{"gene":"NFIL3","run_date":"2026-04-29T11:37:56","timeline":{"discoveries":[{"year":2001,"finding":"E4BP4/NFIL3 functions as a transcriptional repressor that competes with PAR family proteins (DBP, HLF, TEF) for the same DNA binding sites but cannot heterodimerize with them; E4BP4 and PAR proteins oscillate in antiphase in the SCN and liver, forming a reciprocating on/off switch for target gene transcription.","method":"Transcriptional reporter assays in vitro, electrophoretic mobility shift assay (EMSA), mRNA rhythm profiling in SCN and liver, analysis of mCry-deficient mice","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 — multiple orthogonal methods (EMSA, reporter assay, in vivo expression profiling, genetic model) in a single well-cited study","pmids":["11316793"],"is_preprint":false},{"year":1994,"finding":"E4BP4 contains a 65-amino-acid minimal repression domain near its C-terminus that is sufficient to repress transcription when fused to the GAL4 DNA-binding domain; a charge-configuration mutation in this domain abolishes repressor activity, and the mechanism involves interaction with a component of the general transcription machinery rather than resembling known repression domains.","method":"Domain mapping by GAL4 fusion reporter assays, site-directed mutagenesis","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 — reconstitution and mutagenesis of repression domain with functional readout","pmids":["8127655"],"is_preprint":false},{"year":1996,"finding":"The E4BP4 repression domain interacts specifically with the TBP-binding repressor protein Dr1; E4BP4 mutants deficient in repression are also deficient in Dr1 binding, suggesting that recruitment of Dr1 mediates transcriptional repression by E4BP4.","method":"Protein-protein interaction mapping, pulldown assays, correlation of repression-defective mutants with Dr1 binding","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 3 — single-lab protein interaction study with functional mutant correlation","pmids":["8836190"],"is_preprint":false},{"year":1995,"finding":"NFIL3/NF-IL3A binds the sequence TAATTACGTCTG (minimal: ATTACG) in the IL-3 promoter and transactivates IL-3 promoter-reporter constructs in resting T cells in a binding-site-dependent manner, establishing it as a transcriptional activator of the human IL-3 gene.","method":"DNase I footprinting, gel shift assay, cotransfection reporter assays with mutant promoters","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 — in vitro binding assays plus functional reporter assays with site-specific mutations","pmids":["7565758"],"is_preprint":false},{"year":1995,"finding":"E4BP4 is a phosphoprotein; phosphorylation produced in baculovirus-infected Sf9 cells (but not in E. coli) enhances its DNA-binding activity, and the leucine heptad repeat domain is required for both DNA binding and repression activity.","method":"Comparison of bacterially vs. baculovirus-produced protein by gel shift assay, mutagenesis of leucine zipper, post-translational modification analysis","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 1 method (in vitro biochemistry + mutagenesis) but single lab, limited follow-up","pmids":["8547328"],"is_preprint":false},{"year":1997,"finding":"NFIL3/E4BP4 is a delayed-early IL-3-responsive gene in pro-B lymphocytes regulated through the Ras signaling pathway; enforced expression of NFIL3 promotes survival but not proliferation of IL-3-deprived pro-B cells, identifying it as a downstream mediator of IL-3 survival signaling.","method":"Northern blot, enforced cDNA expression in IL-3-dependent pro-B cell lines (Baf-3, FL5.12), survival assays upon growth factor withdrawal","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — gain-of-function with defined survival phenotype, replicated across two cell lines","pmids":["9122243"],"is_preprint":false},{"year":1999,"finding":"NFIL3 expression is regulated by oncogenic