Affinage

DDX54

ATP-dependent RNA helicase DDX54 · UniProt Q8TDD1

Round 2 corrected
Length
881 aa
Mass
98.6 kDa
Annotated
2026-04-28
42 papers in source corpus 11 papers cited in narrative 11 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

DDX54 is a nucleolar DEAD-box RNA helicase with RNA-dependent ATPase activity that functions at the intersection of transcriptional co-regulation, pre-mRNA splicing, myelination, and innate immune modulation. It acts as a nuclear receptor co-regulator—repressing estrogen receptor-mediated transcription through a discrete repression domain homologous to NCoR2/SMRT (PMID:12466272) and gene-selectively co-activating the constitutive androstane receptor (PMID:22910411)—and as a DNA damage–responsive splicing factor that promotes U2 snRNP and spliceosomal B complex interactions to reduce intron retention at weak splice sites after ionizing radiation, thereby supporting cell survival (PMID:28596291). DDX54 is essential for both developmental myelination and adult myelin homeostasis: it binds MBP mRNA and protein, and oligodendrocyte-specific conditional knockout causes progressive myelin breakdown, oligodendrocyte apoptosis, and lethality (PMID:23239230, PMID:37720086). Upon viral infection, DDX54 relocalizes from the nucleolus to the nucleoplasm, where its ATPase activity is required to recruit and stimulate the m6A demethylase ALKBH5 on selected transcripts including mavs mRNA, promoting their nuclear retention and thereby suppressing type I interferon signaling (PMID:40793791).

Mechanistic history

Synthesis pass · year-by-year structured walk · 6 steps
  1. 2002 High

    The discovery that DDX54 possesses RNA-dependent ATPase activity and functions as a hormone-dependent co-repressor of estrogen receptors—through a discrete C-terminal repression domain—established it as the first DEAD-box helicase directly engaged in nuclear receptor transcriptional regulation.

    Evidence Co-immunoprecipitation, domain-mapping deletions, reporter assays, ATPase assay, and siRNA/antisense knockdown in human cells

    PMID:12466272

    Open questions at the time
    • Whether helicase/ATPase activity contributes to transcriptional co-repression is unknown
    • No structural information for the repression domain or the ER interaction interface
    • Genome-wide set of ER target genes affected by DDX54 not defined
  2. 2011 Medium

    Identification of DDX54 as an oligodendrocyte-lineage protein that physically associates with all four MBP isoforms and influences the nuclear localization of the 21.5-kDa MBP isoform opened a new functional context—myelination—for this helicase.

    Evidence Co-immunoprecipitation from brain tissue and cultured oligodendrocytes, co-transfection localization assay

    PMID:21932369

    Open questions at the time
    • Whether the DDX54–MBP interaction is direct or mediated by RNA was not resolved
    • Functional consequence for myelin formation not yet tested in vivo
  3. 2012 High

    In vivo knockdown of Ddx54 in neonatal mouse brain demonstrated that it is required for proper MBP mRNA metabolism and developmental myelination, with DDX54 binding MBP mRNA directly and regulating MBP promoter activity, while its role as a gene-selective CAR co-activator expanded its nuclear-receptor regulatory repertoire.

    Evidence Intraventricular Ad-shRNA injection with immunohistochemistry/immunoblot; RNA-IP; MBP promoter reporter; siRNA in HepG2 cells for CAR target genes

    PMID:22910411 PMID:23239230

    Open questions at the time
    • Specific RNA motifs on MBP mRNA bound by DDX54 not mapped
    • Whether CAR co-activation requires DDX54 ATPase activity is untested
    • Whether DDX54 controls MBP mRNA transport, stability, or translation is unclear
  4. 2017 High

    Systematic interactome and iCLIP analysis revealed DDX54 as an immediate-to-early DNA damage response splicing regulator: upon ionizing radiation it increases binding to pre-mRNAs with weak acceptor splice sites and engages U2 snRNP/B complex components, reducing intron retention and promoting cell survival, thereby establishing a direct mechanistic link between DDX54 helicase activity and spliceosomal function.

    Evidence UV crosslinking poly(A) pulldown-MS, iCLIP, RNA-seq splicing analysis, co-IP with spliceosomal components, siRNA survival assays

    PMID:28596291

    Open questions at the time
    • Whether ATPase/helicase activity is catalytically required for U2 snRNP recruitment was not tested
    • Upstream signal linking IR to increased DDX54–RNA binding unknown
    • Overlap between DDX54 splicing targets and its nuclear receptor target genes not explored
  5. 2023 High

    Oligodendrocyte-specific conditional knockout after developmental myelination proved DDX54 is indispensable for adult myelin homeostasis: loss causes progressive inner sheath breakdown, oligodendrocyte apoptosis, neuroinflammation, and death within months, and DDX54 expression is reduced in MS patient corpus callosum.

