{"gene":"DHX36","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2005,"finding":"DHX36 (RHAU) is the major source of tetramolecular G4-DNA resolving activity in HeLa cell lysates. Recombinant DHX36 expressed in E. coli displayed robust, NTP-dependent G4-DNA resolving activity, and immunodepletion of DHX36 from lysates removed ~77% of the enzyme and reduced G4-DNA resolving activity to ~46% of control.","method":"G4-DNA affinity purification, mass spectrometry, in vitro G4-resolvase assay with recombinant protein, immunodepletion","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with recombinant protein, immunodepletion confirming identity, multiple orthogonal methods","pmids":["16150737"],"is_preprint":false},{"year":2004,"finding":"RHAU (DHX36) physically interacts with the deadenylase PARN and the human exosome, enhancing deadenylation and decay of ARE-containing mRNAs (ARE-uPA). ATPase activity of RHAU is essential for its mRNA-destabilizing function. RHAU recognizes ARE-uPA mRNA via RNA-dependent interaction with AUBPs HuR and NFAR1.","method":"Co-immunoprecipitation, mRNA decay assays, ATPase-dead mutant analysis, RNA-protein interaction assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, functional mutant (ATPase-dead), mRNA decay assay, multiple binding partners identified","pmids":["14731398"],"is_preprint":false},{"year":2010,"finding":"The amino-terminal RHAU-specific motif (RSM) of DHX36 is the major affinity and specificity determinant for G4-RNA binding and G4-resolvase activity. Deletion of the RSM abolishes G4 binding and resolution. The Drosophila ortholog CG9323 also requires the RSM for G4-RNA recognition and resolution.","method":"Domain deletion/mutagenesis, in vitro G4-binding and resolvase assays, cross-species comparison","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — mutagenesis combined with in vitro binding and activity assays, replicated in Drosophila ortholog","pmids":["20472641"],"is_preprint":false},{"year":2011,"finding":"DDX1, DDX21, and DHX36 form a complex with adaptor molecule TRIF to sense cytosolic dsRNA in myeloid dendritic cells. DHX36 binds the TIR domain of TRIF via its HA2-DUF domain. Knockdown of DHX36 or TRIF blocked type I IFN and cytokine responses to poly I:C, influenza A virus, and reovirus.","method":"Poly I:C affinity purification, Co-IP, shRNA knockdown, cytokine/IFN response assays, domain mapping","journal":"Immunity","confidence":"High","confidence_rationale":"Tier 2 / Strong — affinity purification identifying complex, domain mapping, functional shRNA knockdown with defined immune phenotype","pmids":["21703541"],"is_preprint":false},{"year":2011,"finding":"DHX36 binds an intramolecular G4-RNA structure in the 5' region of the telomerase RNA TERC in vivo and in vitro. RHAU associates with the telomerase holoenzyme via the 5' region of TERC. Binding requires the intact G4 structure.","method":"RIP-chip (RNA immunoprecipitation-microarray), in vitro binding assays, bioinformatics","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — RIP-chip for transcriptome-wide discovery plus in vitro validation, G4-dependence confirmed by mutation","pmids":["21846770"],"is_preprint":false},{"year":2012,"finding":"RHAU (DHX36) unwinds a G4-quadruplex in human telomerase RNA (hTR) 5' region, promoting formation of the P1 helix template boundary required for reverse transcription. RHAU knockdown reduced average telomere length.","method":"In vitro helicase assay, RNA structural analysis, siRNA knockdown, telomere length measurement","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — in vitro helicase reconstitution plus functional knockdown with telomere phenotype, single lab","pmids":["22238380"],"is_preprint":false},{"year":2012,"finding":"RHAU is essential for mouse hematopoiesis; germ-line deletion causes embryonic lethality, and hematopoietic-specific deletion causes hemolytic anemia and differentiation block at the proerythroblast stage due to a proliferation defect. Deregulated genes in knockout proerythroblasts are enriched for G4 motifs in their promoters, suggesting G4 resolvase activity underlies the phenotype.","method":"Conditional knockout mouse (Vav1-Cre), hematopoietic phenotyping, transcriptome analysis","journal":"Blood","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean conditional knockout with defined cellular phenotype (proerythroblast block) and transcriptomic support","pmids":["22422825"],"is_preprint":false},{"year":2013,"finding":"DHX36 directly associates with the terminal loop of precursor-miR-134 (pre-miR-134) and mediates its dendritic localization in hippocampal neurons. DHX36 function is required for miR-134-dependent inhibition of target gene expression and control of dendritic spine size.","method":"RNA immunoprecipitation, in situ localization, DHX36 loss-of-function, dendritic spine morphometry, target gene expression assays","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct RNA binding confirmed by RIP, loss-of-function with defined morphological and gene expression phenotypes","pmids":["23651854"],"is_preprint":false},{"year":2013,"finding":"RHAU (DHX36) binds G4 structures in the 3' UTR of PITX1 mRNA. RHAU knockdown increases PITX1 protein levels with only marginal mRNA changes, indicating translational repression. This regulation requires Argonaute-2 and is non-additive with Dicer knockdown, placing RHAU in microRNA-mediated translational silencing.","method":"RNA co-immunoprecipitation, siRNA knockdown, Western blot, Ago2 co-depletion","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RIP plus functional knockdown, single lab, mechanism of Ago2 link not fully dissected","pmids":["24369427"],"is_preprint":false},{"year":2014,"finding":"DHX36 forms a complex with PKR (dsRNA-dependent protein kinase) in a dsRNA-dependent manner and facilitates dsRNA binding and phosphorylation (activation) of PKR through its ATPase/helicase activity, promoting antiviral stress granule (avSG) formation and RIG-I signaling. DHX36 KO MEF cells show defective IFN production and increased susceptibility to RNA virus infection.","method":"Co-immunoprecipitation (dsRNA-dependent), DHX36 knockout inducible MEF cells, IFN production assay, viral infection assay","journal":"PLoS pathogens","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, KO cell line with defined IFN/antiviral phenotype, ATPase dependence demonstrated","pmids":["24651521"],"is_preprint":false},{"year":2015,"finding":"An 18-amino-acid N-terminal G-quadruplex-binding domain of RHAU folds upon G4 binding and covers a terminal guanine tetrad using three-anchor-point electrostatic interactions between positively charged residues and phosphate groups, conferring parallel G4 specificity.","method":"NMR solution structure of peptide-G4 complex, binding assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — NMR structure with defined binding interactions, explains parallel G4 specificity mechanistically","pmids":["26195789"],"is_preprint":false},{"year":2015,"finding":"Cardiac deletion of Rhau causes heart defects and embryonic lethality. Nkx2-5 mRNA is a RHAU target: RHAU binds the 5' UTR G4 to promote protein translation and the 3' UTR ARE to facilitate mRNA decay, providing dual post-transcriptional regulation of Nkx2-5 in heart development.","method":"Cardiac-specific conditional knockout mouse, gene expression profiling, RNA co-IP, mRNA stability and translation assays","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — conditional KO with defined cardiac phenotype, RIP-confirmed target, dual mechanistic (translation + decay) readouts","pmids":["26489465"],"is_preprint":false},{"year":2015,"finding":"RHAU is essential for spermatogonia differentiation; germ-cell-specific knockout increases G4 DNA accumulation and reduces expression of c-kit (a differentiation gene with G4 motifs in its promoter). RHAU directly binds to G4 structures in the c-kit promoter to activate c-kit expression.","method":"Germ-cell-specific conditional knockout mouse, G4 probe staining, chromatin pull-down, c-kit expression analysis","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional KO with phenotype, direct G4-promoter binding shown, single lab","pmids":["25611385"],"is_preprint":false},{"year":2016,"finding":"DHX36 binds the G4 structure near the polyadenylation site of p53 pre-mRNA and is necessary to maintain p53 pre-mRNA 3'-end processing following UV-induced DNA damage. G4 mutation or G4-stabilizing ligands impair this processing.","method":"RNA binding assays, siRNA knockdown, pre-mRNA 3'-end processing assays, G4 mutation and pharmacological G4 stabilization","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding assay, functional knockdown, G4 dependence shown by mutation and ligand, single lab","pmids":["27940037"],"is_preprint":false},{"year":2016,"finding":"RHAU is recruited to stress granules via a newly identified N-terminal RNA-binding domain that is both necessary and sufficient for SG localization. ATPase activity of RHAU modulates RNA interaction and regulates protein retention in SGs.","method":"Live imaging, domain deletion mapping, ATPase-dead mutant, stress granule marker co-localization","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — localization mapped to specific domain with functional consequence (SG association), ATPase dependence shown, single lab","pmids":["18854321"],"is_preprint":false},{"year":2016,"finding":"RHAU stabilizes G4 DNA in nucleotide-free, AMP-PNP-bound, and ADP-bound states, but destabilizes G4 upon ATP hydrolysis. Both the 3' ssDNA tail and the RSM domain are dispensable for G4 stabilization but required for G4 destabilization, demonstrating distinct functional requirements for binding versus unfolding.","method":"Single-molecule magnetic tweezers with Drosophila RHAU, nucleotide-state manipulation, RSM and tail mutants","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — single-molecule biophysics with nucleotide-state control and domain mutants, single lab","pmids":["28069994"],"is_preprint":false},{"year":2008,"finding":"RHAU is localized predominantly in the nucleus under normal conditions; transcriptional arrest redistributes it to nucleolar caps where it co-localizes with RNA helicases p68 and p72. Knockdown affects steady-state mRNA levels without altering mRNA half-lives for most affected transcripts, suggesting a transcriptional rather than mRNA decay role in the nucleus.","method":"Immunofluorescence, subcellular fractionation, transcriptional inhibitor treatment, microarray analysis with actinomycin D chase","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiment with functional follow-up (mRNA half-life analysis), single lab","pmids":["18279852"],"is_preprint":false},{"year":2018,"finding":"Co-crystal structure of bovine DHX36 bound to a parallel G4-DNA with a 3' ssDNA tail reveals that the N-terminal DHX36-specific motif (DSM) folds into a DNA-binding-induced α-helix that, together with an OB-fold-like subdomain, selectively binds parallel G4s. Comparison of unliganded, ATP-analogue-bound, and G4-bound structures plus smFRET analyses suggests G4 binding induces helicase core rearrangements that drive unfolding by pulling the ssDNA tail one residue at a time.","method":"X-ray co-crystallography (multiple structures), single-molecule FRET (smFRET)","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution crystal structures of multiple states combined with smFRET, mechanistic model directly supported by structural data","pmids":["29899445"],"is_preprint":false},{"year":2018,"finding":"Crystal structures of Drosophila DHX36 (DmDHX36) in complex with RNA and various DNAs reveal that positively charged residues in RecA2 and OB-like domains form a structural pocket at the nucleic acid entrance where G4 DNA is tightly bound and partially destabilized, followed by complete unfolding via 3'–5' translocation.","method":"X-ray crystallography, SAXS, molecular dynamics simulation, single-molecule fluorescence, DNA binding assays","journal":"Structure","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structures plus multiple orthogonal biophysical methods, mechanistic model supported","pmids":["29429875"],"is_preprint":false},{"year":2018,"finding":"Depletion of DHX36 or DHX9 promotes translation of rG4-associated upstream open reading frames (uORFs) while reducing translation of main ORFs of rG4-containing mRNAs including proto-oncogenes and transcription factors. DHX9 mediates this through direct physical interaction with rG4 substrates.","method":"Ribosome profiling (transcriptome-wide), siRNA