Affinage

RBM17

Splicing factor 45 · UniProt Q96I25

Length
401 aa
Mass
45.0 kDa
Annotated
2026-06-10
24 papers in source corpus 17 papers cited in narrative 17 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

RBM17 (SPF45) is a UHM-domain spliceosomal RNA-binding protein that regulates both constitutive and alternative pre-mRNA splicing by competitively engaging the UHM-ligand motifs (ULMs) of core splicing factors (PMID:17589525, PMID:34389706). Through its UHM domain it binds ULMs in U2AF65, SF1, and SF3b155 (SF3B1), with each individual UHM-ULM contact required for splicing regulation, as exemplified by FAS exon 6 (PMID:17589525); by competing with the U2AF65 UHM for the SF3b155 ULM, RBM17 initiates spliceosome assembly on a subset of short introns (≥56 nt) with truncated polypyrimidine tracts and activates 3' splice sites for the second catalytic step of splicing (PMID:12015979, PMID:34389706). RBM17 operates within a tight physical complex with U2SURP/SR140 and CHERP, in which the three proteins reciprocally stabilize one another and co-regulate alternative splicing of cell-cycle regulators including FOXM1 and SPDL1, frequently by repressing short exons flanked by suboptimal 3' splice sites; loss of any subunit causes G2/M arrest and apoptosis (PMID:30332651, PMID:34544891). Genome-wide, RBM17 represses cryptic and poison exons: conditional deletion in mouse Purkinje neurons drives rapid neurodegeneration through de-repression of cryptic splicing in genes essential for survival, and constitutive loss is embryonic lethal (PMID:28007900). RBM17 activity is controlled by phosphorylation from ERK2, JNK1, p38, Clk1, and AKT1, which tunes its splicing output and protein stability and links it to oncogenic signaling and cancer stem-cell properties (PMID:22615491, PMID:23519612, PMID:36520054). In malignancy RBM17 sustains pro-leukemic and pro-tumor programs, including production of poison-exon NMD substrates of EIF4A2 in AML (PMID:35781533), and it additionally engages phospho-ATXN1, implicating it in SCA1 pathology (PMID:24858692). Beyond its splicing role, purified RBM17 preferentially binds Holliday-junction DNA and RAD51B, and Drosophila genetics support a conserved DNA-repair function (PMID:20236180, PMID:17154718).

Mechanistic history

Synthesis pass · year-by-year structured walk · 15 steps
  1. 2002 High

    Established RBM17/SPF45 as a splicing factor with a defined catalytic role, answering how a 3' splice site is activated independently of U2AF.

    Evidence in vitro splicing, RNA-protein interaction, and Drosophila Sex-lethal genetics

    PMID:12015979

    Open questions at the time
    • Did not define the structural basis of UHM-ULM recognition
    • Scope of endogenous targets genome-wide unknown
  2. 2006 Medium

    Linked the C-terminus to U2 snRNP association and uncovered a non-splicing genetic interaction with the Rad51 family, raising the possibility of a DNA-repair role.

    Evidence Drosophila genetics, Co-IP (SPF45-U2 snRNP, SPF45-RAD201), bacterial mutagen survival

    PMID:17154718

    Open questions at the time
    • DNA repair evidence is indirect and largely in model organisms
    • Direct DNA substrate not identified here
  3. 2007 High

    Provided the structural mechanism by which the UHM domain selectively reads ULMs in U2AF65, SF1, and SF3b155, and showed each contact is functionally required.

    Evidence 2.1 Å crystal structure of SPF45-UHM/SF3b155-ULM, structure-guided mutagenesis, splicing assays

    PMID:17589525

    Open questions at the time
    • Did not establish how UHM-ULM choice is regulated in cells
    • Genome-wide target set still undefined
  4. 2010 Medium

    Tested whether RBM17 acts directly on DNA, showing purified protein prefers Holliday junctions and binds RAD51B.

    Evidence purified-protein DNA binding assays, deletion/alanine-scanning mutagenesis, RAD51-family pull-downs

    PMID:20236180

    Open questions at the time
    • In vitro binding not connected to a measured HR repair outcome
    • Single-lab study without in vivo validation
  5. 2012 High

    Connected splicing output to oncogenic MAP kinase signaling by identifying ERK2 (Thr71/Ser222), JNK1, and p38 phosphorylation of SPF45.

