{"gene":"CSNK1E","run_date":"2026-06-09T22:57:19","timeline":{"discoveries":[{"year":2005,"finding":"CKIepsilon phosphorylates PER2 at a specific site that recruits the ubiquitin ligase adapter protein beta-TrCP, leading to PER2 ubiquitination and degradation by the 26S proteasome; dominant negative beta-TrCP blocks this phosphorylation-dependent degradation, and CKIepsilon inhibition slows PER2 degradation and lengthens circadian period in Rat-1 cells.","method":"Cell-based PER2 degradation assay, proteasome inhibitor treatment, CKIepsilon inhibitor treatment, dominant-negative beta-TrCP expression, circadian period measurement in Rat-1 cells","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (pharmacological inhibition, dominant-negative, cell-based biochemical assay) in a single rigorous study with functional readout","pmids":["15767683"],"is_preprint":false},{"year":2002,"finding":"CKIepsilon phosphorylates mPer1, mPer2, and mPer3, causing their rapid degradation via the ubiquitin-proteasome pathway and inducing nuclear translocation of mPer3 in a manner dependent on its nuclear localization signal; mutation of potential CKIepsilon phosphorylation sites on mPer3 reduced both nuclear translocation and degradation; CKIepsilon affects the inhibitory effect of mPer proteins (but not mCry proteins) on BMAL1-CLOCK transcriptional activity.","method":"Cell-based phosphorylation and degradation assays, ubiquitin-proteasome pathway inhibition, site-directed mutagenesis of mPer3 phosphorylation sites, subcellular localization imaging, transcriptional reporter assay","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (mutagenesis, localization, degradation assay, transcriptional reporter) in a single study with clear mechanistic readouts","pmids":["11865049"],"is_preprint":false},{"year":2009,"finding":"CKIepsilon/delta-dependent phosphorylation of PER2 controls the rate of PER2 degradation in living clock cells; this degradation rate is temperature-insensitive in cells and in vitro with a synthetic peptide, revealing that CKIepsilon/delta-dependent phosphorylation is a temperature-insensitive, period-determining step in the mammalian circadian clock.","method":"Cell-based bioluminescence period assay with pharmacological CKI inhibitors (1,260 compound screen), in vitro CKI phosphorylation of synthetic peptide at varying temperatures, central and peripheral clock tissue analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro kinase assay with temperature manipulation combined with cell-based functional assay and multi-tissue validation","pmids":["19805222"],"is_preprint":false},{"year":2007,"finding":"AMPK phosphorylates CKIepsilon at Ser-389, increasing CKIepsilon kinase activity, which in turn phosphorylates and induces degradation of mPer2, shortening the circadian period; metformin (via AMPK activation) causes mPer2 degradation and circadian phase advance in wild-type but not AMPK alpha2 knockout mice.","method":"In vitro kinase assay, site-specific phosphorylation mapping (Ser-389), mPer2 degradation assay in fibroblasts, metformin treatment of wild-type and AMPK alpha2 KO mice, circadian expression analysis in peripheral tissues","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro kinase assay with site mapping plus genetic KO validation in vivo using two orthogonal approaches","pmids":["17525164"],"is_preprint":false},{"year":2004,"finding":"Direct and stable interaction between mPER proteins and CKIepsilon is critical for circadian clock function; mPER3 lacks this direct stable interaction with CKIepsilon (shown by chimeric protein in vitro studies), which contributes to its inability to support clock function; the CKIepsilon-binding domain of PER proteins is required not only for phosphorylation but for clock function.","method":"In vitro chimeric protein binding studies, in vivo phosphorylation and subcellular localization analysis in mouse liver, co-immunoprecipitation of clock proteins, analysis of Per double-mutant mice","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal in vitro binding with chimeric proteins combined with in vivo liver analysis across multiple mutant mouse backgrounds","pmids":["14701732"],"is_preprint":false},{"year":2009,"finding":"CKIepsilon is essential for the mammalian circadian clockwork: disruption of both CKIdelta and CKIepsilon (via dominant-negative CKIepsilon in CKIdelta-deficient MEFs) eliminates circadian bioluminescence rhythms and severely compromises PER abundance and phosphorylation rhythms; overexpression of the CKIepsilon/delta-binding domain of PER2 (CKBD-P2) abolishes circadian rhythms and dramatically lowers PER levels, whereas kinase-inactive DN-CKIepsilon (which still binds PER) does not lower PER levels, suggesting a non-catalytic stabilizing role of CKIepsilon for PER.","method":"Dominant-negative CKIepsilon overexpression in CKIdelta-deficient Per2-Luc MEFs, bioluminescence rhythm recording, immunoblot for PER phosphorylation and abundance, CKI-binding domain (CKBD-P2) overexpression","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic loss-of-function combined with dominant-negative and peptide-disruption approaches with clear molecular and functional readouts","pmids":["19948962"],"is_preprint":false},{"year":2009,"finding":"CKIepsilon binds and phosphorylates both Period (circadian pathway) and Dishevelled (planar cell polarity pathway); two key residues in CKIalpha's kinase domain prevent binding of these substrates to CKIalpha; the unique C-terminus of CKIepsilon plays an auxiliary role in stabilizing (but is not essential for) substrate binding; autophosphorylation of CKIepsilon's C-terminal tail prevents substrate binding and phosphorylation through a phosphorylation-dependent interaction between the C-terminal tail and the kinase domain.","method":"GST pull-down assays, mass spectrometry (autophosphorylation site mapping), chemical crosslinking, site-directed mutagenesis of CKIalpha kinase domain residues, in vitro kinase assay","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1 / Moderate — reconstitution with pull-down, mutagenesis, MS, and crosslinking in a single study; single lab but multiple orthogonal methods","pmids":["19274088"],"is_preprint":false},{"year":2006,"finding":"In Drosophila, DBT (CKIepsilon homolog) activity is required for phase-specific hyperphosphorylation and enhanced degradation of CLK in vivo; DBT directly hyperphosphorylates CLK and evokes modest inhibition of CLK-dependent transactivation in cultured Drosophila cells; DBT functions in partnership with PER-relevant protein phosphatase 2A to