{"gene":"DCP1A","run_date":"2026-06-09T23:54:41","timeline":{"discoveries":[{"year":2002,"finding":"DCP1A (SMIF) was identified as a Smad4-interacting transcriptional co-activator that forms a TGFβ/BMP4-inducible complex specifically with Smad4 (not other Smads), translocates to the nucleus in a TGFβ/BMP4-inducible and Smad4-dependent manner, and requires p300/CBP for its transcriptional activity. A point mutation in Smad4 abolished binding to DCP1A and impaired transcriptional activity.","method":"Co-immunoprecipitation, transcriptional reporter assays, dominant-negative mutant overexpression, morpholino knockdown in zebrafish","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, mutagenesis, functional transcriptional assays, and in vivo knockdown across multiple orthogonal methods in a single study","pmids":["11836524"],"is_preprint":false},{"year":2011,"finding":"JNK phosphorylates DCP1A at serine 315 in vivo and in vitro, coimmunoprecipitates and colocalizes with DCP1A in P bodies, and sustained JNK activation leads to DCP1A dispersion from P bodies. Phosphomimetic mutation S315 stabilized IL-8 mRNA. Overexpressed DCP1A blocked IL-8 transcription and suppressed p65 NF-κB nuclear activity.","method":"In vitro kinase assay, co-immunoprecipitation, live-cell imaging, phosphomimetic mutagenesis, transcriptome analysis","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro kinase assay plus mutagenesis plus Co-IP plus imaging with functional mRNA readouts, multiple orthogonal methods","pmids":["21859862"],"is_preprint":false},{"year":2013,"finding":"DCP1A interacts with Ddx6 and Edc3 through its proline-rich C-terminal extension, while its N-terminal EVH1 domain shows stronger interaction with Dcp2. ERK pathway mediates dual phosphorylation of Dcp1a at Ser315 and Ser319; phosphorylated Dcp1a enhances its interaction with Dcp2 without affecting interactions with Ddx6, Edc3, or Edc4.","method":"Co-immunoprecipitation, mass spectrometry, site-directed mutagenesis, kinase assay, phosphomimetic mutant pulldown","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — mass spectrometry identification of phosphosites, mutagenesis, kinase assay, and Co-IP all in one study","pmids":["23637887"],"is_preprint":false},{"year":2013,"finding":"DCP1A is hyper-phosphorylated during mitosis; P bodies disassemble as cells prepare for division and reassemble during cytokinesis. Serine 315 is critical for hyper-phosphorylation, and serine mutations in other regions affect the dynamics of DCP1A association with P bodies as shown by live-cell imaging.","method":"Live-cell imaging, electrophoresis of mitotic cell extracts, truncation and mutational analysis, phosphorylation assays","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — live-cell imaging plus mutagenesis plus biochemical fractionation, single lab","pmids":["23300942"],"is_preprint":false},{"year":2013,"finding":"DCP1A and DCP2 are encoded by maternal mRNAs that are recruited for translation during oocyte maturation via cytoplasmic polyadenylation elements. Both proteins are phosphorylated during maturation (CDC2A likely responsible, MAPK may contribute to DCP1A phosphorylation). Inhibiting DCP1A and DCP2 accumulation by RNAi or morpholinos decreased maternal mRNA degradation during meiotic maturation and reduced zygotic genome transcription.","method":"RNA interference, morpholino knockdown, mRNA stability assays, kinase inhibitor experiments","journal":"Biology of reproduction","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNAi and morpholino knockdown with defined mRNA decay and genome activation phenotypes, single lab","pmids":["23136299"],"is_preprint":false},{"year":2013,"finding":"DCP1A expression of its N-terminal EVH1 domain is required for activation of PKR, which leads to phosphorylation of eIF2α and translational inhibition. This DCP1A-induced translational arrest is specific to DCP1A, as expression of other P-body components (Pan2, Pan3, Ccr4, Caf1) did not induce eIF2α phosphorylation.","method":"GFP-Dcp1a domain mutant expression, eIF2α phosphorylation assays, PKR activation assays, poliovirus infection model","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain mutagenesis with defined PKR activation readout, single lab with multiple mutant constructs","pmids":["24382890"],"is_preprint":false},{"year":2008,"finding":"Dcp1a is hyperphosphorylated during brain development, neuronal differentiation, and cellular stress; specific amino acid residues responsible for phosphorylation were identified.","method":"Phosphorylation analysis during neuronal development and stress conditions, residue identification","journal":"FEBS letters","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, limited methodological detail in abstract, no functional consequence rigorously established","pmids":["19084008"],"is_preprint":false},{"year":2012,"finding":"Malin E3 ubiquitin ligase is recruited to P bodies and promotes DCP1A degradation via the ubiquitin–proteasome system. Depletion of malin results in elevated DCP1A levels and altered microRNA-mediated gene silencing activity.","method":"Co-localization, ubiquitin-proteasome inhibitor experiments, malin depletion with DCP1A protein level measurement, miRNA silencing assays","journal":"RNA biology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — genetic depletion with mechanistic follow-up on protein degradation pathway, single lab","pmids":["23131811"],"is_preprint":false},{"year":2018,"finding":"PRRSV nonstructural protein 4 (nsp4), a 3C-like proteinase, cleaves porcine DCP1A at glutamic acid 238 (E238), and the two cleavage products lose anti-PRRSV activity. The cleavage-resistant mutant pDCP1A-E238A retains higher antiviral activity than wild-type, establishing DCP1A as an interferon-stimulated gene with antiviral function that is targeted by viral protease.","method":"Overexpression, knockdown, protease cleavage assay, site-directed mutagenesis (E238A), viral infection assays","journal":"Journal of immunology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — protease cleavage assay with defined cleavage site plus mutagenesis plus functional antiviral readout","pmids":["30158128"],"is_preprint":false},{"year":2020,"finding":"PDCoV nsp5 (3C-like protease) cleaves DCP1A at glutamine 343 (Q343); the cleaved fragments DCP1A1-343 and DCP1A344-580 are unable to inhibit PDCoV infection. The cleavage-resistant mutant DCP1A-Q343A exhibits stronger antiviral activity. The Q343 cleavage site is conserved in mammalian DCP1A homologs, and nsp5 from seven other CoVs also cleaved DCP1A.","method":"Protease cleavage assay, site-directed mutagenesis (Q343A), viral infection assays, sequence conservation analysis","journal":"Journal of virology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — protease cleavage with defined site, mutagenesis, functional antiviral assay, replicated across multiple CoV nsp5 proteins","pmids":["32461317"],"is_preprint":false},{"year":2023,"finding":"SARS-CoV-2 main protease (Mpro) cleaves DCP1A at residue Q343, abolishing its ISG effector activity. Mpro from multiple coronavirus genera also cleaves DCP1A, though alphacoronavirus Mpro shows weaker activity.","method":"Protease cleavage assay, site-directed mutagenesis, ISG reporter assays in mammalian cell lines","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — defined cleavage site plus functional assay, replicated across multiple coronavirus proteases in two mammalian cell lines","pmids":["36758802"],"is_preprint":false},{"year":2023,"finding":"SADS-CoV nsp5 cleaves DCP1A via its protease activity (requiring H41 and C144 residues); DCP1A-Q343A mutant resists cleavage and shows stronger ability to inhibit SADS-CoV infection. DCP1A cleavage by nsp5 inhibits IRF3 and NF-κB signaling pathways to decrease IFN-β and inflammatory cytokine production.","method":"Protease cleavage assay, active-site mutagenesis of nsp5 (H41, C144), DCP1A Q343A mutant, viral infection assays, IFN-β and cytokine production assays","journal":"Frontiers in immunology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — active site mutagenesis of protease plus substrate site mutagenesis plus functional signaling and antiviral readouts","pmids":["37283741"],"is_preprint":false},{"year":2024,"finding":"MEK1 