Affinage

RNPS1

RNA-binding protein with serine-rich domain 1 · UniProt Q15287

Length
305 aa
Mass
34.2 kDa
Annotated
2026-06-10
21 papers in source corpus 18 papers cited in narrative 18 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 7/7 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

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).

Mechanistic history

Synthesis pass · year-by-year structured walk · 17 steps
  1. 1999 High

    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

    PMID:10449421

    Open questions at the time
    • Did not define the RNA sequence elements bound
    • Mechanism of SR-protein synergy not resolved
  2. 1998 Medium

    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

    PMID:9580558

    Open questions at the time
    • Functional consequence of PITSLRE interaction unknown
    • Speckle disruption phenotype mechanism unclear
  3. 2001 High

    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

    PMID:11546874

    Open questions at the time
    • Direct vs. indirect UPF contacts not mapped
    • Quantitative contribution to global NMD not measured
  4. 2001 Medium

    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

    PMID:11477570

    Open questions at the time
    • Single lab
    • Endogenous SART3-RNPS1 stoichiometry undefined
  5. 2003 Medium

    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

    PMID:14517304

    Open questions at the time
    • Direct export role vs. indirect effect not separated
    • Single lab
  6. 2004 High

    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

    PMID:14729963

    Open questions at the time
    • Structural basis of domain-specific contacts unknown
    • Target-element specificity not defined transcriptome-wide
  7. 2005 High

    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

    PMID:15684395

    Open questions at the time
    • Upstream signals controlling CK2 phosphorylation unknown
    • Effect on endogenous targets not surveyed
  8. 2007 Medium

    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

    PMID:17586820

    Open questions at the time
    • Which NMD targets are most sensitive not defined
    • Single cell-line system
  9. 2007 Medium

    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

    PMID:17959926

    Open questions at the time
    • Direct R-loop detection not performed
    • Mechanistic link to genome integrity inferred
  10. 2018 Medium

    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

    PMID:29366779

    Open questions at the time
    • Binding-element consensus not generalized
    • EJC-independence asserted but not exhaustively tested here
  11. 2022 High

    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

    PMID:35640609

    Open questions at the time
    • Individual interactor contributions not deconvolved
    • Direct vs. proximity-only partners not separated
  12. 2022 High

    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

    PMID:35482923

    Open questions at the time
    • How aberrant splicing triggers TNF signaling not resolved
    • Allele is hypomorphic, not null
  13. 2022 Medium

    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

    PMID:36300671

    Open questions at the time
    • Direct binding to these targets not shown
    • Tumor relevance correlative
  14. 2023 Medium

    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

    PMID:37204171

    Open questions at the time
    • Endogenous domain cooperation not reconstituted
    • Single lab
  15. 2024 High

    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

    PMID:39687031

    Open questions at the time
    • E3 ligase driving cyclical degradation not identified
    • Structural organization of PSAP not resolved
  16. 2024 Medium

    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

    PMID:38246918

    Open questions at the time
    • Mechanism by which RNPS1 shields NAT10 not defined
    • Single lab
  17. 2026 Low

    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

    PMID:41371758

    Open questions at the time
    • mRNA stabilization mechanism not characterized molecularly
    • Epistasis by knockdown only
    • Single lab, not independently confirmed

Open questions

Synthesis pass · forward-looking unresolved questions
  • 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.
  • 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

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 3 GO:0140110 transcription regulator activity 3 GO:0060090 molecular adaptor activity 2 GO:0098772 molecular function regulator activity 2
Localization
GO:0005634 nucleus 2 GO:0005654 nucleoplasm 2
Pathway
R-HSA-8953854 Metabolism of RNA 4 R-HSA-74160 Gene expression (Transcription) 3 R-HSA-1640170 Cell Cycle 2
Partners
CDC2LNAT10PNNSAP18SART3UPF2UPF3USP4
Complex memberships
PSAP complex (RNPS1-PNN-SAP18)exon junction complex (post-splicing complex)