establish dynamic equilibrium between hypo- and hyperphosphorylated CLK isoforms; DBT also alters CLK subcellular localization from nuclear to cytoplasmic in the presence of PER.","method":"In vivo CLK phosphorylation analysis, cultured Drosophila cell transfection with DBT, transcriptional reporter assay, protein stability assay, subcellular localization imaging","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cell-based functional assay with localization and reporter readouts, single lab, Drosophila ortholog (DBT)","pmids":["16603629"],"is_preprint":false},{"year":2005,"finding":"In Drosophila, DBT (CKIepsilon homolog) and CKIalpha cooperatively phosphorylate Ci (Gli homolog) at three clusters of serine residues primed by PKA and GSK3; this CKI phosphorylation creates binding sites for the F-box protein Slimb/beta-TRCP, recruiting the SCF(Slimb) ubiquitin ligase for Ci proteolytic processing; CKI phosphorylation sites act cooperatively in vivo.","method":"In vivo genetic analysis in Drosophila, in vitro phosphorylation assay, co-immunoprecipitation for Slimb/beta-TRCP binding, site-directed mutagenesis of Ci phosphorylation clusters, canonical beta-TRCP motif substitution","journal":"Developmental cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro kinase assay combined with in vivo Drosophila genetics, Co-IP, and mutagenesis in a single study","pmids":["16326393"],"is_preprint":false},{"year":2006,"finding":"In Drosophila in vivo, CKIepsilon (discs overgrown) acts positively in both Wnt/beta-catenin and Fz/PCP signaling pathways; kinase activity of CKIepsilon is required for peak Wnt/beta-catenin signaling but CKIepsilon may act through a kinase-independent mechanism in the Fz/PCP pathway; the primary CKIepsilon phosphorylation target residue on Dishevelled was identified.","method":"Loss-of-function and coexpression assays in Drosophila in vivo, identification of primary kinase target residue on Dsh","journal":"Current biology : CB","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo genetic loss-of-function with coexpression in Drosophila, primary phosphorylation site identified; single lab","pmids":["16824922"],"is_preprint":false},{"year":2011,"finding":"Csnk1e functions as a negative regulator of sensitivity to psychostimulants (methamphetamine) and opioids (fentanyl): Csnk1e null mice and mice treated with a selective CKIepsilon inhibitor (PF-4800567) both showed increased locomotor activity following MA and fentanyl administration.","method":"Csnk1e knockout mice, selective pharmacological inhibitor (PF-4800567), locomotor activity assay, QTL mapping with congenic lines","journal":"Neuropsychopharmacology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO plus pharmacological inhibition with defined behavioral phenotype; single lab but two orthogonal approaches (genetic and pharmacological)","pmids":["22089318"],"is_preprint":false},{"year":2023,"finding":"CHCHD2 T61I mutant (mislocalized to cytosol) recruits Csnk1e/d, which then phosphorylates neurofilament and alpha-Synuclein, forming cytosolic aggresomes in dopaminergic neurons; a Csnk1e/d inhibitor substantially suppressed phosphorylation of these substrates, reduced cellular damage in CHCHD2-T61I-expressing cells, and improved neurodegenerative phenotypes in knock-in mice.","method":"Cell transfection (Neuro2a), knock-in and transgenic mouse models, co-immunoprecipitation/localization of Csnk1e/d with CHCHD2-T61I, phosphorylation assays for alpha-Synuclein and neurofilament, Csnk1e/d inhibitor treatment, patient-derived iPS cell-derived dopaminergic neurons, postmortem PD brain analysis","journal":"EMBO molecular medicine","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (cell model, knock-in mouse, patient iPS cells, pharmacological inhibition) with consistent mechanistic readouts across systems","pmids":["37578019"],"is_preprint":false},{"year":2023,"finding":"CSNK1E is upregulated in stemlike drug-persistent DLBCL cells in part through activation of the APRIL-TNFRSF13B axis; CSNK1E inhibition impaired growth and tumor-initiating capacity of drug-persistent cells and potentiated R-CHOP efficacy both in vitro and in vivo.","method":"Single-cell RNA sequencing, B-cell receptor sequencing on paired patient samples, CSNK1E inhibition in vitro and in vivo xenograft models, clonogenicity assay, tumor-initiating capacity assay","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional in vitro and in vivo experiments with defined phenotypic readout; single lab, pathway placement is partially inferred","pmids":["41758931"],"is_preprint":false},{"year":2025,"finding":"Pathogenic DVL frameshift variants interfere with CSNK1E-induced phosphorylation of DVL, offering a mechanism for impaired WNT signaling response; mutant DVL proteins fail to change their localization in response to WNT ligands and fail to activate canonical WNT signaling.","method":"TOPFlash reporter assay, immunocytochemistry for DVL localization, in vitro transfection of WT and frameshift DVL constructs, assessment of CSNK1E-induced phosphorylation","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab preprint, phosphorylation interference shown by cell-based assay without direct in vitro reconstitution of CSNK1E-DVL phosphorylation","pmids":["bio_10.1101_2025.08.02.668297"],"is_preprint":true}],"current_model":"CSNK1E (CKIepsilon) is a serine/threonine kinase whose primary established mechanism is the phosphorylation of PER proteins (PER1, PER2, PER3) at specific sites that recruit the beta-TrCP ubiquitin ligase adapter, targeting PERs for 26S proteasome-mediated degradation and controlling their nuclear translocation, thereby setting the period of the mammalian circadian clock; its activity is itself regulated by AMPK-mediated phosphorylation at Ser-389 and by autophosphorylation of its C-terminal tail (which inhibits substrate binding); additionally, CKIepsilon phosphorylates Dishevelled to promote both Wnt/beta-catenin and PCP signaling, phosphorylates CLK in Drosophila to regulate its stability and transcriptional activity, and phosphorylates alpha-Synuclein and neurofilament when recruited by mislocalized CHCHD2-T61I in a Parkinson's disease context."