phosphorylates DCP1A at S563; dephosphorylation of S563 promotes P body formation and RNA storage, facilitating both self-renewal and differentiation of mouse embryonic stem cells. DCP1A, along with P body components EDC4 and DCP2, is required for ESC self-renewal and differentiation.","method":"Quantitative phosphoproteomics, in vitro kinase assay, site-directed mutagenesis (S563), P body imaging, ESC self-renewal and differentiation assays","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — phosphoproteomics identification plus in vitro kinase assay plus mutagenesis plus defined cellular phenotypes","pmids":["39671288"],"is_preprint":false},{"year":2024,"finding":"DCP1a and DCP1b are non-redundant cofactors of the mRNA cap hydrolase DCP2 with distinct roles: DCP1a is essential for decapping complex assembly and interactions with mRNA cap-binding proteins, while DCP1b is essential for interactions with protein degradation and translational machinery. DCP1a and DCP1b regulate turnover of distinct sets of mRNAs.","method":"Functional dissection by knockdown/knockout, Co-immunoprecipitation of decapping complex components, mRNA turnover profiling","journal":"Life science alliance","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and mRNA turnover assays with functional knockdown, single lab, distinct paralog roles established","pmids":["39256052"],"is_preprint":false},{"year":2021,"finding":"Dcp1a-deficient mice generated by CRISPR/Cas9 die around embryonic day 10.5 with massive growth retardation and cardiac developmental defects; lethality is fully rescued by transgenic expression of human DCP1A, establishing DCP1A as essential for embryonic growth.","method":"CRISPR/Cas9 knockout, transgenic rescue, embryonic phenotyping","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic knockout with defined embryonic lethal phenotype fully rescued by transgenic human DCP1A","pmids":["33813271"],"is_preprint":false},{"year":2021,"finding":"Dcp1a puncta are absent in quiescent muscle satellite cells but appear during activation/proliferation. Dcp1a knockdown leads to increased cell proliferation and higher cyclin expression during proliferation but compromised differentiation. Knockdown of Dcp1a leads to increased Fmrp accumulation in puncta, indicating cross-regulation between decay and storage mRNP granules.","method":"Single myofiber isolation, live-cell imaging, polysome profiling, siRNA knockdown with proliferation and differentiation assays","journal":"Skeletal muscle","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — knockdown with defined proliferation/differentiation phenotypes plus imaging, single lab","pmids":["34238354"],"is_preprint":false},{"year":2023,"finding":"Cordycepin suppresses the elevation of DCP1A protein during postovulatory oocyte aging by inhibiting polyadenylation of DCP1A mRNA, consequently impeding maternal mRNA decapping and degradation. Increased DCP1A protein accelerates maternal mRNA degradation during postovulatory aging in both mouse and human oocytes.","method":"Proteomic and RNA sequencing analyses, mRNA injection/siRNA in oocytes, polyadenylation assays","journal":"Cellular and molecular life sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — siRNA/mRNA injection functional assays plus proteomic/transcriptomic evidence, single lab","pmids":["38001238"],"is_preprint":false},{"year":2024,"finding":"Exogenous Dcp1a mRNA injection into MII oocytes accelerates degradation of maternal mRNAs, while siRNA knockdown of DCP1A reduces maternal mRNA decay in postovulatory-aged oocytes, directly establishing DCP1A as a driver of premature maternal mRNA degradation during postovulatory aging.","method":"mRNA microinjection, siRNA knockdown in oocytes, RNA-seq, proteomics","journal":"Cell proliferation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — gain- and loss-of-function in oocytes with transcriptomic readout, single lab","pmids":["39629683"],"is_preprint":false},{"year":2025,"finding":"SVV 3C protease cleaves DCP1A at Q343, generating fragments that lose the ability to restrict SVV replication. Wild-type DCP1A targets the viral 3D RNA-dependent RNA polymerase for OPTN-mediated autophagic degradation; this antiviral mechanism is abolished after DCP1A cleavage. The cleavage-resistant DCP1A-Q343A mutant retains stronger antiviral effects.","method":"Protease cleavage assay, site-directed mutagenesis (Q343A), viral infection assay, autophagy pathway analysis","journal":"Veterinary research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cleavage assay with mutagenesis and viral functional readout, single lab, novel antiviral mechanism proposed with supporting data","pmids":["40022242"],"is_preprint":false},{"year":2025,"finding":"DCP1A-containing HOPS condensates under hyperosmotic stress exhibit sub-diffusion due to endoplasmic reticulum attachment and occasional super-diffusion due to coupling to microtubule-dependent active transport, as established by live-cell single-particle tracking.","method":"Live-cell single-particle tracking (SPT), ER and microtubule fluorescence labeling, GEM accessibility mapping","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single preprint, localization/dynamics data without functional mechanistic follow-up on DCP1A activity","pmids":[],"is_preprint":true}],"current_model":"DCP1A is an mRNA decapping cofactor of DCP2 that localizes to cytoplasmic P bodies and is regulated by multiple kinases (JNK, ERK, MEK1, CDK1) via phosphorylation at key serine residues (S315, S319, S563), controlling P body dynamics, mRNA stability, and mRNA decay; it also functions as an interferon-stimulated gene with antiviral activity that is counteracted by coronavirus and other viral proteases cleaving DCP1A at Q343 (or E238 in porcine PRRSV), and it additionally acts as a Smad4-interacting transcriptional co-activator in TGFβ signaling."},"narrative":{"mechanistic_narrative":"DCP1A is a cofactor of the mRNA cap hydrolase DCP2 that nucleates cytoplasmic P bodies and couples mRNA decapping and decay to cell-state transitions, antiviral defense, and TGFβ-dependent transcription [PMID:39256052, PMID:21859862, PMID:11836524]. Within the decapping machinery, its N-terminal EVH1 domain mediates the strongest interaction with DCP2, while its proline-rich C-terminal extension engages Ddx6 and Edc3 [PMID:23637887]; DCP1A and the paralog DCP1B act non-redundantly, with DCP1A required for decapping-complex assembly and contacts with cap-binding proteins and DCP1B linking to degradation and translational machinery, such that each governs turnover of distinct mRNA sets [PMID:39256052]. DCP1A activity and P body dynamics are set by phosphorylation through multiple kinases: JNK phosphorylates Ser315 and sustained activation disperses DCP1A from P bodies and stabilizes IL-8 mRNA [PMID:21859862], ERK drives dual Ser315/Ser319 phosphorylation that enhances DCP1A–DCP2 association [PMID:23637887], mitotic hyperphosphorylation at Ser315 accompanies P body disassembly during division [PMID:23300942], and MEK1 phosphorylation of Ser563 antagonizes P body formation and RNA storage to control embryonic stem cell self-renewal and differentiation [PMID:39671288]. DCP1A protein levels are additionally limited by malin-mediated ubiquitin–proteasome degradation, which tunes microRNA silencing [PMID:23131811]. Through this decapping function DCP1A drives developmental and physiological mRNA clearance: it is essential for mouse embryonic growth and cardiac development [PMID:33813271], mediates maternal mRNA degradation during oocyte maturation and postovulatory aging [PMID:23136299, PMID:38001238, PMID:39629683], and regulates muscle satellite cell proliferation and differentiation [PMID:34238354]. Independently, DCP1A (SMIF) functions as a Smad4-specific transcriptional co-activator that translocates to the nucleus upon TGFβ/BMP4 signaling and requires p300/CBP for activity [PMID:11836524]. DCP1A is also an interferon-stimulated gene with broad antiviral activity that is neutralized by viral 3C-like proteases, which cleave it at Q343 (or E238 in porcine DCP1A), with cleavage-resistant mutants retaining enhanced antiviral function [PMID:30158128, PMID:32461317, PMID:36758802, PMID:37283741, PMID:40022242].","teleology":[{"year":2002,"claim":"Established