Ras through both the Raf-MAPK and PI3K pathways; NFIL3 inhibits apoptosis independently of Bcl-xL, defining two distinct IL-3 survival pathways.","method":"Constitutively active Ras mutant expression, pathway inhibitors, cell survival assays in IL-3-dependent pro-B cells","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 — epistasis via pathway inhibitors and genetic mutants with defined survival readout","pmids":["10082541"],"is_preprint":false},{"year":2002,"finding":"GATA-1 and GATA-2 bind the E4bp4 promoter GATA motif in vitro and in vivo; GATA-1 overexpression transactivates the E4bp4 reporter and modulates IL-3-withdrawal apoptosis, placing GATA factors upstream of NFIL3 in the IL-3 survival pathway.","method":"Promoter deletion analysis, gel shift assay, chromatin immunoprecipitation (ChIP), stable overexpression of GATA-1 and GATA-1 DNA-binding mutant, apoptosis assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 — ChIP confirming in vivo binding plus functional genetic epistasis with defined apoptosis readout","pmids":["12023274"],"is_preprint":false},{"year":2004,"finding":"Casein kinase 1ε (CK1ε) physically associates with E4BP4, phosphorylates it at Ser182, and promotes proteasomal degradation of E4BP4 protein; CK1ε also attenuates E4BP4 nuclear accumulation independently of its kinase activity, thereby reducing E4BP4-mediated repression of cPer2.","method":"Co-immunoprecipitation, in vitro kinase assay, site-directed mutagenesis (Ser182), proteasome inhibitor rescue, nuclear localization assay","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 1 — physical association, in vitro phosphorylation, mutagenesis, and proteasomal mechanism all demonstrated","pmids":["15182670"],"is_preprint":false},{"year":2006,"finding":"E4BP4 binds a novel D-box-like element (B-site) in the Per2 promoter and negatively regulates Per2 mRNA oscillation; the B-site together with the E2 enhancer is required for robust circadian Per2 expression in cell-autonomous clocks.","method":"siRNA knockdown, luciferase reporter assays with promoter deletion/mutation constructs, chromatin immunoprecipitation (ChIP)","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1–2 — multiple orthogonal methods (siRNA KD, mutagenesis, ChIP) in a single study","pmids":["17182630"],"is_preprint":false},{"year":2007,"finding":"E4BP4 physically interacts with PER2 (via E4BP4's C-terminal repression domain) and with CRY2, placing E4BP4 within the negative regulator complex of the mammalian circadian clock.","method":"Co-immunoprecipitation, deletion mapping of interaction domain","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 — single-lab co-IP with domain mapping","pmids":["17274955"],"is_preprint":false},{"year":2009,"finding":"E4BP4/NFIL3 is essential for NK cell development in a cell-intrinsic manner, acting downstream of the IL-15 receptor and upstream of the transcription factor Id2; Nfil3−/− mice specifically lack NK cells but retain B, T, and NKT cells, and NK cell-mediated cytotoxicity is severely impaired.","method":"Gene-targeted Nfil3−/− mice, mixed bone marrow chimeras (cell-intrinsic test), hematopoietic progenitor overexpression, NK cytotoxicity assays","journal":"Nature immunology","confidence":"High","confidence_rationale":"Tier 2 — independently generated KO mouse with defined cellular phenotype, cell-intrinsic rescue, replicated across multiple labs","pmids":["19749763"],"is_preprint":false},{"year":2009,"finding":"NFIL3 is an anti-apoptotic transcription factor in NK cells; Nfil3−/− mice show a specific NK cell intrinsic developmental block with severely reduced mature NK cells, impaired IFN-γ production and cytolytic activity, and failure to reject MHC-I-deficient cells in vivo.","method":"Gene-targeted Nfil3−/− mice, NK cell-intrinsic bone marrow transfer, in vitro cytotoxicity and IFN-γ assays, in vivo rejection assay","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 