},"narrative":{"mechanistic_narrative":"CSNK1E (CKIepsilon) is a serine/threonine protein kinase that functions as a core period-determining enzyme of the mammalian circadian clock by phosphorylating PERIOD proteins (PER1, PER2, PER3) to control their stability, localization, and inhibitory activity [PMID:11865049, PMID:19805222]. CKIepsilon-dependent phosphorylation of PER2 creates a recognition motif for the beta-TrCP ubiquitin ligase adapter, driving PER2 ubiquitination and 26S proteasome-mediated degradation; this phosphorylation-coupled degradation is temperature-insensitive and sets the pace of the clock [PMID:15767683, PMID:19805222]. A stable, direct interaction between CKIepsilon and the CKI-binding domain of PER proteins is required for both phosphorylation and clock function, and the kinase contributes non-catalytically to PER stabilization in addition to its degradative phosphorylation role [PMID:14701732, PMID:19948962]. CKIepsilon activity is itself regulated: AMPK phosphorylates CKIepsilon at Ser-389 to increase kinase activity and accelerate PER2 turnover, shortening circadian period, while autophosphorylation of the C-terminal tail folds back onto the kinase domain to block substrate binding [PMID:17525164, PMID:19274088]. Beyond the clock, CKIepsilon phosphorylates Dishevelled and acts positively in Wnt/beta-catenin and planar cell polarity signaling [PMID:19274088, PMID:16824922], and in a Parkinson's disease context it is recruited by cytosol-mislocalized CHCHD2-T61I to phosphorylate alpha-Synuclein and neurofilament, promoting aggresome formation and neurodegeneration that is reversed by CKIepsilon/delta inhibition [PMID:37578019]. CKIepsilon also negatively regulates behavioral sensitivity to psychostimulants and opioids [PMID:22089318] and supports growth and tumor-initiating capacity of drug-persistent DLBCL cells [PMID:41758931].","teleology":[{"year":2002,"claim":"Established that CKIepsilon directly governs PER protein fate, answering how a kinase controls clock-protein levels: it phosphorylates mPer1/2/3 to drive proteasomal degradation and regulate nuclear translocation and PER inhibitory activity on BMAL1-CLOCK.","evidence":"Cell-based phosphorylation/degradation assays, mPer3 phospho-site mutagenesis, localization imaging, and transcriptional reporter assays","pmids":["11865049"],"confidence":"High","gaps":["Did not identify the specific PER phospho-acceptor sites that recruit downstream degradation machinery","Mechanism linking phosphorylation to ubiquitination not yet defined"]},{"year":2004,"claim":"Showed that a direct, stable CKIepsilon-PER physical interaction (absent in mPER3) is required not just for phosphorylation but for clock function, defining substrate engagement as a determinant of clock competence.","evidence":"In vitro chimeric protein binding, in vivo mouse liver phosphorylation/localization, Co-IP, and Per mutant mouse analysis","pmids":["14701732"],"confidence":"High","gaps":["Structural basis of the CKIepsilon-PER binding interface not resolved","Why mPER3 fails to bind stably not mechanistically explained at residue level"]},{"year":2005,"claim":"Defined the degradation mechanism: CKIepsilon phosphorylation of PER2 recruits the beta-TrCP ubiquitin ligase adapter to target PER2 for proteasomal destruction, linking kinase activity to period length.","evidence":"Cell-based PER2 degradation assays, proteasome and CKIepsilon inhibition, dominant-negative beta-TrCP, and circadian period measurement in Rat-1 cells","pmids":["15767683"],"confidence":"High","gaps":["Exact phosphodegron residues on PER2 not mapped in this study","Did not address how multiple phospho-events are temporally coordinated"]},{"year":2006,"claim":"Extended CKIepsilon function beyond the clock by showing the Drosophila ortholog DBT regulates CLK stability and CLK-PP2A phosphorylation equilibrium, and cooperates with CKIalpha to create beta-TrCP/Slimb phosphodegrons on the Hedgehog effector Ci.","evidence":"In vivo Drosophila genetics, in vitro phosphorylation, Co-IP for Slimb binding, reporter and localization assays","pmids":["16603629","16326393"],"confidence":"Medium","gaps":["CLK regulation demonstrated for the Drosophila ortholog, not directly for mammalian CSNK1E","Whether mammalian CSNK1E phosphorylates Gli/Ci homologs not tested"]},{"year":2006,"claim":"Placed CKIepsilon in Wnt and PCP signaling by showing it acts positively in both pathways and phosphorylates a defined target residue on Dishevelled, with kinase-dependent and kinase-independent modes.","evidence":"Drosophila in vivo loss-of-function and coexpression assays with phospho-site identification on Dsh","pmids":["16824922"],"confidence":"Medium","gaps":["Kinase-independent PCP mechanism not molecularly defined","Demonstrated in Drosophila; direct mammalian DVL phosphorylation by CSNK1E not reconstituted here"]},{"year":2007,"claim":"Identified upstream regulation of CKIepsilon, answering how metabolic state tunes the clock: AMPK phosphorylates CKIepsilon at Ser-389 to boost kinase activity, accelerate PER2 degradation, and shorten period.","evidence":"In vitro kinase assay with Ser-389 mapping, fibroblast PER2 degradation, and metformin treatment of WT vs AMPK alpha2 KO mice","pmids":["17525164"],"confidence":"High","gaps":["Stoichiometry and dynamics of Ser-389 phosphorylation in vivo not quantified","Whether other kinases regulate CKIepsilon similarly not addressed"]},{"year":2009,"claim":"Resolved how CKIepsilon achieves clock robustness and autoregulation: phosphorylation-driven PER2 degradation is temperature-insensitive (a period-determining step), and autophosphorylation of the C-terminal tail folds back to inhibit substrate binding shared between PER and Dishevelled.","evidence":"Compound screen with cell bioluminescence assays, in vitro temperature-varied kinase assays on synthetic peptide; and GST pull-down, MS, crosslinking, mutagenesis of the autoinhibitory tail","pmids":["19805222","19274088"],"confidence":"High","gaps":["Physiological trigger relieving C-terminal autoinhibition in vivo not identified","How temperature insensitivity is enforced enzymatically not fully explained"]},{"year":2009,"claim":"Demonstrated CKIepsilon is essential for the clockwork and revealed a dual role: kinase activity drives PER degradation rhythms, but the kinase also stabilizes PER non-catalytically through binding.","evidence":"Dominant-negative CKIepsilon in CKIdelta-deficient Per2-Luc MEFs, bioluminescence recording, immunoblot, and CKBD-P2 peptide disruption","pmids":["19948962"],"confidence":"High","gaps":["Mechanism by which binding stabilizes PER independent of catalysis unresolved","Relative contributions of CKIdelta vs CKIepsilon not fully separated"]},{"year":2011,"claim":"Linked CKIepsilon to behavior, showing it negatively regulates sensitivity to psychostimulants and opioids, broadening its physiological reach beyond timekeeping.","evidence":"Csnk1e knockout mice and selective inhibitor PF-4800567 with locomotor assays and QTL