a transcriptional, signaling role for DCP1A before its decapping function was known, showing it acts as a Smad4-specific nuclear co-activator in TGFβ/BMP4 signaling.","evidence":"Co-IP, transcriptional reporter assays, Smad4 point mutant, and zebrafish morpholino knockdown","pmids":["11836524"],"confidence":"High","gaps":["Does not connect the nuclear co-activator role to DCP1A's cytoplasmic decapping function","Mechanism of nuclear/cytoplasmic partitioning not resolved"]},{"year":2008,"claim":"First indicated that DCP1A phosphorylation is a regulated event tied to neuronal development and stress, raising the question of which kinases and sites are involved.","evidence":"Phosphorylation analysis across neuronal development and stress with residue identification","pmids":["19084008"],"confidence":"Low","gaps":["Limited methodological detail and no rigorously established functional consequence","Responsible kinases not identified"]},{"year":2011,"claim":"Identified JNK as a kinase that phosphorylates DCP1A at Ser315, linking stress kinase signaling to P body dynamics and mRNA stability.","evidence":"In vitro kinase assay, Co-IP, live-cell imaging, S315 phosphomimetic mutagenesis with IL-8 mRNA readout","pmids":["21859862"],"confidence":"High","gaps":["Mechanism linking DCP1A overexpression to NF-κB suppression not fully resolved","Whether dispersion reflects loss of decapping activity not tested directly"]},{"year":2013,"claim":"Mapped DCP1A's modular interactions and showed ERK-driven dual Ser315/Ser319 phosphorylation selectively strengthens DCP1A–DCP2 binding, defining how signaling tunes decapping-complex composition.","evidence":"Co-IP, mass spectrometry, site-directed mutagenesis, kinase assay, phosphomimetic pulldown","pmids":["23637887"],"confidence":"High","gaps":["Effect on decapping catalytic output not quantified","Interplay between ERK and JNK phosphorylation not resolved"]},{"year":2013,"claim":"Connected DCP1A phosphorylation to the cell cycle, showing mitotic hyperphosphorylation (Ser315-dependent) accompanies P body disassembly and reassembly.","evidence":"Live-cell imaging, mitotic extract electrophoresis, truncation and mutational analysis","pmids":["23300942"],"confidence":"Medium","gaps":["Mitotic kinase not definitively identified","Functional consequence of mitotic P body disassembly for mRNA fate unclear"]},{"year":2013,"claim":"Demonstrated a physiological decay role in reproduction, with DCP1A/DCP2 driving maternal mRNA degradation and zygotic genome activation during oocyte maturation.","evidence":"RNAi, morpholino knockdown, mRNA stability assays, kinase inhibitor experiments","pmids":["23136299"],"confidence":"Medium","gaps":["Direct kinase responsible for DCP1A phosphorylation during maturation not confirmed","Target mRNA specificity not defined"]},{"year":2013,"claim":"Revealed a translation-control activity distinct from decapping, showing the DCP1A EVH1 domain activates PKR to phosphorylate eIF2α and arrest translation.","evidence":"GFP-Dcp1a domain mutants, eIF2α phosphorylation and PKR activation assays, poliovirus model","pmids":["24382890"],"confidence":"Medium","gaps":["Mechanism by which EVH1 engages PKR unresolved","Relationship to canonical decapping activity unclear"]},{"year":2012,"claim":"Established that DCP1A protein abundance is controlled by ubiquitin-proteasome turnover via the malin E3 ligase, linking DCP1A levels to microRNA silencing.","evidence":"Co-localization, proteasome inhibition, malin depletion with DCP1A level and miRNA silencing assays","pmids":["23131811"],"confidence":"Medium","gaps":["Ubiquitination sites on DCP1A not mapped","Signals controlling malin recruitment to P bodies unknown"]},{"year":2018,"claim":"Defined DCP1A as an interferon-stimulated antiviral effector that viral proteases neutralize, showing PRRSV nsp4 cleaves porcine DCP1A at E238 to abrogate antiviral activity.","evidence":"Overexpression, knockdown, protease cleavage assay, E238A mutagenesis, viral infection assays","pmids":["30158128"],"confidence":"High","gaps":["Molecular basis of DCP1A antiviral restriction not defined","Whether antiviral function requires decapping activity untested"]},{"year":2020,"claim":"Identified Q343 as a conserved cleavage site exploited by coronavirus 3C-like proteases, generalizing the protease-counteraction strategy across CoVs.","evidence":"Protease cleavage assay, Q343A mutagenesis, viral infection assays, sequence conservation analysis","pmids":["32461317"],"confidence":"High","gaps":["Downstream antiviral effector mechanism not yet defined","Fragment fates after cleavage unclear"]},{"year":2021,"claim":"Established DCP1A as essential in vivo, with knockout causing embryonic lethality and cardiac defects rescued by human DCP1A.","evidence":"CRISPR/Cas9 knockout, transgenic rescue, embryonic phenotyping in mice","pmids":["33813271"],"confidence":"High","gaps":["Molecular cause of cardiac defect not defined","Which DCP1A activity (decapping vs. transcriptional) underlies essentiality unknown"]},{"year":2021,"claim":"Showed DCP1A controls muscle satellite cell fate, with puncta appearing on activation and knockdown shifting proliferation versus differentiation and altering mRNP granule cross-regulation.","evidence":"Single myofiber isolation, live-cell imaging, polysome profiling, siRNA knockdown with proliferation/differentiation assays","pmids":["34238354"],"confidence":"Medium","gaps":["Target mRNAs driving the phenotype not identified","Mechanism of Fmrp granule cross-regulation unresolved"]},{"year":2023,"claim":"Confirmed Q343 cleavage by SARS-CoV-2 Mpro and across coronavirus genera abolishes DCP1A ISG effector activity, strengthening DCP1A as a pan-coronavirus antiviral target.","evidence":"Protease cleavage assay, site-directed mutagenesis, ISG reporter assays in two mammalian cell lines","pmids":["36758802"],"confidence":"High","gaps":["Effector pathway of ISG activity not mechanistically defined here","Alphacoronavirus weaker cleavage basis unexplained"]},{"year":2023,"claim":"Linked DCP1A cleavage to suppression of innate immune signaling, showing SADS-CoV nsp5 cleavage at Q343 inhibits IRF3/NF-κB and reduces IFN-β and cytokine output.","evidence":"Protease cleavage assay, nsp5 active-site mutagenesis, DCP1A-Q343A mutant, IFN-β and cytokine assays","pmids":["37283741"],"confidence":"High","gaps":["Direct molecular connection between DCP1A and IRF3/NF-κB unresolved","Whether intact DCP1A acts upstream or as scaffold not defined"]},{"year":2023,"claim":"Identified DCP1A as a driver of premature maternal mRNA degradation in postovulatory oocyte aging, regulated at the level of DCP1A mRNA polyadenylation.","evidence":"Proteomics, RNA-seq, oocyte mRNA injection/siRNA, polyadenylation assays in mouse and human oocytes","pmids":["38001238"],"confidence":"Medium","gaps":["Polyadenylation machinery acting on DCP1A mRNA not identified","Target maternal transcript specificity not defined"]},{"year":2024,"claim":"Confirmed DCP1A dose directly sets maternal mRNA decay rate in oocytes via gain- and loss-of-function, cementing its causal role in postovulatory aging.","evidence":"mRNA microinjection and siRNA knockdown in oocytes with RNA-seq and proteomics","pmids":["39629683"],"confidence":"Medium","gaps":["Upstream regulators of DCP1A in aged oocytes not defined","Selectivity of degraded transcripts unresolved"]},{"year":2024,"claim":"Resolved DCP1A and DCP1B as non-redundant DCP2 cofactors with distinct interaction partners and distinct target mRNA repertoires, refining the architecture of the decapping complex.","evidence":"Knockdown/knockout functional dissection, Co-IP of decapping components, mRNA turnover profiling","pmids":["39256052"],"confidence":"Medium","gaps":["Structural basis of paralog-specific interactions not determined","Single-lab; reciprocal validation of partner specificity limited"]},{"year":2024,"claim":"Defined MEK1-dependent Ser563 phosphorylation as a switch governing P body formation and RNA storage in embryonic stem cell self-renewal and differentiation.","evidence":"Quantitative phosphoproteomics, in vitro kinase assay, S563 mutagenesis, P body imaging, ESC assays","pmids":["39671288"],"confidence":"High","gaps":["Stored mRNA targets governing ESC fate not identified","Integration with ERK/JNK phosphorylation inputs unresolved"]},{"year":2025,"claim":"Extended the antiviral mechanism by showing intact DCP1A targets viral RdRp for OPTN-mediated autophagic degradation, an activity destroyed by Q343 cleavage.","evidence":"Protease cleavage assay, Q343A mutagenesis, viral infection assay, autophagy pathway analysis","pmids":["40022242"],"confidence":"Medium","gaps":["Single lab; OPTN-DCP1A interaction not reciprocally validated","Whether this mechanism generalizes beyond SVV unknown"]},{"year":null,"claim":"It remains unresolved how DCP1A's distinct activities—decapping cofactor, Smad4 transcriptional co-activator, PKR/translation regulator, and antiviral effector—are mechanistically partitioned, and which underlies its essential developmental role.