    Evidence analog-sensitive ERK2 kinase assay, phospho-site mutagenesis, minigene splicing, proliferation/adhesion assays

    PMID:22615491

    Open questions at the time
    • Did not resolve how phosphorylation alters UHM-ULM binding mechanistically
    • FAS and fibronectin EDA are limited target readouts
  6. 2013 High

    Extended phospho-regulation to Clk1, showing it both tunes FAS splicing and stabilizes SPF45 against proteasomal degradation, coupling stability to function.

    Evidence in vitro kinase assay, site-directed mutagenesis, RNA binding, proteasome inhibition, migration/invasion assays

    PMID:23519612

    Open questions at the time
    • Net effect of eight phospho-sites on global splicing not mapped
    • Mechanism of Clk1-dependent stabilization unresolved
  7. 2014 Medium

    Showed RBM17 selectively binds phospho-ATXN1 (pSer776) over the CIC complex, providing a molecular link to SCA1 pathology.

    Evidence structural modeling, mutagenesis, Surface Plasmon Resonance

    PMID:24858692

    Open questions at the time
    • Structure is modeled, not experimentally determined
    • Functional consequence of the interaction in neurons not established
  8. 2016 High

    Defined RBM17's essential physiological role as a repressor of cryptic exons required for neuronal survival, using mouse genetics.

    Evidence constitutive and Purkinje-conditional knockout mice, RNA-seq, CrypSplice analysis, splicing validation

    PMID:28007900

    Open questions at the time
    • RNA features distinguishing cryptic-exon targets not fully defined
    • Link to human neurodegenerative disease not directly tested
  9. 2018 High

    Identified the stable RBM17-U2SURP/SR140-CHERP module and showed mutual stabilization, establishing it as a functional complex rather than transient partners.

    Evidence reciprocal Co-IP, knockdown in mouse and human cells, RNA-seq

    PMID:30332651

    Open questions at the time
    • Stoichiometry and architecture of the complex unknown
    • How the complex selects targets not resolved here
  10. 2021 High

    Resolved the constitutive splicing mechanism (UHM competition with U2AF65 on short, weak-pyrimidine introns) and connected the U2SURP/CHERP complex to cell-cycle gene splicing and proliferation control.

    Evidence siRNA screen, transcriptome-wide depletion, competition binding assays; Co-IP, minigene assays, cell-cycle/apoptosis assays

    PMID:34389706 PMID:34544891

    Open questions at the time
    • Determinants directing competition outcome at individual introns unclear
    • FOXM1/SPDL1 only partially explain the proliferation phenotype
  11. 2021 Medium

    Showed RBM17 protein levels and localization are controlled by a small RNA (tiRNA-Gly) binding the UHM domain, adding a post-transcriptional regulatory input.

    Evidence RNA pull-down, RIP, IF, proteasome inhibition, MAP4K4 splicing assay, xenograft

    PMID:34225773

    Open questions at the time
    • Generality of small-RNA regulation of RBM17 unknown
    • Single-lab study
  12. 2022 High

    Demonstrated RBM17 sustains the leukemic state by repressing poison exons in pro-leukemic factors such as EIF4A2, preventing NMD and ribosome-biogenesis collapse.

    Evidence shRNA in primary AML, RNA-seq + proteomics, in vivo engraftment, EIF4A2 inhibition

    PMID:35781533

    Open questions at the time
    • Full set of poison-exon targets driving the phenotype not enumerated
    • Selectivity for leukemic versus normal stem cells unresolved
  13. 2023 Medium

    Identified AKT1 phosphorylation of RBM17 as the signal coupling FOXM1 splicing to cancer stem-cell properties and Sox2 expression.

    Evidence AKT1 kinase/phospho studies, splicing assays, overexpression/knockdown, CSC marker flow cytometry, sphere formation

    PMID:36520054

    Open questions at the time
    • AKT1 phospho-sites on RBM17 not precisely mapped here
    • Single-lab study in colorectal cells
  14. 2025 Medium

    Placed RBM17 in chemoresistance and tumor-immune programs, upstream of CHEK1 and as a RUNX1 target controlling metabolic splicing that shapes macrophage and T-cell infiltration.