2 — independent KO mouse replication confirming NK-intrinsic requirement","pmids":["19995955"],"is_preprint":false},{"year":2009,"finding":"NFIL3 is induced by IL-4 in B cells in a STAT6-dependent manner, binds the Iε promoter in vivo, and is required for IL-4-induced germline epsilon (GLε) transcription and IgE class switching in a B-cell-intrinsic manner.","method":"Nfil3−/− mice, ChIP (in vivo binding to Iε promoter), enforced NFIL3 expression rescue, cycloheximide experiment to show direct induction of GLε","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1–2 — ChIP, genetic KO, gain-of-function rescue, multiple orthogonal methods","pmids":["20080759"],"is_preprint":false},{"year":2010,"finding":"E4BP4 binds a D-box element in the distal Fgf21 promoter and suppresses FGF21 transcription; insulin increases E4BP4 expression and promoter binding via AKT activation, linking E4BP4 to circadian and feeding-state repression of FGF21.","method":"E4BP4 overexpression/depletion in hepatocytes, luciferase reporter with D-box mutation, ChIP, FGF21 secretion assay, AKT inhibitor experiments","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 — multiple orthogonal methods (ChIP, reporter, KD, OE, secretion assay) in a single study","pmids":["20851878"],"is_preprint":false},{"year":2011,"finding":"NFIL3/E4BP4 is essential for development of CD8α+ conventional DCs in a cell-intrinsic manner, in part through regulation of Batf3 expression; Nfil3−/− mice lack CD8α+ cDCs, show impaired cross-priming of CD8+ T cells and reduced IL-12 production after TLR3 stimulation.","method":"Nfil3−/− mice, Flt3L bone marrow cultures, cross-priming assay, IL-12 production assay","journal":"Blood","confidence":"High","confidence_rationale":"Tier 2 — KO mouse with cell-intrinsic test and defined functional readouts","pmids":["21474667"],"is_preprint":false},{"year":2011,"finding":"E4BP4 directly binds to and negatively regulates the Il13 gene in TH2 cells, while positively regulating IL-4 production; E4BP4 controls TH2 cytokine balance in a T-cell-intrinsic manner.","method":"Nfil3−/− mice, enforced E4BP4 expression, ChIP, cytokine assays in TH2 cells","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1–2 — ChIP demonstrating direct binding, KO and OE with defined cytokine phenotype","pmids":["21499227"],"is_preprint":false},{"year":2011,"finding":"NFIL3 is induced by IL-10 via STAT3 in myeloid cells and binds a single 10-bp site in a distal enhancer 10 kb upstream of the Il12b transcription start site, mediating transcriptional repression of IL-12p40 as part of a negative feedback loop.","method":"Chromatin immunoprecipitation (ChIP), enhancer deletion analysis, NFIL3-deficient myeloid cells, IL-10/STAT3 pathway analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 — ChIP, site-specific mutagenesis, genetic KO cells with defined cytokine readout","pmids":["21566115"],"is_preprint":false},{"year":2011,"finding":"NFIL3 binds the Il12b promoter and represses IL-12p40 production in macrophages induced by bacterial products; repression requires a C-terminal minimal repression domain of NFIL3 and is IL-10-independent.","method":"ChIP, Il12b-BAC-GFP reporter macrophage line with NFIL3 overexpression/shRNA knockdown, Nfil3−/− macrophages","journal":"Journal of immunology (Baltimore, Md. : 1950)","confidence":"High","confidence_rationale":"Tier 1–2 — ChIP, reporter assay, KO/KD, domain requirement all demonstrated","pmids":["21383239"],"is_preprint":false},{"year":2011,"finding":"E4BP4 controls IL-10 and IL-13 production in CD4+ T cells; enforced E4bp4 expression induces IL-10 and IL-13 in TH1 cells, and E4bp4−/− TH1, Treg, and NKT cells show attenuated IL-10 and IL-13 expression.","method":"Nfil3−/− mice, enforced expression vectors, cytokine measurement in multiple T cell subsets","journal":"Nature immunology","confidence":"High","confidence_rationale":"Tier 