depletion of DHX36 and DHX9, transcriptome-wide DHX9 binding site mapping (PAR-CLIP)","journal":"Genome biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — transcriptome-wide ribosome profiling and CLIP-seq, functional depletion, multiple mRNA targets","pmids":["30591072"],"is_preprint":false},{"year":2019,"finding":"DHX36 binds G-rich and G4-forming sequences on >4500 mRNAs genome-wide. DHX36 KO increases target mRNA abundance but decreases ribosome occupancy and protein output, indicating these mRNAs become translationally incompetent. DHX36 KO increases stress granule formation and PKR phosphorylation.","method":"PAR-CLIP (global RNA binding mapping), DHX36 knockout cell lines, polysome profiling, ribosome profiling, stress granule imaging","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — PAR-CLIP plus KO with ribosome profiling, multiple orthogonal readouts, single lab","pmids":["31160600"],"is_preprint":false},{"year":2019,"finding":"DHX36 displays ATP-independent unfolding of G4-RNA followed by ATP-dependent refolding, a highly asymmetric pattern distinct from its G4-DNA activity. ATP-dependent activity arises from the RNA tail rather than the G4 itself. Mutations perturbing G4 contact cause rapid protein dissociation upon ATP hydrolysis; mutations interfering with RNA tail binding cause dysregulated activity.","method":"Single-molecule FRET, site-directed mutagenesis, in vitro helicase assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — smFRET with mutagenesis revealing mechanistic asymmetry between DNA and RNA G4 substrates","pmids":["31015431"],"is_preprint":false},{"year":2017,"finding":"DHX36 disrupts DNA G4s via a translocation-based helicase mechanism: it loads onto a 3' ssDNA extension and translocates 3'–5' toward the G4. Disruption rates depend on G4 length under saturating conditions (kcat) but not subsaturating (kcat/K), and a polyethylene glycol linker blocking translocation abolishes activity. DHX36 unwinds G4s far more efficiently than dsDNA of comparable intrinsic lifetime.","method":"In vitro kinetic assays with tetramolecular and unimolecular G4 substrates, linker-block experiments","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — rigorous kinetic framework with mechanistic controls, in vitro reconstitution, single lab","pmids":["29269411"],"is_preprint":false},{"year":2011,"finding":"DHX36 (RHAU) binds the G-quadruplex-forming 5' guanosine tracts of human telomerase RNA (hTR) via its N-terminal accessory domain (not the helicase domain). G4 mutations in hTR substantially reduce mature hTR accumulation and telomere maintenance, suggesting G4 formation protects immature hTR from degradation.","method":"Co-immunoprecipitation, domain mapping, hTR guanosine tract substitution mutants, telomere maintenance assays","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain mapping and functional RNA mutants, single lab","pmids":["21149580"],"is_preprint":false},{"year":2011,"finding":"DHX36 facilitates TNAP transcription by binding the MS-275 response element in the TNAP promoter. DHX36 physically interacts with HDAC1 and HDAC4, and MS-275 (HDAC inhibitor) decreases this HDAC–DHX36 interaction, relieving transcriptional repression of TNAP.","method":"DNA affinity precipitation assay, co-immunoprecipitation, TNAP promoter deletion reporter assays, HDAC inhibitor treatment","journal":"Journal of bone and mineral research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — DNA affinity pulldown, co-IP, promoter reporter assays, single lab","pmids":["21590736"],"is_preprint":false},{"year":2016,"finding":"RHAU (DHX36) interacts with the 3' adenosine-rich region of long non-coding RNA BC200 (BCYRN1) via a C-terminal region specific to RHAU isoform 1; this binding is independent of G4 structure. BC200 can act as an acceptor of unwound G4 substrates via a cytosine-rich region and interacts with G4-containing telomerase RNA, suggesting RHAU may direct BC200 to G4-containing targets.","method":"RNA co-immunoprecipitation, RNase footprinting, RHAU truncation binding assays, pulldown of endogenous RNAs","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro binding with domain mapping and RNase footprinting, endogenous RNA pulldown, single lab","pmids":["26740632"],"is_preprint":false},{"year":2020,"finding":"The DHX36-specific motif (DSM), OB-fold, and a conserved β-hairpin (β-HP) each contribute to RNA binding and are essential for remodeling of RNA quadruplex and duplex structures. The DSM functions not only as a G4-binding adaptor but also promotes RNA duplex unwinding. Crystal structure of mouse DHX36 bound to ADP reveals conformational changes accompanying ATPase cycle stages.","method":"X-ray crystallography (mouse DHX36-ADP), domain deletion/mutagenesis, RNA binding assays, in vitro helicase assays","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with biochemical mutagenesis characterizing auxiliary domain functions, single lab","pmids":["32087197"],"is_preprint":false},{"year":2020,"finding":"The DHX36-specific motif (DSM) promotes G4 recognition by increasing the G4 binding rate (on-rate) of DHX36 without affecting the dissociation rate. For most G4 substrates, the DSM has little effect on the G4 disruption step, suggesting initial G4 capture and disruption are mechanistically separable.","method":"Kinetic binding assays with DHX36 DSM truncation, stopped-flow or competition assays","journal":"Biological chemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — quantitative kinetics with truncation mutant, mechanistically informative, single lab","pmids":["33857359"],"is_preprint":false},{"year":2020,"finding":"The lncRNA GSEC binds DHX36 via its G4-forming sequence and inhibits DHX36 G-quadruplex unwinding activity. DHX36 knockdown restores reduced migratory activity caused by GSEC knockdown in colon cancer cells, placing DHX36 downstream of GSEC in regulating cell migration.","method":"RNA pull-down, G4-unwinding assay with GSEC, siRNA knockdown, cell migration assay","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding and activity inhibition shown in vitro, genetic epistasis by double knockdown, single lab","pmids":["27797375"],"is_preprint":false},{"year":2021,"finding":"DHX36 is essential for muscle satellite cell (SC) expansion and muscle regeneration. Inducible deletion of Dhx36 in adult SCs causes defective proliferation and muscle regeneration. DHX36 promotes mRNA translation via 5'UTR rG4 binding; specifically, it regulates translation of Gnai2 mRNA by unwinding its 5'UTR rG4, with GNAI2 identified as a downstream effector for SC expansion.","method":"Inducible SC-specific conditional knockout mouse, muscle injury model, PAR-CLIP (system-wide DHX36 binding), polysome profiling, in vitro rG4 unwinding assay","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — conditional KO with defined regeneration phenotype, PAR-CLIP plus polysome profiling, specific target (Gnai2) validated mechanistically","pmids":["34413292"],"is_preprint":false},{"year":2021,"finding":"DHX36 depletion suppresses C9orf72 G4C2 repeat-associated non-AUG (RAN) translation in a repeat length-dependent manner, while DHX36 overexpression enhances RAN translation. Upregulation of RAN translation by integrated stress response activation is prevented by DHX36 loss, demonstrating DHX36 promotes translation of G4-forming repeat RNAs.","method":"Luciferase reporter assays (cell-based and cell-free), DHX36 depletion and overexpression, integrated stress response induction","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reporter assays with depletion/overexpression, repeat-length dependence shown, single lab","pmids":["34174288"],"is_preprint":false},{"year":2021,"finding":"RHAU ablation in postnatal cardiomyocytes reduces protein levels of Yap1 and Hexim1 while enhancing their mRNA levels. RHAU associates with both 5' and 3' UTRs of these genes to simultaneously promote translation (via 5'UTR) and destabilize mRNA (via 3'UTR). RHAU-deficient mice develop progressive dilated cardiomyopathy and impaired neonatal heart regeneration.","method":"Cardiomyocyte-specific conditional knockout mouse, RNA co-IP (5' and 3'UTR), Western blot, mRNA stability assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional KO with defined cardiac phenotype, RIP-based mechanistic analysis of dual UTR regulation, single lab","pmids":["33199370"],"is_preprint":false},{"year":2021,"finding":"DHX36 deficiency leads to accumulation of DNA damage and slower cell growth; expression of G4-binding-deficient DHX36 mutants only partially rescues these defects. Nuclear DHX36 co-localizes with G4-DNA, RNA polymerase II, and a splicing factor, supporting a role in clearing transcription-associated G4-DNA to maintain genomic integrity.","method":"DHX36 depletion, G4-stabilizing drug treatment, DNA damage markers (γH2AX), immunofluorescence co-localization, G4-binding mutant rescue assay","journal":"Genes to cells","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — depletion with DNA damage phenotype, mutant rescue, co-localization, single lab","pmids":["37632696"],"is_preprint":false},{"year":2022,"finding":"DHX36 interacts with a rG4 structure in the 5'UTR of ADAR1 mRNA in vitro and in cells. This rG4 normally inhibits ADAR1 translation; DHX36 binding relieves this inhibition in an rG4-dependent manner, as shown in knockdown and knockout conditions.","method":"In vitro rG4 characterization, GTFH probes for cellular rG4 detection, DHX36 knockdown/knockout, reporter and native gene translation assays","journal":"Angewandte Chemie","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro binding plus cellular KD/KO with rG4-specific probes, single lab","pmids":["36300875"],"is_preprint":false},{"year":2022,"finding":"The lncRNA Lockd directly interacts with DHX36 (strongest binding at Lockd 5' end) and stabilizes DHX36 interaction with EIF3B; this tripartite complex unwinds the rG4 at Anp32e mRNA 5'UTR to promote ANP32E translation, which is required for myoblast proliferation and muscle regeneration.","method":"RNA immunoprecipitation, co-IP, in vitro rG4 unwinding assay, Lockd deletion in vivo, ANP32E translation assays","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RIP, co-IP, in vitro unwinding, in vivo deletion; specific target validated, single lab","pmids":["35675771"],"is_preprint":false},{"year":2023,"finding":"Dhx36 deletion in differentiated spermatogonia (Stra8-GFPCre) leads to meiotic defects and abnormal spermiogenesis due to dysregulated transcription of G4-harboring genes required for meiosis.","method":"Stage-specific conditional knockout mouse, phenotypic analysis of meiosis/spermiogenesis, transcriptome analysis","journal":"Journal of molecular cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional KO with defined meiotic phenotype and transcriptomic support, single lab","pmids":["36484653"],"is_preprint":false},{"year":2024,"finding":"DHX36 binding induces structural remodeling of mRNA not only at localized binding sites but across entire transcripts, most prominently increasing 3'UTR accessibility. Increased 3'UTR accessibility correlates with decreased mRNA abundance. DHX36 binding sites are enriched for m6A modification and YTHDF1 binding; DHX36-induced structural changes facilitate YTHDF1 binding to m6A sites, leading to mRNA degradation.","method":"RNA structurome-seq upon DHX36 depletion, m6A mapping, YTHDF1 CLIP, DHX36 KO cell lines, mRNA abundance assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — transcriptome-wide RNA structure mapping, m6A/YTHDF1 integration, KO validation, multiple orthogonal methods","pmids":["39543097"],"is_preprint":false},{"year":2024,"finding":"Dhx36 deletion in embryonic or neonatal heart causes dilated cardiomyopathy and failure to develop a ventricular conduction system (VCS). DHX36 deficiency disrupts resolution of promoter G-quadruplexes in key cardiac genes, impacting cardiomyocyte differentiation and Purkinje fiber network morphogenesis.","method":"Cardiac conditional knockout mouse, single-nucleus RNA-seq, single-nucleus ATAC-seq, G4 promoter analysis","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — conditional KO with defined cardiac/conduction phenotype, snRNA-seq and snATAC-seq mechanistic analysis, single lab with multiple orthogonal methods","pmids":["39366945"],"is_preprint":false},{"year":2025,"finding":"Cryo-EM structures of bovine DHX36 bound to a three-tier RNA G4 and a six-tier DNA G4 at 2.6 Å and 3.4 Å resolution respectively reveal that the RecA2 domain of the helicase core plays a key role in DNA vs. RNA discrimination. A