls periodic pre-mRNA splicing over the cell cycle.","date":"2024","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/39687031","citation_count":3,"is_preprint":false},{"pmid":"35939184","id":"PMC_35939184","title":"Molecular cloning, expression and generation of a polyclonal antibody specific for RNPS1.","date":"2022","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/35939184","citation_count":1,"is_preprint":false},{"pmid":"37705863","id":"PMC_37705863","title":"miR-6893-3p is a bonafide negative regulator of splicing activator, RNPS1.","date":"2023","source":"3 Biotech","url":"https://pubmed.ncbi.nlm.nih.gov/37705863","citation_count":1,"is_preprint":false},{"pmid":"37204171","id":"PMC_37204171","title":"Serine-rich domain of RNPS1 functions in activation of alternative splicing.","date":"2023","source":"Genes to cells : devoted to molecular & cellular mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/37204171","citation_count":0,"is_preprint":false},{"pmid":"41371758","id":"PMC_41371758","title":"RNPS1 Promotes the Progression of Nonsmall Cell Lung Cancer via ETV4-Mediated Ferroptosis.","date":"2026","source":"DNA and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/41371758","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11122,"output_tokens":5013,"usd":0.054281,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":13181,"output_tokens":5038,"usd":0.095927,"stage2_stop_reason":"end_turn"},"total_usd":0.150208,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1999,\n      \"finding\": \"RNPS1 was biochemically purified from HeLa cells as a general activator of pre-mRNA splicing; recombinant RNPS1 expressed in baculovirus functionally synergizes with SR proteins and strongly activates splicing of both constitutively and alternatively spliced pre-mRNAs. RNPS1 contains an RNA-recognition motif (RRM) preceded by a serine-rich domain.\",\n      \"method\": \"Biochemical purification from HeLa cells, baculovirus-expressed recombinant protein in splicing assays, in vitro splicing activation assay\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — direct biochemical purification and reconstituted in vitro splicing assay with recombinant protein\",\n      \"pmids\": [\"10449421\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"RNPS1 specifically interacts in vitro and in vivo with the 110 kDa isoforms (p110) of the PITSLRE protein kinase family (CDC2L). Both RNPS1 and PITSLRE p110 localize to nuclear speckles; overexpression of RNPS1 disrupts normal nuclear speckle organization, causing aggregation into ~6 'mega' speckles.\",\n      \"method\": \"In vitro binding assay, co-immunoprecipitation in vivo, immunofluorescence/subcellular localization\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal in vitro and in vivo interaction confirmed, localization phenotype documented, single lab\",\n      \"pmids\": [\"9580558\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"RNPS1, as a component of the post-splicing complex deposited 5' to exon-exon junctions, interacts with the human Upf complex (UPF1/UPF2/UPF3), a central component of NMD. Tethering RNPS1 to the 3' UTR of beta-globin mRNA triggers NMD, demonstrating its direct role in mRNA surveillance.\",\n      \"method\": \"Co-immunoprecipitation, tethering assay (MS2 coat protein fusion), NMD reporter assay\",\n      \"journal\": \"Science (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP plus functional tethering assay demonstrating NMD activation, replicated by subsequent studies\",\n      \"pmids\": [\"11546874\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"SART3 (a tumor-rejection antigen/RNA-binding protein) interacts with RNPS1 through the N-terminal domains of RNPS1, as shown by yeast two-hybrid, in vitro pull-down, and co-immunoprecipitation. Co-transfection of SART3 with RNPS1 relocalized SART3 from diffuse nucleoplasmic to nuclear speckled domains. SART3 cooperates with RNPS1 to stimulate proximal alternative 3' splicing.\",\n      \"method\": \"Yeast two-hybrid, in vitro pull-down, co-immunoprecipitation, immunofluorescence, in vitro splicing assay\",\n      \"journal\": \"International journal of cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (Y2H, pulldown, co-IP, functional splicing assay), single lab\",\n      \"pmids\": [\"11477570\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Pnn/DRS protein directly interacts with RNPS1; overexpression of the N-terminal fragment of Pnn that binds RNPS1 blocks pre-mRNA splicing. Pnn binds spliced mRNAs immediately upstream of the splice junction. Suppression of Pnn leads to nuclear accumulation of poly(A)+ RNA, suggesting Pnn participates in mRNA export via its interaction with RNPS1.