Affinage

CSNK1E

Casein kinase I isoform epsilon · UniProt P49674

Length
416 aa
Mass
47.3 kDa
Annotated
2026-06-09
24 papers in source corpus 14 papers cited in narrative 14 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

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).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 2002 High

    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

    PMID:11865049

    Open questions at the time
    • Did not identify the specific PER phospho-acceptor sites that recruit downstream degradation machinery
    • Mechanism linking phosphorylation to ubiquitination not yet defined
  2. 2004 High

    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

    PMID:14701732

    Open questions at the time
    • Structural basis of the CKIepsilon-PER binding interface not resolved
    • Why mPER3 fails to bind stably not mechanistically explained at residue level
  3. 2005 High

    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

    PMID:15767683

    Open questions at the time
    • Exact phosphodegron residues on PER2 not mapped in this study
    • Did not address how multiple phospho-events are temporally coordinated
  4. 2006 Medium

    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

    PMID:16326393 PMID:16603629

    Open questions at the time
    • CLK regulation demonstrated for the Drosophila ortholog, not directly for mammalian CSNK1E
    • Whether mammalian CSNK1E phosphorylates Gli/Ci homologs not tested
  5. 2006 Medium

    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

    PMID:16824922

    Open questions at the time
    • Kinase-independent PCP mechanism not molecularly defined
    • Demonstrated in Drosophila; direct mammalian DVL phosphorylation by CSNK1E not reconstituted here
  6. 2007 High

    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

    PMID:17525164

    Open questions at the time
    • Stoichiometry and dynamics of Ser-389 phosphorylation in vivo not quantified
    • Whether other kinases regulate CKIepsilon similarly not addressed
  7. 2009 High

    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

    PMID:19274088 PMID:19805222

    Open questions at the time
    • Physiological trigger relieving C-terminal autoinhibition in vivo not identified
    • How temperature insensitivity is enforced enzymatically not fully explained
  8. 2009 High

    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

    PMID:19948962

    Open questions at the time
    • Mechanism by which binding stabilizes PER independent of catalysis unresolved
    • Relative contributions of CKIdelta vs CKIepsilon not fully separated
  9. 2011 Medium

    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

    PMID:22089318

    Open questions at the time
    • Molecular substrate mediating the drug-sensitivity phenotype not identified
    • Neural circuit or cell type of action undefined
  10. 2023 High

    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

    PMID:37578019

    Open questions at the time
    • Phospho-acceptor sites on alpha-Synuclein/neurofilament not mapped
    • Whether CSNK1E is dysregulated in sporadic PD not established
  11. 2023 Medium

    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

    PMID:41758931

    Open questions at the time
    • Direct CSNK1E substrates driving the persistence phenotype not identified
    • Pathway placement relative to APRIL-TNFRSF13B partially inferred
  12. 2025 Low

    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)

    PMID:bio_10.1101_2025.08.02.668297

    Open questions at the time
    • Awaits direct in vitro reconstitution of CSNK1E-DVL phosphorylation
    • Single-lab preprint not peer-reviewed
    • Specific DVL phospho-sites affected by variants not mapped

Open questions

Synthesis pass · forward-looking unresolved questions
  • 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.
  • 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

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 6 GO:0016740 transferase activity 3 GO:0140110 transcription regulator activity 2
Pathway
R-HSA-9909396 Circadian clock 5 R-HSA-392499 Metabolism of proteins 3 R-HSA-162582 Signal Transduction 2

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2005 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. Cell-based PER2 degradation assay, proteasome inhibitor treatment, CKIepsilon inhibitor treatment, dominant-negative beta-TrCP expression, circadian period measurement in Rat-1 cells Molecular and cellular biology High 15767683
2002 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. Cell-based phosphorylation and degradation assays, ubiquitin-proteasome pathway inhibition, site-directed mutagenesis of mPer3 phosphorylation sites, subcellular localization imaging, transcriptional reporter assay Molecular and cellular biology High 11865049
2009 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. 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 Proceedings of the National Academy of Sciences of the United States of America High 19805222
2007 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. 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 The Journal of biological chemistry High 17525164
2004 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. 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 Molecular and cellular biology High 14701732
2009 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. 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 Proceedings of the National Academy of Sciences of the United States of America High 19948962
2009 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. GST pull-down assays, mass spectrometry (autophosphorylation site mapping), chemical crosslinking, site-directed mutagenesis of CKIalpha kinase domain residues, in vitro kinase assay PloS one High 19274088
2006 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. In vivo CLK phosphorylation analysis, cultured Drosophila cell transfection with DBT, transcriptional reporter assay, protein stability assay, subcellular localization imaging Proceedings of the National Academy of Sciences of the United States of America Medium 16603629
2005 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. 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 Developmental cell High 16326393
2006 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. Loss-of-function and coexpression assays in Drosophila in vivo, identification of primary kinase target residue on Dsh Current biology : CB Medium 16824922
2011 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. Csnk1e knockout mice, selective pharmacological inhibitor (PF-4800567), locomotor activity assay, QTL mapping with congenic lines Neuropsychopharmacology Medium 22089318
2023 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. 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 EMBO molecular medicine High 37578019
2023 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. 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 Blood Medium 41758931
2025 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. TOPFlash reporter assay, immunocytochemistry for DVL localization, in vitro transfection of WT and frameshift DVL constructs, assessment of CSNK1E-induced phosphorylation bioRxivpreprint Low bio_10.1101_2025.08.02.668297

