HNRNPA3

HNRNPA3 is a nuclear RNA-binding protein that governs RNA processing and translation, with a prominent role in C9orf72-linked neurodegeneration (PMID:27461252, PMID:33469008). It directly binds both sense and antisense GGGGCC repeat RNAs of C9orf72 and negatively regulates repeat RNA levels; reducing nuclear HNRNPA3 increases repeat RNA, dipeptide repeat protein (DPR) production, and DNA double-strand breaks, whereas elevating it in vivo suppresses repeat RNA, RNA foci, DPR accumulation, and neurodegeneration (PMID:27461252, PMID:31642962, PMID:36611007). In disease, the protein is depleted from the nucleus through cytoplasmic sequestration—by poly-GA inclusions and by RNA-dependent recruitment into mutant FUS aggregates—linking its nuclear loss to pathology (PMID:31642962, PMID:29131108, PMID:34915152). Beyond repeat biology, HNRNPA3 shapes mRNA fate through several mechanisms: it physically associates with the CPSF complex to drive site-specific intronic polyadenylation of GRHL3, maintaining keratinocyte progenitor identity (PMID:33469008), and it acts as an m6A reader on AML1-ETO pre-mRNA to regulate alternative splicing in t(8;21) AML and on the CHOP uORF cassette to relieve translational repression during ER stress (PMID:38797229, PMID:41902934). HNRNPA3 also stabilizes GLI2 by blocking FBXW11-mediated ubiquitination, thereby activating Hedgehog signaling to promote hepatocellular carcinoma proliferation (PMID:41191267), and is required for proper alternative splicing of viral RNAs, with its activity targeted by viral proteins through autophagic degradation and SUMOylation [PMID:39138195, PMID:bio_10.1101_2025.03.26.645526]. Its nucleocytoplasmic distribution and activity are regulated by partner proteins including ENDOU-1, which drives cytoplasmic translocation during ER stress (PMID:41902934).

1. 2016 High

   Established that HNRNPA3 directly binds the C9orf72 GGGGCC repeat RNA and acts as a brake on toxic DPR production, defining its first link to ALS/FTD pathology.

   Evidence RNA binding assays plus knockdown in primary neurons and patient fibroblasts with DPR readout and patient tissue immunostaining

   PMID:27461252

   Open questions at the time

   • Mechanism by which binding lowers repeat RNA levels not resolved
   • Does not establish whether the effect is on transcription, stability, or transport
2. 2017 Medium

   Showed HNRNPA3 is specifically mislocalized to the cytoplasm in C9orf72 ALS motor neurons, distinguishing it from related hnRNPA1/A2B1 and implicating nuclear depletion in disease.

   Evidence Immunostaining of patient spinal cord and HNRNPA3 coding-region mutation screen

   PMID:29131108

   Open questions at the time

   • No functional rescue of mislocalization phenotype
   • No causative HNRNPA3 mutation identified
3. 2019 High

   Extended the repeat model to antisense RNA and identified poly-GA-driven cytoplasmic sequestration as the mechanism depleting nuclear HNRNPA3 and exacerbating DNA damage.

   Evidence Antisense RNA binding assays, siRNA knockdown, poly-GA co-localization, and DNA damage foci in patient dentate gyri

   PMID:31642962

   Open questions at the time

   • Causal chain linking nuclear depletion to DNA double-strand breaks not fully defined
   • Sequestration stoichiometry and reversibility unknown
4. 2021 High

   Identified HNRNPA3 as a mutant FUS aggregate-specific component recruited in an RNA-dependent manner, generalizing its sequestration across distinct ALS proteinopathies.

   Evidence Affinity purification/proteomics of mFAs vs stress granules, Co-IP, RNase treatment, and Drosophila genetic epistasis

   PMID:34915152

   Open questions at the time

   • RNA species mediating recruitment not identified
   • Whether sequestration drives or merely accompanies toxicity unresolved
5. 2021 High

   Revealed a physiological RNA-processing role: HNRNPA3 works with the CPSF complex to direct intronic polyadenylation, controlling cell identity in keratinocytes.