\",\n      \"method\": \"Co-immunoprecipitation, in vitro splicing assay, oligonucleotide-directed RNase H mapping, heterokaryon export assay, siRNA knockdown\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal biochemical methods in one study, single lab\",\n      \"pmids\": [\"14517304\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Yeast two-hybrid screening identified four RNPS1-interacting factors: p54/SRp54, hTra2β, hLucA, and pinin. Domain mapping showed the S domain interacts with p54, the RRM interacts with pinin, and the C-terminal RS/P domain interacts with hTra2β. Interaction was verified in vitro and in vivo. Overexpression of RNPS1 induced exon skipping in beta-globin and tra-2β pre-mRNAs; co-expression with p54 cooperatively stimulated exon inclusion in ATP synthase γ-subunit pre-mRNA. The RS/P domain and RRM are required for exon-skipping activity; the S domain mediates cooperative effect with p54.\",\n      \"method\": \"Yeast two-hybrid, in vitro binding, co-immunoprecipitation, domain-deletion/mutation analysis, in vivo splicing reporter assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods, domain-mapping by mutagenesis, functional assays in vivo and in vitro\",\n      \"pmids\": [\"14729963\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"RNPS1 incorporates into active spliceosomes and enhances formation of the ATP-dependent A complex, promoting generation of both splicing intermediates and final products. RNPS1 is phosphorylated in vivo by CK2 (casein kinase II), with Ser-53 identified as the major CK2 phosphorylation site in vitro and in vivo. The phosphorylation status of Ser-53 significantly affects splicing activation in vitro and influences splicing and translation efficiencies in vivo, but does not affect nuclear localization.\",\n      \"method\": \"In vitro spliceosome assembly assay, co-immunoprecipitation with CK2, in vitro kinase assay, site-directed mutagenesis (S53A/S53D), in vivo splicing and translation reporter assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro kinase assay with mutagenesis plus in vivo functional validation, multiple orthogonal methods\",\n      \"pmids\": [\"15684395\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Cellular RNPS1 protein abundance directly modulates NMD efficiency: a HeLa cell strain with low NMD efficiency has reduced RNPS1 levels, and restoration of functional RNPS1 (but not NMD-inactive mutant proteins) rescues efficient NMD.\",\n      \"method\": \"Quantitative NMD reporter assay, RNPS1 knockdown/rescue, NMD-inactive mutant rescue experiment\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional rescue with wild-type vs. inactive mutant, single lab, two orthogonal methods\",\n      \"pmids\": [\"17586820\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Overexpression of RNPS1 suppresses high-molecular-weight DNA fragmentation, hypermutation, and G2 cell cycle arrest caused by ASF/SF2 depletion. Knockdown of RNPS1 alone leads to accumulation of HMW DNA fragments. RNPS1 does not compensate for ASF/SF2 in splicing, suggesting RNPS1 prevents transcriptional R-loop formation by forming RNP complexes on nascent transcripts.\",\n      \"method\": \"RNAi knockdown of ASF/SF2 and RNPS1, overexpression rescue assay, DNA fragmentation assay, cell cycle analysis\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KD and OE with defined phenotypic readouts, single lab\",\n      \"pmids\": [\"17959926\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"USP4 (ubiquitin-specific protease 4) is a binding partner of RNPS1 and specifically deubiquitinates K63-linked (but not K48-linked) polyubiquitin chains on RNPS1. SART3 elevates the catalytic activity of USP4 on ubiquitinated RNPS1.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, deubiquitinase assay with K48/K63 linkage-specific analysis\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct enzymatic deubiquitinase assay with linkage specificity, single lab\",\n      \"pmids\": [\"27990632\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Knockdown of RNPS1 induces aberrant splicing of AURKB pre-mRNA at upstream pseudo 5' and 3' splice sites in intron 5, reducing wild-type AURKB protein and causing multinucleation. Rescue by ectopic AURKB expression confirmed AURKB as a key functional target. RNPS1 (not as an EJC component) directly binds a specific exonic element upstream of the authentic 5' splice site in AURKB. RNPS1 knockdown also causes parallel aberrant splicing of MDM2 pre-mRNA, indicating a global role in splicing fidelity.