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model integrating EVH1, proline-rich, and phosphosite regions with each function","No unified account of nuclear vs. cytoplasmic vs. condensate DCP1A pools","Decapping-independence of antiviral and transcriptional roles not directly tested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2,13]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,13]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[13]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1,3,12]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[2,13]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[8,9,10,11]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[14,12]}],"complexes":["DCP2 decapping complex","P body","Smad4 transcriptional complex"],"partners":["DCP2","DDX6","EDC3","EDC4","SMAD4","MALIN"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NPI6","full_name":"mRNA-decapping enzyme 1A","aliases":["Smad4-interacting transcriptional co-activator","Transcription factor SMIF"],"length_aa":582,"mass_kda":63.3,"function":"Necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay (PubMed:12417715). Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP (PubMed:12417715). Contributes to the transactivation of target genes after stimulation by TGFB1 (PubMed:11836524). Essential for embryonic development (PubMed:33813271)","subcellular_location":"Cytoplasm, P-body; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9NPI6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DCP1A","classification":"Not Classified","n_dependent_lines":9,"n_total_lines":74,"dependency_fraction":0.12162162162162163},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000272886","cell_line_id":"CID000837","localizations":[{"compartment":"vesicles","grade":3},{"compartment":"cytoplasmic","grade":1}],"interactors":[{"gene":"EDC3","stoichiometry":10.0},{"gene":"DCP1B","stoichiometry":10.0},{"gene":"EDC4","stoichiometry":10.0},{"gene":"DDX6","stoichiometry":4.0},{"gene":"ARHGAP18","stoichiometry":0.2},{"gene":"ATG4B","stoichiometry":0.2},{"gene":"CLTA","stoichiometry":0.2},{"gene":"CLTB","stoichiometry":0.2},{"gene":"HNRNPA2B1","stoichiometry":0.2},{"gene":"RAB2A","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000837","total_profiled":1310},"omim":[{"mim_id":"617748","title":"TUDOR DOMAIN-CONTAINING PROTEIN 5; TDRD5","url":"https://www.omim.org/entry/617748"},{"mim_id":"614295","title":"BICC FAMILY RNA-BINDING PROTEIN 1; BICC1","url":"https://www.omim.org/entry/614295"},{"mim_id":"611882","title":"PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2; PNRC2","url":"https://www.omim.org/entry/611882"},{"mim_id":"611008","title":"MEX3 RNA-BINDING FAMILY MEMBER B; MEX3B","url":"https://www.omim.org/entry/611008"},{"mim_id":"611007","title":"MEX3 RNA-BINDING FAMILY MEMBER A; MEX3A","url":"https://www.omim.org/entry/611007"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytoplasmic bodies","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/DCP1A"},"hgnc":{"alias_symbol":["HSA275986","SMIF","SMAD4IP1"],"prev_symbol":[]},"alphafold":{"accession":"Q9NPI6","domains":[{"cath_id":"2.30.29.30","chopping":"2-139","consensus_level":"high","plddt":95.2264,"start":2,"end":139}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NPI6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NPI6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NPI6-F1-predicted_aligned_error_v6.png","plddt_mean":57.78},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DCP1A","jax_strain_url":"https://www.jax.org/strain/search?query=DCP1A"},"sequence":{"accession":"Q9NPI6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NPI6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NPI6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NPI6"}},"corpus_meta":[{"pmid":"21859862","id":"PMC_21859862","title":"c-Jun N-terminal kinase phosphorylates DCP1a to control formation of P bodies.","date":"2011","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/21859862","citation_count":75,"is_preprint":false},{"pmid":"11836524","id":"PMC_11836524","title":"SMIF, a Smad4-interacting protein that functions as a co-activator in TGFbeta signalling.","date":"2002","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/11836524","citation_count":72,"is_preprint":false},{"pmid":"23136299","id":"PMC_23136299","title":"Maternally recruited DCP1A and DCP2 contribute to messenger RNA degradation during oocyte maturation and genome activation in mouse.","date":"2013","source":"Biology of reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/23136299","citation_count":66,"is_preprint":false},{"pmid":"23300942","id":"PMC_23300942","title":"The P body protein Dcp1a is hyper-phosphorylated during mitosis.","date":"2013","source":"PloS 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1950)","url":"https://pubmed.ncbi.nlm.nih.gov/30158128","citation_count":31,"is_preprint":false},{"pmid":"24382890","id":"PMC_24382890","title":"mRNA decapping enzyme 1a (Dcp1a)-induced translational arrest through protein kinase R (PKR) activation requires the N-terminal enabled vasodilator-stimulated protein homology 1 (EVH1) domain.","date":"2013","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/24382890","citation_count":27,"is_preprint":false},{"pmid":"36758802","id":"PMC_36758802","title":"The main protease of SARS-CoV-2 cleaves histone deacetylases and DCP1A, attenuating the immune defense of the interferon-stimulated genes.","date":"2023","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/36758802","citation_count":26,"is_preprint":false},{"pmid":"23637887","id":"PMC_23637887","title":"Phosphorylation of mRNA decapping protein Dcp1a by the ERK signaling pathway during early differentiation of 3T3-L1 preadipocytes.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23637887","citation_count":23,"is_preprint":false},{"pmid":"31278739","id":"PMC_31278739","title":"Bta-miR-34b regulates milk fat biosynthesis by targeting mRNA decapping enzyme 1A (DCP1A) in cultured bovine mammary epithelial cells1.","date":"2019","source":"Journal of animal science","url":"https://pubmed.ncbi.nlm.nih.gov/31278739","citation_count":21,"is_preprint":false},{"pmid":"31188482","id":"PMC_31188482","title":"LINC00339 promotes gastric cancer progression by elevating DCP1A expression via inhibiting miR-377-3p.","date":"2019","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/31188482","citation_count":19,"is_preprint":false},{"pmid":"27578485","id":"PMC_27578485","title":"Genetic variants in the PIWI-piRNA pathway gene DCP1A predict melanoma disease-specific survival.","date":"2016","source":"International journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/27578485","citation_count":18,"is_preprint":false},{"pmid":"23131811","id":"PMC_23131811","title":"Lafora disease E3 ubiquitin ligase malin is recruited to the processing bodies and regulates the microRNA-mediated gene silencing process via the decapping enzyme Dcp1a.","date":"2012","source":"RNA biology","url":"https://pubmed.ncbi.nlm.nih.gov/23131811","citation_count":17,"is_preprint":false},{"pmid":"19084008","id":"PMC_19084008","title":"Dcp1a phosphorylation along neuronal development and stress.","date":"2008","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/19084008","citation_count":17,"is_preprint":false},{"pmid":"32982440","id":"PMC_32982440","title":"Circ_0007031 Serves as a Sponge of miR-760 to Regulate the Growth and Chemoradiotherapy Resistance of Colorectal Cancer via