2 — KO with gain-of-function validation across multiple cell types","pmids":["21460847"],"is_preprint":false},{"year":2013,"finding":"E4BP4 interacts with histone methyltransferase G9a; E4BP4-dependent repression of Fgf21 requires G9a catalytic activity (SET domain), and E4BP4 overexpression increases H3K9me2 at the Fgf21 promoter, defining an epigenetic repression mechanism.","method":"Co-immunoprecipitation (E4BP4–G9a interaction), G9a inhibitor (BIX01294), SET domain deletion mutant, ChIP for H3K9me2, adenoviral shRNA knockdown in vivo","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — physical interaction, catalytic mutant, ChIP for histone mark, and in vivo KD all demonstrated","pmids":["23283977"],"is_preprint":false},{"year":2014,"finding":"E4BP4 is required at the CLP stage for NK lineage commitment and directly binds the regulatory regions of Eomes and Id2, promoting their transcription; Eomes and Id2 overexpression rescues NK production from E4bp4−/− progenitors.","method":"Conditional/stage-specific E4bp4 deletion, ChIP (E4BP4 binding to Eomes and Id2 loci), rescue experiments with Eomes/Id2 overexpression","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 1–2 — ChIP plus genetic epistasis (rescue) defining direct transcriptional targets","pmids":["24663216"],"is_preprint":false},{"year":2014,"finding":"NFIL3 directs differentiation of a committed ILC precursor (αLP/CXCR6+ cells) that gives rise to all ILC lineages; NFIL3 governs ILC development by directly regulating expression of the transcription factor TOX.","method":"Nfil3−/− mice, clonal differentiation assays, bone marrow precursor identification, ChIP/reporter for TOX regulation","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 — genetic KO with clonal assays and identification of direct downstream target","pmids":["25310240"],"is_preprint":false},{"year":2014,"finding":"NFIL3 is required for the CHILP (common helper innate lymphoid cell progenitor) and acts via direct Id2 regulation; NFIL3 expression in lymphoid progenitors is controlled by IL-7, and ectopic Id2 expression rescues defective ILC lineage development in Nfil3-null precursors in vivo.","method":"Conditional Nfil3 targeting, mixed bone marrow chimeras, Id2 rescue experiments in vivo, promoter binding assays","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 — conditional KO, cell-intrinsic demonstration, genetic rescue defining direct pathway","pmids":["25801035"],"is_preprint":false},{"year":2014,"finding":"Nfil3 is required for Eomes-expressing conventional NK cells but not for TRAIL+Eomes− NK cells; restoration of Eomes in Nfil3−/− progenitors rescues NK cell development, placing Eomes as the key downstream effector of Nfil3 in NK commitment.","method":"Nfil3−/− mice, Eomes reporter/flow cytometry, retroviral Eomes overexpression rescue in Nfil3−/− progenitors","journal":"Journal of immunology (Baltimore, Md. : 1950)","confidence":"High","confidence_rationale":"Tier 2 — genetic KO plus gain-of-function rescue defining Eomes as direct downstream effector","pmids":["24532575"],"is_preprint":false},{"year":2015,"finding":"IL-27 induces NFIL3, which promotes permissive chromatin remodeling at the Tim-3 locus and drives Tim-3 and IL-10 expression in T cells; the inhibitory effect of IL-27-conditioned TH1 cells is NFIL3-dependent.","method":"NFIL3 KO/KD, chromatin remodeling assays (ATAC/accessibility), Tim-3 and IL-10 expression assays, IL-27R−/− mice","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — genetic KO in vitro and in vivo with chromatin remodeling and functional readouts","pmids":["25614966"],"is_preprint":false},{"year":2015,"finding":"PDK1 connects IL-15 signaling to E4BP4 induction via mTOR during early NK cell development; PDK1-deficient NK cells show reduced mTOR activation and E4BP4 induction, and ectopic E4BP4 expression or mTOR activation partially rescues NK cell