\",\n      \"method\": \"siRNA knockdown, RT-PCR splicing analysis, ectopic rescue experiment, RNA binding/pulldown to identify RNPS1 binding element, cell division phenotype assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KD with rescue, direct RNA binding, multiple phenotypic readouts, single lab\",\n      \"pmids\": [\"29366779\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The main function of RNPS1 is splicing regulation (suppressing cryptic/mis-splicing), with a moderate but non-essential contribution to NMD. RNPS1 core interactome (defined by complementary co-immunoprecipitations and proximity labeling) includes splicing-regulatory factors whose interaction depends on either the C-terminal domain or the RRM domain of RNPS1. Both RRM and C-terminal domain partially contribute to RNPS1-dependent splicing regulation.\",\n      \"method\": \"Transcriptome-wide RNA-seq after RNPS1/EJC knockdown, complementary co-immunoprecipitation, proximity labeling (BioID), domain-deletion rescue analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (interactome by co-IP and proximity labeling, transcriptome-wide splicing analysis, domain rescue), two human cell lines\",\n      \"pmids\": [\"35640609\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"A missense allele (F181I) of mouse Rnps1 causes defective hematopoiesis via stem cell-intrinsic excessive apoptosis driven by TNF-dependent death signaling. Numerous splice variants with retained introns and skipped exons accumulate in Rnps1F181I/F181I cells, but NMD appeared normal. TNF knockout rescued hematopoietic cells to near-normal levels and dramatically reduced intron retention, placing RNPS1 upstream of TNF signaling in the hematopoietic context.\",\n      \"method\": \"ENU mutagenesis screen, homozygous mouse model, transcriptome analysis (RNA-seq), genetic epistasis (Tnf knockout rescue), flow cytometry of hematopoietic cells\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis with Tnf KO rescue, transcriptome-wide splicing analysis in vivo, well-controlled mouse model\",\n      \"pmids\": [\"35482923\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RNPS1 regulates the alternative splicing of Rac1 pre-mRNA to promote the tumorigenic splice variant Rac1b, and knockdown of RNPS1 in cervical cancer cells causes exon skipping of the RAS domain-encoding exons of RhoA, decreasing RhoA expression. RNPS1-mediated alternative splicing of key targets including MDM4 and WDR1 was also identified.\",\n      \"method\": \"siRNA knockdown, genome-wide RNA-seq isoform analysis, RT-PCR splicing validation\",\n      \"journal\": \"IUBMB life\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — transcriptome-wide analysis with RT-PCR validation, single lab, no mutagenesis\",\n      \"pmids\": [\"36300671\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Tethering RNPS1 or its isolated S (serine-rich) domain alone causes exon inclusion of an HIV-1 splicing substrate. Overexpression of the isolated RRM domain acts in a dominant negative manner and causes exon skipping of endogenous apoptotic pre-mRNAs (Bcl-X, MCL-1). Tethering of core EJC proteins (eIF4A3, MAGOH, Y14) does not produce exon inclusion, indicating the splicing activity is RNPS1-specific and not attributable to EJC core components.\",\n      \"method\": \"Tethering assay, domain overexpression, splicing reporter assay, RT-PCR of endogenous targets\",\n      \"journal\": \"Genes to cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain dissection with tethering and dominant-negative experiments, functional splicing readouts, single lab\",\n      \"pmids\": [\"37204171\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RNPS1 forms the PSAP complex with PNN and SAP18 (distinct from the ASAP complex containing ACIN1 and SAP18), and this PSAP complex is required for precise splicing of AURKB intron 5 and a subset of other introns. RNPS1 protein level oscillates periodically through the cell cycle, coordinating with cyclical splicing of PSAP-controlled introns including AURKB; this periodic decrease in RNPS1 protein is mediated by the ubiquitin-proteasome pathway.\",\n      \"method\": \"Co-immunoprecipitation (defining PSAP vs ASAP complexes), siRNA knockdown of RNPS1 and PNN, whole-transcriptome RNA-seq, cell-cycle synchronization and protein level analysis, proteasome inhibitor treatment\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — complex composition defined by co-IP, transcriptome-wide splicing analysis, cell-cycle functional linkage with proteasome inhibitor confirmation, multiple orthogonal methods\",\n      \"pmids\": [\"39687031\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RNPS1 directly interacts with NAT10 and inhibits its ubiquitination-mediated degradation by the E3 ubiquitin ligase ZSWIM6, thereby stabilizing NAT10 protein. Elevated NAT10 stability promotes tRNA ac4C modification, which enhances translation of genes in IL-6, IL-8, and PTEN signaling pathways.