Affinage

RNF125

E3 ubiquitin-protein ligase RNF125 · UniProt Q96EQ8

Length
232 aa
Mass
26.5 kDa
Annotated
2026-06-10
26 papers in source corpus 21 papers cited in narrative 21 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

RNF125 is a membrane-associated RING-type E3 ubiquitin ligase that functions as a negative regulator of innate immune signaling and a tumor suppressor by catalyzing ubiquitin-dependent proteasomal degradation of diverse substrates (PMID:17460044, PMID:28476934). Its catalytic competence requires more than the canonical C3HC4 RING: an adjacent C2HC zinc finger stabilizes the RING fold and is essential for binding the E2 enzyme UbcH5a (with M112 as a critical contact), while a first zinc finger (ZF1) and residues N-terminal to the RING activate the E2~Ub conjugate (PMID:27411375, PMID:37541247). The protein carries a ubiquitin-interacting motif (UIM) that binds polyubiquitin chains, is targeted to membranes and excluded from the nucleus via N-terminal myristoylation, and undergoes rapid RING- and UIM-dependent auto-ubiquitination, giving it a half-life under 30 minutes (PMID:17990982). In innate immunity RNF125 restrains type-I interferon and proinflammatory cytokine output by conjugating ubiquitin to the RIG-I/MDA5/IPS-1 sensing axis and to the mitochondrial adaptor TRIM14, driving their K48-linked degradation; RIG-I is targeted at Lys181 (PMID:17460044, PMID:28476934, PMID:37978243). Beyond immunity, RNF125 ubiquitinates and degrades a broad set of substrates—JAK1, p53, PD-L1, SRSF1, HMGB1, MCM6, and DDX5—to modulate immune checkpoint, oncogenic, and inflammatory outputs across melanoma, hepatocellular carcinoma, and lung and cervical cancers (PMID:26027934, PMID:25591766, PMID:35965501, PMID:37142680, PMID:41605025, PMID:41824200). RNF125 expression is set transcriptionally by the mTORC2/AKT/FOXO1 axis and by NFATC2, and post-transcriptionally by MBNL1 (PMID:37951197, PMID:41329937, PMID:40341413). A Tenorio syndrome–associated UIM variant (p.Glu224Gln) retains ligase activity but loses K63-linked ubiquitin chain binding, linking RNF125 dysfunction to human disease (PMID:37986019).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 2007 High

    Established RNF125 as a bona fide E3 ligase and defined its core biological role as a brake on antiviral innate immunity by degrading the RIG-I/MDA5/IPS-1 sensing machinery.

    Evidence Ubiquitination and proteasome-inhibitor assays with overexpression/knockdown in cell lines

    PMID:17460044

    Open questions at the time
    • Did not resolve ubiquitin chain linkage type
    • Did not map substrate lysine acceptor sites
  2. 2007 Medium

    Showed RNF125 E3 activity is functionally consequential against viral transcription, linking RING integrity to antiviral restriction of HIV-1.

    Evidence RING-domain mutagenesis with reporter and Northern assays in primary PBMCs

    PMID:17643463

    Open questions at the time
    • Direct substrate for HIV-1 transcription restriction not identified
    • Single lab
  3. 2008 High

    Defined the domain architecture and regulatory features of RNF125, explaining its membrane targeting, nuclear exclusion, and short half-life through myristoylation and UIM/RING-dependent auto-ubiquitination.

    Evidence Domain truncation, mutagenesis, fractionation, pulse-chase, and UIM–ubiquitin binding assays

    PMID:17990982

    Open questions at the time
    • UIM chain-linkage specificity assigned to K48 here, later revised toward K63
    • Single lab
  4. 2015 High

    Extended RNF125 substrate repertoire beyond immunity to JAK1 and p53, implicating it in RTK signaling/drug resistance and in suppression of p53-dependent growth control.

    Evidence Reciprocal Co-IP, GST pull-down, ubiquitination assays, knockdown, reporter assays, and xenografts

    PMID:25591766 PMID:26027934

    Open questions at the time
    • Ubiquitin chain linkage on these substrates not fully defined
    • Acceptor lysines not mapped
  5. 2016 High

    Resolved why RNF125 needs more than its RING domain, demonstrating the C2HC zinc finger stabilizes the RING and is required for E2 (UbcH5a) binding.