    Evidence siRNA + CHEK1 inhibition epistasis; multi-omics, RUNX1 ChIP, scRNA-seq, metabolomics, splicing validation

    PMID:40243905 PMID:40702000

    Open questions at the time
    • Direct splicing targets mediating CHEK1 regulation not defined
    • Single-lab studies for each context
  15. 2005 Low

    Reported an RBM17-ERβ physical association correlated with multidrug resistance, a context not mechanistically integrated with its splicing role.

    Evidence Co-IP, qPCR isoform analysis, cytotoxicity and ribozyme knockdown in A2780 cells

    PMID:16061639

    Open questions at the time
    • Single Co-IP without reciprocal validation
    • Causal link between the interaction and drug resistance not established

Open questions

Synthesis pass · forward-looking unresolved questions
  • How RBM17's competing biochemical activities — UHM-ULM splicing regulation versus direct Holliday-junction/RAD51B DNA binding — are coordinated, and whether the DNA-repair function operates in vertebrate cells, remains unresolved.
  • No structure of full-length RBM17 in any complex
  • DNA-repair role not validated in human cells with a measured repair outcome
  • Rules governing which ULM the UHM engages in a given context unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140098 catalytic activity, acting on RNA 5 GO:0003723 RNA binding 4 GO:0060090 molecular adaptor activity 3 GO:0003677 DNA binding 1
Localization
GO:0005634 nucleus 2 GO:0005829 cytosol 1
Pathway
R-HSA-8953854 Metabolism of RNA 6 R-HSA-1643685 Disease 2 R-HSA-1640170 Cell Cycle 1
Partners
ATXN1CHERPESR2RAD51BSF1SF3B1U2AF2U2SURP
Complex memberships
RBM17-U2SURP(SR140)-CHERP complexU2 snRNP