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, tRNA ac4C sequencing (TRMC-seq), translation analysis\",\n      \"journal\": \"International journal of oral science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus ubiquitination assay establishing the protein-protein interaction and stabilization mechanism, single lab\",\n      \"pmids\": [\"38246918\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"RNPS1 stabilizes ETV4 mRNA in NSCLC cells; knockdown of RNPS1 destabilizes ETV4 mRNA, and blocking ETV4 expression partially reverses RNPS1-mediated suppression of erastin-triggered ferroptosis (lipid ROS accumulation, malondialdehyde, glutathione depletion).\",\n      \"method\": \"Lentiviral overexpression/knockdown, erastin-induced ferroptosis assay, lipid ROS/MDA/GSH measurement, ETV4 mRNA stability assay, ETV4 siRNA epistasis\",\n      \"journal\": \"DNA and cell biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, mRNA stabilization mechanism not deeply characterized at molecular level, epistasis by knockdown only\",\n      \"pmids\": [\"41371758\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RNPS1 is a multifunctional RNA-binding protein that acts as a general activator and fidelity guardian of pre-mRNA splicing by binding directly to specific exonic elements and nucleating splicing-regulatory complexes (including the PSAP complex with PNN and SAP18), suppresses cryptic splice site usage transcriptome-wide, contributes to nonsense-mediated mRNA decay by bridging the exon junction complex to the UPF surveillance machinery, prevents transcriptional R-loop formation on nascent transcripts, is regulated by CK2-mediated phosphorylation at Ser-53 and by K63-linked deubiquitination via USP4/SART3, undergoes periodic proteasomal degradation to coordinate cell-cycle-dependent splicing of targets like AURKB, and additionally stabilizes the NAT10 protein by blocking its E3 ligase (ZSWIM6)-mediated ubiquitination.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RNPS1 is a multifunctional nuclear RNA-binding protein that acts as a general activator and fidelity guardian of pre-mRNA splicing, originally purified from HeLa cells as a factor that synergizes with SR proteins to activate both constitutive and alternative splicing through an RRM preceded by a serine-rich domain [#0]. It incorporates into active spliceosomes and promotes ATP-dependent A-complex formation [#6], and works combinatorially with multiple splicing regulators (SART3, pinin/PNN, p54/SRp54, hTra2\\u03b2) via distinct domains \\u2014 the S domain, RRM, and C-terminal RS/P domain each engaging different partners to direct exon inclusion or skipping [#3, #5, #14]. Genome-wide, RNPS1 suppresses cryptic and aberrant splicing: it binds a specific exonic element upstream of the authentic 5' splice site of AURKB to enforce correct splicing, with loss causing pseudo-splice-site usage and multinucleation, and it similarly governs splicing fidelity of MDM2, Rac1, RhoA, and other targets [#10, #13]. This precise splicing function is executed through the PSAP complex (RNPS1\\u2013PNN\\u2013SAP18), which is required for accurate splicing of AURKB intron 5 and a subset of other introns; RNPS1 protein abundance oscillates through the cell cycle via ubiquitin-proteasome\\u2013mediated degradation, coordinating cyclical splicing of PSAP-controlled targets [#15]. Independent of splicing, RNPS1 functions in nonsense-mediated mRNA decay as a post-splicing complex component deposited 5' to exon junctions that bridges to the UPF1/UPF2/UPF3 surveillance machinery, and its cellular level directly tunes NMD efficiency [#2, #7]. RNPS1 activity is post-translationally regulated by CK2-mediated phosphorylation at Ser-53, which modulates splicing activation [#6], and by USP4-mediated removal of K63-linked polyubiquitin chains, stimulated by SART3 [#9]. A missense Rnps1 allele in mouse causes intron-retention\\u2013driven defective hematopoiesis through TNF-dependent apoptosis, establishing RNPS1 upstream of TNF death signaling in vivo [#12].\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Established RNPS1 as a bona fide splicing activator, answering whether it had intrinsic biochemical activity rather than merely associating with the splicing machinery.