Source papers

Stage 0 corpus · 24 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2005 Control of mammalian circadian rhythm by CKIepsilon-regulated proteasome-mediated PER2 degradation. Molecular and cellular biology 408 15767683
2002 Control of intracellular dynamics of mammalian period proteins by casein kinase I epsilon (CKIepsilon) and CKIdelta in cultured cells. Molecular and cellular biology 249 11865049
2009 CKIepsilon/delta-dependent phosphorylation is a temperature-insensitive, period-determining process in the mammalian circadian clock. Proceedings of the National Academy of Sciences of the United States of America 206 19805222
2007 Activation of 5'-AMP-activated kinase with diabetes drug metformin induces casein kinase Iepsilon (CKIepsilon)-dependent degradation of clock protein mPer2. The Journal of biological chemistry 193 17525164
2009 Essential roles of CKIdelta and CKIepsilon in the mammalian circadian clock. Proceedings of the National Academy of Sciences of the United States of America 140 19948962
2004 Direct association between mouse PERIOD and CKIepsilon is critical for a functioning circadian clock. Molecular and cellular biology 135 14701732
2005 Phosphorylation by double-time/CKIepsilon and CKIalpha targets cubitus interruptus for Slimb/beta-TRCP-mediated proteolytic processing. Developmental cell 118 16326393
2006 Balance between DBT/CKIepsilon kinase and protein phosphatase activities regulate phosphorylation and stability of Drosophila CLOCK protein. Proceedings of the National Academy of Sciences of the United States of America 108 16603629
2006 CKIepsilon/discs overgrown promotes both Wnt-Fz/beta-catenin and Fz/PCP signaling in Drosophila. Current biology : CB 82 16824922
2011 Csnk1e is a genetic regulator of sensitivity to psychostimulants and opioids. Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology 50 22089318
2014 Dopaminergic pathway polymorphisms and heroin addiction: further support for association of CSNK1E variants. Pharmacogenomics 31 25521358
2009 Interactions between Casein kinase Iepsilon (CKIepsilon) and two substrates from disparate signaling pathways reveal mechanisms for substrate-kinase specificity. PloS one 29 19274088
2016 Altered CSNK1E, FABP4 and NEFH protein levels in the dorsolateral prefrontal cortex in schizophrenia. Schizophrenia research 24 27236410
2022 circ_CSNK1E modulates airway smooth muscle cells proliferation and migration via miR-34a-5p/VAMP2 axis in asthma. Cellular signalling 22 35483563
2014 The circadian clock gene Csnk1e regulates rapid eye movement sleep amount, and nonrapid eye movement sleep architecture in mice. Sleep 22 24744456
2019 FENDRR reduces tumor invasiveness in prostate cancer PC-3 cells by targeting CSNK1E. European review for medical and pharmacological sciences 14 31539119
2018 Genetic association study of CSNK1E gene in bipolar disorder and circadian characteristics. Nordic journal of psychiatry 11 30445897
2023 Involvement of casein kinase 1 epsilon/delta (Csnk1e/d) in the pathogenesis of familial Parkinson's disease caused by CHCHD2. EMBO molecular medicine 10 37578019
2018 A de novo pathogenic CSNK1E mutation identified by exome sequencing in family trios with epileptic encephalopathy. Human mutation 10 30488659
2025 Identifying CSNK1E as a therapeutic target in thyroid cancer among the core circadian clock genes. Histochemistry and cell biology 3 39904793
2025 CSNK1E is involved in TGF-β1 induced epithelial mesenchymal transformationas and related to melanoma immune heterogeneity. Frontiers in pharmacology 1 39872053
2025 Casein kinase 1 family member CSNK1E can regulate proliferation and migration in hepatocellular carcinoma. Journal of cancer research and clinical oncology 1 41014359
2026 CSNK1E sustains stemlike drug persistence in diffuse large B-cell lymphoma. Blood 0 41758931
2025 A CGG Repeat Expansion in CSNK1E Associated with Progressive Myoclonic Epilepsy with Incomplete Penetrance. Movement disorders : official journal of the Movement Disorder Society 0 40751262

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