development.","method":"Conditional PDK1 KO, E4BP4 ectopic expression rescue, mTOR activation bypass, IL-15/CD122 signaling assays","journal":"The Journal of experimental medicine","confidence":"High","confidence_rationale":"Tier 2 — conditional KO with genetic epistasis rescue, defining PDK1-mTOR-E4BP4-CD122 pathway","pmids":["25624444"],"is_preprint":false},{"year":2016,"finding":"E4BP4 binds the Fgf21 promoter D-box element and represses FGF21 expression; E4bp4 knockout mice show upregulated hepatic Fgf21. E4BP4 interacts with nuclear SREBP-1c to preserve its acetylation and protect it from ubiquitination-dependent degradation, thereby amplifying lipogenesis.","method":"E4bp4−/− mice, co-immunoprecipitation (E4BP4–SREBP-1c), ubiquitination assay, adenoviral shRNA in vivo, lipogenic enzyme expression assays","journal":"Journal of lipid research","confidence":"High","confidence_rationale":"Tier 1–2 — KO mice, co-IP for protein interaction, ubiquitination assay with in vivo validation","pmids":["27252523"],"is_preprint":false},{"year":2017,"finding":"Smad3 directly suppresses E4BP4/NFIL3 transcription; deletion of Smad3 expands NK cells and enhances their anti-tumor functions via E4BP4, and Smad3 suppresses IFN-γ production via E4BP4 in a T-bet-independent manner.","method":"Smad3−/− bone marrow transfer, ChIP (Smad3 binding to E4BP4 locus), E4BP4 rescue in Smad3−/− cells, tumor models, SIS3 inhibitor","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1–2 — ChIP establishing direct transcriptional regulation, genetic KO with functional rescue","pmids":["28262747"],"is_preprint":false},{"year":2017,"finding":"The intestinal microbiota controls the amplitude of NFIL3 circadian oscillation in intestinal epithelial cells via group 3 ILCs, STAT3, and the epithelial cell circadian clock; NFIL3 in turn regulates a circadian lipid metabolic program controlling lipid absorption and export.","method":"Germ-free vs. colonized mice, ILC3 depletion, STAT3 inhibition, Nfil3−/− mice, lipid absorption/export assays","journal":"Science (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 — multiple genetic and pharmacological manipulations with defined metabolic phenotype and signaling pathway","pmids":["28860383"],"is_preprint":false},{"year":2017,"finding":"NFIL3 represses hepatic gluconeogenesis by competing with CREB for binding to cAMP response elements in gluconeogenic gene promoters (e.g., Pepck, G6pc); the repression requires the bZIP DNA-binding domain, and hepatic NFIL3 overexpression ameliorates hyperglycemia in insulin-resistant mice.","method":"ChIP (NFIL3 binding to CRE elements), luciferase reporter with CRE mutations, adenoviral overexpression/knockdown in mice, glucose tolerance tests","journal":"Metabolism: clinical and experimental","confidence":"High","confidence_rationale":"Tier 1–2 — ChIP, mutagenesis of binding site, gain/loss of function in vivo","pmids":["29132537"],"is_preprint":false},{"year":2018,"finding":"E4BP4 regulates carboxylesterase 2 (Ces) enzymes by physically interacting with REV-ERBα and antagonizing its trans-repressive activity on Ces2b promoter; E4bp4−/− mice show reduced Ces expression and altered pharmacokinetics of CPT-11.","method":"Co-immunoprecipitation (E4BP4–REV-ERBα), luciferase reporter, EMSA (REV-ERBα binding site), E4bp4−/− mice, pharmacokinetic study","journal":"Biochemical pharmacology","confidence":"High","confidence_rationale":"Tier 1–2 — co-IP, EMSA, reporter, and in vivo pharmacokinetics in KO mice","pmids":["29653076"],"is_preprint":false},{"year":2018,"finding":"E4BP4 mediates transcriptional inhibition of Bcl6 by recruiting the repressive epigenetic modifiers HDAC1 and EZH2, thereby inhibiting T follicular helper (Tfh) cell differentiation; E4BP4 phosphorylation site mutants cannot inhibit Tfh differentiation.","method":"Conditional E4bp4 KO and knockin mice, co-IP/ChIP (HDAC1, EZH2 recruitment), phosphorylation mutant