\",\n      \"evidence\": \"Biochemical purification from HeLa and reconstituted in vitro splicing assays with baculovirus-expressed recombinant protein\",\n      \"pmids\": [\"10449421\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the RNA sequence elements bound\", \"Mechanism of SR-protein synergy not resolved\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Linked RNPS1 to nuclear speckle architecture and the PITSLRE/CDC2L kinase, situating it within nuclear RNA-processing compartments.\",\n      \"evidence\": \"In vitro binding, in vivo co-IP, and immunofluorescence localization in human cells\",\n      \"pmids\": [\"9580558\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of PITSLRE interaction unknown\", \"Speckle disruption phenotype mechanism unclear\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Defined a splicing-independent role for RNPS1 in mRNA surveillance, showing it bridges the post-splicing exon-junction complex to the UPF NMD machinery.\",\n      \"evidence\": \"Co-IP with UPF1/UPF2/UPF3 and MS2 tethering NMD reporter assays\",\n      \"pmids\": [\"11546874\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct vs. indirect UPF contacts not mapped\", \"Quantitative contribution to global NMD not measured\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Identified SART3 as a domain-specific partner that cooperates with RNPS1 in alternative 3' splice site selection, beginning the dissection of its combinatorial partnerships.\",\n      \"evidence\": \"Yeast two-hybrid, pull-down, co-IP, immunofluorescence, and in vitro splicing assay\",\n      \"pmids\": [\"11477570\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Endogenous SART3-RNPS1 stoichiometry undefined\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Established Pnn/PNN as a direct RNPS1 partner coupling splicing to mRNA export.\",\n      \"evidence\": \"Co-IP, in vitro splicing, RNase H mapping, heterokaryon export assay, and siRNA knockdown\",\n      \"pmids\": [\"14517304\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct export role vs. indirect effect not separated\", \"Single lab\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Mapped RNPS1 domains to specific partners and splicing outcomes, showing it can drive either exon skipping or inclusion depending on cofactor and domain engaged.\",\n      \"evidence\": \"Yeast two-hybrid, in vitro/in vivo binding, domain-deletion mutagenesis, and splicing reporters\",\n      \"pmids\": [\"14729963\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of domain-specific contacts unknown\", \"Target-element specificity not defined transcriptome-wide\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Connected RNPS1 to spliceosome assembly and identified CK2 phosphorylation of Ser-53 as a regulatory switch on its splicing activity.\",\n      \"evidence\": \"In vitro spliceosome assembly assay, CK2 kinase assay, S53A/S53D mutagenesis, and in vivo reporters\",\n      \"pmids\": [\"15684395\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Upstream signals controlling CK2 phosphorylation unknown\", \"Effect on endogenous targets not surveyed\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Showed RNPS1 abundance is rate-limiting for NMD efficiency, distinguishing functional from inactive forms.\",\n      \"evidence\": \"Quantitative NMD reporter with knockdown/rescue using wild-type vs. NMD-inactive mutants\",\n      \"pmids\": [\"17586820\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Which NMD targets are most sensitive not defined\", \"Single cell-line system\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Revealed a genome-protective role: RNPS1 suppresses DNA fragmentation and is proposed to prevent R-loop formation on nascent transcripts.\",\n      \"evidence\": \"RNAi of ASF/SF2 and RNPS1, overexpression rescue, DNA fragmentation, and cell-cycle assays\",\n      \"pmids\": [\"17959926\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct R-loop detection not performed\", \"Mechanistic link to genome integrity inferred\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Demonstrated RNPS1 enforces splicing fidelity at specific targets by direct exonic binding, with AURKB mis-splicing causing multinucleation.\",\n      \"evidence\": \"siRNA knockdown, RT-PCR splicing analysis, RNA binding/pulldown, ectopic AURKB rescue, and division phenotype\",\n      \"pmids\": [\"29366779\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Binding-element consensus not generalized\", \"EJC-independence asserted but not exhaustively tested here\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defined RNPS1's primary function transcriptome-wide as suppression of cryptic splicing with a moderate, non-essential NMD contribution, and mapped its core interactome to RRM- and C-terminal-dependent partnerships.