Affinage

DDX43

Probable ATP-dependent RNA helicase DDX43 · UniProt Q9NXZ2

Length
648 aa
Mass
72.8 kDa
Annotated
2026-06-09
26 papers in source corpus 13 papers cited in narrative 12 extracted findings
Cross-family judge faithfulness: 7/7 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

DDX43 (HAGE) is an ATP-dependent dual RNA/DNA helicase that couples nucleic-acid unwinding to chromatin remodeling, oncogenic signaling, and antiviral defense (PMID:28468824, PMID:37120627). Biochemically it unwinds RNA with 5'-to-3' polarity and DNA with 3'-to-5' directionality, functioning as a monomer in which the N-terminal K-homology (KH) domain — not the helicase core alone — is required for nucleic-acid binding and full unwinding activity (PMID:28468824). The KH domain preferentially recognizes pyrimidine-rich single-stranded substrates (optimal TTGT/UUGU) through its GXXG loop, thereby imposing sequence specificity and processivity on the full-length enzyme (PMID:33199368). In vivo, DDX43 ATPase/helicase activity is essential for chromatin remodeling during spermiogenesis: testis-specific knockout or an ATPase-dead knock-in mutation causes male infertility through defective histone-to-protamine exchange and post-meiotic condensation, with eCLIP-seq linking DDX43 to RNA regulatory programs in spermatids (Elfn2 hub target) (PMID:37120627). In malignant melanoma-initiating cells, DDX43 promotes oncogenic RAS protein expression (NRAS, KRAS, HRAS) by unwinding RAS mRNAs to drive AKT/ERK signaling and tumor growth and to confer MEK-inhibitor resistance (PMID:22393060, PMID:24899684), and it represses the PML tumor suppressor by promoting SOCS1 expression to inhibit JAK-STAT signaling (PMID:24525737). DDX43 expression is epigenetically controlled by promoter CpG methylation, with demethylation restoring expression in hematological malignancies (PMID:17296563, PMID:24656837, PMID:23495895). DDX43 additionally restricts HSV-2 replication in an interferon-independent manner (PMID:41157636).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 2007 Medium

    Established the regulatory layer controlling DDX43 abundance, showing its expression is set epigenetically rather than constitutively.

    Evidence methylation-specific PCR and bisulfite sequencing in CML cell lines and patient samples

    PMID:17296563 PMID:23495895 PMID:24656837

    Open questions at the time
    • Does not address DDX43 molecular activity or downstream targets
    • Correlative for expression control; trans-acting factors driving methylation not defined
  2. 2012 Medium

    Connected DDX43 helicase activity to a concrete oncogenic output by showing it unwinds NRAS mRNA to sustain AKT/ERK signaling.

    Evidence siRNA knockdown with helicase-dependent NRAS rescue, in vitro unwinding, and NOD/SCID tumor model in melanoma-initiating cells

    PMID:22393060

    Open questions at the time
    • Direct binding of DDX43 to NRAS mRNA not mapped to specific sequence elements
    • Single lab; in vitro unwinding does not establish cellular target selectivity
  3. 2014 Medium

    Extended the oncogenic mechanism to immune evasion, showing DDX43 represses PML via SOCS1-mediated JAK-STAT inhibition, and broadened the RAS axis to MEK-inhibitor resistance.

    Evidence siRNA knockdown with helicase-dependent SOCS1 rescue and xenografts; ectopic DDX43 expression inducing RAS and conferring MEK-inhibitor resistance in uveal melanoma

    PMID:24525737 PMID:24899684

    Open questions at the time
    • Whether RAS and SOCS1 effects share a common mRNA-unwinding mechanism not resolved
    • Single-lab studies; structural basis of mRNA target recognition unaddressed
  4. 2017 High

    Defined the core enzymology, establishing DDX43 as a monomeric dual RNA/DNA helicase with opposite polarities on RNA versus DNA and a KH domain required for activity.

    Evidence purified recombinant protein with helicase/ATPase assays, truncations, and point mutagenesis

    PMID:28468824

    Open questions at the time
    • Physiological DNA versus RNA substrates not defined
    • No high-resolution structure of the full-length enzyme
  5. 2019 Medium

    Tested how the multidomain architecture contributes to binding, finding that all domains must be physically connected for full single-stranded substrate affinity.