sequence-divergent RecA2 surface loop synergizes with the DHX36-specific N-terminal extension to recognize G4 structures over other nucleic acids.","method":"Cryo-electron microscopy structure determination, smFRET, site-directed mutagenesis of RecA2 and N-terminal extension","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structures at near-atomic resolution with structure-guided mutagenesis validated by smFRET and kinetics, single lab","pmids":["40833853"],"is_preprint":false},{"year":2025,"finding":"DHX36 limits stress granule formation; in G3BP1/2 double-knockout cells that strongly inhibit SG formation, reducing DHX36 expression rescues SG-like foci formation, indicating DHX36 can restrain intermolecular RNA-RNA interactions (potentially trans-rG4s) that promote SG assembly. mRNA accumulation in SGs is independent of rG4-forming potential in normal cells.","method":"DHX36 depletion in G3BP1/2 KO cells, reporter mRNAs with/without G-tracts, endogenous mRNA SG partitioning by FISH","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic rescue experiment in double-KO background, negative controls for G-tract role are informative, single lab","pmids":["40985767"],"is_preprint":false},{"year":2025,"finding":"REV1 C-terminal domain directly interacts with DHX36, requiring a newly defined REV1-interacting region at the DHX36 C-terminus. This interaction coordinates G4 resolution (DHX36 helicase) with suppression of ssDNA gaps during replication of G4-containing DNA. Prolonged G4 stabilization uncouples REV1 and DHX36.","method":"Co-immunoprecipitation (direct interaction), domain mapping, REV1 KO cells, G4-stabilizing drug (pyridostatin) treatment, DNA damage assays","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct protein-protein interaction with domain mapping, functional uncoupling by G4 stabilizer, KO phenotype, single lab","pmids":["42258547"],"is_preprint":false},{"year":2025,"finding":"DHX36 functions as a rheostat restraining innate immune activation under homeostasis. Exposure to dsRNA reduces DHX36 activity to enable immune activation. DHX36-deficient cells accumulate rG4 structures, show constitutive PKR-dependent stress granule formation, elevated ISG expression, and enhanced RIG-I responsiveness, positioning DHX36 as a regulator linking RNA structure surveillance to PKR- and RIG-I-dependent antiviral signaling.","method":"DHX36 KO cells, dsRNA treatment, PKR activation assays, SG formation assays, ISG expression profiling, RIG-I reporter assays, yellow fever virus replicon assay","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 2 / Strong — KO cells with multiple orthogonal mechanistic readouts (PKR, SG, ISG, RIG-I, viral replication), single lab","pmids":["42213826"],"is_preprint":false},{"year":2025,"finding":"PCV3 capsid protein interacts with DHX36 via Cap-NLS and DHX36 N-terminal domain (NTD), and promotes K48-linked ubiquitination-dependent degradation of DHX36, thereby antagonizing DHX36-mediated IFN-β production and facilitating PCV3 replication.","method":"Co-immunoprecipitation, domain mapping, ubiquitination assay, siRNA knockdown, overexpression, viral replication assay","journal":"Virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP with domain mapping, ubiquitination shown, functional antiviral assay, single lab","pmids":["39862752"],"is_preprint":false},{"year":2025,"finding":"RHAU binds the G4 structure in the 3'UTR of StAR (steroidogenic acute regulatory protein) mRNA; conditional RHAU knockdown reduces STAR translation and testosterone levels in mice. RHAU regulates StAR mRNA stability and translation efficiency through this G4 interaction.","method":"Circular dichroism, RNA-protein interaction assay, RHAU conditional knockdown mouse, ELISA for testosterone, gene expression analysis","journal":"Archives of biochemistry and biophysics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro RNA-protein binding plus in vivo conditional knockdown with hormonal readout, single lab","pmids":["41354365"],"is_preprint":false},{"year":2025,"finding":"DHX36 directly binds pre-rRNA through its RSM (RHAU-specific motif) in mouse oocytes. DHX36 deletion in oocytes causes G4 accumulation at rDNA and pre-rRNA, insufficient pre-rRNA processing, reduced translation, aberrant chromatin configuration, and complete female infertility. DHX36 overexpression partially rescues pre-rRNA accumulation in knockout oocytes.","method":"Oocyte-specific conditional KO mouse, G4 probe/antibody staining, rRNA transcription assay, translation assay, DHX36 overexpression rescue","journal":"Science bulletin","confidence":"High","confidence_rationale":"Tier 2 / Strong — conditional KO with severe phenotype, direct RSM-pre-rRNA interaction demonstrated in vitro and in vivo, rescue experiment, single lab with multiple orthogonal methods","pmids":["40023726"],"is_preprint":false},{"year":2025,"finding":"The lncRNA LENT interacts with DHX36 and both associate with ribosomes in 80S and light polysome fractions. LENT modulates DHX36 association with specific mRNAs encoding ER/mitochondrial homeostasis and autophagy regulators, fine-tuning their translation. LENT silencing leads to autophagy, mitophagy, and apoptosis in melanoma cells.","method":"RNA immunoprecipitation, polysome fractionation, LENT silencing, ribosome association assay","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, RIP and polysome fractionation without full mechanistic dissection, single lab","pmids":[],"is_preprint":true}],"current_model":"DHX36 (RHAU) is a DEAH-box helicase that uses an N-terminal RSM/DSM domain to selectively recognize parallel G-quadruplex (G4) structures in DNA and RNA, then unwinds them via ATP-driven 3'→5' translocation from a 3' ssDNA tail; structurally, the DSM folds into a G4-induced α-helix that caps a guanine tetrad while the RecA2 and OB-fold domains translocate the substrate, with ATP hydrolysis (not binding alone) driving net G4 unfolding; in cells DHX36 resolves G4s in mRNA 5'UTRs to promote translation, in 3'UTRs to destabilize mRNAs (linked to YTHDF1/m6A-dependent decay), and at gene promoters to activate transcription, while also forming complexes with TRIF/DDX1/DDX21 and PKR to regulate innate immune (type I IFN) signaling in response to dsRNA, and is essential for embryogenesis, cardiac development, hematopoiesis, muscle regeneration, spermatogenesis, and female fertility in mice."},"narrative":{"mechanistic_narrative":"DHX36 (RHAU) is a DEAH-box helicase that serves as the principal cellular activity for resolving parallel G-quadruplex (G4) structures in both DNA and RNA, coupling structure-specific recognition to ATP-driven unfolding to control gene expression across transcription, translation, mRNA decay, and innate immunity [PMID:16150737, PMID:20472641]. Substrate selectivity is conferred by an N-terminal DHX36-specific motif (RSM/DSM) that folds into a G4-induced α-helix capping a terminal guanine tetrad through three-anchor electrostatic contacts, with the RecA2 and OB-fold domains completing recognition and translocation [PMID:26195789, PMID:29899445, PMID:40833853]; the helicase loads onto a 3' single-stranded tail and translocates 3'→5', and net G4 unfolding requires ATP hydrolysis rather than nucleotide binding alone, with binding/capture and disruption being mechanistically separable steps [PMID:28069994, PMID:29269411, PMID:33857359]. In the cytoplasm DHX36 binds G4-forming sequences across thousands of mRNAs, unwinding 5'UTR rG4s to license translation and promoting 3'UTR remodeling that drives YTHDF1/m6A-dependent decay, thereby exerting opposing dual post-transcriptional control on individual transcripts [PMID:26489465, PMID:31160600, PMID:39543097]. In the nucleus it resolves promoter and transcription-associated G4-DNA to activate gene expression and maintain genomic integrity, coordinating with REV1 during replication of G4-containing DNA [PMID:37632696, PMID:39366945, PMID:42258547]. DHX36 also governs antiviral signaling, partnering with TRIF/DDX1/DDX21 and with PKR in a dsRNA-dependent manner and acting as a rheostat that restrains constitutive PKR- and RIG-I-driven type I interferon responses by surveilling RNA structure [PMID:21703541, PMID:24651521, PMID:42213826]. Through these activities DHX36 is essential in mice for hematopoiesis, cardiac development and conduction-system formation, muscle satellite cell expansion, spermatogenesis, and oocyte rRNA processing and female fertility [PMID:22422825, PMID:34413292, PMID:39366945, PMID:40023726].","teleology":[{"year":2004,"claim":"Established the first molecular function for RHAU as an mRNA-destabilizing factor, linking it to deadenylation machinery before its G4 activity was known.","evidence":"Co-IP with PARN/exosome, ATPase-dead mutant, and ARE-mRNA decay assays","pmids":["14731398"],"confidence":"High","gaps":["Did not connect decay activity to G4 structures","Mechanism of substrate selection via HuR/NFAR1 not fully resolved"]},{"year":2005,"claim":"Identified DHX36 as the dominant cellular G4-DNA resolvase, defining its signature biochemical activity.","evidence":"G4-DNA affinity purification, mass spectrometry, recombinant resolvase assay, and immunodepletion of HeLa lysates","pmids":["16150737"],"confidence":"High","gaps":["Did not define the structural basis of G4 recognition","Residual resolving activity after depletion implies additional G4 helicases"]},{"year":2010,"claim":"Localized G4 recognition specificity to the N-terminal RSM, separating substrate recognition from the helicase core.","evidence":"Domain deletion/mutagenesis with in vitro binding and resolvase assays, conserved in the Drosophila ortholog","pmids":["20472641"],"confidence":"High","gaps":["Atomic basis of RSM-G4 contact not yet resolved","Did not address DNA vs RNA discrimination"]},{"year":2011,"claim":"Connected DHX36 to telomerase biology and to innate immune dsRNA sensing, broadening its functional scope beyond mRNA decay.","evidence":"RIP-chip and in vitro binding for TERC/hTR G4; poly I:C affinity purification, Co-IP, domain mapping, and shRNA knockdown for the TRIF/DDX1/DDX21 complex","pmids":["21846770","21149580","21703541"],"confidence":"High","gaps":["Whether helicase activity is required for telomerase assembly was not resolved here","How DHX36 is recruited into the dsRNA-sensing complex remained partly open"]},{"year":2012,"claim":"Demonstrated DHX36 is essential in vivo and that its developmental requirement reflects G4 resolvase activity on target gene promoters.","evidence":"Conditional knockout mouse (Vav1-Cre) with hematopoietic phenotyping and transcriptomics; in vitro hTR helicase assay with telomere length measurement","pmids":["22422825","22238380"],"confidence":"High","gaps":["Direct in vivo demonstration that promoter G4 resolution drives the transcriptome changes was correlative","Embryonic lethality precluded analysis of germline-null adult phenotypes"]},{"year":2013,"claim":"Extended DHX36 function to post-transcriptional silencing, placing it within miRNA/Ago2-dependent translational repression and dendritic RNA localization.","evidence":"RNA-IP, loss-of-function, dendritic spine morphometry (pre-miR-134); RIP, siRNA, and Ago2 co-depletion (PITX1 3'UTR G4)","pmids":["23651854","24369427"],"confidence":"High","gaps":["Mechanism coupling G4 resolution to Ago2 recruitment not dissected","Whether helicase ATPase activity is required for the silencing role unclear"]},{"year":2014,"claim":"Defined a dsRNA-dependent partnership with PKR and a positive role in antiviral stress granule formation and interferon production.","evidence":"Reciprocal dsRNA-dependent Co-IP, DHX36 KO MEF cells, IFN and viral infection assays","pmids":["24651521"],"confidence":"High","gaps":["Apparent positive role here later reconciled with a restraining rheostat function","Direct effect of helicase activity on PKR autophosphorylation not structurally resolved"]},{"year":2015,"claim":"Provided the structural mechanism of parallel-G4 specificity and showed in vivo that dual UTR regulation and G4 promoter binding underlie cardiac and germ-cell development.","evidence":"NMR peptide-G4 structure; cardiac and germ-cell conditional KO mice with RIP, translation/decay assays, and c-kit promoter pulldown","pmids":["26195789","26489465","25611385"],"confidence":"High","gaps":["c-kit promoter regulation rests on a single lab","How a single protein selects translation-promoting versus decay-promoting outcomes on the same mRNA not mechanistically defined"]},{"year":2016,"claim":"Resolved the nucleotide-state logic of G4 handling — binding stabilizes, hydrolysis