Regulating DCP1A.","date":"2020","source":"Cancer management and research","url":"https://pubmed.ncbi.nlm.nih.gov/32982440","citation_count":16,"is_preprint":false},{"pmid":"38001238","id":"PMC_38001238","title":"Cordycepin delays postovulatory aging of oocytes through inhibition of maternal mRNAs degradation via DCP1A polyadenylation suppression.","date":"2023","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/38001238","citation_count":13,"is_preprint":false},{"pmid":"28488892","id":"PMC_28488892","title":"Dcp1a and GW182 Induce Distinct Cellular Aggregates and Have Different Effects on microRNA Pathway.","date":"2017","source":"DNA and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/28488892","citation_count":10,"is_preprint":false},{"pmid":"34238354","id":"PMC_34238354","title":"mRNP granule proteins Fmrp and Dcp1a differentially regulate mRNP complexes to contribute to control of muscle stem cell quiescence and activation.","date":"2021","source":"Skeletal muscle","url":"https://pubmed.ncbi.nlm.nih.gov/34238354","citation_count":9,"is_preprint":false},{"pmid":"37283741","id":"PMC_37283741","title":"Swine acute diarrhoea syndrome coronavirus (SADS-CoV) Nsp5 antagonizes type I interferon signaling by cleaving DCP1A.","date":"2023","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/37283741","citation_count":9,"is_preprint":false},{"pmid":"32646734","id":"PMC_32646734","title":"Expression of DCP1a in gastric cancer and its biological function and mechanism in chemotherapy resistance in gastric cancer cells.","date":"2020","source":"Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver","url":"https://pubmed.ncbi.nlm.nih.gov/32646734","citation_count":7,"is_preprint":false},{"pmid":"33813271","id":"PMC_33813271","title":"mRNA decapping factor Dcp1a is essential for embryonic growth in mice.","date":"2021","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/33813271","citation_count":6,"is_preprint":false},{"pmid":"37065560","id":"PMC_37065560","title":"LncRNA HOXD-AS2 regulates miR-3681-5p/DCP1A axis to promote the progression of non-small cell lung cancer.","date":"2023","source":"Journal of thoracic disease","url":"https://pubmed.ncbi.nlm.nih.gov/37065560","citation_count":6,"is_preprint":false},{"pmid":"40022242","id":"PMC_40022242","title":"The Seneca Valley virus 3C protease cleaves DCP1A to attenuate its antiviral effects.","date":"2025","source":"Veterinary research","url":"https://pubmed.ncbi.nlm.nih.gov/40022242","citation_count":6,"is_preprint":false},{"pmid":"39629683","id":"PMC_39629683","title":"Multi-omics revealed that DCP1A and SPDL1 determine embryogenesis defects in postovulatory ageing oocytes.","date":"2024","source":"Cell proliferation","url":"https://pubmed.ncbi.nlm.nih.gov/39629683","citation_count":3,"is_preprint":false},{"pmid":"39671288","id":"PMC_39671288","title":"DCP1A, a MEK substrate, regulates the self-renewal and differentiation of mouse embryonic stem cells.","date":"2024","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/39671288","citation_count":2,"is_preprint":false},{"pmid":"39256052","id":"PMC_39256052","title":"Non-redundant roles for the human mRNA decapping cofactor paralogs DCP1a and DCP1b.","date":"2024","source":"Life science alliance","url":"https://pubmed.ncbi.nlm.nih.gov/39256052","citation_count":2,"is_preprint":false},{"pmid":"39348227","id":"PMC_39348227","title":"RETRACTION: LINC00339 promotes gastric cancer progression by elevating DCP1A expression via inhibiting miR-377-3p.","date":"2024","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/39348227","citation_count":0,"is_preprint":false},{"pmid":"38410577","id":"PMC_38410577","title":"Erratum to lncRNA HOXD-AS2 regulates miR-3681-5p/DCP1A axis to promote the progression of non-small cell lung cancer.","date":"2024","source":"Journal of thoracic disease","url":"https://pubmed.ncbi.nlm.nih.gov/38410577","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.10.16.681898","title":"Calcium: Modulator of Post-transcriptional and post-translational process in mESCs","date":"2025-10-16","source":"bioRxiv","url":"https://doi.org/10.1101/2025.10.16.681898","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.06.13.659610","title":"ER tethering and active transport govern condensate diffusion during hyperosmotic stress","date":"2025-06-17","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.13.659610","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.04.16.649117","title":"Statistical Molecular Interaction Fields: A Fast and Informative Tool for Characterizing RNA and Protein Binding Pockets","date":"2025-04-18","source":"bioRxiv","url":"https://doi.org/10.1101/2025.04.16.649117","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":17553,"output_tokens":4827,"usd":0.062532,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":13047,"output_tokens":5700,"usd":0.103868,"stage2_stop_reason":"end_turn"},"total_usd":0.1664,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2002,\n      \"finding\": \"DCP1A (SMIF) was identified as a Smad4-interacting transcriptional co-activator that forms a TGFβ/BMP4-inducible complex specifically with Smad4 (not other Smads), translocates to the nucleus in a TGFβ/BMP4-inducible and Smad4-dependent manner, and requires p300/CBP for its transcriptional activity. A point mutation in Smad4 abolished binding to DCP1A and impaired transcriptional activity.\",\n      \"method\": \"Co-immunoprecipitation, transcriptional reporter assays, dominant-negative mutant overexpression, morpholino knockdown in zebrafish\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, mutagenesis, functional transcriptional assays, and in vivo knockdown across multiple orthogonal methods in a single study\",\n      \"pmids\": [\"11836524\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"JNK phosphorylates DCP1A at serine 315 in vivo and in vitro, coimmunoprecipitates and colocalizes with DCP1A in P bodies, and sustained JNK activation leads to DCP1A dispersion from P bodies. Phosphomimetic mutation S315 stabilized IL-8 mRNA. Overexpressed DCP1A blocked IL-8 transcription and suppressed p65 NF-κB nuclear activity.\",\n      \"method\": \"In vitro kinase assay, co-immunoprecipitation, live-cell imaging, phosphomimetic mutagenesis, transcriptome analysis\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro kinase assay plus mutagenesis plus Co-IP plus imaging with functional mRNA readouts, multiple orthogonal methods\",\n      \"pmids\": [\"21859862\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"DCP1A interacts with Ddx6 and Edc3 through its proline-rich C-terminal extension, while its N-terminal EVH1 domain shows stronger interaction with Dcp2. ERK pathway mediates dual phosphorylation of Dcp1a at Ser315 and Ser319; phosphorylated Dcp1a enhances its interaction with Dcp2 without affecting interactions with Ddx6, Edc3, or Edc4.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, site-directed mutagenesis, kinase assay, phosphomimetic mutant pulldown\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — mass spectrometry identification of phosphosites, mutagenesis, kinase assay, and Co-IP all in one study\",\n      \"pmids\": [\"23637887\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"DCP1A is hyper-phosphorylated during mitosis; P bodies disassemble as cells prepare for division and reassemble during cytokinesis. Serine 315 is critical for hyper-phosphorylation, and serine mutations in other regions affect the dynamics of DCP1A association with P bodies as shown by live-cell imaging.\",\n      \"method\": \"Live-cell imaging, electrophoresis of mitotic cell extracts, truncation and mutational analysis, phosphorylation assays\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — live-cell imaging plus mutagenesis plus biochemical fractionation, single lab\",\n      \"pmids\": [\"23300942\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"DCP1A and DCP2 are encoded by maternal mRNAs that are recruited for translation during oocyte maturation via cytoplasmic polyadenylation elements. Both proteins are phosphorylated during maturation (CDC2A likely responsible, MAPK may contribute to DCP1A phosphorylation). Inhibiting DCP1A and DCP2 accumulation by RNAi or morpholinos decreased maternal mRNA degradation during meiotic maturation and reduced zygotic genome transcription.