HNRNPA3

HNRNPA3 is a multifunctional RNA-binding protein that governs post-transcriptional gene regulation through RNA processing, translational control, and protein homeostasis. It binds C9orf72 G4C2 hexanucleotide repeat RNA (both sense and antisense strands) and suppresses dipeptide repeat protein production and RNA foci formation; loss of nuclear HNRNPA3—whether by knockdown or sequestration into poly-GA or mutant FUS inclusions—elevates pathological repeat translation and exacerbates DNA damage in ALS/FTD models (PMID:27461252, PMID:31642962, PMID:36611007, PMID:34915152). HNRNPA3 interacts with CPSF complex components to promote intronic polyadenylation of the differentiation activator GRHL3, thereby maintaining keratinocyte progenitor identity, and functions as an N6-methyladenosine (m6A) reader that recognizes methylated sequences to regulate alternative splicing of AML1-ETO pre-mRNA and translational control of CHOP mRNA during ER stress (PMID:33469008, PMID:38797229, PMID:41902934). Beyond RNA metabolism, HNRNPA3 stabilizes GLI2 protein by blocking FBXW11-mediated ubiquitination to activate Hedgehog signaling in hepatocellular carcinoma, and is itself targeted for autophagic degradation by SARS-CoV-2 N protein, linking its depletion to impaired splicing, DNA damage, and pneumonia severity (PMID:41191267, PMID:39138195).

1. 2016 High

   Identification of HNRNPA3 as a direct binder of C9orf72 G4C2 repeat RNA established it as a nuclear suppressor of pathological repeat translation, answering how repeat RNA levels and DPR production are normally kept in check.

   Evidence siRNA knockdown in primary neurons, tissue culture, and patient fibroblasts with RNA pulldown interaction assay

   PMID:27461252

   Open questions at the time

   • Mechanism by which HNRNPA3 binding reduces repeat RNA levels (degradation vs. export block) not resolved
   • Whether HNRNPA3 acts on repeat RNA co-transcriptionally or post-transcriptionally unknown
2. 2019 High

   Discovery that poly-GA sequesters HNRNPA3 into cytoplasmic inclusions, and that HNRNPA3 binds both sense and antisense repeat RNA, revealed a feed-forward toxicity loop in which DPRs deplete their own suppressor and simultaneously impair DNA damage repair by co-sequestering phospho-ATM.

   Evidence Co-localization and co-IP in patient dentate gyri; siRNA knockdown with DPR and DNA damage quantification across multiple DPR types

   PMID:31642962

   Open questions at the time

   • Whether HNRNPA3 sequestration is reversible in vivo not tested
   • Relative contribution of HNRNPA3 loss vs. pATM sequestration to DNA damage unclear
3. 2021 High

   Demonstrating that HNRNPA3 interacts with the CPSF complex to promote intronic polyadenylation of GRHL3 expanded its role beyond repeat RNA biology to site-specific pre-mRNA 3′-end processing that controls epidermal progenitor maintenance.

   Evidence Targeted genetic screen, CRISPR knockout of GRHL3 IpA site, co-IP of HNRNPA3 with CPSF components in keratinocytes

   PMID:33469008

   Open questions at the time

   • Whether HNRNPA3-CPSF interaction modulates IpA at other loci genome-wide not determined
   • Structural basis of HNRNPA3-CPSF interaction unknown
4. 2021 High

   Identification of HNRNPA3 as specifically enriched in mutant FUS assemblies (but not normal stress granules) demonstrated that ALS-linked FUS mutations co-opt HNRNPA3, and loss of its ortholog potentiates FUS toxicity in Drosophila.

   Evidence Quantitative affinity purification proteomics of mFAs vs. SGs; RNA-dependent co-IP; immunofluorescence in FUS transgenic mice; Drosophila genetic epistasis

   PMID:34915152

   Open questions at the time

   • Which HNRNPA3-dependent RNA processing events are disrupted by FUS sequestration not catalogued
   • Whether HNRNPA3 sequestration into FUS inclusions occurs in human patient tissue not shown
5. 2023 Medium

   In vivo overexpression of HNRNPA3 in a Drosophila C9-ALS/FTD model reduced repeat RNA, RNA foci, DPR accumulation, and neurodegeneration, providing proof-of-concept that restoring HNRNPA3 levels is neuroprotective.

   Evidence Drosophila transgenic overexpression with multi-readout quantification of repeat RNA, foci, DPRs, and neurodegeneration

   PMID:36611007

   Open questions at the time

   • Mammalian in vivo validation of overexpression rescue not yet performed
   • Mechanism by which HNRNPA3 reduces repeat RNA levels still unresolved
6. 2024 Medium

   Three parallel studies broadened HNRNPA3 biology: it was shown to function as an m6A reader regulating AML1-ETO alternative splicing in AML, to be targeted for autophagic degradation by SARS-CoV-2 N protein causing splicing defects and pneumonia, and to interact with PEDV NSP9 while its loss promotes lipid synthesis via SREBF1.

   Evidence Activity-based protein profiling and siRNA in AML cells (PMID:38797229); siRNA/overexpression in mouse pneumonia model with autophagic degradation assays (PMID:39138195); LC-MS/MS NSP9 interactome plus miRNA and lipid assays (PMID:38259103)

   PMID:38259103 PMID:38797229 PMID:39138195

   Open questions at the time

   • Structural basis for m6A recognition by HNRNPA3 not defined
   • Whether autophagic degradation of HNRNPA3 is a general viral immune evasion strategy beyond SARS-CoV-2 unknown
   • PEDV findings rely on single-lab porcine system
7. 2025 Medium

   Discovery that HNRNPA3 stabilizes GLI2 by blocking FBXW11-mediated ubiquitination connected HNRNPA3 to Hedgehog signaling activation and HCC proliferation, revealing a protein-level regulatory function independent of its RNA-binding activities.

   Evidence Co-IP, LC-MS/MS, ubiquitination assays, xenograft mouse model with GANT61 pharmacological rescue

   PMID:41191267

   Open questions at the time

   • Whether HNRNPA3-GLI2 interaction is direct or bridged by RNA not fully excluded
   • Relevance to non-HCC Hedgehog-driven cancers untested
8. 2026 Medium

   Showing that ENDOU-1-dependent nuclear-to-cytoplasmic relocalization enables HNRNPA3 to act as an m6A reader on CHOP mRNA uORFs unified its m6A reader function with ER stress signaling and demonstrated stimulus-dependent compartment switching as a regulatory mechanism.

   Evidence Subcellular fractionation, co-IP with ENDOU-1, m6A reader functional assays and time-course analysis during ER stress

   PMID:41902934

   Open questions at the time

   • Transcriptome-wide scope of HNRNPA3 m6A reading targets not mapped
   • Whether ENDOU-1 directly modifies HNRNPA3 or acts indirectly on its localization unclear

• Key unresolved questions include the structural basis of HNRNPA3's m6A recognition, the genome-wide catalog of its IpA and splicing targets, the mechanism by which it reduces G4C2 repeat RNA levels, and whether its protein-stabilizing function on GLI2 extends to other substrates.
• No crystal/cryo-EM structure of HNRNPA3 bound to m6A or G4C2 RNA
• Genome-wide CLIP-seq or eCLIP map not reported
• In vivo mammalian rescue of C9-ALS phenotypes by HNRNPA3 overexpression not demonstrated