   Evidence Genetic screen, CRISPR knockout of GRHL3 IpA site, Co-IP with CPSF, and differentiation assays

   PMID:33469008

   Open questions at the time

   • Direct CPSF subunit contact not mapped
   • Genome-wide scope of HNRNPA3-dependent IpA not defined
6. 2023 Medium

   Demonstrated in vivo that raising HNRNPA3 is protective, confirming it negatively regulates GGGGCC repeat RNA and neurodegeneration.

   Evidence Drosophila transgenic overexpression of human hnRNPA3 with repeat RNA, foci, DPR, and neurodegeneration readouts

   PMID:36611007

   Open questions at the time

   • Single-lab Drosophila model
   • Therapeutic translatability to mammalian neurons untested
7. 2024 Medium

   Defined HNRNPA3 as an m6A reader regulating AML1-ETO splicing and a druggable target via covalent inhibition in leukemia.

   Evidence Covalent probe target ID, m6A reader and splicing assays, and AML differentiation upon neratinib inhibition

   PMID:38797229

   Open questions at the time

   • m6A reader designation is putative
   • Direct m6A-binding interface not structurally defined
8. 2024 Medium

   Showed viral targeting of HNRNPA3 stability, with SARS-CoV-2 N protein driving its autophagic degradation to impair splicing and worsen disease.

   Evidence Autophagy-inhibitor rescue of degradation, knockdown/overexpression in cell and mouse pneumonia models

   PMID:39138195

   Open questions at the time

   • HNRNPA3 studied alongside three other degraded proteins, limiting specific attribution
   • Splicing targets affected not identified
9. 2024 Medium

   Identified HNRNPA3 as a host interactor of PEDV NSP9 that restricts viral replication by limiting lipid synthesis.

   Evidence LC-MS/MS interactor ID, siRNA knockdown, lipid and SREBF1 reporter assays, pathway inhibitor experiments

   PMID:38259103

   Open questions at the time

   • Direct vs indirect control of SREBF1/lipid pathway unclear
   • Single interaction screen without reciprocal validation
10. 2025 High

    Established a non-RNA, protein-stabilizing function: HNRNPA3 binds GLI2 and blocks its FBXW11-mediated ubiquitination to activate Hedgehog signaling in hepatocellular carcinoma.

    Evidence Co-IP, LC-MS/MS, ubiquitination assays, luciferase reporter, proliferation assays, xenograft, and GANT61 rescue

    PMID:41191267

    Open questions at the time

    • How HNRNPA3 sterically blocks FBXW11 not defined
    • Whether RNA binding contributes to GLI2 stabilization unknown
11. 2025 Medium

    Showed HIV-1 Vif induces HNRNPA3 SUMOylation and that HNRNPA3 is required for proper viral RNA splicing and infectivity.

    Evidence Proteome-wide SUMOylation MS screen, biochemical validation, knockdown with splice isoform and infectivity analysis (preprint)

    PMID:bio_10.1101_2025.03.26.645526

    Open questions at the time

    • Functional consequence of SUMOylation on splicing not directly tested
    • Preprint, not yet peer-reviewed
12. 2026 Medium

    Defined regulated nucleocytoplasmic shuttling: ENDOU-1 drives cytoplasmic translocation during ER stress, where HNRNPA3 reads m6A on the CHOP uORF to enable maximal CHOP translation.

    Evidence ENDOU-1 overexpression, subcellular fractionation, m6A reader and uORF reporter assays, Co-IP with ENDOU-1

    PMID:41902934

    Open questions at the time

    • Mechanism by which ENDOU-1 triggers translocation unclear
    • Breadth of cytoplasmic m6A targets undefined

• How HNRNPA3's distinct activities—repeat RNA suppression, intronic polyadenylation, m6A reading, and GLI2 stabilization—are integrated and selectively deployed across cell types and stress states remains unknown.
• No unifying structural or domain-level explanation linking RNA-binding and protein-stabilizing functions
• Determinants of nuclear vs cytoplasmic activity not mechanistically resolved