    Evidence NMR RING–E2 binding, partial X-ray structure, and Cys-to-Ala/M112 mutagenesis

    PMID:27411375

    Open questions at the time
    • Full-length structure not determined
    • Substrate-bound catalytic geometry unresolved
  6. 2017 High

    Broadened immune regulation by showing RNF125 degrades the mitochondrial adaptor TRIM14 via K48 chains and, distinctly, K63-ubiquitinates the IL-36 receptor to drive its trafficking and signaling.

    Evidence Co-IP, linkage-specific ubiquitination assays, KO MEFs, substrate-lysine mutagenesis, and live-cell trafficking

    PMID:28476934 PMID:29176319

    Open questions at the time
    • How RNF125 chooses between K48 (degradative) and K63 (signaling) outputs unclear
    • Context-dependence of receptor activation vs degradation not resolved
  7. 2022 High

    Identified PD-L1 as a degradative RNF125 substrate, positioning RNF125 as a positive regulator of anti-tumor immunity through immune-checkpoint control.

    Evidence Co-IP, K48-specific ubiquitination, KO cell lines, syngeneic tumor models, and flow cytometry

    PMID:35965501

    Open questions at the time
    • PD-L1 acceptor lysines not mapped
    • Relationship to other PD-L1 ligases not addressed
  8. 2023 High

    Completed the mechanistic picture of catalysis by showing ZF1 recruits the E2 and N-terminal residues activate the E2~Ub conjugate, complementing the C2HC role.

    Evidence Structural analysis with mutagenesis and in vitro ubiquitination assays

    PMID:37541247

    Open questions at the time
    • Mechanism of linkage-type selection still unresolved
    • Single lab
  9. 2023 Medium

    Expanded RNF125 substrates and upstream control, identifying SRSF1, HMGB1, MCM6 as degradation targets and NFATC2 as a direct transcriptional activator of RNF125.

    Evidence MS, Co-IP, domain mapping, ubiquitination assays, ChIP/luciferase/DNA pull-down, and in vivo models

    PMID:37142680 PMID:37599832 PMID:37951197 PMID:38298426

    Open questions at the time
    • Each substrate validated in a single disease context
    • Acceptor lysines and chain linkages largely unmapped
  10. 2023 Medium

    Reassigned UIM specificity to K63-linked chains and tied UIM function to human disease through a Tenorio syndrome variant that loses chain binding while retaining catalysis.

    Evidence Disease-variant characterization with in vitro chain-binding and E3 activity assays

    PMID:37986019

    Open questions at the time
    • Downstream consequence of impaired K63 binding for substrate selection unclear
    • Single lab
  11. 2023 Medium

    Mapped a precise RIG-I acceptor site and placed RNF125 downstream of CD97, refining how RNF125 terminates IFN-I signaling at Lys181 of RIG-I.

    Evidence K48-specific ubiquitination, site-directed mutagenesis of RIG-I Lys181, Co-IP, and CD97-deficient mice

    PMID:37978243

    Open questions at the time
    • Generality of K181 targeting across cell types not established
    • Single lab
  12. 2025 Medium

    Defined upstream regulation by mTORC2/AKT/FOXO1 and demonstrated tumor-suppressive function of RNF125 in inducible in vivo HCC models, and added DDX5 and renal RIG-I as substrates with anti-fibrotic/anti-metastatic outputs.

    Evidence Rictor ablation, FOXO1 ChIP, doxycycline-inducible in vivo system, Co-IP/ubiquitination/CHX chase, and xenograft/UUO models

    PMID:40566706 PMID:41329937 PMID:41605025

    Open questions at the time
    • MBNL1 post-transcriptional control rests on a single low-confidence study
    • Integration of transcriptional vs post-transcriptional control of RNF125 not unified

Open questions

Synthesis pass · forward-looking unresolved questions
  • How RNF125 selects between K48-degradative and K63-signaling outputs on different substrates, and how its many substrate engagements are coordinated across tissues, remains unresolved.
  • No unifying model of substrate/linkage selection
  • Most substrates validated in single contexts without cross-validation
  • Structural basis of substrate recognition undetermined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 5 GO:0016740 transferase activity 4 GO:0016874 ligase activity 3 GO:0098772 molecular function regulator activity 3
Localization
GO:0005829 cytosol 1 GO:0005886 plasma membrane 1
Pathway
R-HSA-168256 Immune System 3 R-HSA-392499 Metabolism of proteins 3 R-HSA-1643685 Disease 1
Partners
CD274DDX5JAK1MAVSMDA5RIGITP53TRIM14