Evidence

Reading pass · 18 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1999 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. Biochemical purification from HeLa cells, baculovirus-expressed recombinant protein in splicing assays, in vitro splicing activation assay The EMBO journal High 10449421
1998 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. In vitro binding assay, co-immunoprecipitation in vivo, immunofluorescence/subcellular localization Journal of cell science Medium 9580558
2001 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. Co-immunoprecipitation, tethering assay (MS2 coat protein fusion), NMD reporter assay Science (New York, N.Y.) High 11546874
2001 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. Yeast two-hybrid, in vitro pull-down, co-immunoprecipitation, immunofluorescence, in vitro splicing assay International journal of cancer Medium 11477570
2003 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. Co-immunoprecipitation, in vitro splicing assay, oligonucleotide-directed RNase H mapping, heterokaryon export assay, siRNA knockdown Molecular and cellular biology Medium 14517304
2004 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. Yeast two-hybrid, in vitro binding, co-immunoprecipitation, domain-deletion/mutation analysis, in vivo splicing reporter assays Molecular and cellular biology High 14729963
2005 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. 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 Molecular and cellular biology High 15684395
2007 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. Quantitative NMD reporter assay, RNPS1 knockdown/rescue, NMD-inactive mutant rescue experiment Nucleic acids research Medium 17586820
2007 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. RNAi knockdown of ASF/SF2 and RNPS1, overexpression rescue assay, DNA fragmentation assay, cell cycle analysis RNA (New York, N.Y.) Medium 17959926
2017 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. Co-immunoprecipitation, ubiquitination assay, deubiquitinase assay with K48/K63 linkage-specific analysis FEBS letters Medium 27990632
2018 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. siRNA knockdown, RT-PCR splicing analysis, ectopic rescue experiment, RNA binding/pulldown to identify RNPS1 binding element, cell division phenotype assay Biochemical and biophysical research communications Medium 29366779
2022 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. Transcriptome-wide RNA-seq after RNPS1/EJC knockdown, complementary co-immunoprecipitation, proximity labeling (BioID), domain-deletion rescue analysis Nucleic acids research High 35640609
2022 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. ENU mutagenesis screen, homozygous mouse model, transcriptome analysis (RNA-seq), genetic epistasis (Tnf knockout rescue), flow cytometry of hematopoietic cells Proceedings of the National Academy of Sciences of the United States of America High 35482923
2022 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. siRNA knockdown, genome-wide RNA-seq isoform analysis, RT-PCR splicing validation IUBMB life Medium 36300671
2023 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. Tethering assay, domain overexpression, splicing reporter assay, RT-PCR of endogenous targets Genes to cells Medium 37204171
2024 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. 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 iScience High 39687031
2024 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. Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, tRNA ac4C sequencing (TRMC-seq), translation analysis International journal of oral science Medium 38246918
2026 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). Lentiviral overexpression/knockdown, erastin-induced ferroptosis assay, lipid ROS/MDA/GSH measurement, ETV4 mRNA stability assay, ETV4 siRNA epistasis DNA and cell biology Low 41371758

Source papers

Stage 0 corpus · 21 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2001 Communication of the position of exon-exon junctions to the mRNA surveillance machinery by the protein RNPS1. Science (New York, N.Y.) 330 11546874
1999 Purification and characterization of human RNPS1: a general activator of pre-mRNA splicing. The EMBO journal 128 10449421
2007 The abundance of RNPS1, a protein component of the exon junction complex, can determine the variability in efficiency of the Nonsense Mediated Decay pathway. Nucleic acids research 102 17586820
2004 Human RNPS1 and its associated factors: a versatile alternative pre-mRNA splicing regulator in vivo. Molecular and cellular biology 92 14729963
1998 The RNP protein, RNPS1, associates with specific isoforms of the p34cdc2-related PITSLRE protein kinase in vivo. Journal of cell science 83 9580558
2003 Nuclear Pnn/DRS protein binds to spliced mRNPs and participates in mRNA processing and export via interaction with RNPS1. Molecular and cellular biology 61 14517304
2007 The RNA binding protein RNPS1 alleviates ASF/SF2 depletion-induced genomic instability. RNA (New York, N.Y.) 53 17959926
2005 Activation of pre-mRNA splicing by human RNPS1 is regulated by CK2 phosphorylation. Molecular and cellular biology 43 15684395
2001 Binding of a SART3 tumor-rejection antigen to a pre-mRNA splicing factor RNPS1: a possible regulation of splicing by a complex formation. International journal of cancer 30 11477570
2024 RNPS1 stabilizes NAT10 protein to facilitate translation in cancer via tRNA ac4C modification. International journal of oral science 16 38246918
2022 Exon junction complex-associated multi-adapter RNPS1 nucleates splicing regulatory complexes to maintain transcriptome surveillance. Nucleic acids research 16 35640609
2022 RNPS1 functions as an oncogenic splicing factor in cervical cancer cells. IUBMB life 13 36300671
2019 RNPS1 inhibition aggravates ischemic brain injury and promotes neuronal death. Biochemical and biophysical research communications 13 31831174
2018 Splicing activator RNPS1 suppresses errors in pre-mRNA splicing: A key factor for mRNA quality control. Biochemical and biophysical research communications 13 29366779
2017 RNPS1 is modulated by ubiquitin-specific protease 4. FEBS letters 12 27990632
2022 RNPS1 inhibits excessive tumor necrosis factor/tumor necrosis factor receptor signaling to support hematopoiesis in mice. Proceedings of the National Academy of Sciences of the United States of America 11 35482923
2024 RNPS1 in PSAP complex controls periodic pre-mRNA splicing over the cell cycle. iScience 3 39687031
2023 miR-6893-3p is a bonafide negative regulator of splicing activator, RNPS1. 3 Biotech 1 37705863
2022 Molecular cloning, expression and generation of a polyclonal antibody specific for RNPS1. Molecular biology reports 1 35939184
2026 RNPS1 Promotes the Progression of Nonsmall Cell Lung Cancer via ETV4-Mediated Ferroptosis. DNA and cell biology 0 41371758
2023 Serine-rich domain of RNPS1 functions in activation of alternative splicing. Genes to cells : devoted to molecular & cellular mechanisms 0 37204171

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