mapping","pmids":["22089318"],"confidence":"Medium","gaps":["Molecular substrate mediating the drug-sensitivity phenotype not identified","Neural circuit or cell type of action undefined"]},{"year":2023,"claim":"Connected CKIepsilon to neurodegeneration, showing mislocalized CHCHD2-T61I recruits Csnk1e/d to phosphorylate alpha-Synuclein and neurofilament and drive aggresome formation, with inhibition rescuing phenotypes.","evidence":"Neuro2a cells, knock-in/transgenic mice, Co-IP/localization, phospho-assays, inhibitor treatment, patient iPSC-derived neurons, and postmortem PD brain","pmids":["37578019"],"confidence":"High","gaps":["Phospho-acceptor sites on alpha-Synuclein/neurofilament not mapped","Whether CSNK1E is dysregulated in sporadic PD not established"]},{"year":2023,"claim":"Implicated CSNK1E in cancer cell persistence, showing it is upregulated via the APRIL-TNFRSF13B axis in drug-persistent DLBCL and that its inhibition impairs tumor-initiating capacity and potentiates chemotherapy.","evidence":"Single-cell RNA-seq, BCR sequencing of paired patient samples, in vitro/in vivo CSNK1E inhibition and clonogenicity/tumor-initiating assays","pmids":["41758931"],"confidence":"Medium","gaps":["Direct CSNK1E substrates driving the persistence phenotype not identified","Pathway placement relative to APRIL-TNFRSF13B partially inferred"]},{"year":2025,"claim":"Tied CSNK1E-DVL phosphorylation to human disease, showing pathogenic DVL frameshift variants interfere with CSNK1E-induced phosphorylation and fail to activate canonical WNT signaling.","evidence":"TOPFlash reporter, DVL localization imaging, and transfection of WT/frameshift DVL constructs (preprint)","pmids":["bio_10.1101_2025.08.02.668297"],"confidence":"Low","gaps":["Awaits direct in vitro reconstitution of CSNK1E-DVL phosphorylation","Single-lab preprint not peer-reviewed","Specific DVL phospho-sites affected by variants not mapped"]},{"year":null,"claim":"The structural basis of CKIepsilon substrate selection and how its C-terminal autoinhibition is relieved in vivo to switch between substrates (PER, Dishevelled, alpha-Synuclein) across distinct cellular contexts remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of CKIepsilon bound to a physiological substrate","Triggers governing context-specific substrate engagement undefined","Whether non-catalytic substrate-stabilizing role generalizes beyond PER unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,2,3,6,11]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1,6]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[1,7]}],"localization":[],"pathway":[{"term_id":"R-HSA-9909396","term_label":"Circadian clock","supporting_discovery_ids":[0,1,2,3,5]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[6,9]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,8]}],"complexes":[],"partners":["PER1","PER2","PER3","DVL","CHCHD2","BTRC"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P49674","full_name":"Casein kinase I isoform epsilon","aliases":[],"length_aa":416,"mass_kda":47.3,"function":"Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates (Probable). Participates in Wnt signaling (PubMed:12556519, PubMed:23413191). Phosphorylates DVL1 (PubMed:12556519). Phosphorylates DVL2 (PubMed:23413191). Phosphorylates NEDD9/HEF1 (By similarity). Central component of the circadian clock (PubMed:16790549). In balance with PP1, determines the circadian period length, through the regulation of the speed and rhythmicity of PER1 and PER2 phosphorylation (PubMed:15917222, PubMed:16790549). Controls PER1 and PER2 nuclear transport and degradation (By similarity). Inhibits cytokine-induced granuloytic differentiation (PubMed:15070676)","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/P49674/entry"},"depmap":{"release":"DepMap","has_data":false,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CSNK1E"},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000213923","cell_line_id":"CID001163","localizations":[{"compartment":"centrosome","grade":3},{"compartment":"cytoplasmic","grade":2},{"compartment":"nucleoplasm","grade":2}],"interactors":[{"gene":"CSNK1E;CSNK1D","stoichiometry":10.0},{"gene":"GAPVD1","stoichiometry":4.0},{"gene":"MCC","stoichiometry":0.2},{"gene":"CRY1","stoichiometry":0.2},{"gene":"FAM207A","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001163","total_profiled":1310},"omim":[{"mim_id":"621522","title":"SCAFFOLDING CK1-ANCHORING PROTEIN F; SACK1F","url":"https://www.omim.org/entry/621522"},{"mim_id":"621521","title":"SCAFFOLDING CK1-ANCHORING PROTEIN E; SACK1E","url":"https://www.omim.org/entry/621521"},{"mim_id":"621520","title":"SCAFFOLDING CK1-ANCHORING PROTEIN C; SACK1C","url":"https://www.omim.org/entry/621520"},{"mim_id":"621519","title":"SCAFFOLDING CK1-ANCHORING PROTEIN B; SACK1B","url":"https://www.omim.org/entry/621519"},{"mim_id":"621022","title":"SCAFFOLDING CK1-ANCHORING PROTEIN A; SACK1A","url":"https://www.omim.org/entry/621022"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CSNK1E"},"hgnc":{"alias_symbol":["HCKIE","CKIE","CKIepsilon"],"prev_symbol":[]},"alphafold":{"accession":"P49674","domains":[{"cath_id":"3.30.200.20","chopping":"15-22_36-84","consensus_level":"medium","plddt":90.923,"start":15,"end":84},{"cath_id":"1.10.510.10","chopping":"86-294","consensus_level":"high","plddt":97.2924,"start":86,"end":294}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P49674","model_url":"https://alphafold.ebi.ac.uk/files/AF-P49674-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P49674-F1-predicted_aligned_error_v6.png","plddt_mean":79.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CSNK1E","jax_strain_url":"https://www.jax.org/strain/search?query=CSNK1E"},"sequence":{"accession":"P49674","fasta_url":"https://rest.uniprot.org/uniprotkb/P49674.