Evidence

Reading pass · 21 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2007 RNF125 acts as an E3 ubiquitin ligase that conjugates ubiquitin to RIG-I, MDA5, and IPS-1, targeting them for proteasomal degradation and thereby negatively regulating IFN and cytokine production induced by pathogens. Ubiquitination assay, proteasome inhibitor experiments, overexpression/knockdown in cell lines Proceedings of the National Academy of Sciences of the United States of America High 17460044
2008 RNF125/TRAC-1 is membrane-associated and excluded from the nucleus through N-terminal myristoylation; it contains a C3HC4 RING domain, a C2HC zinc finger, two C2H2 zinc fingers, and a ubiquitin-interacting motif (UIM) that binds K48-linked polyubiquitin chains; the UIM together with the RING domain is required for auto-ubiquitination, which gives RNF125 a half-life shorter than 30 minutes. Domain truncation analysis, mutagenesis, Co-IP, subcellular fractionation, pulse-chase/half-life assay, UIM-ubiquitin binding assay The Biochemical journal High 17990982
2007 RNF125/TRAC-1 down-modulates HIV-1 replication at the viral transcription step in PBMCs and cell lines; mutations in the RING finger domain abolish this activity, indicating that E3 ligase activity is required. RING domain mutagenesis, reporter gene assay, Northern blotting, overexpression in primary PBMCs Virology Medium 17643463
2015 RNF125 physically interacts with JAK1, ubiquitinates it, and promotes its proteasomal degradation, thereby suppressing RTK expression and contributing to BRAF inhibitor resistance in melanoma. Co-IP, ubiquitination assay, overexpression/knockdown, in vivo xenograft Cell reports High 26027934
2015 RNF125 physically interacts with p53, ubiquitinates it, and promotes its proteasomal degradation; a RING domain C72/75A mutation does not abolish p53 binding but is expected to eliminate E3 activity; RNF125 represses p53-dependent transactivation and growth inhibition. Co-IP, GST pull-down, ubiquitination assay, Western blot dose-response, siRNA knockdown, transcriptional reporter assay Cellular physiology and biochemistry Medium 25591766
2016 In addition to the RING domain, the C2HC zinc finger (ZF) of RNF125 is essential for E3 ligase activity because it stabilizes the RING domain and is required for binding to the E2 enzyme UbcH5a; the linker region Li2(120-128) enhances activity; the conserved residue M112 in the C2HC ZF is a critical contact residue whose mutation abolishes ubiquitin ligase activity. Truncated protein activity assays, Cys-to-Ala mutagenesis of zinc-chelating residues, NMR RING–E2 binding assay, partial X-ray crystal structure of RNF125, site-directed mutagenesis of M112 Scientific reports High 27411375
2017 RNF125 interacts with TRIM14, a mitochondrial innate immune adaptor, catalyzes its K48-linked polyubiquitination, and mediates its proteasomal degradation, thereby negatively regulating type-I IFN and proinflammatory cytokine production during viral infection; TRIM14 protein is retained in RNF125-deficient MEFs late after viral infection. Co-IP, ubiquitination assay (K48-linkage specific), RNF125 KO MEFs, overexpression/knockdown Journal of immunology High 28476934
2017 RNF125 co-immunoprecipitates with the IL-36 receptor subunit IL-1Rrp2, ubiquitinates it primarily at K63 (with minor K48), activates IL-36R signaling, and traffics with IL-1Rrp2 from the cell surface to lysosomes; mutations of Lys568 and Lys569 in IL-1Rrp2 decrease ubiquitination by RNF125 and increase its steady-state levels. siRNA screen, Co-IP, ubiquitination assay (K63/K48 specific), site-directed mutagenesis of IL-1Rrp2 lysines, live-cell trafficking/co-localization Journal of innate immunity High 29176319
2022 RNF125 interacts with PD-L1 and promotes its K48-linked polyubiquitination and proteasomal degradation; RNF125 knockout in MC-38 and H22 cells elevates PD-L1 and accelerates tumor growth in syngeneic mice, while overexpression has the opposite effect and increases CD4+/CD8+ T cell and macrophage infiltration. Co-IP, ubiquitination assay, RNF125 KO cell lines, syngeneic in vivo tumor models, flow cytometry Frontiers in oncology High 35965501