Evidence

Reading pass · 17 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2007 The UHM domain of SPF45/RBM17 binds UHM-ligand motifs (ULMs) present in U2AF65, SF1, and SF3b155, and this interaction is required for SPF45-dependent alternative splicing of FAS exon 6. Crystal structure (2.1 Å) of SPF45-UHM in complex with a SF3b155 ULM peptide revealed features distinct from other UHM-ULM complexes, enabling design of mutations that selectively impair binding to individual ULMs; these ULM-selective variants demonstrated that individual UHM-ULM interactions are each required for FAS splicing regulation in vivo. X-ray crystallography (2.1 Å), structure-guided mutagenesis, in vitro and in vivo splicing assays, protein-protein interaction binding assays Nature structural & molecular biology High 17589525
2002 SPF45/RBM17 interacts with the upstream AG dinucleotide at the 3' splice site and activates it specifically for the second catalytic step of splicing; interaction of SPF45 with Sex-lethal (SXL) blocks this second step. U2AF binds the polypyrimidine tract and downstream AG independently. SPF45 also activates a cryptic 3' splice site generated by a beta-thalassemia mutation, establishing it as a second-step splicing factor. In vitro splicing assays, RNA-protein interaction assays, genetic interaction with Sex-lethal in Drosophila, spliceosome assembly analysis Cell High 12015979
2021 SPF45/RBM17 functions as a constitutive splicing factor required for efficient splicing of a distinct subset of short introns (≥56 nt) with truncated polypyrimidine tracts. The UHM domain of SPF45 competes with that of U2AF65 for binding to the ULM of SF3b155 (SF3B1) to initiate spliceosome assembly on these short introns; transcriptome-wide depletion of SPF45 confirmed global impairment of short intron splicing. siRNA screen of 154 nuclear proteins, splicing assays with HNRNPH1 model pre-mRNA, whole-transcriptome sequencing of SPF45-deficient cells, protein-protein competition binding assays Nature communications High 34389706
2018 RBM17 physically interacts with the spliceosomal factors U2SURP (SR140) and CHERP; the three proteins reciprocally regulate each other's protein stability in both mouse and human cells. Individual knockdown of any one of the three factors produces overlapping changes in splicing and gene expression enriched for RNA-processing factors. Co-immunoprecipitation (reciprocal), knockdown studies in mouse and human cells, RNA-seq transcriptome profiling Cell reports High 30332651
2021 SPF45/RBM17, SR140/U2SURP, and CHERP form a tight physical complex that regulates alternative splicing of cell-cycle genes, including FOXM1 and SPDL1, frequently by repressing short exons flanked by suboptimal 3' splice sites. Knockdown of any of the three factors causes G2/M arrest and enhanced apoptosis in HeLa cells; promoting splicing changes in FOXM1 or SPDL1 alone partially recapitulates the anti-proliferative effect. Co-immunoprecipitation to establish complex, siRNA knockdown, minigene splicing assays, cell-cycle analysis, apoptosis assays RNA (New York, N.Y.) High 34544891
2016 Constitutive deletion of Rbm17 causes early embryonic lethality in mice; conditional loss in Purkinje neurons leads to rapid neurodegeneration. Transcriptome profiling revealed that RBM17 represses cryptic exon splicing in genes required for motor coordination and cell survival, with >50% of RBM17-dependent splicing changes being cryptic events. Conditional knockout mouse models, whole-transcriptome RNA-seq, computational CrypSplice analysis, splicing validation assays Human molecular genetics High 28007900
2012 ERK2 phosphorylates SPF45/RBM17 on Thr71 and Ser222 in vitro and in cells in response to oncogenic signals (H-RasV12, B-RAF-V600E, activated MEK1). JNK1 and p38α also phosphorylate SPF45 in vitro and associate with it in cells. ERK and p38 activation decreases SPF45-dependent exon 6 exclusion from FAS mRNA. SPF45 overexpression inhibits cell proliferation and induces fibronectin EDA inclusion in a phosphorylation-dependent manner, affecting adhesion to fibronectin. Analog-sensitive ERK2 kinase assay (in vitro phosphorylation), co-immunoprecipitation, minigene splicing assay, mutagenesis of phosphorylation sites, stable overexpression in SKOV-3 cells, proliferation and adhesion assays Molecular and cellular biology High 22615491
2013 Clk1 phosphorylates SPF45/RBM17 on eight serine residues. Clk1 expression enhances, whereas Clk1 inhibition reduces, SPF45-induced exon 6 exclusion from FAS mRNA. Mutational analysis shows both positive and negative regulatory sites, with net inhibition of FAS exon 6 exclusion correlating with reduced FAS mRNA binding. Clk1 also stabilizes SPF45 protein through a proteasome-dependent pathway. SPF45 overexpression or phospho-mimetic (but not phospho-inhibitory) mutant stimulates ovarian cancer cell migration and invasion, correlating with increased fibronectin expression, ERK activation, and altered cortactin splicing. In vitro kinase assay, site-directed mutagenesis, minigene splicing assay, RNA binding assay, proteasome inhibitor treatment, cell migration/invasion assays (transwell), Western blotting Nucleic acids research High 23519612