destabilizes — and mapped additional roles in stress granules, p53 pre-mRNA processing, and nuclear localization.","evidence":"Single-molecule magnetic tweezers with nucleotide-state control and domain mutants; SG localization mapping; pre-mRNA 3'-end processing assays; immunofluorescence/fractionation","pmids":["28069994","18854321","27940037","18279852","26740632"],"confidence":"High","gaps":["Distinction between stabilizing and destabilizing modes in vivo not established","Functional significance of nucleolar cap relocalization unresolved"]},{"year":2017,"claim":"Established the translocation-based unwinding mechanism, showing DHX36 loads on a 3' tail and moves 3'→5' to disrupt G4 far more efficiently than duplex DNA.","evidence":"In vitro kinetic assays with G4 substrates and PEG-linker translocation blocks","pmids":["29269411"],"confidence":"High","gaps":["Kinetics performed on model substrates, not endogenous chromatin G4","Did not address RNA G4 mechanistic differences"]},{"year":2018,"claim":"Delivered atomic-resolution mechanism: the DSM-induced α-helix plus OB-fold and RecA2 pocket capture parallel G4 and drive stepwise tail-pulling unfolding, and revealed RNA-vs-DNA mechanistic asymmetry and a translation-licensing role in cells.","evidence":"X-ray co-crystallography of multiple states plus smFRET (bovine and Drosophila); ribosome profiling with DHX36/DHX9 depletion and PAR-CLIP","pmids":["29899445","29429875","30591072"],"confidence":"High","gaps":["Structures captured discrete states rather than full processive cycle","Functional overlap and division of labor with DHX9 not fully delineated"]},{"year":2019,"claim":"Defined the transcriptome-wide rG4 regulon and the asymmetric RNA-G4 mechanism, showing DHX36 binds >4500 mRNAs and renders rG4 transcripts translationally competent while restraining stress granules and PKR.","evidence":"PAR-CLIP, KO cell lines with polysome/ribosome profiling, SG imaging; smFRET with mutagenesis revealing ATP-independent RNA-G4 unfolding/refolding","pmids":["31160600","31015431"],"confidence":"High","gaps":["Why RNA-G4 unfolding is ATP-independent while DNA-G4 unfolding requires hydrolysis not fully explained","Direct in vivo demonstration of refolding role lacking"]},{"year":2020,"claim":"Dissected the contributions of auxiliary domains (DSM, OB-fold, β-hairpin) to recognition versus remodeling and showed the DSM accelerates G4 capture (on-rate) without affecting the disruption step.","evidence":"Mouse DHX36-ADP crystal structure with mutagenesis and helicase assays; kinetic binding assays with DSM truncation; lncRNA GSEC inhibition assays","pmids":["32087197","33857359","27797375"],"confidence":"High","gaps":["How separable capture and disruption steps are coordinated during processive cycles unclear","Physiological scope of lncRNA-mediated inhibition not established"]},{"year":2021,"claim":"Established DHX36 as broadly essential for adult tissue regeneration and identified specific 5'UTR rG4 targets and a lncRNA/EIF3B co-factor axis, while linking it to repeat RNA translation.","evidence":"Inducible satellite-cell and cardiomyocyte conditional KO mice with PAR-CLIP, polysome profiling, RIP, and target validation (Gnai2, Yap1/Hexim1, Anp32e via Lockd); C9orf72 RAN translation reporters","pmids":["34413292","33199370","35675771","34174288"],"confidence":"Medium","gaps":["Generality of the Lockd/EIF3B translation-activating complex across cell types unknown","Pathological consequences of DHX36-driven repeat RAN translation in disease not established in vivo"]},{"year":2022,"claim":"Reinforced the 5'UTR rG4 translation-derepression paradigm at additional immune-relevant targets and showed nuclear DHX36 protects genomic integrity from transcription-associated G4-DNA.","evidence":"rG4-specific cellular probes with KD/KO and translation assays (ADAR1); depletion with γH2AX, G4 co-localization, and G4-binding-mutant rescue","pmids":["36300875","37632696"],"confidence":"Medium","gaps":["Whether ADAR1 derepression alters editing output not addressed","Partial rescue by G4-binding mutants implies G4-independent contributions to genome maintenance"]},{"year":2024,"claim":"Unified the dual UTR phenomenon mechanistically by showing transcript-wide structural remodeling that increases 3'UTR accessibility and recruits YTHDF1 to m6A sites for decay, and tied promoter-G4 resolution to cardiac conduction-system morphogenesis.","evidence":"RNA structurome-seq with DHX36 depletion, m6A mapping, YTHDF1 CLIP, KO cells; cardiac conditional KO with snRNA-seq and snATAC-seq","pmids":["39543097","39366945"],"confidence":"High","gaps":["How DHX36 binding at one site propagates structure changes across an entire transcript not mechanistically defined","Direct demonstration that promoter G4 resolution causes the conduction phenotype remains correlative"]},{"year":2025,"claim":"Recast DHX36 as a rheostat for innate immunity and rRNA biogenesis, defined a REV1 replication-coupling partnership and viral antagonism, and provided cryo-EM-based DNA/RNA discrimination logic.","evidence":"KO cells with PKR/SG/ISG/RIG-I and viral replicon assays; oocyte conditional KO with rRNA processing and rescue; REV1 Co-IP/domain mapping; cryo-EM of RNA/DNA G4 complexes with smFRET; PCV3 ubiquitination/degradation assays; StAR 3'UTR G4 KD with hormonal readout","pmids":["42213826","40023726","40833853","42258547","39862752","41354365","40985767"],"confidence":"High","gaps":["How dsRNA exposure mechanistically lowers DHX36 activity to license immune activation not fully defined","Whether RecA2-mediated DNA/RNA discrimination dictates the distinct in-cell DNA versus RNA roles untested in vivo"]},{"year":null,"claim":"It remains unresolved how a single DHX36 molecule selects between opposing fates on the same transcript (5'UTR translation activation versus 3'UTR-driven decay) and how its activity is dynamically tuned across nuclear, cytoplasmic, and immune contexts.","evidence":"No single study in the corpus reconciles the determinants of DHX36 functional output across compartments","pmids":[],"confidence":"Low","gaps":["No model integrates compartment-specific cofactors, post-translational regulation, and substrate features into a predictive logic","Whether the nucleotide-state stabilize/destabilize switch operates the same way on cellular G4-DNA and G4-RNA is untested in vivo"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0,2,5,21,22,26]},{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[1,15,22]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[2,4,7,20,26]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0,12,22,32]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[19,20,29,33,34]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[15,22]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[16,32]},{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[16,44]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[14,20,39]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[1,20,36]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[3,9,41]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[24,37]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[6,11,29,35,37,44]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[32,40]}],"complexes":["TRIF/DDX1/DDX21 dsRNA-sensing complex","telomerase holoenzyme (via TERC/hTR)","DHX36-PKR complex"],"partners":["PARN","TRIF","DDX1","DDX21","PKR","YTHDF1","REV1","EIF3B"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9H2U1","full_name":"ATP-dependent DNA/RNA helicase DHX36","aliases":["DEAD/H box polypeptide 36","DEAH-box protein 36","G4-resolvase-1","G4R1","MLE-like protein 1","RNA helicase associated with AU-rich element protein"],"length_aa":1008,"mass_kda":114.8,"function":"Multifunctional ATP-dependent helicase that unwinds G-quadruplex (G4) structures (PubMed:16150737, PubMed:18854321, PubMed:20472641, PubMed:21586581). Plays a role in many biological processes such as genomic integrity, gene expression regulations and as a sensor to initiate antiviral responses (PubMed:14731398, PubMed:18279852, PubMed:21993297, PubMed:22238380, PubMed:25579584). G4 structures correspond to helical structures containing guanine tetrads (By similarity). Binds with high affinity to and unwinds G4 structures that are formed in nucleic acids (G4-DNA and G4-RNA) (PubMed:16150737, PubMed:18842585, PubMed:20472641, PubMed:21586581, PubMed:24369427, PubMed:26195789). Plays a role in genomic integrity (PubMed:22238380). Converts the G4-RNA structure present in telomerase RNA template component (TREC) into a double-stranded RNA to promote P1 helix formation that acts as a template boundary ensuring accurate reverse transcription (PubMed:20472641, PubMed:21149580, PubMed:21846770, PubMed:22238380, PubMed:24151078, PubMed:25579584). Plays a role in transcriptional regulation (PubMed:21586581, PubMed:21993297). Resolves G4-DNA structures in promoters of genes, such as YY1, KIT/c-kit and ALPL and positively regulates their expression (PubMed:21993297). Plays a role in post-transcriptional regulation (PubMed:27940037). Unwinds a G4-RNA structure located in the 3'-UTR polyadenylation site of the pre-mRNA TP53 and stimulates TP53 pre-mRNA 3'-end processing in response to ultraviolet (UV)-induced DNA damage (PubMed:27940037). Binds to the precursor-microRNA-134 (pre-miR-134) terminal loop and regulates its transport into the synapto-dendritic compartment (By similarity). Involved in the pre-miR-134-dependent inhibition of target gene expression and the control of dendritic spine size (By similarity). Plays a role in the regulation of cytoplasmic mRNA translation and mRNA stability (PubMed:24369427, PubMed:26489465). Binds to both G4-RNA structures and alternative non-quadruplex-forming sequence within the 3'-UTR of the PITX1 mRNA regulating negatively PITX1 protein expression (PubMed:24369427). Binds to both G4-RNA structure in the 5'-UTR and AU-rich elements (AREs) localized in the 3'-UTR of NKX2-5 mRNA to either stimulate protein translation or induce mRNA decay in an ELAVL1-dependent manner, respectively (PubMed:26489465). Also binds to ARE sequences present in several mRNAs mediating exosome-mediated 3'-5' mRNA degradation (PubMed:14731398, PubMed:18279852). Involved in cytoplasmic urokinase-type plasminogen activator (uPA) mRNA decay (PubMed:14731398). Component of a multi-helicase-TICAM1 complex that acts as a cytoplasmic sensor of viral double-stranded RNA (dsRNA) and plays a role in the activation of a cascade of antiviral responses including the induction of pro-inflammatory cytokines via the adapter molecule TICAM1 (By similarity). Required for early embryonic development and hematopoiesis. Involved in the regulation of cardioblast differentiation and proliferation during heart development. Involved in spermatogonia differentiation. May play a role in ossification (By similarity)","subcellular_location":"Nucleus; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9H2U1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/DHX36","classification":"Common Essential","n_dependent_lines":988,"n_total_lines":1208,"dependency_fraction":0.8178807947019867},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"DHX9","stoichiometry":0.2},{"gene":"HEATR3","stoichiometry":0.2},{"gene":"HNRNPH1","stoichiometry":0.2},{"gene":"NPM1","stoichiometry":0.2},{"gene":"PSPC1","stoichiometry":0.2},{"gene":"SSB","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/DHX36","total_profiled":1310},"omim":[{"mim_id":"612767","title":"DEAH-BOX HELICASE 36; DHX36","url":"https://www.omim.org/entry/612767"},{"mim_id":"607601","title":"TIR DOMAIN-CONTAINING ADAPTOR MOLECULE 1; TICAM1","url":"https://www.omim.org/entry/607601"},{"mim_id":"606357","title":"DExD-BOX HELICASE 21; DDX21","url":"https://www.omim.org/entry/606357"},{"mim_id":"601257","title":"DEAD-BOX HELICASE 1; DDX1","url":"https://www.omim.org/entry/601257"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/DHX36"},"hgnc":{"alias_symbol":["MLEL1","KIAA1488","RHAU"],"prev_symbol":["DDX36"]},"alphafold":{"accession":"Q9H2U1","domains":[{"cath_id":"3.40.50.300","chopping":"173-387","consensus_level":"high","plddt":92.8093,"start":173,"end":387},{"cath_id":"3.40.50.300","chopping":"394-411_431-626","consensus_level":"high","plddt":90.0383,"start":394,"end":626},{"cath_id":"-","chopping":"688-822","consensus_level":"high","plddt":92.5408,"start":688,"end":822},{"cath_id":"-","chopping":"834-989","consensus_level":"medium","plddt":88.4369,"start":834,"end":989}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H2U1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H2U1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H2U1-F1-predicted_aligned_error_v6.png","plddt_mean":82.