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P49674/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P49674"}},"corpus_meta":[{"pmid":"15767683","id":"PMC_15767683","title":"Control of mammalian circadian rhythm by CKIepsilon-regulated proteasome-mediated PER2 degradation.","date":"2005","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/15767683","citation_count":408,"is_preprint":false},{"pmid":"11865049","id":"PMC_11865049","title":"Control of intracellular dynamics of mammalian period proteins by casein kinase I epsilon (CKIepsilon) and CKIdelta in cultured cells.","date":"2002","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/11865049","citation_count":249,"is_preprint":false},{"pmid":"19805222","id":"PMC_19805222","title":"CKIepsilon/delta-dependent phosphorylation is a temperature-insensitive, period-determining process in the mammalian circadian clock.","date":"2009","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/19805222","citation_count":206,"is_preprint":false},{"pmid":"17525164","id":"PMC_17525164","title":"Activation of 5'-AMP-activated kinase with diabetes drug metformin induces casein kinase Iepsilon (CKIepsilon)-dependent degradation of clock protein mPer2.","date":"2007","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/17525164","citation_count":193,"is_preprint":false},{"pmid":"19948962","id":"PMC_19948962","title":"Essential roles of CKIdelta and CKIepsilon in the mammalian circadian clock.","date":"2009","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/19948962","citation_count":140,"is_preprint":false},{"pmid":"14701732","id":"PMC_14701732","title":"Direct association between mouse PERIOD and CKIepsilon is critical for a functioning circadian clock.","date":"2004","source":"Molecular and cellular 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medicine","url":"https://pubmed.ncbi.nlm.nih.gov/37578019","citation_count":10,"is_preprint":false},{"pmid":"30488659","id":"PMC_30488659","title":"A de novo pathogenic CSNK1E mutation identified by exome sequencing in family trios with epileptic encephalopathy.","date":"2018","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/30488659","citation_count":10,"is_preprint":false},{"pmid":"39904793","id":"PMC_39904793","title":"Identifying CSNK1E as a therapeutic target in thyroid cancer among the core circadian clock genes.","date":"2025","source":"Histochemistry and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/39904793","citation_count":3,"is_preprint":false},{"pmid":"41014359","id":"PMC_41014359","title":"Casein kinase 1 family member CSNK1E can regulate proliferation and migration in hepatocellular carcinoma.","date":"2025","source":"Journal of cancer research and clinical 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Society","url":"https://pubmed.ncbi.nlm.nih.gov/40751262","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.08.02.668297","title":"Pathogenic  <i>DVL</i>  frameshifting variants in Robinow syndrome disrupt WNT signaling and cellular dynamics","date":"2025-08-03","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.02.668297","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":15128,"output_tokens":4239,"usd":0.054484,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12139,"output_tokens":4470,"usd":0.086222,"stage2_stop_reason":"end_turn"},"total_usd":0.140706,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2005,\n      \"finding\": \"CKIepsilon phosphorylates PER2 at a specific site that recruits the ubiquitin ligase adapter protein beta-TrCP, leading to PER2 ubiquitination and degradation by the 26S proteasome; dominant negative beta-TrCP blocks this phosphorylation-dependent degradation, and CKIepsilon inhibition slows PER2 degradation and lengthens circadian period in Rat-1 cells.\",\n      \"method\": \"Cell-based PER2 degradation assay, proteasome inhibitor treatment, CKIepsilon inhibitor treatment, dominant-negative beta-TrCP expression, circadian period measurement in Rat-1 cells\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (pharmacological inhibition, dominant-negative, cell-based biochemical assay) in a single rigorous study with functional readout\",\n      \"pmids\": [\"15767683\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"CKIepsilon phosphorylates mPer1, mPer2, and mPer3, causing their rapid degradation via the ubiquitin-proteasome pathway and inducing nuclear translocation of mPer3 in a manner dependent on its nuclear localization signal; mutation of potential CKIepsilon phosphorylation sites on mPer3 reduced both nuclear translocation and degradation; CKIepsilon affects the inhibitory effect of mPer proteins (but not mCry proteins) on BMAL1-CLOCK transcriptional activity.\",\n      \"method\": \"Cell-based phosphorylation and degradation assays, ubiquitin-proteasome pathway inhibition, site-directed mutagenesis of mPer3 phosphorylation sites, subcellular localization imaging, transcriptional reporter assay\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (mutagenesis, localization, degradation assay, transcriptional reporter) in a single study with clear mechanistic readouts\",\n      \"pmids\": [\"11865049\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"CKIepsilon/delta-dependent phosphorylation of PER2 controls the rate of PER2 degradation in living clock cells; this degradation rate is temperature-insensitive in cells and in vitro with a synthetic peptide, revealing that CKIepsilon/delta-dependent phosphorylation is a temperature-insensitive, period-determining step in the mammalian circadian clock.\",\n      \"method\": \"Cell-based bioluminescence period assay with pharmacological CKI inhibitors (1,260 compound screen), in vitro CKI phosphorylation of synthetic peptide at varying temperatures, central and peripheral clock tissue analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro kinase assay with temperature manipulation combined with cell-based functional assay and multi-tissue validation\",\n      \"pmids\": [\"19805222\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"AMPK phosphorylates CKIepsilon at Ser-389, increasing CKIepsilon kinase activity, which in turn phosphorylates and induces degradation of mPer2, shortening the circadian period; metformin (via AMPK activation) causes mPer2 degradation and circadian phase advance in wild-type but not AMPK alpha2 knockout mice.\",\n      \"method\": \"In vitro kinase assay, site-specific phosphorylation mapping (Ser-389), mPer2 degradation assay in fibroblasts, metformin treatment of wild-type and AMPK alpha2 KO mice, circadian expression analysis in peripheral tissues\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro kinase assay with site mapping plus genetic KO validation in vivo using two orthogonal approaches\",\n      \"pmids\": [\"17525164\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Direct and stable interaction between mPER proteins and CKIepsilon is critical for circadian clock function; mPER3 lacks this direct stable interaction with CKIepsilon (shown by chimeric protein in vitro studies), which contributes to its inability to support clock function; the CKIepsilon-binding domain of PER proteins is required not only for phosphorylation but for clock function.