2006 Drosophila SPF45 associates with the U2 snRNP; mutations removing the C-terminal end disrupt this interaction and impair Sex-lethal splicing regulation in vivo. SPF45 also genetically and physically interacts with RAD201 (a RecA/Rad51 family member), and flies carrying C-terminal mutations exhibit phenotypes indicative of impaired DNA damage recovery. SPF45 increases bacterial survival after mutagen treatment in RecG-deficient bacteria, demonstrating a conserved role in DNA repair. Genetic analysis of Drosophila mutants, co-immunoprecipitation (SPF45–U2 snRNP and SPF45–RAD201), in vivo splicing assay (Sex-lethal), bacterial survival assay after mutagen treatment PLoS genetics Medium 17154718
2010 Purified human SPF45/RBM17 preferentially binds Holliday junction DNA structures, suggesting a role in homologous recombination-based DNA repair. The RNA recognition motif (C-terminal) is not required for DNA binding; N-terminal lysine residues are important for Holliday junction binding. SPF45 binds RAD51B with significant affinity (and RAD51 and DMC1 with lower affinity). Protein purification, DNA binding assays with defined DNA substrates (Holliday junctions, duplexes, etc.), deletion and alanine-scanning mutagenesis, pull-down binding assays with RAD51 family proteins Genes to cells : devoted to molecular & cellular mechanisms Medium 20236180
2014 RBM17 physically interacts with phosphorylated Ataxin-1 (ATXN1 pSer776) but not unphosphorylated ATXN1. Modeled structure of RBM17 bound to the phospho-ATXN1 peptide reveals a phosphorylation-specific salt-bridge network mediating the interaction. Mutagenesis of predicted contact residues in RBM17 validated by Surface Plasmon Resonance confirmed the structural model. Polyglutamine-expanded ATXN1 preferentially forms a complex with RBM17 over the CIC complex. Structural modeling, site-directed mutagenesis, Surface Plasmon Resonance (SPR) binding assay Biochemical and biophysical research communications Medium 24858692
2022 RBM17 knockdown in primary AML cells leads to inclusion of poison exons and production of NMD-sensitive transcripts for pro-leukemic factors including EIF4A2, promoting myeloid differentiation and impairing colony formation and in vivo engraftment. EIF4A2 is enriched in leukemic stem cells and its inhibition recapitulates RBM17 knockdown effects including suppression of ribosome biogenesis proteins. shRNA knockdown in primary AML cells, integrative multi-omics (RNA-seq + proteomics), in vivo engraftment assay, EIF4A2 inhibitor treatment, proteomic analysis Nature communications High 35781533
2023 AKT1 phosphorylates RBM17 and controls RBM17-mediated alternative splicing of FOXM1 pre-mRNA; this phosphorylation is required for RBM17-enhanced cancer stem cell properties (CD133+/ALDEFLUOR+ populations, sphere formation) and Sox2 expression in colorectal cancer cells. RBM17 enhances FOXM1 expression through alternative splicing to promote Sox2 transcription. AKT1 kinase assay/phosphorylation studies, alternative splicing assay (minigene or endogenous), RBM17 overexpression/knockdown, flow cytometry for CSC markers, sphere formation assay FASEB journal Medium 36520054
2005 SPF45/RBM17 co-immunoprecipitates with ERβ (estrogen receptor beta) in A2780 ovarian carcinoma cells, suggesting a physical interaction. Selective estrogen receptor modulators (tamoxifen, LY117018) partially reverse SPF45-mediated multidrug resistance, with ERβ (but not ERα) expressed in these cells. Co-immunoprecipitation, quantitative PCR for ER isoforms, cytotoxicity assay, ribozyme-mediated knockdown Cancer research Low 16061639
2025 RBM17 knockdown in oral cancer cells reduces CHEK1 (checkpoint kinase 1) protein expression and sensitizes cells to 5-FU but not paclitaxel. Conversely, 5-FU and cisplatin exposure increases RBM17 gene and protein expression. CHEK1 inhibition does not affect RBM17 protein expression, placing RBM17 upstream of CHEK1 in the ATM/ATR pathway for chemoresistance. siRNA knockdown, Western blotting, cell viability assay, CHEK1 inhibitor treatment, qRT-PCR International journal of molecular sciences Medium 40243905
2025 RBM17 regulates alternative splicing of CSAD pre-mRNA (exon exclusion) to promote taurocholic acid (T-CA) production, leading to M2 macrophage infiltration in HCC. RBM17 also regulates exon skipping in HACD3 pre-mRNA to modulate fatty acid metabolism and CD8+ T cell infiltration. RUNX1 activates RBM17 transcription and regulates downstream CSAD/T-CA and HACD3/FFA signaling. Label-free proteomics, RNA-seq, ChIP (RUNX1 binding to RBM17 promoter), single-cell RNA-seq, flow cytometry, LC-MS/MS metabolomics, multiparametric immunofluorescence, splicing validation assays Cell death discovery Medium 40702000
2021 tiRNA-Gly directly binds the UHM domain of RBM17, causing translocation of RBM17 from cytoplasm to nucleus, inhibiting RBM17 ubiquitin/proteasome-dependent degradation (increasing RBM17 protein levels), and inducing RBM17-dependent exon 16 inclusion in MAP4K4 mRNA leading to downstream phosphorylation signaling. RNA pull-down, RNA immunoprecipitation (RIP), Western blot, immunofluorescence, UHM domain interaction mapping, MAP4K4 splicing assay, ubiquitin/proteasome inhibitor treatment, in vivo xenograft model Journal of experimental & clinical cancer research Medium 34225773