    Evidence domain-deletion and domain-disconnection constructs with EMSA and in vitro unwinding

    PMID:31623828

    Open questions at the time
    • Reported guanosine-rich substrate preference and weak unwinding partially conflict with other in vitro studies
    • Single lab; physiological relevance of disconnected-domain behavior unclear
  6. 2020 High

    Resolved the basis of substrate specificity, showing the KH domain reads pyrimidine-rich TTGT/UUGU motifs via its GXXG loop to direct full-length unwinding.

    Evidence EMSA, NMR (15N-HSQC), SELEX, ChIP-seq, CLIP-seq, and GXXG-loop mutagenesis

    PMID:33199368

    Open questions at the time
    • How motif recognition couples to processive unwinding mechanistically not detailed
    • Genome-wide functional targets bearing this motif not validated
  7. 2023 High

    Provided in vivo proof of an essential physiological role, demonstrating that DDX43 ATPase/helicase activity drives chromatin remodeling during spermiogenesis.

    Evidence conditional and global knockout mice, ATPase-dead knock-in phenocopy, scRNA-seq, and eCLIP-seq

    PMID:37120627

    Open questions at the time
    • Mechanism linking RNA targets (e.g. Elfn2) to histone-to-protamine exchange not defined
    • Whether the same RNA-unwinding activity underlies its oncogenic roles untested
  8. 2025 Medium

    Identified an antiviral function, showing human DDX43 restricts HSV-2 replication independently of interferon.

    Evidence reciprocal overexpression and knockdown in HeLa and ARPE-19 cells with viral replication readouts and confirmed IFN independence

    PMID:41157636

    Open questions at the time
    • Molecular mechanism of restriction (target, step inhibited) unknown
    • Single lab; relationship to the fish-ortholog innate-immune adaptor interactions unestablished

Open questions

Synthesis pass · forward-looking unresolved questions
  • It remains unknown whether the in vitro RNA/DNA helicase activity and KH-domain motif recognition mechanistically unify DDX43's distinct roles in spermatid chromatin remodeling, RAS/SOCS1 mRNA regulation in cancer, and antiviral restriction.
  • No structural model of substrate-engaged full-length DDX43
  • Cellular target spectrum and recruitment determinants not mapped across tissues

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003677 DNA binding 2 GO:0003723 RNA binding 2 GO:0016787 hydrolase activity 2 GO:0140098 catalytic activity, acting on RNA 2 GO:0140657 ATP-dependent activity 2 GO:0140097 catalytic activity, acting on DNA 1
Localization
GO:0005829 cytosol 1
Pathway
R-HSA-162582 Signal Transduction 3 R-HSA-1643685 Disease 2 R-HSA-8953854 Metabolism of RNA 2 R-HSA-1474165 Reproduction 1 R-HSA-168256 Immune System 1
Partners
MAVSSOCS1TRIF