\",\n      \"method\": \"In vitro chimeric protein binding studies, in vivo phosphorylation and subcellular localization analysis in mouse liver, co-immunoprecipitation of clock proteins, analysis of Per double-mutant mice\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal in vitro binding with chimeric proteins combined with in vivo liver analysis across multiple mutant mouse backgrounds\",\n      \"pmids\": [\"14701732\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"CKIepsilon is essential for the mammalian circadian clockwork: disruption of both CKIdelta and CKIepsilon (via dominant-negative CKIepsilon in CKIdelta-deficient MEFs) eliminates circadian bioluminescence rhythms and severely compromises PER abundance and phosphorylation rhythms; overexpression of the CKIepsilon/delta-binding domain of PER2 (CKBD-P2) abolishes circadian rhythms and dramatically lowers PER levels, whereas kinase-inactive DN-CKIepsilon (which still binds PER) does not lower PER levels, suggesting a non-catalytic stabilizing role of CKIepsilon for PER.\",\n      \"method\": \"Dominant-negative CKIepsilon overexpression in CKIdelta-deficient Per2-Luc MEFs, bioluminescence rhythm recording, immunoblot for PER phosphorylation and abundance, CKI-binding domain (CKBD-P2) overexpression\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic loss-of-function combined with dominant-negative and peptide-disruption approaches with clear molecular and functional readouts\",\n      \"pmids\": [\"19948962\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"CKIepsilon binds and phosphorylates both Period (circadian pathway) and Dishevelled (planar cell polarity pathway); two key residues in CKIalpha's kinase domain prevent binding of these substrates to CKIalpha; the unique C-terminus of CKIepsilon plays an auxiliary role in stabilizing (but is not essential for) substrate binding; autophosphorylation of CKIepsilon's C-terminal tail prevents substrate binding and phosphorylation through a phosphorylation-dependent interaction between the C-terminal tail and the kinase domain.\",\n      \"method\": \"GST pull-down assays, mass spectrometry (autophosphorylation site mapping), chemical crosslinking, site-directed mutagenesis of CKIalpha kinase domain residues, in vitro kinase assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — reconstitution with pull-down, mutagenesis, MS, and crosslinking in a single study; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"19274088\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"In Drosophila, DBT (CKIepsilon homolog) activity is required for phase-specific hyperphosphorylation and enhanced degradation of CLK in vivo; DBT directly hyperphosphorylates CLK and evokes modest inhibition of CLK-dependent transactivation in cultured Drosophila cells; DBT functions in partnership with PER-relevant protein phosphatase 2A to establish dynamic equilibrium between hypo- and hyperphosphorylated CLK isoforms; DBT also alters CLK subcellular localization from nuclear to cytoplasmic in the presence of PER.\",\n      \"method\": \"In vivo CLK phosphorylation analysis, cultured Drosophila cell transfection with DBT, transcriptional reporter assay, protein stability assay, subcellular localization imaging\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cell-based functional assay with localization and reporter readouts, single lab, Drosophila ortholog (DBT)\",\n      \"pmids\": [\"16603629\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"In Drosophila, DBT (CKIepsilon homolog) and CKIalpha cooperatively phosphorylate Ci (Gli homolog) at three clusters of serine residues primed by PKA and GSK3; this CKI phosphorylation creates binding sites for the F-box protein Slimb/beta-TRCP, recruiting the SCF(Slimb) ubiquitin ligase for Ci proteolytic processing; CKI phosphorylation sites act cooperatively in vivo.\",\n      \"method\": \"In vivo genetic analysis in Drosophila, in vitro phosphorylation assay, co-immunoprecipitation for Slimb/beta-TRCP binding, site-directed mutagenesis of Ci phosphorylation clusters, canonical beta-TRCP motif substitution\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro kinase assay combined with in vivo Drosophila genetics, Co-IP, and mutagenesis in a single study\",\n      \"pmids\": [\"16326393\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"In Drosophila in vivo, CKIepsilon (discs overgrown) acts positively in both Wnt/beta-catenin and Fz/PCP signaling pathways; kinase activity of CKIepsilon is required for peak Wnt/beta-catenin signaling but CKIepsilon may act through a kinase-independent mechanism in the Fz/PCP pathway; the primary CKIepsilon phosphorylation target residue on Dishevelled was identified.\",\n      \"method\": \"Loss-of-function and coexpression assays in Drosophila in vivo, identification of primary kinase target residue on Dsh\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo genetic loss-of-function with coexpression in Drosophila, primary phosphorylation site identified; single lab\",\n      \"pmids\": [\"16824922\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Csnk1e functions as a negative regulator of sensitivity to psychostimulants (methamphetamine) and opioids (fentanyl): Csnk1e null mice and mice treated with a selective CKIepsilon inhibitor (PF-4800567) both showed increased locomotor activity following MA and fentanyl administration.\",\n      \"method\": \"Csnk1e knockout mice, selective pharmacological inhibitor (PF-4800567), locomotor activity assay, QTL mapping with congenic lines\",\n      \"journal\": \"Neuropsychopharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO plus pharmacological inhibition with defined behavioral phenotype; single lab but two orthogonal approaches (genetic and pharmacological)\",\n      \"pmids\": [\"22089318\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CHCHD2 T61I mutant (mislocalized to cytosol) recruits Csnk1e/d, which then phosphorylates neurofilament and alpha-Synuclein, forming cytosolic aggresomes in dopaminergic neurons; a Csnk1e/d inhibitor substantially suppressed phosphorylation of these substrates, reduced cellular damage in CHCHD2-T61I-expressing cells, and improved neurodegenerative phenotypes in knock-in mice.\",\n      \"method\": \"Cell transfection (Neuro2a), knock-in and transgenic mouse models, co-immunoprecipitation/localization of Csnk1e/d with CHCHD2-T61I, phosphorylation assays for alpha-Synuclein and neurofilament, Csnk1e/d inhibitor treatment, patient-derived iPS cell-derived dopaminergic neurons, postmortem PD brain analysis\",\n      \"journal\": \"EMBO molecular medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (cell model, knock-in mouse, patient iPS cells, pharmacological inhibition) with consistent mechanistic readouts across systems\",\n      \"pmids\": [\"37578019\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CSNK1E is upregulated in stemlike drug-persistent DLBCL cells in part through activation of the APRIL-TNFRSF13B axis; CSNK1E inhibition impaired growth and tumor-initiating capacity of drug-persistent cells and potentiated R-CHOP efficacy both in vitro and in vivo.