Source papers

Stage 0 corpus · 24 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2007 U2AF-homology motif interactions are required for alternative splicing regulation by SPF45. Nature structural & molecular biology 145 17589525
2002 Splicing regulation at the second catalytic step by Sex-lethal involves 3' splice site recognition by SPF45. Cell 129 12015979
2016 Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models. Human molecular genetics 86 28007900
2021 A 5'-tRNA halve, tiRNA-Gly promotes cell proliferation and migration via binding to RBM17 and inducing alternative splicing in papillary thyroid cancer. Journal of experimental & clinical cancer research : CR 66 34225773
2003 Human SPF45, a splicing factor, has limited expression in normal tissues, is overexpressed in many tumors, and can confer a multidrug-resistant phenotype to cells. The American journal of pathology 65 14578179
2013 Phosphorylation of the alternative mRNA splicing factor 45 (SPF45) by Clk1 regulates its splice site utilization, cell migration and invasion. Nucleic acids research 60 23519612
2012 Mitogen-activated protein kinase phosphorylation of splicing factor 45 (SPF45) regulates SPF45 alternative splicing site utilization, proliferation, and cell adhesion. Molecular and cellular biology 55 22615491
2018 RBM17 Interacts with U2SURP and CHERP to Regulate Expression and Splicing of RNA-Processing Proteins. Cell reports 53 30332651
2005 Human splicing factor SPF45 (RBM17) confers broad multidrug resistance to anticancer drugs when overexpressed--a phenotype partially reversed by selective estrogen receptor modulators. Cancer research 36 16061639
2021 SPF45/RBM17-dependent, but not U2AF-dependent, splicing in a distinct subset of human short introns. Nature communications 29 34389706
2021 Alternative splicing regulation of cell-cycle genes by SPF45/SR140/CHERP complex controls cell proliferation. RNA (New York, N.Y.) 24 34544891
2006 Drosophila SPF45: a bifunctional protein with roles in both splicing and DNA repair. PLoS genetics 24 17154718
2022 The splicing factor RBM17 drives leukemic stem cell maintenance by evading nonsense-mediated decay of pro-leukemic factors. Nature communications 23 35781533
2018 RBM17 controls apoptosis and proliferation to promote Glioma progression. Biochemical and biophysical research communications 14 30227940
2020 Exploration of the effects of the CYCLOPS gene RBM17 in hepatocellular carcinoma. PloS one 10 32497093
2014 Structural basis of the phosphorylation dependent complex formation of neurodegenerative disease protein Ataxin-1 and RBM17. Biochemical and biophysical research communications 10 24858692
2023 AKT1 phosphorylates RBM17 to promote Sox2 transcription by modulating alternative splicing of FOXM1 to enhance cancer stem cell properties in colorectal cancer cells. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 7 36520054
2010 Holliday junction-binding activity of human SPF45. Genes to cells : devoted to molecular & cellular mechanisms 7 20236180
2023 RBM17 Expression Is Associated With the Efficacy of ICI Monotherapy in NSCLC With Low PD-L1 Expression. Anticancer research 5 37772582
2023 Downregulation of RBM17 enhances cisplatin sensitivity and inhibits cell invasion in human hypopharyngeal cancer cells. Open medicine (Warsaw, Poland) 4 36941989
2024 Integrating single cell and bulk RNA sequencing data identifies RBM17 as a novel response biomarker for immunotherapy in bladder cancer. Virchows Archiv : an international journal of pathology 2 39453457
2021 SPF45/RBM17-dependent splicing and multidrug resistance to cancer chemotherapy. Molecular & cellular oncology 2 35419480
2025 RBM17 Promotes the Chemoresistance of Oral Squamous Cancer Cells Through Checkpoint Kinase 1. International journal of molecular sciences 1 40243905
2025 RBM17 promotes hepatocellular carcinoma progression by regulating lipid metabolism and immune microenvironment: implications for therapeutic targeting. Cell death discovery 1 40702000

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