    Evidence Ddx54 fl/fl;MBP-Cre conditional KO mouse with behavioral, histological, and immunohistochemical characterization; in vitro myelination assay; human MS tissue analysis

    PMID:37720086

    Open questions at the time
    • The molecular targets of DDX54 in mature oligodendrocytes (specific mRNAs or splicing events) are not defined
    • Whether DDX54 loss phenocopies MBP loss or involves additional substrates is unknown
    • Causal role of DDX54 reduction in MS pathogenesis not established
  6. 2025 High

    During viral infection, DDX54 relocalizes from the nucleolus to the nucleoplasm and uses its ATPase activity to bind m6A-modified transcripts and recruit/stimulate the m6A demethylase ALKBH5, causing nuclear retention of demethylated transcripts (including mavs) and suppressing type I interferon signaling—revealing an epitranscriptomic mechanism for DDX54-mediated immune regulation.

    Evidence VSV infection model, DDX54 OE/KO/KD, ALKBH5 KO epistasis, m6A-seq, RIP, subcellular fractionation/imaging, ATPase mutant analysis, interferon response assays

    PMID:40793791

    Open questions at the time
    • How viral infection triggers DDX54 nucleolar-to-nucleoplasm relocalization is unknown
    • Whether DDX54–ALKBH5 cooperation extends to other viral infections beyond VSV is untested
    • Structural basis for DDX54 stimulation of ALKBH5 enzymatic activity not determined

Open questions

Synthesis pass · forward-looking unresolved questions
  • A unifying structural and regulatory framework—explaining how DDX54 ATPase/helicase activity is directed toward distinct substrate classes (nuclear receptor complexes, spliceosomal intermediates, MBP mRNA, m6A-modified transcripts) and how these functions are coordinated or segregated in different cellular contexts—remains to be established.
  • No high-resolution structure of DDX54 or its complexes exists
  • Context-dependent regulatory inputs (post-translational modifications, relocalization signals) are largely uncharacterized
  • Genome-wide catalog of direct DDX54 RNA targets across physiological contexts is incomplete

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 5 GO:0140098 catalytic activity, acting on RNA 2 GO:0140110 transcription regulator activity 2 GO:0140657 ATP-dependent activity 2 GO:0098772 molecular function regulator activity 1
Localization
GO:0005634 nucleus 4 GO:0005654 nucleoplasm 2 GO:0005730 nucleolus 1
Pathway
R-HSA-74160 Gene expression (Transcription) 2 R-HSA-8953854 Metabolism of RNA 2 R-HSA-168256 Immune System 1 R-HSA-73894 DNA Repair 1
Partners
ALKBH5ESR1MBPNR1I3PBX3SNRNP200
Complex memberships
spliceosomal B complex (functional interaction)