\",\n      \"method\": \"Single-cell RNA sequencing, B-cell receptor sequencing on paired patient samples, CSNK1E inhibition in vitro and in vivo xenograft models, clonogenicity assay, tumor-initiating capacity assay\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional in vitro and in vivo experiments with defined phenotypic readout; single lab, pathway placement is partially inferred\",\n      \"pmids\": [\"41758931\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Pathogenic DVL frameshift variants interfere with CSNK1E-induced phosphorylation of DVL, offering a mechanism for impaired WNT signaling response; mutant DVL proteins fail to change their localization in response to WNT ligands and fail to activate canonical WNT signaling.\",\n      \"method\": \"TOPFlash reporter assay, immunocytochemistry for DVL localization, in vitro transfection of WT and frameshift DVL constructs, assessment of CSNK1E-induced phosphorylation\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab preprint, phosphorylation interference shown by cell-based assay without direct in vitro reconstitution of CSNK1E-DVL phosphorylation\",\n      \"pmids\": [\"bio_10.1101_2025.08.02.668297\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"CSNK1E (CKIepsilon) is a serine/threonine kinase whose primary established mechanism is the phosphorylation of PER proteins (PER1, PER2, PER3) at specific sites that recruit the beta-TrCP ubiquitin ligase adapter, targeting PERs for 26S proteasome-mediated degradation and controlling their nuclear translocation, thereby setting the period of the mammalian circadian clock; its activity is itself regulated by AMPK-mediated phosphorylation at Ser-389 and by autophosphorylation of its C-terminal tail (which inhibits substrate binding); additionally, CKIepsilon phosphorylates Dishevelled to promote both Wnt/beta-catenin and PCP signaling, phosphorylates CLK in Drosophila to regulate its stability and transcriptional activity, and phosphorylates alpha-Synuclein and neurofilament when recruited by mislocalized CHCHD2-T61I in a Parkinson's disease context.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CSNK1E (CKIepsilon) is a serine/threonine protein kinase that functions as a core period-determining enzyme of the mammalian circadian clock by phosphorylating PERIOD proteins (PER1, PER2, PER3) to control their stability, localization, and inhibitory activity [#1, #2]. CKIepsilon-dependent phosphorylation of PER2 creates a recognition motif for the beta-TrCP ubiquitin ligase adapter, driving PER2 ubiquitination and 26S proteasome-mediated degradation; this phosphorylation-coupled degradation is temperature-insensitive and sets the pace of the clock [#0, #2]. A stable, direct interaction between CKIepsilon and the CKI-binding domain of PER proteins is required for both phosphorylation and clock function, and the kinase contributes non-catalytically to PER stabilization in addition to its degradative phosphorylation role [#4, #5]. CKIepsilon activity is itself regulated: AMPK phosphorylates CKIepsilon at Ser-389 to increase kinase activity and accelerate PER2 turnover, shortening circadian period, while autophosphorylation of the C-terminal tail folds back onto the kinase domain to block substrate binding [#3, #6]. Beyond the clock, CKIepsilon phosphorylates Dishevelled and acts positively in Wnt/beta-catenin and planar cell polarity signaling [#6, #9], and in a Parkinson's disease context it is recruited by cytosol-mislocalized CHCHD2-T61I to phosphorylate alpha-Synuclein and neurofilament, promoting aggresome formation and neurodegeneration that is reversed by CKIepsilon/delta inhibition [#11]. CKIepsilon also negatively regulates behavioral sensitivity to psychostimulants and opioids [#10] and supports growth and tumor-initiating capacity of drug-persistent DLBCL cells [#12].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Established that CKIepsilon directly governs PER protein fate, answering how a kinase controls clock-protein levels: it phosphorylates mPer1/2/3 to drive proteasomal degradation and regulate nuclear translocation and PER inhibitory activity on BMAL1-CLOCK.\",\n      \"evidence\": \"Cell-based phosphorylation/degradation assays, mPer3 phospho-site mutagenesis, localization imaging, and transcriptional reporter assays\",\n      \"pmids\": [\"11865049\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify the specific PER phospho-acceptor sites that recruit downstream degradation machinery\", \"Mechanism linking phosphorylation to ubiquitination not yet defined\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Showed that a direct, stable CKIepsilon-PER physical interaction (absent in mPER3) is required not just for phosphorylation but for clock function, defining substrate engagement as a determinant of clock competence.\",\n      \"evidence\": \"In vitro chimeric protein binding, in vivo mouse liver phosphorylation/localization, Co-IP, and Per mutant mouse analysis\",\n      \"pmids\": [\"14701732\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the CKIepsilon-PER binding interface not resolved\", \"Why mPER3 fails to bind stably not mechanistically explained at residue level\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Defined the degradation mechanism: CKIepsilon phosphorylation of PER2 recruits the beta-TrCP ubiquitin ligase adapter to target PER2 for proteasomal destruction, linking kinase activity to period length.\",\n      \"evidence\": \"Cell-based PER2 degradation assays, proteasome and CKIepsilon inhibition, dominant-negative beta-TrCP, and circadian period measurement in Rat-1 cells\",\n      \"pmids\": [\"15767683\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Exact phosphodegron residues on PER2 not mapped in this study\", \"Did not address how multiple phospho-events are temporally coordinated\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Extended CKIepsilon function beyond the clock by showing the Drosophila ortholog DBT regulates CLK stability and CLK-PP2A phosphorylation equilibrium, and cooperates with CKIalpha to create beta-TrCP/Slimb phosphodegrons on the Hedgehog effector Ci.