analysis, Tfh differentiation assays","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 1–2 — conditional KO/KI, co-IP for epigenetic complex, mutagenesis of phosphorylation sites","pmids":["32191636"],"is_preprint":false},{"year":2018,"finding":"E4BP4 interacts with G9a to form a multi-molecular complex that silences SOSTDC1 through G9a-mediated epigenetic modification, thereby regulating hepcidin expression and iron homeostasis in thyroid cancer cells.","method":"Co-immunoprecipitation (E4BP4–G9a), ChIP, E4BP4/G9a siRNA knockdown, in vivo xenograft","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2–3 — co-IP and ChIP but single lab, cancer context","pmids":["30250199"],"is_preprint":false},{"year":2019,"finding":"An Nfil3-Zeb2-Id2 transcriptional circuit is required for cDC1 progenitor development; Nfil3 drives the transition from Zeb2hi/Id2lo CDPs to Zeb2lo/Id2hi committed cDC1 progenitors, enabling the switch in Irf8 enhancer usage from the +41-kb to the +32-kb element.","method":"Single-cell RNA-seq of CDPs, genetic epistasis (Nfil3, Zeb2, Id2 KO combinations), Irf8 enhancer reporter","journal":"Nature immunology","confidence":"High","confidence_rationale":"Tier 2 — scRNA-seq plus multi-gene epistasis defining transcriptional circuit","pmids":["31406377"],"is_preprint":false},{"year":2019,"finding":"NFIL3 directly binds the PRNP promoter and acts as a transcriptional activator of PrPc expression; NFIL3-driven PrPc upregulation promotes lung cancer cell lamellipodium formation and migration through JNK signaling.","method":"NFIL3 KD, luciferase reporter with PRNP promoter, ChIP (NFIL3 binding to PRNP promoter), JNK inhibitor, migration/invasion assays","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2–3 — ChIP and reporter for direct binding, KD with defined phenotype, but single lab","pmids":["31477838"],"is_preprint":false},{"year":2019,"finding":"NFIL3 directly binds and negatively regulates Foxp3 expression, and induces methylation at Foxp3 regulatory CpG sites, thereby impairing Treg cell function and stability.","method":"ChIP (NFIL3 binding to Foxp3 locus), bisulfite sequencing for CpG methylation, NFIL3 overexpression in Treg cells, suppression assays in vitro and in vivo","journal":"Experimental & molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP, methylation assay, functional suppression assay in single study","pmids":["31311918"],"is_preprint":false},{"year":2019,"finding":"E4BP4 directly binds to the Notch1 locus and regulates its expression; SUMOylation and phosphorylation of E4BP4 modulate its activity and NK cell development; brief Notch ligand exposure completely rescues NK cell development from E4bp4−/− progenitors.","method":"E4BP4 PTM mutants, ChIP (E4BP4 at Notch1 locus), Notch inhibition/rescue experiments, NK cell development assays","journal":"Journal of immunology (Baltimore, Md. : 1950)","confidence":"Medium","confidence_rationale":"Tier 2–3 — ChIP for novel target, PTM mutant analysis, genetic rescue; single lab","pmids":["29311361"],"is_preprint":false},{"year":2020,"finding":"PBX1 directly binds the Nfil3 promoter and upregulates NFIL3 expression to promote NK cell development; knockout of the PBX1 binding site in the Nfil3 promoter reduces NK precursor and NK cell numbers analogously to Nfil3 KO.","method":"PBX1 conditional KO, ChIP/EMSA (PBX1 binding to Nfil3 promoter), CRISPR deletion of binding site, NK progenitor flow cytometry","journal":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","confidence":"High","confidence_rationale":"Tier 1–2 — ChIP, CRISPR binding site deletion, and conditional KO all converge on same conclusion","pmids":["32190943"],"is_preprint":false},{"year":2021,"finding":"REV-ERBα and REV-ERBβ directly repress E4bp4 expression in cardiomyocytes; loss of Rev-erbs induces E4BP4, which in turn directly represses Nampt via D-box elements, reducing NAD+ biosynthesis and causing