\",\n      \"method\": \"RNA interference, morpholino knockdown, mRNA stability assays, kinase inhibitor experiments\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNAi and morpholino knockdown with defined mRNA decay and genome activation phenotypes, single lab\",\n      \"pmids\": [\"23136299\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"DCP1A expression of its N-terminal EVH1 domain is required for activation of PKR, which leads to phosphorylation of eIF2α and translational inhibition. This DCP1A-induced translational arrest is specific to DCP1A, as expression of other P-body components (Pan2, Pan3, Ccr4, Caf1) did not induce eIF2α phosphorylation.\",\n      \"method\": \"GFP-Dcp1a domain mutant expression, eIF2α phosphorylation assays, PKR activation assays, poliovirus infection model\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain mutagenesis with defined PKR activation readout, single lab with multiple mutant constructs\",\n      \"pmids\": [\"24382890\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Dcp1a is hyperphosphorylated during brain development, neuronal differentiation, and cellular stress; specific amino acid residues responsible for phosphorylation were identified.\",\n      \"method\": \"Phosphorylation analysis during neuronal development and stress conditions, residue identification\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, limited methodological detail in abstract, no functional consequence rigorously established\",\n      \"pmids\": [\"19084008\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Malin E3 ubiquitin ligase is recruited to P bodies and promotes DCP1A degradation via the ubiquitin–proteasome system. Depletion of malin results in elevated DCP1A levels and altered microRNA-mediated gene silencing activity.\",\n      \"method\": \"Co-localization, ubiquitin-proteasome inhibitor experiments, malin depletion with DCP1A protein level measurement, miRNA silencing assays\",\n      \"journal\": \"RNA biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — genetic depletion with mechanistic follow-up on protein degradation pathway, single lab\",\n      \"pmids\": [\"23131811\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PRRSV nonstructural protein 4 (nsp4), a 3C-like proteinase, cleaves porcine DCP1A at glutamic acid 238 (E238), and the two cleavage products lose anti-PRRSV activity. The cleavage-resistant mutant pDCP1A-E238A retains higher antiviral activity than wild-type, establishing DCP1A as an interferon-stimulated gene with antiviral function that is targeted by viral protease.\",\n      \"method\": \"Overexpression, knockdown, protease cleavage assay, site-directed mutagenesis (E238A), viral infection assays\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — protease cleavage assay with defined cleavage site plus mutagenesis plus functional antiviral readout\",\n      \"pmids\": [\"30158128\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"PDCoV nsp5 (3C-like protease) cleaves DCP1A at glutamine 343 (Q343); the cleaved fragments DCP1A1-343 and DCP1A344-580 are unable to inhibit PDCoV infection. The cleavage-resistant mutant DCP1A-Q343A exhibits stronger antiviral activity. The Q343 cleavage site is conserved in mammalian DCP1A homologs, and nsp5 from seven other CoVs also cleaved DCP1A.\",\n      \"method\": \"Protease cleavage assay, site-directed mutagenesis (Q343A), viral infection assays, sequence conservation analysis\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — protease cleavage with defined site, mutagenesis, functional antiviral assay, replicated across multiple CoV nsp5 proteins\",\n      \"pmids\": [\"32461317\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SARS-CoV-2 main protease (Mpro) cleaves DCP1A at residue Q343, abolishing its ISG effector activity. Mpro from multiple coronavirus genera also cleaves DCP1A, though alphacoronavirus Mpro shows weaker activity.\",\n      \"method\": \"Protease cleavage assay, site-directed mutagenesis, ISG reporter assays in mammalian cell lines\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — defined cleavage site plus functional assay, replicated across multiple coronavirus proteases in two mammalian cell lines\",\n      \"pmids\": [\"36758802\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SADS-CoV nsp5 cleaves DCP1A via its protease activity (requiring H41 and C144 residues); DCP1A-Q343A mutant resists cleavage and shows stronger ability to inhibit SADS-CoV infection. DCP1A cleavage by nsp5 inhibits IRF3 and NF-κB signaling pathways to decrease IFN-β and inflammatory cytokine production.\",\n      \"method\": \"Protease cleavage assay, active-site mutagenesis of nsp5 (H41, C144), DCP1A Q343A mutant, viral infection assays, IFN-β and cytokine production assays\",\n      \"journal\": \"Frontiers in immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — active site mutagenesis of protease plus substrate site mutagenesis plus functional signaling and antiviral readouts\",\n      \"pmids\": [\"37283741\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"MEK1 phosphorylates DCP1A at S563; dephosphorylation of S563 promotes P body formation and RNA storage, facilitating both self-renewal and differentiation of mouse embryonic stem cells. DCP1A, along with P body components EDC4 and DCP2, is required for ESC self-renewal and differentiation.\",\n      \"method\": \"Quantitative phosphoproteomics, in vitro kinase assay, site-directed mutagenesis (S563), P body imaging, ESC self-renewal and differentiation assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — phosphoproteomics identification plus in vitro kinase assay plus mutagenesis plus defined cellular phenotypes\",\n      \"pmids\": [\"39671288\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"DCP1a and DCP1b are non-redundant cofactors of the mRNA cap hydrolase DCP2 with distinct roles: DCP1a is essential for decapping complex assembly and interactions with mRNA cap-binding proteins, while DCP1b is essential for interactions with protein degradation and translational machinery. DCP1a and DCP1b regulate turnover of distinct sets of mRNAs.\",\n      \"method\": \"Functional dissection by knockdown/knockout, Co-immunoprecipitation of decapping complex components, mRNA turnover profiling\",\n      \"journal\": \"Life science alliance\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and mRNA turnover assays with functional knockdown, single lab, distinct paralog roles established\",\n      \"pmids\": [\"39256052\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Dcp1a-deficient mice generated by CRISPR/Cas9 die around embryonic day 10.5 with massive growth retardation and cardiac developmental defects; lethality is fully rescued by transgenic expression of human DCP1A, establishing DCP1A as essential for embryonic growth.\",\n      \"method\": \"CRISPR/Cas9 knockout, transgenic rescue, embryonic phenotyping\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic knockout with defined embryonic lethal phenotype fully rescued by transgenic human DCP1A\",\n      \"pmids\": [\"33813271\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Dcp1a puncta are absent in quiescent muscle satellite cells but appear during activation/proliferation. Dcp1a knockdown leads to increased cell proliferation and higher cyclin expression during proliferation but compromised differentiation. Knockdown of Dcp1a leads to increased Fmrp accumulation in puncta, indicating cross-regulation between decay and storage mRNP granules.\",\n      \"method\": \"Single myofiber isolation, live-cell imaging, polysome profiling, siRNA knockdown with proliferation and differentiation assays\",\n      \"journal\": \"Skeletal muscle\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — knockdown with defined proliferation/differentiation phenotypes plus imaging, single lab\",\n      \"pmids\": [\"34238354\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Cordycepin suppresses the elevation of DCP1A protein during postovulatory oocyte aging by inhibiting polyadenylation of DCP1A mRNA, consequently impeding maternal mRNA decapping and degradation. Increased DCP1A protein accelerates maternal mRNA degradation during postovulatory aging in both mouse and human oocytes.