Evidence

Reading pass · 11 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2002 DDX54 (DP97), a DEAD-box RNA helicase, was identified as a novel nuclear receptor co-regulator that interacts with estrogen receptors (ER) and other nuclear receptors in a hormone-dependent manner and represses their transcriptional activity. Mapping studies localized the interaction to the C-terminal region of DP97 and the hormone-binding/AF-2 region of ERs. A small repression domain (aa 589–631) with homology to NCoR2/SMRTe was identified as necessary and sufficient for intrinsic repressor activity, while the N-terminal helicase region was dispensable for transcriptional repression. DDX54 possesses RNA-dependent ATPase activity. Knockdown of endogenous DDX54 by antisense or siRNA enhanced estradiol-ER-stimulated gene expression and attenuated ER-mediated repression. Co-immunoprecipitation, domain-mapping deletion studies, reporter assays, RNA-dependent ATPase activity assay, siRNA/antisense knockdown with gene expression readouts The Journal of biological chemistry High 12466272
2012 DP97 (DDX54) was identified as a novel interacting protein of the constitutive androstane receptor (CAR) and acts as a gene-selective co-activator: siRNA knockdown of DP97 suppressed CAR-induced expression of CYP2B6 and UGT1A1 but not CYP3A4. DP97-mediated CAR transactivation was synergistically enhanced by co-expression of SRC-1 or PGC1α, suggesting DP97 acts as a mediator between CAR and co-activators. siRNA knockdown with mRNA expression readouts, co-expression/transactivation reporter assays in HepG2 cells Biochemical and biophysical research communications Medium 22910411
2011 DDX54 (Ddx54) was identified as the antigen recognized by the 4F2 monoclonal antibody specific for oligodendrocyte lineage cells. Ddx54 was found to co-immunoprecipitate with all four isoforms of myelin basic protein (MBP) from brain homogenates and cultured oligodendrocyte cell lysates, indicating direct association. Co-transfection of Ddx54 with MBP isoform genes increased nuclear localization of the 21.5-kDa MBP isoform. Co-immunoprecipitation, immunohistochemistry, co-transfection localization assay Journal of neuroscience research Medium 21932369
2012 Ddx54 knockdown in mouse brain (via intraventricular injection of Ad-shRNA:Ddx54 on postnatal day 2) caused defective myelination: MBP immunosignals accumulated in the subplate layer and failed to intrude into emerging white matter; the 21.5 kDa MBP isoform was specifically decreased while other MBP isoforms and oligodendrocyte markers were unchanged. Ddx54 transfection into neuroepithelial cells upregulated MBP promoter activity, and immunoprecipitation in HEK293 cells indicated Ddx54 directly interacts with MBP mRNA, suggesting a role in MBP mRNA metabolism and myelination. In vivo shRNA knockdown with immunohistochemistry/immunoblot, MBP promoter luciferase reporter assay, co-immunoprecipitation of Ddx54 with MBP mRNA Journal of neuroscience research High 23239230
2017 DDX54 is an immediate-to-early DNA damage response (DDR) regulator that is required for splicing efficacy of IR-induced pre-mRNAs. Upon ionizing radiation (IR), DDX54 increases its interaction with a defined class of pre-mRNAs harboring introns with weak acceptor splice sites, and forms protein-protein contacts with components of U2 snRNP and the spliceosomal B complex, resulting in reduced intron retention and higher processing rates of target transcripts. DDX54 promotes cell survival after IR exposure. Systematic interactome capture (UV crosslinking + poly(A) pulldown + MS), iCLIP, RNA-seq (splicing analysis), co-immunoprecipitation with spliceosomal components, siRNA knockdown with survival assays Genome research High 28596291
2020 DDX54 binds to the lncRNA SNHG10 and to PBX3 mRNA, and SNHG10 maintains PBX3 mRNA stability by recruiting DDX54, forming a regulatory feedback loop that promotes gastric cancer cell growth. RNA immunoprecipitation (RIP), RNA pulldown, siRNA knockdown, rescue overexpression assays Digestive diseases and sciences Low 32712782
2021 DDX54 overexpression in colorectal cancer cells promotes proliferation and mobility by increasing phosphorylation of p65 and AKT, implicating DDX54 in activation of NF-κB and PI3K/AKT signaling pathways. siRNA knockdown and overexpression with phosphorylation analysis by western blot, proliferation/migration assays Frontiers in oncology Low 33968751
2021 DDX54 protein is recruited by lncRNA PITPNA-AS1 and contributes to upregulation of SIK2 expression in triple-negative breast cancer cells, functioning downstream of PITPNA-AS1 sponging of miR-520d-5p. RNA pulldown, RIP assay, siRNA/overexpression rescue assays Journal of translational medicine Low 34353336
2022 DDX54 is recruited by lncRNA CBR3-AS1 (which sponges miR-140-5p) to upregulate NUCKS1 expression, thereby activating the mTOR signaling pathway and promoting stemness and EMT in osteosarcoma cells. RIP, RNA pulldown, luciferase reporter, siRNA knockdown, rescue assays, in vivo xenograft Molecular therapy oncolytics Low 35592388
2023 Oligodendrocyte-specific conditional knockout of Ddx54 (MBP-Cre driven) in mice, after completion of normal postnatal myelination, leads to progressive inner myelin sheath breakdown, loss of myelinated axons, oligodendrocyte apoptosis, glial activation, and death within 7 months, demonstrating that Ddx54 is indispensable for adult myelin homeostasis. Ddx54 knockdown also greatly impairs myelination in vitro, and Ddx54 expression is decreased in corpus callosum of MS patients. Conditional knockout mouse model (Ddx54 fl/fl;MBP-Cre), behavioral/histological/immunohistochemical analysis, in vitro myelination knockdown assay, human MS tissue analysis iScience High 37720086
2025 DDX54 inhibits the type I interferon antiviral response by facilitating m6A demethylation of selected transcripts including mavs mRNA via ALKBH5. Upon VSV infection, DDX54 relocalizes from the nucleolus to the nucleoplasm, where it and ALKBH5 independently bind m6A-modified transcripts forming m6A RNA/protein complexes. DDX54 interaction with ALKBH5 on these selected transcripts promotes ALKBH5 demethylase enzymatic activity (which is otherwise impaired during VSV infection), causing nuclear retention of demethylated transcripts and limiting their cytoplasmic translation, thereby impairing interferon signaling. ATPase activity of DDX54 is required both for binding selected transcripts and for promoting ALKBH5 activity. ALKBH5 knockout abrogated DDX54's suppressive effect on interferon response. VSV infection model, DDX54 overexpression/knockout/knockdown, ALKBH5 knockout, m6A-seq, RIP, subcellular fractionation/relocalization imaging, ATPase activity mutant analysis, interferon response assays Journal of virology High 40793791