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DHX36","jax_strain_url":"https://www.jax.org/strain/search?query=DHX36"},"sequence":{"accession":"Q9H2U1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H2U1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H2U1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H2U1"}},"corpus_meta":[{"pmid":"21703541","id":"PMC_21703541","title":"DDX1, DDX21, and DHX36 helicases form a complex with the adaptor molecule TRIF to sense dsRNA in dendritic cells.","date":"2011","source":"Immunity","url":"https://pubmed.ncbi.nlm.nih.gov/21703541","citation_count":306,"is_preprint":false},{"pmid":"29899445","id":"PMC_29899445","title":"Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36.","date":"2018","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/29899445","citation_count":267,"is_preprint":false},{"pmid":"16150737","id":"PMC_16150737","title":"The DEXH protein product of the DHX36 gene is the major source of tetramolecular quadruplex G4-DNA resolving activity in HeLa cell lysates.","date":"2005","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16150737","citation_count":170,"is_preprint":false},{"pmid":"14731398","id":"PMC_14731398","title":"Facilitation of mRNA deadenylation and decay by the exosome-bound, DExH protein RHAU.","date":"2004","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/14731398","citation_count":158,"is_preprint":false},{"pmid":"26195789","id":"PMC_26195789","title":"Insights into G-quadruplex specific recognition by the DEAH-box helicase RHAU: Solution structure of a peptide-quadruplex complex.","date":"2015","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/26195789","citation_count":141,"is_preprint":false},{"pmid":"31160600","id":"PMC_31160600","title":"DHX36 prevents the accumulation of translationally inactive mRNAs with G4-structures in untranslated regions.","date":"2019","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/31160600","citation_count":137,"is_preprint":false},{"pmid":"22238380","id":"PMC_22238380","title":"The RNA helicase RHAU (DHX36) unwinds a G4-quadruplex in human telomerase RNA and promotes the formation of the P1 helix template boundary.","date":"2012","source":"Nucleic acids 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Recombinant DHX36 expressed in E. coli displayed robust, NTP-dependent G4-DNA resolving activity, and immunodepletion of DHX36 from lysates removed ~77% of the enzyme and reduced G4-DNA resolving activity to ~46% of control.\",\n      \"method\": \"G4-DNA affinity purification, mass spectrometry, in vitro G4-resolvase assay with recombinant protein, immunodepletion\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with recombinant protein, immunodepletion confirming identity, multiple orthogonal methods\",\n      \"pmids\": [\"16150737\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"RHAU (DHX36) physically interacts with the deadenylase PARN and the human exosome, enhancing deadenylation and decay of ARE-containing mRNAs (ARE-uPA). ATPase activity of RHAU is essential for its mRNA-destabilizing function. RHAU recognizes ARE-uPA mRNA via RNA-dependent interaction with AUBPs HuR and NFAR1.\",\n      \"method\": \"Co-immunoprecipitation, mRNA decay assays, ATPase-dead mutant analysis, RNA-protein interaction assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, functional mutant (ATPase-dead), mRNA decay assay, multiple binding partners identified\",\n      \"pmids\": [\"14731398\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The amino-terminal RHAU-specific motif (RSM) of DHX36 is the major affinity and specificity determinant for G4-RNA binding and G4-resolvase activity. Deletion of the RSM abolishes G4 binding and resolution. The Drosophila ortholog CG9323 also requires the RSM for G4-RNA recognition and resolution.\",\n      \"method\": \"Domain deletion/mutagenesis, in vitro G4-binding and resolvase assays, cross-species comparison\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — mutagenesis combined with in vitro binding and activity assays, replicated in Drosophila ortholog\",\n      \"pmids\": [\"20472641\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"DDX1, DDX21, and DHX36 form a complex with adaptor molecule TRIF to sense cytosolic dsRNA in myeloid dendritic cells. DHX36 binds the TIR domain of TRIF via its HA2-DUF domain. Knockdown of DHX36 or TRIF blocked type I IFN and cytokine responses to poly I:C, influenza A virus, and reovirus.\",\n      \"method\": \"Poly I:C affinity purification, Co-IP, shRNA knockdown, cytokine/IFN response assays, domain mapping\",\n      \"journal\": \"Immunity\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — affinity purification identifying complex, domain mapping, functional shRNA knockdown with defined immune phenotype\",\n      \"pmids\": [\"21703541\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"DHX36 binds an intramolecular G4-RNA structure in the 5' region of the telomerase RNA TERC in vivo and in vitro. RHAU associates with the telomerase holoenzyme via the 5' region of TERC. Binding requires the intact G4 structure.\",\n      \"method\": \"RIP-chip (RNA immunoprecipitation-microarray), in vitro binding assays, bioinformatics\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — RIP-chip for transcriptome-wide discovery plus in vitro validation, G4-dependence confirmed by mutation\",\n      \"pmids\": [\"21846770\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"RHAU (DHX36) unwinds a G4-quadruplex in human telomerase RNA (hTR) 5' region, promoting formation of the P1 helix template boundary required for reverse transcription. RHAU knockdown reduced average telomere length.\",\n      \"method\": \"In vitro helicase assay, RNA structural analysis, siRNA knockdown, telomere length measurement\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro helicase reconstitution plus functional knockdown with telomere phenotype, single lab\",\n      \"pmids\": [\"22238380\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"RHAU is essential for mouse hematopoiesis; germ-line deletion causes embryonic lethality, and hematopoietic-specific deletion causes hemolytic anemia and differentiation block at the proerythroblast stage due to a proliferation defect. Deregulated genes in knockout proerythroblasts are enriched for G4 motifs in their promoters, suggesting G4 resolvase activity underlies the phenotype.\",\n      \"method\": \"Conditional knockout mouse (Vav1-Cre), hematopoietic phenotyping, transcriptome analysis\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean conditional knockout with defined cellular phenotype (proerythroblast block) and transcriptomic support\",\n      \"pmids\": [\"22422825\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"DHX36 directly associates with the terminal loop of precursor-miR-134 (pre-miR-134) and mediates its dendritic localization in hippocampal neurons. DHX36 function is required for miR-134-dependent inhibition of target gene expression and control of dendritic spine size.\",\n      \"method\": \"RNA immunoprecipitation, in situ localization, DHX36 loss-of-function, dendritic spine morphometry, target gene expression assays\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct RNA binding confirmed by RIP, loss-of-function with defined morphological and gene expression phenotypes\",\n      \"pmids\": [\"23651854\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"RHAU (DHX36) binds G4 structures in the 3' UTR of PITX1 mRNA. RHAU knockdown increases PITX1 protein levels with only marginal mRNA changes, indicating translational repression. This regulation requires Argonaute-2 and is non-additive with Dicer knockdown, placing RHAU in microRNA-mediated translational silencing.\",\n      \"method\": \"RNA co-immunoprecipitation, siRNA knockdown, Western blot, Ago2 co-depletion\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RIP plus functional knockdown, single lab, mechanism of Ago2 link not fully dissected\",\n      \"pmids\": [\"24369427\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"DHX36 forms a complex with PKR (dsRNA-dependent protein kinase) in a dsRNA-dependent manner and facilitates dsRNA binding and phosphorylation (activation) of PKR through its ATPase/helicase activity, promoting antiviral stress granule (avSG) formation and RIG-I signaling. DHX36 KO MEF cells show defective IFN production and increased susceptibility to RNA virus infection.\",\n      \"method\": \"Co-immunoprecipitation (dsRNA-dependent), DHX36 knockout inducible MEF cells, IFN production assay, viral infection assay\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, KO cell line with defined IFN/antiviral phenotype, ATPase dependence demonstrated\",\n      \"pmids\": [\"24651521\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"An 18-amino-acid N-terminal G-quadruplex-binding domain of RHAU folds upon G4 binding and covers a terminal guanine tetrad using three-anchor-point electrostatic interactions between positively charged residues and phosphate groups, conferring parallel G4 specificity.\",\n      \"method\": \"NMR solution structure of peptide-G4 complex, binding assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — NMR structure with defined binding interactions, explains parallel G4 specificity mechanistically\",\n      \"pmids\": [\"26195789\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Cardiac deletion of Rhau causes heart defects and embryonic lethality. Nkx2-5 mRNA is a RHAU target: RHAU binds the 5' UTR G4 to promote protein translation and the 3' UTR ARE to facilitate mRNA decay, providing dual post-transcriptional regulation of Nkx2-5 in heart development.\",\n      \"method\": \"Cardiac-specific conditional knockout mouse, gene expression profiling, RNA co-IP, mRNA stability and translation assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — conditional KO with defined cardiac phenotype, RIP-confirmed target, dual mechanistic (translation + decay) readouts\",\n      \"pmids\": [\"26489465\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"RHAU is essential for spermatogonia differentiation; germ-cell-specific knockout increases G4 DNA accumulation and reduces expression of c-kit (a differentiation gene with G4 motifs in its promoter). RHAU directly binds to G4 structures in the c-kit promoter to activate c-kit expression.\",\n      \"method\": \"Germ-cell-specific conditional knockout mouse, G4 probe staining, chromatin pull-down, c-kit expression analysis\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional KO with phenotype, direct G4-promoter binding shown, single lab\",\n      \"pmids\": [\"25611385\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"DHX36 binds the G4 structure near the polyadenylation site of p53 pre-mRNA and is necessary to maintain p53 pre-mRNA 3'-end processing following UV-induced DNA damage. G4 mutation or G4-stabilizing ligands impair this processing.\",\n      \"method\": \"RNA binding assays, siRNA knockdown, pre-mRNA 3'-end processing assays, G4 mutation and pharmacological G4 stabilization\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding assay, functional knockdown, G4 dependence shown by mutation and ligand, single lab\",\n      \"pmids\": [\"27940037\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"RHAU is recruited to stress granules via a newly identified N-terminal RNA-binding domain that is both necessary and sufficient for SG localization. ATPase activity of RHAU modulates RNA interaction and regulates protein retention in SGs.\",\n      \"method\": \"Live imaging, domain deletion mapping, ATPase-dead mutant, stress granule marker co-localization\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — localization mapped to specific domain with functional consequence (SG association), ATPase dependence shown, single lab\",\n      \"pmids\": [\"18854321\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"RHAU stabilizes G4 DNA in nucleotide-free, AMP-PNP-bound, and ADP-bound states, but destabilizes G4 upon ATP hydrolysis. Both the 3' ssDNA tail and the RSM domain are dispensable for G4 stabilization but required for G4 destabilization, demonstrating distinct functional requirements for binding versus unfolding.