Evidence

Reading pass · 12 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2017 DDX43 is an ATP-dependent dual RNA and DNA helicase. It exhibits 5' to 3' polarity on RNA and 3' to 5' directionality on DNA. The N-terminal K-homology (KH) domain is required for nucleic acid binding and full unwinding activity; the C-terminal helicase domain alone has no RNA unwinding activity and significantly reduced DNA unwinding activity. DDX43 exists as a monomer in solution. Purified recombinant protein, in vitro helicase/ATPase assays, truncation mutations, site-directed mutagenesis The Journal of biological chemistry High 28468824
2020 The KH domain of DDX43 preferentially binds pyrimidine-rich ssDNA and ssRNA; the GXXG loop and an adjacent alanine residue are critical for pyrimidine binding. The optimal binding sequence is TTGT/UUGU. The KH domain facilitates substrate sequence specificity and unwinding processivity of the full-length DDX43 helicase. EMSA, NMR (15N-HSQC), SELEX, ChIP-seq, CLIP-seq, mutational analysis of GXXG loop The Journal of biological chemistry High 33199368
2019 Full binding activity of DDX43 to single-stranded DNA or RNA (preferring substrates ≥12 nt and guanosine-rich sequences) requires physical connection of all protein domains; absence or disjunction of any domain reduces binding affinity approximately 10-fold. The unwinding activity of DDX43 in vitro was found to be neither efficient nor sustainable. Recombinant protein expression in E. coli, purification, EMSA, in vitro binding and unwinding assays with domain deletion and disconnection constructs Biochemical and biophysical research communications Medium 31623828
2012 HAGE (DDX43) knockdown in ABCB5+ malignant melanoma-initiating cells reduces NRAS protein expression and decreases AKT and ERK pathway activation, inhibiting tumor growth in vivo. HAGE promotes NRAS mRNA unwinding in vitro, and NRAS expression silenced by siRNA can be rescued by re-introduction of HAGE, confirming dependence on helicase activity. siRNA knockdown, NRAS rescue experiment, in vitro unwinding assay, tumor transplantation in NOD/SCID mice The Journal of biological chemistry Medium 22393060
2014 HAGE (DDX43) prevents PML tumor suppressor expression in ABCB5+ malignant melanoma-initiating cells by promoting SOCS1 expression, which inhibits JAK-STAT pathway activation. HAGE promotes SOCS1 mRNA unwinding in vitro. HAGE knockdown reduces SOCS1, activates JAK-STAT, and increases PML. SOCS1 silenced by siRNA can be rescued by re-introduction of HAGE, confirming helicase-activity dependence. HAGE promotes tumor initiation and growth by preventing anti-proliferative effects of IFN-α. siRNA knockdown, SOCS1 rescue experiment, in vitro mRNA unwinding assay, stem cell proliferation assay, tumor xenotransplantation in NOD/SCID mice Cell death & disease Medium 24525737
2014 Overexpression of DDX43 in MEK inhibitor-resistant uveal melanoma cells mediates resistance by upregulating RAS (KRAS, HRAS, NRAS) protein levels and activating ERK and AKT pathways. Depletion of DDX43 decreases RAS proteins and inhibits downstream signaling. Ectopic expression of DDX43 in parental cells induces RAS protein levels and renders cells resistant to MEK inhibition. siRNA knockdown, ectopic overexpression, Western blotting for pathway activation, analysis of MEK inhibitor-resistant cell lines Molecular cancer therapeutics Medium 24899684
2018 DDX43 overexpression in CML cell lines enhances survival and colony formation and inhibits apoptosis. DDX43 regulates H19 lncRNA expression through demethylation. miR-186 directly targets DDX43 (overexpression of miR-186 increases apoptosis and decreases cell survival). Silencing H19 inhibits cell survival downstream of DDX43. DDX43 overexpression and siRNA knockdown, colony formation assay, apoptosis assay, miRNA-target validation, H19 expression analysis with methylation studies Oncogene Medium 29449695
2023 DDX43 is an essential regulator of chromatin remodeling during spermiogenesis. Testis-specific Ddx43 knockout mice are male-infertile with defective histone-to-protamine replacement and post-meiotic chromatin condensation defects. Loss of ATP hydrolysis activity via a missense mutation replicates the infertility phenotype, demonstrating that ATPase/helicase activity is required. DDX43 regulates dynamic RNA regulatory processes in spermatids, and eCLIP-seq identified Elfn2 as a DDX43-targeted hub gene. Conditional and global knockout mice, ATPase-dead missense mutation knock-in, single-cell RNA-seq, eCLIP-seq, chromatin analysis Nature communications High 37120627
2007 HAGE (DDX43) promoter CpG island methylation status directly correlates with HAGE expression in CML cell lines and patient samples; demethylation of the promoter is associated with gene overexpression, establishing promoter methylation as the epigenetic mechanism controlling HAGE expression. Quantitative methylation-specific PCR, bisulfite sequencing, quantitative RT-PCR in cell lines and patient samples Haematologica Medium 17296563 23495895 24656837
2014 Restoration of DDX43 expression in K562 cells by 5-aza-2'-deoxycytidine (DNA demethylating agent) treatment confirms that promoter methylation directly regulates DDX43 gene expression. 5-aza-2'-deoxycytidine demethylation treatment, quantitative RT-PCR Leukemia research Medium 24656837
2022 In Nile tilapia, OnDDX43 is localized to the cytoplasm and positively regulates IFN-β expression. Pull-down assays showed that OnDDX43 interacts with the antiviral adaptor proteins IPS-1 (MAVS) and TRIF, identifying these as binding partners in the innate immune signaling pathway. Subcellular localization, overexpression in 293T cells, IFN-β reporter assay, pull-down assay Molecular immunology Low 34990938
2025 Human DDX43 overexpression inhibits HSV-2 replication, and knockdown of endogenous DDX43 enhances HSV-2 replication, in an interferon-independent manner. Overexpression and knockdown experiments in HeLa and ARPE-19 cells, viral replication assay, IFN independence confirmed experimentally Viruses Medium 41157636