\",\n      \"evidence\": \"In vivo Drosophila genetics, in vitro phosphorylation, Co-IP for Slimb binding, reporter and localization assays\",\n      \"pmids\": [\"16603629\", \"16326393\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"CLK regulation demonstrated for the Drosophila ortholog, not directly for mammalian CSNK1E\", \"Whether mammalian CSNK1E phosphorylates Gli/Ci homologs not tested\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Placed CKIepsilon in Wnt and PCP signaling by showing it acts positively in both pathways and phosphorylates a defined target residue on Dishevelled, with kinase-dependent and kinase-independent modes.\",\n      \"evidence\": \"Drosophila in vivo loss-of-function and coexpression assays with phospho-site identification on Dsh\",\n      \"pmids\": [\"16824922\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Kinase-independent PCP mechanism not molecularly defined\", \"Demonstrated in Drosophila; direct mammalian DVL phosphorylation by CSNK1E not reconstituted here\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Identified upstream regulation of CKIepsilon, answering how metabolic state tunes the clock: AMPK phosphorylates CKIepsilon at Ser-389 to boost kinase activity, accelerate PER2 degradation, and shorten period.\",\n      \"evidence\": \"In vitro kinase assay with Ser-389 mapping, fibroblast PER2 degradation, and metformin treatment of WT vs AMPK alpha2 KO mice\",\n      \"pmids\": [\"17525164\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry and dynamics of Ser-389 phosphorylation in vivo not quantified\", \"Whether other kinases regulate CKIepsilon similarly not addressed\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Resolved how CKIepsilon achieves clock robustness and autoregulation: phosphorylation-driven PER2 degradation is temperature-insensitive (a period-determining step), and autophosphorylation of the C-terminal tail folds back to inhibit substrate binding shared between PER and Dishevelled.\",\n      \"evidence\": \"Compound screen with cell bioluminescence assays, in vitro temperature-varied kinase assays on synthetic peptide; and GST pull-down, MS, crosslinking, mutagenesis of the autoinhibitory tail\",\n      \"pmids\": [\"19805222\", \"19274088\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological trigger relieving C-terminal autoinhibition in vivo not identified\", \"How temperature insensitivity is enforced enzymatically not fully explained\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Demonstrated CKIepsilon is essential for the clockwork and revealed a dual role: kinase activity drives PER degradation rhythms, but the kinase also stabilizes PER non-catalytically through binding.\",\n      \"evidence\": \"Dominant-negative CKIepsilon in CKIdelta-deficient Per2-Luc MEFs, bioluminescence recording, immunoblot, and CKBD-P2 peptide disruption\",\n      \"pmids\": [\"19948962\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which binding stabilizes PER independent of catalysis unresolved\", \"Relative contributions of CKIdelta vs CKIepsilon not fully separated\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Linked CKIepsilon to behavior, showing it negatively regulates sensitivity to psychostimulants and opioids, broadening its physiological reach beyond timekeeping.\",\n      \"evidence\": \"Csnk1e knockout mice and selective inhibitor PF-4800567 with locomotor assays and QTL mapping\",\n      \"pmids\": [\"22089318\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular substrate mediating the drug-sensitivity phenotype not identified\", \"Neural circuit or cell type of action undefined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Connected CKIepsilon to neurodegeneration, showing mislocalized CHCHD2-T61I recruits Csnk1e/d to phosphorylate alpha-Synuclein and neurofilament and drive aggresome formation, with inhibition rescuing phenotypes.\",\n      \"evidence\": \"Neuro2a cells, knock-in/transgenic mice, Co-IP/localization, phospho-assays, inhibitor treatment, patient iPSC-derived neurons, and postmortem PD brain\",\n      \"pmids\": [\"37578019\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Phospho-acceptor sites on alpha-Synuclein/neurofilament not mapped\", \"Whether CSNK1E is dysregulated in sporadic PD not established\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Implicated CSNK1E in cancer cell persistence, showing it is upregulated via the APRIL-TNFRSF13B axis in drug-persistent DLBCL and that its inhibition impairs tumor-initiating capacity and potentiates chemotherapy.\",\n      \"evidence\": \"Single-cell RNA-seq, BCR sequencing of paired patient samples, in vitro/in vivo CSNK1E inhibition and clonogenicity/tumor-initiating assays\",\n      \"pmids\": [\"41758931\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct CSNK1E substrates driving the persistence phenotype not identified\", \"Pathway placement relative to APRIL-TNFRSF13B partially inferred\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Tied CSNK1E-DVL phosphorylation to human disease, showing pathogenic DVL frameshift variants interfere with CSNK1E-induced phosphorylation and fail to activate canonical WNT signaling.\",\n      \"evidence\": \"TOPFlash reporter, DVL localization imaging, and transfection of WT/frameshift DVL constructs (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.08.02.668297\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Awaits direct in vitro reconstitution of CSNK1E-DVL phosphorylation\", \"Single-lab preprint not peer-reviewed\", \"Specific DVL phospho-sites affected by variants not mapped\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural basis of CKIepsilon substrate selection and how its C-terminal autoinhibition is relieved in vivo to switch between substrates (PER, Dishevelled, alpha-Synuclein) across distinct cellular contexts remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of CKIepsilon bound to a physiological substrate\", \"Triggers governing context-specific substrate engagement undefined\", \"Whether non-catalytic substrate-stabilizing role generalizes beyond PER unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 2, 3, 6, 11]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 6]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [1, 7]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9909396\", \"supporting_discovery_ids\": [0, 1, 2, 3, 5]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [6, 9]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 8]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"PER1\", \"PER2\", \"PER3\", \"DVL\", \"CHCHD2\", \"BTRC\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}