\",\n      \"method\": \"Proteomic and RNA sequencing analyses, mRNA injection/siRNA in oocytes, polyadenylation assays\",\n      \"journal\": \"Cellular and molecular life sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — siRNA/mRNA injection functional assays plus proteomic/transcriptomic evidence, single lab\",\n      \"pmids\": [\"38001238\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Exogenous Dcp1a mRNA injection into MII oocytes accelerates degradation of maternal mRNAs, while siRNA knockdown of DCP1A reduces maternal mRNA decay in postovulatory-aged oocytes, directly establishing DCP1A as a driver of premature maternal mRNA degradation during postovulatory aging.\",\n      \"method\": \"mRNA microinjection, siRNA knockdown in oocytes, RNA-seq, proteomics\",\n      \"journal\": \"Cell proliferation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — gain- and loss-of-function in oocytes with transcriptomic readout, single lab\",\n      \"pmids\": [\"39629683\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SVV 3C protease cleaves DCP1A at Q343, generating fragments that lose the ability to restrict SVV replication. Wild-type DCP1A targets the viral 3D RNA-dependent RNA polymerase for OPTN-mediated autophagic degradation; this antiviral mechanism is abolished after DCP1A cleavage. The cleavage-resistant DCP1A-Q343A mutant retains stronger antiviral effects.\",\n      \"method\": \"Protease cleavage assay, site-directed mutagenesis (Q343A), viral infection assay, autophagy pathway analysis\",\n      \"journal\": \"Veterinary research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cleavage assay with mutagenesis and viral functional readout, single lab, novel antiviral mechanism proposed with supporting data\",\n      \"pmids\": [\"40022242\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"DCP1A-containing HOPS condensates under hyperosmotic stress exhibit sub-diffusion due to endoplasmic reticulum attachment and occasional super-diffusion due to coupling to microtubule-dependent active transport, as established by live-cell single-particle tracking.\",\n      \"method\": \"Live-cell single-particle tracking (SPT), ER and microtubule fluorescence labeling, GEM accessibility mapping\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single preprint, localization/dynamics data without functional mechanistic follow-up on DCP1A activity\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"DCP1A is an mRNA decapping cofactor of DCP2 that localizes to cytoplasmic P bodies and is regulated by multiple kinases (JNK, ERK, MEK1, CDK1) via phosphorylation at key serine residues (S315, S319, S563), controlling P body dynamics, mRNA stability, and mRNA decay; it also functions as an interferon-stimulated gene with antiviral activity that is counteracted by coronavirus and other viral proteases cleaving DCP1A at Q343 (or E238 in porcine PRRSV), and it additionally acts as a Smad4-interacting transcriptional co-activator in TGFβ signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DCP1A is a cofactor of the mRNA cap hydrolase DCP2 that nucleates cytoplasmic P bodies and couples mRNA decapping and decay to cell-state transitions, antiviral defense, and TGFβ-dependent transcription [#13, #1, #0]. Within the decapping machinery, its N-terminal EVH1 domain mediates the strongest interaction with DCP2, while its proline-rich C-terminal extension engages Ddx6 and Edc3 [#2]; DCP1A and the paralog DCP1B act non-redundantly, with DCP1A required for decapping-complex assembly and contacts with cap-binding proteins and DCP1B linking to degradation and translational machinery, such that each governs turnover of distinct mRNA sets [#13]. DCP1A activity and P body dynamics are set by phosphorylation through multiple kinases: JNK phosphorylates Ser315 and sustained activation disperses DCP1A from P bodies and stabilizes IL-8 mRNA [#1], ERK drives dual Ser315/Ser319 phosphorylation that enhances DCP1A–DCP2 association [#2], mitotic hyperphosphorylation at Ser315 accompanies P body disassembly during division [#3], and MEK1 phosphorylation of Ser563 antagonizes P body formation and RNA storage to control embryonic stem cell self-renewal and differentiation [#12]. DCP1A protein levels are additionally limited by malin-mediated ubiquitin–proteasome degradation, which tunes microRNA silencing [#7]. Through this decapping function DCP1A drives developmental and physiological mRNA clearance: it is essential for mouse embryonic growth and cardiac development [#14], mediates maternal mRNA degradation during oocyte maturation and postovulatory aging [#4, #16, #17], and regulates muscle satellite cell proliferation and differentiation [#15]. Independently, DCP1A (SMIF) functions as a Smad4-specific transcriptional co-activator that translocates to the nucleus upon TGFβ/BMP4 signaling and requires p300/CBP for activity [#0]. DCP1A is also an interferon-stimulated gene with broad antiviral activity that is neutralized by viral 3C-like proteases, which cleave it at Q343 (or E238 in porcine DCP1A), with cleavage-resistant mutants retaining enhanced antiviral function [#8, #9, #10, #11, #18].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Established a transcriptional, signaling role for DCP1A before its decapping function was known, showing it acts as a Smad4-specific nuclear co-activator in TGFβ/BMP4 signaling.\",\n      \"evidence\": \"Co-IP, transcriptional reporter assays, Smad4 point mutant, and zebrafish morpholino knockdown\",\n      \"pmids\": [\"11836524\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not connect the nuclear co-activator role to DCP1A's cytoplasmic decapping function\", \"Mechanism of nuclear/cytoplasmic partitioning not resolved\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"First indicated that DCP1A phosphorylation is a regulated event tied to neuronal development and stress, raising the question of which kinases and sites are involved.\",\n      \"evidence\": \"Phosphorylation analysis across neuronal development and stress with residue identification\",\n      \"pmids\": [\"19084008\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Limited methodological detail and no rigorously established functional consequence\", \"Responsible kinases not identified\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Identified JNK as a kinase that phosphorylates DCP1A at Ser315, linking stress kinase signaling to P body dynamics and mRNA stability.\",\n      \"evidence\": \"In vitro kinase assay, Co-IP, live-cell imaging, S315 phosphomimetic mutagenesis with IL-8 mRNA readout\",\n      \"pmids\": [\"21859862\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism linking DCP1A overexpression to NF-κB suppression not fully resolved\", \"Whether dispersion reflects loss of decapping activity not tested directly\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Mapped DCP1A's modular interactions and showed ERK-driven dual Ser315/Ser319 phosphorylation selectively strengthens DCP1A–DCP2 binding, defining how signaling tunes decapping-complex composition.\",\n      \"evidence\": \"Co-IP, mass spectrometry, site-directed mutagenesis, kinase assay, phosphomimetic pulldown\",\n      \"pmids\": [\"23637887\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Effect on decapping catalytic output not quantified\", \"Interplay between ERK and JNK phosphorylation not resolved\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Connected DCP1A phosphorylation to the cell cycle, showing mitotic hyperphosphorylation (Ser315-dependent) accompanies P body disassembly and reassembly.\",\n      \"evidence\": \"Live-cell imaging, mitotic extract electrophoresis, truncation and mutational analysis\",\n      \"pmids\": [\"23300942\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mitotic kinase not definitively identified\", \"Functional consequence of mitotic P body disassembly for mRNA fate unclear\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Demonstrated a physiological decay role in reproduction, with DCP1A/DCP2 driving maternal mRNA degradation and zygotic genome activation during oocyte maturation.