cardiomyopathy.","method":"Cardiomyocyte-specific Rev-erb double KO mice, ChIP (REV-ERB binding to E4bp4; E4BP4 binding to Nampt), NAD+ measurement, cardiac function assessment","journal":"Nature cardiovascular research","confidence":"High","confidence_rationale":"Tier 1–2 — conditional double KO, ChIP for both regulatory steps, metabolite measurement","pmids":["35036997"],"is_preprint":false},{"year":2021,"finding":"mTORC1 mainly promotes E4BP4 expression during early NK cell development, while mTORC2 controls T-bet expression; this differential regulation by the two mTOR complexes coordinates sequential stages of NK cell differentiation.","method":"CD122-Cre and Ncr1-Cre conditional KO of Raptor (mTORC1) and Rictor (mTORC2), E4BP4/T-bet protein measurement, NK cell stage-specific flow cytometry","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 — conditional KO with stage-specific phenotype and molecular readout; single lab","pmids":["33462410"],"is_preprint":false},{"year":2022,"finding":"NFIL3 directly suppresses NFKBIA transcription, thereby enhancing NF-κB signaling and promoting proliferation and metastasis of triple-negative breast cancer cells.","method":"ChIP (NFIL3 binding to NFKBIA promoter), luciferase reporter, gain/loss of function, in vivo xenograft, NF-κB activity assays","journal":"Journal of experimental & clinical cancer research : CR","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP, reporter with functional rescue in vivo; single lab","pmids":["35180863"],"is_preprint":false},{"year":2022,"finding":"E4BP4 restrains microglial activation by directly binding a D-box element in the Mapk1/3 promoter and trans-repressing ERK1/2 (Mapk1/3) expression; microglial-specific E4bp4 deletion exacerbates delirium-associated cognitive decline.","method":"Global and microglial-specific E4bp4 KO, ChIP (E4BP4 at Mapk1/3 promoter), single-cell RNA-seq, LTP measurement, cognitive assays","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"High","confidence_rationale":"Tier 1–2 — ChIP, cell-type-specific KO, scRNA-seq, multiple functional readouts","pmids":["35713240"],"is_preprint":false},{"year":2023,"finding":"E4BP4 promotes lipid droplet biogenesis and liver steatosis by activating Fsp27 (CIDEC) expression; E4BP4 enhances Fsp27 transactivation by CREBH. E4BP4 is SUMOylated on five lysine residues, and HFD-induced deSUMOylation of E4BP4 activates Fsp27 and lipid droplet formation.","method":"E4bp4 liver-specific KO and overexpression, Fsp27 rescue, co-IP (E4BP4–CREBH interaction), SUMOylation site mutagenesis, cAMP signaling experiments","journal":"Diabetes","confidence":"High","confidence_rationale":"Tier 1–2 — LKO, OE, rescue, co-IP, and SUMOylation mutagenesis all in one study","pmids":["36508222"],"is_preprint":false},{"year":2024,"finding":"Hepatocyte E4BP4 promotes liver fibrosis by stabilizing YAP, which activates OPN (osteopontin) expression; OPN secreted from hepatocytes activates hepatic stellate cells (HSCs). Antibody neutralization or shRNA depletion of OPN abrogates E4BP4-induced HSC activation.","method":"Hepatocyte-specific E4bp4 KO, medium transfer experiment, RNA-Seq, co-IP (E4BP4–YAP), OPN neutralization, shRNA, in vivo fibrosis model","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"High","confidence_rationale":"Tier 1–2 — LKO, medium transfer for paracrine mechanism, co-IP, rescue with OPN neutralization","pmids":["39473081"],"is_preprint":false},{"year":2017,"finding":"hnRNP A1 binds a specific region of the Nfil3 5'-UTR IRES and regulates cap-independent, IRES-mediated translation of Nfil3 mRNA in a phase-dependent manner; hnRNP A1 knockdown abolishes NFIL3 protein oscillation without affecting mRNA oscillation.","method":"IRES reporter assay, RNA pulldown of hnRNP A1, hnRNP A1 siRNA knockdown, bioluminescent protein oscillation tracking","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — functional IRES