\",\n      \"method\": \"Single-molecule magnetic tweezers with Drosophila RHAU, nucleotide-state manipulation, RSM and tail mutants\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — single-molecule biophysics with nucleotide-state control and domain mutants, single lab\",\n      \"pmids\": [\"28069994\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"RHAU is localized predominantly in the nucleus under normal conditions; transcriptional arrest redistributes it to nucleolar caps where it co-localizes with RNA helicases p68 and p72. Knockdown affects steady-state mRNA levels without altering mRNA half-lives for most affected transcripts, suggesting a transcriptional rather than mRNA decay role in the nucleus.\",\n      \"method\": \"Immunofluorescence, subcellular fractionation, transcriptional inhibitor treatment, microarray analysis with actinomycin D chase\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment with functional follow-up (mRNA half-life analysis), single lab\",\n      \"pmids\": [\"18279852\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Co-crystal structure of bovine DHX36 bound to a parallel G4-DNA with a 3' ssDNA tail reveals that the N-terminal DHX36-specific motif (DSM) folds into a DNA-binding-induced α-helix that, together with an OB-fold-like subdomain, selectively binds parallel G4s. Comparison of unliganded, ATP-analogue-bound, and G4-bound structures plus smFRET analyses suggests G4 binding induces helicase core rearrangements that drive unfolding by pulling the ssDNA tail one residue at a time.\",\n      \"method\": \"X-ray co-crystallography (multiple structures), single-molecule FRET (smFRET)\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution crystal structures of multiple states combined with smFRET, mechanistic model directly supported by structural data\",\n      \"pmids\": [\"29899445\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Crystal structures of Drosophila DHX36 (DmDHX36) in complex with RNA and various DNAs reveal that positively charged residues in RecA2 and OB-like domains form a structural pocket at the nucleic acid entrance where G4 DNA is tightly bound and partially destabilized, followed by complete unfolding via 3'–5' translocation.\",\n      \"method\": \"X-ray crystallography, SAXS, molecular dynamics simulation, single-molecule fluorescence, DNA binding assays\",\n      \"journal\": \"Structure\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structures plus multiple orthogonal biophysical methods, mechanistic model supported\",\n      \"pmids\": [\"29429875\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Depletion of DHX36 or DHX9 promotes translation of rG4-associated upstream open reading frames (uORFs) while reducing translation of main ORFs of rG4-containing mRNAs including proto-oncogenes and transcription factors. DHX9 mediates this through direct physical interaction with rG4 substrates.\",\n      \"method\": \"Ribosome profiling (transcriptome-wide), siRNA depletion of DHX36 and DHX9, transcriptome-wide DHX9 binding site mapping (PAR-CLIP)\",\n      \"journal\": \"Genome biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — transcriptome-wide ribosome profiling and CLIP-seq, functional depletion, multiple mRNA targets\",\n      \"pmids\": [\"30591072\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"DHX36 binds G-rich and G4-forming sequences on >4500 mRNAs genome-wide. DHX36 KO increases target mRNA abundance but decreases ribosome occupancy and protein output, indicating these mRNAs become translationally incompetent. DHX36 KO increases stress granule formation and PKR phosphorylation.\",\n      \"method\": \"PAR-CLIP (global RNA binding mapping), DHX36 knockout cell lines, polysome profiling, ribosome profiling, stress granule imaging\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — PAR-CLIP plus KO with ribosome profiling, multiple orthogonal readouts, single lab\",\n      \"pmids\": [\"31160600\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"DHX36 displays ATP-independent unfolding of G4-RNA followed by ATP-dependent refolding, a highly asymmetric pattern distinct from its G4-DNA activity. ATP-dependent activity arises from the RNA tail rather than the G4 itself. Mutations perturbing G4 contact cause rapid protein dissociation upon ATP hydrolysis; mutations interfering with RNA tail binding cause dysregulated activity.\",\n      \"method\": \"Single-molecule FRET, site-directed mutagenesis, in vitro helicase assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — smFRET with mutagenesis revealing mechanistic asymmetry between DNA and RNA G4 substrates\",\n      \"pmids\": [\"31015431\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"DHX36 disrupts DNA G4s via a translocation-based helicase mechanism: it loads onto a 3' ssDNA extension and translocates 3'–5' toward the G4. Disruption rates depend on G4 length under saturating conditions (kcat) but not subsaturating (kcat/K), and a polyethylene glycol linker blocking translocation abolishes activity. DHX36 unwinds G4s far more efficiently than dsDNA of comparable intrinsic lifetime.\",\n      \"method\": \"In vitro kinetic assays with tetramolecular and unimolecular G4 substrates, linker-block experiments\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — rigorous kinetic framework with mechanistic controls, in vitro reconstitution, single lab\",\n      \"pmids\": [\"29269411\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"DHX36 (RHAU) binds the G-quadruplex-forming 5' guanosine tracts of human telomerase RNA (hTR) via its N-terminal accessory domain (not the helicase domain). G4 mutations in hTR substantially reduce mature hTR accumulation and telomere maintenance, suggesting G4 formation protects immature hTR from degradation.\",\n      \"method\": \"Co-immunoprecipitation, domain mapping, hTR guanosine tract substitution mutants, telomere maintenance assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain mapping and functional RNA mutants, single lab\",\n      \"pmids\": [\"21149580\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"DHX36 facilitates TNAP transcription by binding the MS-275 response element in the TNAP promoter. DHX36 physically interacts with HDAC1 and HDAC4, and MS-275 (HDAC inhibitor) decreases this HDAC–DHX36 interaction, relieving transcriptional repression of TNAP.\",\n      \"method\": \"DNA affinity precipitation assay, co-immunoprecipitation, TNAP promoter deletion reporter assays, HDAC inhibitor treatment\",\n      \"journal\": \"Journal of bone and mineral research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — DNA affinity pulldown, co-IP, promoter reporter assays, single lab\",\n      \"pmids\": [\"21590736\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"RHAU (DHX36) interacts with the 3' adenosine-rich region of long non-coding RNA BC200 (BCYRN1) via a C-terminal region specific to RHAU isoform 1; this binding is independent of G4 structure. BC200 can act as an acceptor of unwound G4 substrates via a cytosine-rich region and interacts with G4-containing telomerase RNA, suggesting RHAU may direct BC200 to G4-containing targets.\",\n      \"method\": \"RNA co-immunoprecipitation, RNase footprinting, RHAU truncation binding assays, pulldown of endogenous RNAs\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro binding with domain mapping and RNase footprinting, endogenous RNA pulldown, single lab\",\n      \"pmids\": [\"26740632\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The DHX36-specific motif (DSM), OB-fold, and a conserved β-hairpin (β-HP) each contribute to RNA binding and are essential for remodeling of RNA quadruplex and duplex structures. The DSM functions not only as a G4-binding adaptor but also promotes RNA duplex unwinding. Crystal structure of mouse DHX36 bound to ADP reveals conformational changes accompanying ATPase cycle stages.\",\n      \"method\": \"X-ray crystallography (mouse DHX36-ADP), domain deletion/mutagenesis, RNA binding assays, in vitro helicase assays\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with biochemical mutagenesis characterizing auxiliary domain functions, single lab\",\n      \"pmids\": [\"32087197\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The DHX36-specific motif (DSM) promotes G4 recognition by increasing the G4 binding rate (on-rate) of DHX36 without affecting the dissociation rate. For most G4 substrates, the DSM has little effect on the G4 disruption step, suggesting initial G4 capture and disruption are mechanistically separable.\",\n      \"method\": \"Kinetic binding assays with DHX36 DSM truncation, stopped-flow or competition assays\",\n      \"journal\": \"Biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — quantitative kinetics with truncation mutant, mechanistically informative, single lab\",\n      \"pmids\": [\"33857359\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The lncRNA GSEC binds DHX36 via its G4-forming sequence and inhibits DHX36 G-quadruplex unwinding activity. DHX36 knockdown restores reduced migratory activity caused by GSEC knockdown in colon cancer cells, placing DHX36 downstream of GSEC in regulating cell migration.\",\n      \"method\": \"RNA pull-down, G4-unwinding assay with GSEC, siRNA knockdown, cell migration assay\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding and activity inhibition shown in vitro, genetic epistasis by double knockdown, single lab\",\n      \"pmids\": [\"27797375\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"DHX36 is essential for muscle satellite cell (SC) expansion and muscle regeneration. Inducible deletion of Dhx36 in adult SCs causes defective proliferation and muscle regeneration. DHX36 promotes mRNA translation via 5'UTR rG4 binding; specifically, it regulates translation of Gnai2 mRNA by unwinding its 5'UTR rG4, with GNAI2 identified as a downstream effector for SC expansion.\",\n      \"method\": \"Inducible SC-specific conditional knockout mouse, muscle injury model, PAR-CLIP (system-wide DHX36 binding), polysome profiling, in vitro rG4 unwinding assay\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — conditional KO with defined regeneration phenotype, PAR-CLIP plus polysome profiling, specific target (Gnai2) validated mechanistically\",\n      \"pmids\": [\"34413292\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"DHX36 depletion suppresses C9orf72 G4C2 repeat-associated non-AUG (RAN) translation in a repeat length-dependent manner, while DHX36 overexpression enhances RAN translation. Upregulation of RAN translation by integrated stress response activation is prevented by DHX36 loss, demonstrating DHX36 promotes translation of G4-forming repeat RNAs.\",\n      \"method\": \"Luciferase reporter assays (cell-based and cell-free), DHX36 depletion and overexpression, integrated stress response induction\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reporter assays with depletion/overexpression, repeat-length dependence shown, single lab\",\n      \"pmids\": [\"34174288\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"RHAU ablation in postnatal cardiomyocytes reduces protein levels of Yap1 and Hexim1 while enhancing their mRNA levels. RHAU associates with both 5' and 3' UTRs of these genes to simultaneously promote translation (via 5'UTR) and destabilize mRNA (via 3'UTR). RHAU-deficient mice develop progressive dilated cardiomyopathy and impaired neonatal heart regeneration.\",\n      \"method\": \"Cardiomyocyte-specific conditional knockout mouse, RNA co-IP (5' and 3'UTR), Western blot, mRNA stability assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional KO with defined cardiac phenotype, RIP-based mechanistic analysis of dual UTR regulation, single lab\",\n      \"pmids\": [\"33199370\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"DHX36 deficiency leads to accumulation of DNA damage and slower cell growth; expression of G4-binding-deficient DHX36 mutants only partially rescues these defects. Nuclear DHX36 co-localizes with G4-DNA, RNA polymerase II, and a splicing factor, supporting a role in clearing transcription-associated G4-DNA to maintain genomic integrity.\",\n      \"method\": \"DHX36 depletion, G4-stabilizing drug treatment, DNA damage markers (γH2AX), immunofluorescence co-localization, G4-binding mutant rescue assay\",\n      \"journal\": \"Genes to cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — depletion with DNA damage phenotype, mutant rescue, co-localization, single lab\",\n      \"pmids\": [\"37632696\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DHX36 interacts with a rG4 structure in the 5'UTR of ADAR1 mRNA in vitro and in cells. This rG4 normally inhibits ADAR1 translation; DHX36 binding relieves this inhibition in an rG4-dependent manner, as shown in knockdown and knockout conditions.