Source papers

Stage 0 corpus · 42 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2006 Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2861 17081983
2012 Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 1718 22658674
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2015 The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 1118 26186194
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2012 The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Molecular cell 973 22681889
2005 Nucleolar proteome dynamics. Nature 934 15635413
2020 A reference map of the human binary protein interactome. Nature 849 32296183
2002 Directed proteomic analysis of the human nucleolus. Current biology : CB 780 11790298
2007 Large-scale mapping of human protein-protein interactions by mass spectrometry. Molecular systems biology 733 17353931
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2018 High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies. Molecular cell 580 29395067
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2015 A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface. Cell 433 26638075
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
2002 Functional proteomic analysis of human nucleolus. Molecular biology of the cell 391 12429849
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
2016 The cell proliferation antigen Ki-67 organises heterochromatin. eLife 265 26949251
2016 A High-Density Map for Navigating the Human Polycomb Complexome. Cell reports 216 27705803
2011 Toward an understanding of the protein interaction network of the human liver. Molecular systems biology 207 21988832
2018 An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. Nature communications 201 29568061
2009 Structural basis and specificity of human otubain 1-mediated deubiquitination. The Biochemical journal 176 18954305
2013 The protein interaction landscape of the human CMGC kinase group. Cell reports 174 23602568
2020 UFMylation maintains tumour suppressor p53 stability by antagonizing its ubiquitination. Nature cell biology 168 32807901
2019 H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids. Nature cell biology 162 30804502
2019 A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape. Nature immunology 159 30833792
2017 Quantitative proteomics reveals that long non-coding RNA MALAT1 interacts with DBC1 to regulate p53 acetylation. Nucleic acids research 148 28973437
2002 Regulation of nuclear receptor transcriptional activity by a novel DEAD box RNA helicase (DP97). The Journal of biological chemistry 56 12466272
2017 DDX54 regulates transcriptome dynamics during DNA damage response. Genome research 44 28596291
2020 SNHG10/DDX54/PBX3 Feedback Loop Contributes to Gastric Cancer Cell Growth. Digestive diseases and sciences 25 32712782
2021 DDX54 Plays a Cancerous Role Through Activating P65 and AKT Signaling Pathway in Colorectal Cancer. Frontiers in oncology 20 33968751
2012 A DEAD-box RNA helicase Ddx54 protein in oligodendrocytes is indispensable for myelination in the central nervous system. Journal of neuroscience research 18 23239230
2021 MYBL2-induced PITPNA-AS1 upregulates SIK2 to exert oncogenic function in triple-negative breast cancer through miR-520d-5p and DDX54. Journal of translational medicine 17 34353336
2022 LncRNA CBR3-AS1 promotes osteosarcoma progression through the network of miR-140-5p/DDX54-NUCKS1-mTOR signaling pathway. Molecular therapy oncolytics 15 35592388
2012 DP97, a DEAD box DNA/RNA helicase, is a target gene-selective co-regulator of the constitutive androstane receptor. Biochemical and biophysical research communications 11 22910411
2011 A new monoclonal antibody, 4F2, specific for the oligodendroglial cell lineage, recognizes ATP-dependent RNA helicase Ddx54: possible association with myelin basic protein. Journal of neuroscience research 10 21932369
2023 Lethal adulthood myelin breakdown by oligodendrocyte-specific Ddx54 knockout. iScience 4 37720086
2025 DDX54 downregulation enhances anti-PD1 therapy in immune-desert lung tumors with high tumor mutational burden. Proceedings of the National Academy of Sciences of the United States of America 0 40172969
2025 DDX54 drives ALKBH5-mediated demethylation of selected transcripts to suppress interferon antiviral response. Journal of virology 0 40793791