\",\n      \"evidence\": \"RNA-seq after RNPS1/EJC knockdown, co-IP, BioID proximity labeling, and domain-deletion rescue in two human cell lines\",\n      \"pmids\": [\"35640609\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Individual interactor contributions not deconvolved\", \"Direct vs. proximity-only partners not separated\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Provided in vivo physiological evidence: a missense Rnps1 allele causes intron-retention-driven hematopoietic failure through TNF-dependent apoptosis.\",\n      \"evidence\": \"ENU mutagenesis mouse model, RNA-seq, Tnf-knockout genetic epistasis, and flow cytometry\",\n      \"pmids\": [\"35482923\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How aberrant splicing triggers TNF signaling not resolved\", \"Allele is hypomorphic, not null\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Extended RNPS1's splicing regulation to oncogenic isoform choices including Rac1b, RhoA, MDM4, and WDR1.\",\n      \"evidence\": \"siRNA knockdown, genome-wide RNA-seq isoform analysis, and RT-PCR validation\",\n      \"pmids\": [\"36300671\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct binding to these targets not shown\", \"Tumor relevance correlative\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Dissected RNPS1 domain functions in splicing direction, showing the S domain drives exon inclusion while an isolated RRM acts dominant-negative, and confirmed activity is RNPS1-specific rather than EJC-core-derived.\",\n      \"evidence\": \"Tethering assays with isolated domains, dominant-negative overexpression, and RT-PCR of endogenous apoptotic targets\",\n      \"pmids\": [\"37204171\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Endogenous domain cooperation not reconstituted\", \"Single lab\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined the PSAP complex (RNPS1-PNN-SAP18) as the effector for precise intron splicing and linked cell-cycle-periodic, proteasome-mediated RNPS1 turnover to cyclical splicing of targets like AURKB.\",\n      \"evidence\": \"Co-IP defining PSAP vs ASAP, siRNA knockdown, whole-transcriptome RNA-seq, cell-cycle synchronization, and proteasome-inhibitor treatment\",\n      \"pmids\": [\"39687031\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"E3 ligase driving cyclical degradation not identified\", \"Structural organization of PSAP not resolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Uncovered a non-RNA role: RNPS1 stabilizes NAT10 by blocking its ZSWIM6-mediated ubiquitination, downstream affecting tRNA ac4C modification and translation.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, siRNA knockdown, TRMC-seq, and translation analysis\",\n      \"pmids\": [\"38246918\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which RNPS1 shields NAT10 not defined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Reported RNPS1 stabilization of ETV4 mRNA suppressing erastin-induced ferroptosis in NSCLC.\",\n      \"evidence\": \"Lentiviral overexpression/knockdown, ferroptosis and lipid-ROS assays, mRNA stability, and ETV4 siRNA epistasis\",\n      \"pmids\": [\"41371758\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"mRNA stabilization mechanism not characterized molecularly\", \"Epistasis by knockdown only\", \"Single lab, not independently confirmed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RNPS1 distinguishes authentic from cryptic splice sites at the level of RNA recognition, and which E3 ligase and signals drive its cell-cycle-periodic degradation, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural model of RNPS1 bound to a target exonic element\", \"E3 ligase for periodic RNPS1 turnover unidentified\", \"Mechanistic basis of EJC-independent vs. EJC-associated functions not separated\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 10, 11]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 5, 14]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 15]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [9, 16]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 2, 11, 15]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 5, 10]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [10, 15]}\n    ],\n    \"complexes\": [\n      \"PSAP complex (RNPS1-PNN-SAP18)\",\n      \"exon junction complex (post-splicing complex)\"\n    ],\n    \"partners\": [\n      \"PNN\",\n      \"SAP18\",\n      \"SART3\",\n      \"USP4\",\n      \"UPF2\",\n      \"UPF3\",\n      \"NAT10\",\n      \"CDC2L\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}