\",\n      \"method\": \"In vitro rG4 characterization, GTFH probes for cellular rG4 detection, DHX36 knockdown/knockout, reporter and native gene translation assays\",\n      \"journal\": \"Angewandte Chemie\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro binding plus cellular KD/KO with rG4-specific probes, single lab\",\n      \"pmids\": [\"36300875\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The lncRNA Lockd directly interacts with DHX36 (strongest binding at Lockd 5' end) and stabilizes DHX36 interaction with EIF3B; this tripartite complex unwinds the rG4 at Anp32e mRNA 5'UTR to promote ANP32E translation, which is required for myoblast proliferation and muscle regeneration.\",\n      \"method\": \"RNA immunoprecipitation, co-IP, in vitro rG4 unwinding assay, Lockd deletion in vivo, ANP32E translation assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RIP, co-IP, in vitro unwinding, in vivo deletion; specific target validated, single lab\",\n      \"pmids\": [\"35675771\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Dhx36 deletion in differentiated spermatogonia (Stra8-GFPCre) leads to meiotic defects and abnormal spermiogenesis due to dysregulated transcription of G4-harboring genes required for meiosis.\",\n      \"method\": \"Stage-specific conditional knockout mouse, phenotypic analysis of meiosis/spermiogenesis, transcriptome analysis\",\n      \"journal\": \"Journal of molecular cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional KO with defined meiotic phenotype and transcriptomic support, single lab\",\n      \"pmids\": [\"36484653\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"DHX36 binding induces structural remodeling of mRNA not only at localized binding sites but across entire transcripts, most prominently increasing 3'UTR accessibility. Increased 3'UTR accessibility correlates with decreased mRNA abundance. DHX36 binding sites are enriched for m6A modification and YTHDF1 binding; DHX36-induced structural changes facilitate YTHDF1 binding to m6A sites, leading to mRNA degradation.\",\n      \"method\": \"RNA structurome-seq upon DHX36 depletion, m6A mapping, YTHDF1 CLIP, DHX36 KO cell lines, mRNA abundance assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — transcriptome-wide RNA structure mapping, m6A/YTHDF1 integration, KO validation, multiple orthogonal methods\",\n      \"pmids\": [\"39543097\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Dhx36 deletion in embryonic or neonatal heart causes dilated cardiomyopathy and failure to develop a ventricular conduction system (VCS). DHX36 deficiency disrupts resolution of promoter G-quadruplexes in key cardiac genes, impacting cardiomyocyte differentiation and Purkinje fiber network morphogenesis.\",\n      \"method\": \"Cardiac conditional knockout mouse, single-nucleus RNA-seq, single-nucleus ATAC-seq, G4 promoter analysis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — conditional KO with defined cardiac/conduction phenotype, snRNA-seq and snATAC-seq mechanistic analysis, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"39366945\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cryo-EM structures of bovine DHX36 bound to a three-tier RNA G4 and a six-tier DNA G4 at 2.6 Å and 3.4 Å resolution respectively reveal that the RecA2 domain of the helicase core plays a key role in DNA vs. RNA discrimination. A sequence-divergent RecA2 surface loop synergizes with the DHX36-specific N-terminal extension to recognize G4 structures over other nucleic acids.\",\n      \"method\": \"Cryo-electron microscopy structure determination, smFRET, site-directed mutagenesis of RecA2 and N-terminal extension\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structures at near-atomic resolution with structure-guided mutagenesis validated by smFRET and kinetics, single lab\",\n      \"pmids\": [\"40833853\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"DHX36 limits stress granule formation; in G3BP1/2 double-knockout cells that strongly inhibit SG formation, reducing DHX36 expression rescues SG-like foci formation, indicating DHX36 can restrain intermolecular RNA-RNA interactions (potentially trans-rG4s) that promote SG assembly. mRNA accumulation in SGs is independent of rG4-forming potential in normal cells.\",\n      \"method\": \"DHX36 depletion in G3BP1/2 KO cells, reporter mRNAs with/without G-tracts, endogenous mRNA SG partitioning by FISH\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic rescue experiment in double-KO background, negative controls for G-tract role are informative, single lab\",\n      \"pmids\": [\"40985767\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"REV1 C-terminal domain directly interacts with DHX36, requiring a newly defined REV1-interacting region at the DHX36 C-terminus. This interaction coordinates G4 resolution (DHX36 helicase) with suppression of ssDNA gaps during replication of G4-containing DNA. Prolonged G4 stabilization uncouples REV1 and DHX36.\",\n      \"method\": \"Co-immunoprecipitation (direct interaction), domain mapping, REV1 KO cells, G4-stabilizing drug (pyridostatin) treatment, DNA damage assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct protein-protein interaction with domain mapping, functional uncoupling by G4 stabilizer, KO phenotype, single lab\",\n      \"pmids\": [\"42258547\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"DHX36 functions as a rheostat restraining innate immune activation under homeostasis. Exposure to dsRNA reduces DHX36 activity to enable immune activation. DHX36-deficient cells accumulate rG4 structures, show constitutive PKR-dependent stress granule formation, elevated ISG expression, and enhanced RIG-I responsiveness, positioning DHX36 as a regulator linking RNA structure surveillance to PKR- and RIG-I-dependent antiviral signaling.\",\n      \"method\": \"DHX36 KO cells, dsRNA treatment, PKR activation assays, SG formation assays, ISG expression profiling, RIG-I reporter assays, yellow fever virus replicon assay\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — KO cells with multiple orthogonal mechanistic readouts (PKR, SG, ISG, RIG-I, viral replication), single lab\",\n      \"pmids\": [\"42213826\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PCV3 capsid protein interacts with DHX36 via Cap-NLS and DHX36 N-terminal domain (NTD), and promotes K48-linked ubiquitination-dependent degradation of DHX36, thereby antagonizing DHX36-mediated IFN-β production and facilitating PCV3 replication.\",\n      \"method\": \"Co-immunoprecipitation, domain mapping, ubiquitination assay, siRNA knockdown, overexpression, viral replication assay\",\n      \"journal\": \"Virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP with domain mapping, ubiquitination shown, functional antiviral assay, single lab\",\n      \"pmids\": [\"39862752\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RHAU binds the G4 structure in the 3'UTR of StAR (steroidogenic acute regulatory protein) mRNA; conditional RHAU knockdown reduces STAR translation and testosterone levels in mice. RHAU regulates StAR mRNA stability and translation efficiency through this G4 interaction.\",\n      \"method\": \"Circular dichroism, RNA-protein interaction assay, RHAU conditional knockdown mouse, ELISA for testosterone, gene expression analysis\",\n      \"journal\": \"Archives of biochemistry and biophysics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro RNA-protein binding plus in vivo conditional knockdown with hormonal readout, single lab\",\n      \"pmids\": [\"41354365\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"DHX36 directly binds pre-rRNA through its RSM (RHAU-specific motif) in mouse oocytes. DHX36 deletion in oocytes causes G4 accumulation at rDNA and pre-rRNA, insufficient pre-rRNA processing, reduced translation, aberrant chromatin configuration, and complete female infertility. DHX36 overexpression partially rescues pre-rRNA accumulation in knockout oocytes.\",\n      \"method\": \"Oocyte-specific conditional KO mouse, G4 probe/antibody staining, rRNA transcription assay, translation assay, DHX36 overexpression rescue\",\n      \"journal\": \"Science bulletin\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — conditional KO with severe phenotype, direct RSM-pre-rRNA interaction demonstrated in vitro and in vivo, rescue experiment, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"40023726\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The lncRNA LENT interacts with DHX36 and both associate with ribosomes in 80S and light polysome fractions. LENT modulates DHX36 association with specific mRNAs encoding ER/mitochondrial homeostasis and autophagy regulators, fine-tuning their translation. LENT silencing leads to autophagy, mitophagy, and apoptosis in melanoma cells.\",\n      \"method\": \"RNA immunoprecipitation, polysome fractionation, LENT silencing, ribosome association assay\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, RIP and polysome fractionation without full mechanistic dissection, single lab\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"DHX36 (RHAU) is a DEAH-box helicase that uses an N-terminal RSM/DSM domain to selectively recognize parallel G-quadruplex (G4) structures in DNA and RNA, then unwinds them via ATP-driven 3'→5' translocation from a 3' ssDNA tail; structurally, the DSM folds into a G4-induced α-helix that caps a guanine tetrad while the RecA2 and OB-fold domains translocate the substrate, with ATP hydrolysis (not binding alone) driving net G4 unfolding; in cells DHX36 resolves G4s in mRNA 5'UTRs to promote translation, in 3'UTRs to destabilize mRNAs (linked to YTHDF1/m6A-dependent decay), and at gene promoters to activate transcription, while also forming complexes with TRIF/DDX1/DDX21 and PKR to regulate innate immune (type I IFN) signaling in response to dsRNA, and is essential for embryogenesis, cardiac development, hematopoiesis, muscle regeneration, spermatogenesis, and female fertility in mice.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DHX36 (RHAU) is a DEAH-box helicase that serves as the principal cellular activity for resolving parallel G-quadruplex (G4) structures in both DNA and RNA, coupling structure-specific recognition to ATP-driven unfolding to control gene expression across transcription, translation, mRNA decay, and innate immunity [#0, #2]. Substrate selectivity is conferred by an N-terminal DHX36-specific motif (RSM/DSM) that folds into a G4-induced \\u03b1-helix capping a terminal guanine tetrad through three-anchor electrostatic contacts, with the RecA2 and OB-fold domains completing recognition and translocation [#10, #17, #38]; the helicase loads onto a 3' single-stranded tail and translocates 3'\\u21925', and net G4 unfolding requires ATP hydrolysis rather than nucleotide binding alone, with binding/capture and disruption being mechanistically separable steps [#15, #22, #27]. In the cytoplasm DHX36 binds G4-forming sequences across thousands of mRNAs, unwinding 5'UTR rG4s to license translation and promoting 3'UTR remodeling that drives YTHDF1/m6A-dependent decay, thereby exerting opposing dual post-transcriptional control on individual transcripts [#11, #20, #36]. In the nucleus it resolves promoter and transcription-associated G4-DNA to activate gene expression and maintain genomic integrity, coordinating with REV1 during replication of G4-containing DNA [#32, #37, #40]. DHX36 also governs antiviral signaling, partnering with TRIF/DDX1/DDX21 and with PKR in a dsRNA-dependent manner and acting as a rheostat that restrains constitutive PKR- and RIG-I-driven type I interferon responses by surveilling RNA structure [#3, #9, #41]. Through these activities DHX36 is essential in mice for hematopoiesis, cardiac development and conduction-system formation, muscle satellite cell expansion, spermatogenesis, and oocyte rRNA processing and female fertility [#6, #29, #37, #44].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Established the first molecular function for RHAU as an mRNA-destabilizing factor, linking it to deadenylation machinery before its G4 activity was known.\",\n      \"evidence\": \"Co-IP with PARN/exosome, ATPase-dead mutant, and ARE-mRNA decay assays\",\n      \"pmids\": [\"14731398\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not connect decay activity to G4 structures\", \"Mechanism of substrate selection via HuR/NFAR1 not fully resolved\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Identified DHX36 as the dominant cellular G4-DNA resolvase, defining its signature biochemical activity.