\",\n      \"evidence\": \"RNAi, morpholino knockdown, mRNA stability assays, kinase inhibitor experiments\",\n      \"pmids\": [\"23136299\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct kinase responsible for DCP1A phosphorylation during maturation not confirmed\", \"Target mRNA specificity not defined\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Revealed a translation-control activity distinct from decapping, showing the DCP1A EVH1 domain activates PKR to phosphorylate eIF2α and arrest translation.\",\n      \"evidence\": \"GFP-Dcp1a domain mutants, eIF2α phosphorylation and PKR activation assays, poliovirus model\",\n      \"pmids\": [\"24382890\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which EVH1 engages PKR unresolved\", \"Relationship to canonical decapping activity unclear\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Established that DCP1A protein abundance is controlled by ubiquitin-proteasome turnover via the malin E3 ligase, linking DCP1A levels to microRNA silencing.\",\n      \"evidence\": \"Co-localization, proteasome inhibition, malin depletion with DCP1A level and miRNA silencing assays\",\n      \"pmids\": [\"23131811\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitination sites on DCP1A not mapped\", \"Signals controlling malin recruitment to P bodies unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defined DCP1A as an interferon-stimulated antiviral effector that viral proteases neutralize, showing PRRSV nsp4 cleaves porcine DCP1A at E238 to abrogate antiviral activity.\",\n      \"evidence\": \"Overexpression, knockdown, protease cleavage assay, E238A mutagenesis, viral infection assays\",\n      \"pmids\": [\"30158128\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of DCP1A antiviral restriction not defined\", \"Whether antiviral function requires decapping activity untested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identified Q343 as a conserved cleavage site exploited by coronavirus 3C-like proteases, generalizing the protease-counteraction strategy across CoVs.\",\n      \"evidence\": \"Protease cleavage assay, Q343A mutagenesis, viral infection assays, sequence conservation analysis\",\n      \"pmids\": [\"32461317\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream antiviral effector mechanism not yet defined\", \"Fragment fates after cleavage unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Established DCP1A as essential in vivo, with knockout causing embryonic lethality and cardiac defects rescued by human DCP1A.\",\n      \"evidence\": \"CRISPR/Cas9 knockout, transgenic rescue, embryonic phenotyping in mice\",\n      \"pmids\": [\"33813271\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular cause of cardiac defect not defined\", \"Which DCP1A activity (decapping vs. transcriptional) underlies essentiality unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed DCP1A controls muscle satellite cell fate, with puncta appearing on activation and knockdown shifting proliferation versus differentiation and altering mRNP granule cross-regulation.\",\n      \"evidence\": \"Single myofiber isolation, live-cell imaging, polysome profiling, siRNA knockdown with proliferation/differentiation assays\",\n      \"pmids\": [\"34238354\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Target mRNAs driving the phenotype not identified\", \"Mechanism of Fmrp granule cross-regulation unresolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Confirmed Q343 cleavage by SARS-CoV-2 Mpro and across coronavirus genera abolishes DCP1A ISG effector activity, strengthening DCP1A as a pan-coronavirus antiviral target.\",\n      \"evidence\": \"Protease cleavage assay, site-directed mutagenesis, ISG reporter assays in two mammalian cell lines\",\n      \"pmids\": [\"36758802\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Effector pathway of ISG activity not mechanistically defined here\", \"Alphacoronavirus weaker cleavage basis unexplained\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Linked DCP1A cleavage to suppression of innate immune signaling, showing SADS-CoV nsp5 cleavage at Q343 inhibits IRF3/NF-κB and reduces IFN-β and cytokine output.\",\n      \"evidence\": \"Protease cleavage assay, nsp5 active-site mutagenesis, DCP1A-Q343A mutant, IFN-β and cytokine assays\",\n      \"pmids\": [\"37283741\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct molecular connection between DCP1A and IRF3/NF-κB unresolved\", \"Whether intact DCP1A acts upstream or as scaffold not defined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified DCP1A as a driver of premature maternal mRNA degradation in postovulatory oocyte aging, regulated at the level of DCP1A mRNA polyadenylation.\",\n      \"evidence\": \"Proteomics, RNA-seq, oocyte mRNA injection/siRNA, polyadenylation assays in mouse and human oocytes\",\n      \"pmids\": [\"38001238\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Polyadenylation machinery acting on DCP1A mRNA not identified\", \"Target maternal transcript specificity not defined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Confirmed DCP1A dose directly sets maternal mRNA decay rate in oocytes via gain- and loss-of-function, cementing its causal role in postovulatory aging.\",\n      \"evidence\": \"mRNA microinjection and siRNA knockdown in oocytes with RNA-seq and proteomics\",\n      \"pmids\": [\"39629683\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Upstream regulators of DCP1A in aged oocytes not defined\", \"Selectivity of degraded transcripts unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Resolved DCP1A and DCP1B as non-redundant DCP2 cofactors with distinct interaction partners and distinct target mRNA repertoires, refining the architecture of the decapping complex.\",\n      \"evidence\": \"Knockdown/knockout functional dissection, Co-IP of decapping components, mRNA turnover profiling\",\n      \"pmids\": [\"39256052\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis of paralog-specific interactions not determined\", \"Single-lab; reciprocal validation of partner specificity limited\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined MEK1-dependent Ser563 phosphorylation as a switch governing P body formation and RNA storage in embryonic stem cell self-renewal and differentiation.\",\n      \"evidence\": \"Quantitative phosphoproteomics, in vitro kinase assay, S563 mutagenesis, P body imaging, ESC assays\",\n      \"pmids\": [\"39671288\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stored mRNA targets governing ESC fate not identified\", \"Integration with ERK/JNK phosphorylation inputs unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended the antiviral mechanism by showing intact DCP1A targets viral RdRp for OPTN-mediated autophagic degradation, an activity destroyed by Q343 cleavage.\",\n      \"evidence\": \"Protease cleavage assay, Q343A mutagenesis, viral infection assay, autophagy pathway analysis\",\n      \"pmids\": [\"40022242\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; OPTN-DCP1A interaction not reciprocally validated\", \"Whether this mechanism generalizes beyond SVV unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how DCP1A's distinct activities—decapping cofactor, Smad4 transcriptional co-activator, PKR/translation regulator, and antiviral effector—are mechanistically partitioned, and which underlies its essential developmental role.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model integrating EVH1, proline-rich, and phosphosite regions with each function\", \"No unified account of nuclear vs. cytoplasmic vs. condensate DCP1A pools\", \"Decapping-independence of antiviral and transcriptional roles not directly tested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2, 13]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 13]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [13]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 3, 12]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [2, 13]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [8, 9, 10, 11]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [14, 12]}\n    ],\n    \"complexes\": [\"DCP2 decapping complex\", \"P body\", \"Smad4 transcriptional complex\"],\n    \"partners\": [\"DCP2\", \"DDX6\", \"EDC3\", \"EDC4\", \"SMAD4\", \"MALIN\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}