2023 The first zinc finger (ZF1) of RNF125 helps recruit the E2 ubiquitin-conjugating enzyme, while residues N-terminal to the RING domain activate the E2~Ub conjugate; this mechanism is distinct from and complementary to the C2HC ZF role in stabilizing the RING. Structural analysis, binding assays, mutagenesis, in vitro ubiquitination activity assays Structure High 37541247
2023 RNF125 interacts with SRSF1 via Co-IP and mass spectrometry, promotes its proteasomal degradation via ubiquitination, thereby inhibiting the ERK signaling pathway and suppressing HCC proliferation and metastasis. Mass spectrometry, Co-IP, ubiquitination assay, overexpression/knockdown in vitro and in vivo Oncogene Medium 37142680
2023 NFATC2 transcription factor directly binds to the RNF125 promoter and regulates its transcription, as demonstrated by luciferase reporter, ChIP, and DNA pull-down assays; RNF125 in turn ubiquitinates and degrades TRIM14 to suppress Wnt/β-catenin signaling in chondrocytes. Luciferase reporter assay, ChIP, DNA pull-down, Co-IP, ubiquitination assay, adenoviral overexpression in vivo International immunopharmacology Medium 37951197
2023 HMGB1 is a substrate of RNF125; RNF125 interacts with the HMG B-box domain of HMGB1 and induces its ubiquitin-proteasome-mediated degradation, thereby attenuating autophagy and oxidative stress in airway epithelial cells. Co-IP, ubiquitination assay, overexpression/knockdown, in vivo mouse asthma model iScience Medium 37599832
2023 A Tenorio syndrome-associated RNF125 variant (p.Glu224Gln) in the UIM retains E3 ligase activity but has impaired ability to interact with K63-linked ubiquitin chains, indicating that the UIM of RNF125 specifically binds K63-linked ubiquitin chains and that this interaction is required for normal RNF125 function. Clinical variant characterization, in vitro ubiquitin-chain binding assay, E3 ligase activity assay Clinical genetics Medium 37986019
2023 CD97 upregulates RNF125 expression after RNA virus infection, and RNF125 then mediates K48-linked ubiquitination of RIG-I specifically at Lys181, leading to its degradation and suppression of IFN-I signaling. Overexpression, Co-IP, K48-linkage-specific ubiquitination assay, site-directed mutagenesis of RIG-I Lys181, CD97-deficient mice Cellular & molecular immunology Medium 37978243
2024 RNF125 directly interacts with MCM6, mediates its ubiquitination, and promotes the proliferation of HCC cells mainly through this MCM6 axis. Pull-down, Co-IP, ubiquitination assay, co-transfection rescue experiments Oncology letters Medium 38298426
2025 RNF125 is a direct transcriptional target of FOXO1 downstream of the mTORC2/AKT/FOXO1 axis; RNF125 overexpression suppresses tumorigenesis in a c-Met/β-catenin HCC model in vivo, and doxycycline-inducible RNF125 expression in established tumors suppresses progression. Genetic ablation of Rictor (mTORC2), FOXO1 ChIP/transcriptional target analysis, doxycycline-inducible in vivo system, in vitro growth assays Hepatology Medium 41329937
2025 In renal tubular epithelial cells, RNF125 interacts with RIG-I (confirmed by Co-IP) and promotes its K48-linked ubiquitination and proteasomal degradation; reduced RNF125 in UUO-induced renal fibrosis leads to RIG-I accumulation, NF-κB p65 phosphorylation, and inflammatory cytokine production. Co-IP, ubiquitination assay, RNF125 overexpression in UUO mouse model, TGF-β treated tubular cells Sheng li xue bao (Acta physiologica Sinica) Medium 40566706
2025 MBNL1 RNA-binding protein increases the stability of the RNF125 transcript in lung adenocarcinoma cells, acting as an upstream post-transcriptional regulator of RNF125 expression. Knockdown/overexpression rescue experiments, RNA stability assay Oncology reports Low 40341413
2026 RNF125 directly binds DDX5, enhances its ubiquitination, and promotes its proteasomal degradation, thereby suppressing stem cell-like properties and metastasis in NSCLC; knockdown of RNF125 reduces DDX5 degradation. Co-IP, ubiquitination assay, cycloheximide chase, rescue co-transfection, xenograft in vivo Pathology, research and practice Medium 41605025
2026 RNF125 promotes K48-linked ubiquitination and proteasomal degradation of PD-L1 in cervical cancer cells, enhancing CD8+ T cell-mediated anti-tumor immunity; RNF125 is identified as a direct target of miR-574-5p. Co-IP, ubiquitination assay, co-culture with CD8+ T cells, in vivo syngeneic tumor model Molecular and cellular biochemistry Medium 41824200