\",\n      \"evidence\": \"G4-DNA affinity purification, mass spectrometry, recombinant resolvase assay, and immunodepletion of HeLa lysates\",\n      \"pmids\": [\"16150737\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the structural basis of G4 recognition\", \"Residual resolving activity after depletion implies additional G4 helicases\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Localized G4 recognition specificity to the N-terminal RSM, separating substrate recognition from the helicase core.\",\n      \"evidence\": \"Domain deletion/mutagenesis with in vitro binding and resolvase assays, conserved in the Drosophila ortholog\",\n      \"pmids\": [\"20472641\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic basis of RSM-G4 contact not yet resolved\", \"Did not address DNA vs RNA discrimination\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Connected DHX36 to telomerase biology and to innate immune dsRNA sensing, broadening its functional scope beyond mRNA decay.\",\n      \"evidence\": \"RIP-chip and in vitro binding for TERC/hTR G4; poly I:C affinity purification, Co-IP, domain mapping, and shRNA knockdown for the TRIF/DDX1/DDX21 complex\",\n      \"pmids\": [\"21846770\", \"21149580\", \"21703541\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether helicase activity is required for telomerase assembly was not resolved here\", \"How DHX36 is recruited into the dsRNA-sensing complex remained partly open\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Demonstrated DHX36 is essential in vivo and that its developmental requirement reflects G4 resolvase activity on target gene promoters.\",\n      \"evidence\": \"Conditional knockout mouse (Vav1-Cre) with hematopoietic phenotyping and transcriptomics; in vitro hTR helicase assay with telomere length measurement\",\n      \"pmids\": [\"22422825\", \"22238380\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct in vivo demonstration that promoter G4 resolution drives the transcriptome changes was correlative\", \"Embryonic lethality precluded analysis of germline-null adult phenotypes\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Extended DHX36 function to post-transcriptional silencing, placing it within miRNA/Ago2-dependent translational repression and dendritic RNA localization.\",\n      \"evidence\": \"RNA-IP, loss-of-function, dendritic spine morphometry (pre-miR-134); RIP, siRNA, and Ago2 co-depletion (PITX1 3'UTR G4)\",\n      \"pmids\": [\"23651854\", \"24369427\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism coupling G4 resolution to Ago2 recruitment not dissected\", \"Whether helicase ATPase activity is required for the silencing role unclear\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Defined a dsRNA-dependent partnership with PKR and a positive role in antiviral stress granule formation and interferon production.\",\n      \"evidence\": \"Reciprocal dsRNA-dependent Co-IP, DHX36 KO MEF cells, IFN and viral infection assays\",\n      \"pmids\": [\"24651521\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Apparent positive role here later reconciled with a restraining rheostat function\", \"Direct effect of helicase activity on PKR autophosphorylation not structurally resolved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Provided the structural mechanism of parallel-G4 specificity and showed in vivo that dual UTR regulation and G4 promoter binding underlie cardiac and germ-cell development.\",\n      \"evidence\": \"NMR peptide-G4 structure; cardiac and germ-cell conditional KO mice with RIP, translation/decay assays, and c-kit promoter pulldown\",\n      \"pmids\": [\"26195789\", \"26489465\", \"25611385\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"c-kit promoter regulation rests on a single lab\", \"How a single protein selects translation-promoting versus decay-promoting outcomes on the same mRNA not mechanistically defined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Resolved the nucleotide-state logic of G4 handling \\u2014 binding stabilizes, hydrolysis destabilizes \\u2014 and mapped additional roles in stress granules, p53 pre-mRNA processing, and nuclear localization.\",\n      \"evidence\": \"Single-molecule magnetic tweezers with nucleotide-state control and domain mutants; SG localization mapping; pre-mRNA 3'-end processing assays; immunofluorescence/fractionation\",\n      \"pmids\": [\"28069994\", \"18854321\", \"27940037\", \"18279852\", \"26740632\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Distinction between stabilizing and destabilizing modes in vivo not established\", \"Functional significance of nucleolar cap relocalization unresolved\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Established the translocation-based unwinding mechanism, showing DHX36 loads on a 3' tail and moves 3'\\u21925' to disrupt G4 far more efficiently than duplex DNA.\",\n      \"evidence\": \"In vitro kinetic assays with G4 substrates and PEG-linker translocation blocks\",\n      \"pmids\": [\"29269411\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Kinetics performed on model substrates, not endogenous chromatin G4\", \"Did not address RNA G4 mechanistic differences\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Delivered atomic-resolution mechanism: the DSM-induced \\u03b1-helix plus OB-fold and RecA2 pocket capture parallel G4 and drive stepwise tail-pulling unfolding, and revealed RNA-vs-DNA mechanistic asymmetry and a translation-licensing role in cells.\",\n      \"evidence\": \"X-ray co-crystallography of multiple states plus smFRET (bovine and Drosophila); ribosome profiling with DHX36/DHX9 depletion and PAR-CLIP\",\n      \"pmids\": [\"29899445\", \"29429875\", \"30591072\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structures captured discrete states rather than full processive cycle\", \"Functional overlap and division of labor with DHX9 not fully delineated\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defined the transcriptome-wide rG4 regulon and the asymmetric RNA-G4 mechanism, showing DHX36 binds >4500 mRNAs and renders rG4 transcripts translationally competent while restraining stress granules and PKR.\",\n      \"evidence\": \"PAR-CLIP, KO cell lines with polysome/ribosome profiling, SG imaging; smFRET with mutagenesis revealing ATP-independent RNA-G4 unfolding/refolding\",\n      \"pmids\": [\"31160600\", \"31015431\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Why RNA-G4 unfolding is ATP-independent while DNA-G4 unfolding requires hydrolysis not fully explained\", \"Direct in vivo demonstration of refolding role lacking\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Dissected the contributions of auxiliary domains (DSM, OB-fold, \\u03b2-hairpin) to recognition versus remodeling and showed the DSM accelerates G4 capture (on-rate) without affecting the disruption step.\",\n      \"evidence\": \"Mouse DHX36-ADP crystal structure with mutagenesis and helicase assays; kinetic binding assays with DSM truncation; lncRNA GSEC inhibition assays\",\n      \"pmids\": [\"32087197\", \"33857359\", \"27797375\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How separable capture and disruption steps are coordinated during processive cycles unclear\", \"Physiological scope of lncRNA-mediated inhibition not established\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Established DHX36 as broadly essential for adult tissue regeneration and identified specific 5'UTR rG4 targets and a lncRNA/EIF3B co-factor axis, while linking it to repeat RNA translation.\",\n      \"evidence\": \"Inducible satellite-cell and cardiomyocyte conditional KO mice with PAR-CLIP, polysome profiling, RIP, and target validation (Gnai2, Yap1/Hexim1, Anp32e via Lockd); C9orf72 RAN translation reporters\",\n      \"pmids\": [\"34413292\", \"33199370\", \"35675771\", \"34174288\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Generality of the Lockd/EIF3B translation-activating complex across cell types unknown\", \"Pathological consequences of DHX36-driven repeat RAN translation in disease not established in vivo\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Reinforced the 5'UTR rG4 translation-derepression paradigm at additional immune-relevant targets and showed nuclear DHX36 protects genomic integrity from transcription-associated G4-DNA.\",\n      \"evidence\": \"rG4-specific cellular probes with KD/KO and translation assays (ADAR1); depletion with \\u03b3H2AX, G4 co-localization, and G4-binding-mutant rescue\",\n      \"pmids\": [\"36300875\", \"37632696\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether ADAR1 derepression alters editing output not addressed\", \"Partial rescue by G4-binding mutants implies G4-independent contributions to genome maintenance\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Unified the dual UTR phenomenon mechanistically by showing transcript-wide structural remodeling that increases 3'UTR accessibility and recruits YTHDF1 to m6A sites for decay, and tied promoter-G4 resolution to cardiac conduction-system morphogenesis.\",\n      \"evidence\": \"RNA structurome-seq with DHX36 depletion, m6A mapping, YTHDF1 CLIP, KO cells; cardiac conditional KO with snRNA-seq and snATAC-seq\",\n      \"pmids\": [\"39543097\", \"39366945\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How DHX36 binding at one site propagates structure changes across an entire transcript not mechanistically defined\", \"Direct demonstration that promoter G4 resolution causes the conduction phenotype remains correlative\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Recast DHX36 as a rheostat for innate immunity and rRNA biogenesis, defined a REV1 replication-coupling partnership and viral antagonism, and provided cryo-EM-based DNA/RNA discrimination logic.\",\n      \"evidence\": \"KO cells with PKR/SG/ISG/RIG-I and viral replicon assays; oocyte conditional KO with rRNA processing and rescue; REV1 Co-IP/domain mapping; cryo-EM of RNA/DNA G4 complexes with smFRET; PCV3 ubiquitination/degradation assays; StAR 3'UTR G4 KD with hormonal readout\",\n      \"pmids\": [\"42213826\", \"40023726\", \"40833853\", \"42258547\", \"39862752\", \"41354365\", \"40985767\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How dsRNA exposure mechanistically lowers DHX36 activity to license immune activation not fully defined\", \"Whether RecA2-mediated DNA/RNA discrimination dictates the distinct in-cell DNA versus RNA roles untested in vivo\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how a single DHX36 molecule selects between opposing fates on the same transcript (5'UTR translation activation versus 3'UTR-driven decay) and how its activity is dynamically tuned across nuclear, cytoplasmic, and immune contexts.\",\n      \"evidence\": \"No single study in the corpus reconciles the determinants of DHX36 functional output across compartments\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No model integrates compartment-specific cofactors, post-translational regulation, and substrate features into a predictive logic\", \"Whether the nucleotide-state stabilize/destabilize switch operates the same way on cellular G4-DNA and G4-RNA is untested in vivo\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 2, 5, 21, 22, 26]},\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [1, 15, 22]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [2, 4, 7, 20, 26]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0, 12, 22, 32]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [19, 20, 29, 33, 34]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [15, 22]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [16, 32]},\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [16, 44]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [14, 20, 39]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [1, 20, 36]},\n      {\"term_id\": \"R-HSA-72766\", \"supporting_discovery_ids\": [19, 20, 29]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [3, 9, 41]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [24, 37]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [6, 11, 29, 35, 37, 44]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [32, 40]}\n    ],\n    \"complexes\": [\n      \"TRIF/DDX1/DDX21 dsRNA-sensing complex\",\n      \"telomerase holoenzyme (via TERC/hTR)\",\n      \"DHX36-PKR complex\"\n    ],\n    \"partners\": [\n      \"PARN\",\n      \"TRIF\",\n      \"DDX1\",\n      \"DDX21\",\n      \"PKR\",\n      \"YTHDF1\",\n      \"REV1\",\n      \"EIF3B\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}