Source papers

Stage 0 corpus · 26 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2002 Frequent expression of HAGE in presentation chronic myeloid leukaemias. Leukemia 68 12399967
2007 Epigenetic regulation of human cancer/testis antigen gene, HAGE, in chronic myeloid leukemia. Haematologica 44 17296563
2023 Single-cell RNA-seq uncovers dynamic processes orchestrated by RNA-binding protein DDX43 in chromatin remodeling during spermiogenesis. Nature communications 37 37120627
2010 HAGE, a cancer/testis antigen expressed at the protein level in a variety of cancers. Cancer immunity 36 20058853
2017 The DEAD-box protein DDX43 (HAGE) is a dual RNA-DNA helicase and has a K-homology domain required for full nucleic acid unwinding activity. The Journal of biological chemistry 33 28468824
2012 The helicase HAGE expressed by malignant melanoma-initiating cells is required for tumor cell proliferation in vivo. The Journal of biological chemistry 32 22393060
2012 Hydroxybutyrate prevents protein aggregation in the halotolerant bacterium Pseudomonas sp. CT13 under abiotic stress. Extremophiles : life under extreme conditions 32 22527039
2014 Overexpression of DDX43 mediates MEK inhibitor resistance through RAS Upregulation in uveal melanoma cells. Molecular cancer therapeutics 26 24899684
2007 HAGE, a cancer/testis antigen with potential for melanoma immunotherapy: identification of several MHC class I/II HAGE-derived immunogenic peptides. Cancer immunology, immunotherapy : CII 24 17487488
2020 The KH domain facilitates the substrate specificity and unwinding processivity of DDX43 helicase. The Journal of biological chemistry 23 33199368
2018 Arresting of miR-186 and releasing of H19 by DDX43 facilitate tumorigenesis and CML progression. Oncogene 22 29449695
2003 Analysis of the tumour suppressor genes, FHIT and WT-1, and the tumour rejection genes, BAGE, GAGE-1/2, HAGE, MAGE-1, and MAGE-3, in benign and malignant neoplasms of the salivary glands. Molecular pathology : MP 21 12890744
2014 DDX43 promoter is frequently hypomethylated and may predict a favorable outcome in acute myeloid leukemia. Leukemia research 17 24656837
2014 The helicase HAGE prevents interferon-α-induced PML expression in ABCB5+ malignant melanoma-initiating cells by promoting the expression of SOCS1. Cell death & disease 16 24525737
2022 DDX43 recruits TRIF or IPS-1 as an adaptor and activates the IFN-β pathway in Nile tilapia (Oreochromis niloticus). Molecular immunology 10 34990938
2022 Structure-function analysis of DEAD-box helicase DDX43. Methods (San Diego, Calif.) 9 35257897
2021 A Novel HAGE/WT1-ImmunoBody® Vaccine Combination Enhances Anti-Tumour Responses When Compared to Either Vaccine Alone. Frontiers in oncology 7 34262856
2019 DDX43 prefers single strand substrate and its full binding activity requires physical connection of all domains. Biochemical and biophysical research communications 7 31623828
2013 The methylation status of the DDX43 promoter in Chinese patients with chronic myeloid leukemia. Genetic testing and molecular biomarkers 7 23495895
2017 Expression and significance of DDX43 in lung adenocarcinoma. Pakistan journal of pharmaceutical sciences 6 29044003
2021 Helicase antigen (HAGE)-derived vaccines induce immunity to HAGE and ImmunoBody®-HAGE DNA vaccine delays the growth and metastasis of HAGE-expressing tumors in vivo. Immunology and cell biology 5 34105800
2023 DDX43 mRNA expression and protein levels in relation to clinicopathological profile of breast cancer. PloS one 4 37200388
2021 Modification of the multiplex plasmid PCR assay for Borrelia miyamotoi strain LB-2001 based on the complete genome sequence reflecting genomic rearrangements differing from strain CT13-2396. Ticks and tick-borne diseases 3 34656944
2025 Comparative Transcriptomics Analyses Identify DDX43 as a Cellular Regulator Involved in Suppressing HSV-2 Replication. Viruses 1 41157636
2024 Effect of DNMT3A R882H Hot Spot Mutations on DDX43 Promoter Methylation in Acute Myeloid Leukemia. BioMed research international 0 38807916
2024 Correction: DDX43 mRNA expression and protein levels in relation to clinicopathological profile of breast cancer. PloS one 0 39724251

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