Source papers

Stage 0 corpus · 26 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2007 Negative regulation of the RIG-I signaling by the ubiquitin ligase RNF125. Proceedings of the National Academy of Sciences of the United States of America 402 17460044
2015 MicroRNA-15b Modulates Japanese Encephalitis Virus-Mediated Inflammation via Targeting RNF125. Journal of immunology (Baltimore, Md. : 1950) 97 26202983
2008 T-cell regulator RNF125/TRAC-1 belongs to a novel family of ubiquitin ligases with zinc fingers and a ubiquitin-binding domain. The Biochemical journal 73 17990982
2015 Downregulation of the Ubiquitin Ligase RNF125 Underlies Resistance of Melanoma Cells to BRAF Inhibitors via JAK1 Deregulation. Cell reports 62 26027934
2014 A new overgrowth syndrome is due to mutations in RNF125. Human mutation 32 25196541
2017 The Ubiquitin Ligase RNF125 Targets Innate Immune Adaptor Protein TRIM14 for Ubiquitination and Degradation. Journal of immunology (Baltimore, Md. : 1950) 31 28476934
2022 Down-regulation of circPTTG1IP induces hepatocellular carcinoma development via miR-16-5p/RNF125/JAK1 axis. Cancer letters 25 35710093
2023 CD97 negatively regulates the innate immune response against RNA viruses by promoting RNF125-mediated RIG-I degradation. Cellular & molecular immunology 24 37978243
2022 Ubiquitin ligase RNF125 targets PD-L1 for ubiquitination and degradation. Frontiers in oncology 22 35965501
2016 A C2HC zinc finger is essential for the RING-E2 interaction of the ubiquitin ligase RNF125. Scientific reports 22 27411375
2007 The RING finger ubiquitin ligase RNF125/TRAC-1 down-modulates HIV-1 replication in primary human peripheral blood mononuclear cells. Virology 20 17643463
2023 RNF125 attenuates hepatocellular carcinoma progression by downregulating SRSF1-ERK pathway. Oncogene 18 37142680
2022 E3 Ubiquitin Ligase RNF125 Suppresses Immune Escape in Head and Neck Squamous Cell Carcinoma by Regulating PD-L1 Expression. Molecular biotechnology 17 36344734
2015 RNF125 is a ubiquitin-protein ligase that promotes p53 degradation. Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology 17 25591766
2023 Hypermethylation of RNF125 promotes autophagy-induced oxidative stress in asthma by increasing HMGB1 stability. iScience 12 37599832
2023 RNF125, transcriptionally regulated by NFATC2, alleviates osteoarthritis via inhibiting the Wnt/β-catenin signaling pathway through degrading TRIM14. International immunopharmacology 9 37951197
2017 E3 Ubiquitin Ligase RNF125 Activates Interleukin-36 Receptor Signaling and Contributes to Its Turnover. Journal of innate immunity 9 29176319
2023 Zinc finger 1 of the RING E3 ligase, RNF125, interacts with the E2 to enhance ubiquitylation. Structure (London, England : 1993) 8 37541247
2024 RNF125‑mediated ubiquitination of MCM6 regulates the proliferation of human liver hepatocellular carcinoma cells. Oncology letters 7 38298426
2023 Identification of the Shared Gene Signatures of HCK, NOG, RNF125 and Biological Mechanism in Pediatric Acute Lymphoblastic Leukaemia and Pediatric Sepsis. Molecular biotechnology 6 38123749
2025 Targeting mTORC2-dependent AKT/FOXO1/RNF125 signaling exploits a therapeutic vulnerability in c-MET-activated and β-catenin-mutated hepatocellular carcinoma. Hepatology (Baltimore, Md.) 2 41329937
2025 [Reduction in RNF125-mediated RIG-I ubiquitination and degradation promotes renal inflammation and fibrosis progression]. Sheng li xue bao : [Acta physiologica Sinica] 1 40566706
2026 RNF125 suppresses stem cell-like properties and metastasis in non-small cell lung cancer by promoting ubiquitination and degradation of DDX5. Pathology, research and practice 0 41605025
2026 RNF125 promotes CD8 T cell-mediated anticancer immunity and suppresses the malignant phenotype of cervical cancer. Molecular and cellular biochemistry 0 41824200
2025 RNA‑binding protein MBNL1 regulates tumor growth, chemosensitivity and antitumor immunity in lung adenocarcinoma by controlling the expression of tumor suppressor RNF125. Oncology reports 0 40341413
2023 A novel RNF125 variant associated with Tenorio syndrome alters ubiquitin chain binding. Clinical genetics 0 37986019

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