reporter, RNA-protein interaction, KD phenotype; single lab","pmids":["28220845"],"is_preprint":false}],"current_model":"NFIL3/E4BP4 is a bZIP transcription factor that functions primarily as a transcriptional repressor (via a C-terminal repression domain that recruits Dr1 and epigenetic co-repressors such as G9a, HDAC1, and EZH2) but can also activate transcription; it binds D-box/EBPRE elements in target gene promoters to regulate circadian gene expression (competing antagonistically with PAR-family activators DBP/HLF/TEF), immune cell development (acting downstream of IL-15/PDK1/mTOR to drive Eomes and Id2 expression, thereby being essential for NK cell, ILC, and CD8α+ DC lineage commitment), and metabolic programs (repressing FGF21, gluconeogenic genes, and drug-metabolizing enzymes while stabilizing SREBP-1c); its activity is controlled post-translationally by CK1ε-mediated phosphorylation (leading to proteasomal degradation), SUMOylation, and protein–protein interactions with PER2, CRY2, REV-ERB, and YAP."},"narrative":{"teleology":[{"year":1994,"claim":"Identification of how NFIL3 represses transcription resolved a basic mechanistic question: a 65-amino-acid C-terminal minimal repression domain was mapped and shown to function through interaction with general transcription machinery rather than through known silencing motifs.","evidence":"GAL4 fusion reporter assays and site-directed mutagenesis in cell lines","pmids":["8127655"],"confidence":"High","gaps":["The specific general transcription factor target was not identified in this study","Whether the repression domain is sufficient in chromatin context was untested"]},{"year":1996,"claim":"The mechanism of NFIL3-mediated repression was refined by demonstrating that the repression domain physically recruits Dr1, a TBP-associated repressor, and that repression-defective mutants lose Dr1 binding.","evidence":"Pulldown assays and correlation of repression-defective mutants with Dr1 binding","pmids":["8836190"],"confidence":"Medium","gaps":["Single-lab protein interaction without reciprocal validation","Whether Dr1 recruitment is the sole or primary repression mechanism in vivo was not tested"]},{"year":1997,"claim":"NFIL3 was established as a survival factor downstream of IL-3/Ras signaling in pro-B lymphocytes, showing that its function extends beyond transcriptional repression to anti-apoptotic activity in hematopoietic cells.","evidence":"Enforced NFIL3 expression in IL-3-dependent pro-B cell lines (Baf-3, FL5.12) with survival assays upon growth factor withdrawal","pmids":["9122243","10082541"],"confidence":"High","gaps":["Direct transcriptional targets mediating survival were not identified","Whether NFIL3 survival function is relevant in vivo was not addressed"]},{"year":2001,"claim":"The circadian role of NFIL3 was defined: it competes with PAR-family activators (DBP, HLF, TEF) for D-box binding sites, and their antiphase oscillation in the SCN and liver establishes a reciprocating transcriptional switch that shapes circadian gene expression.","evidence":"EMSA, transcriptional reporter assays, mRNA rhythm profiling in SCN and liver, mCry-deficient mice","pmids":["11316793"],"confidence":"High","gaps":["Genome-wide identification of shared D-box target genes was not performed","Whether NFIL3 loss alone disrupts circadian behavior was not tested"]},{"year":2004,"claim":"The post-translational control of NFIL3 protein abundance was established: CK1ε phosphorylates Ser182, promoting proteasomal degradation and reducing nuclear accumulation, thereby linking the core clock kinase to NFIL3 turnover.","evidence":"Co-immunoprecipitation, in vitro kinase assay, Ser182 mutagenesis, proteasome inhibitor rescue, nuclear localization assay","pmids":["15182670"],"confidence":"High","gaps":["Whether other CK1 family members contribute was not tested","In vivo relevance of CK1ε-NFIL3 axis for circadian phenotype was not demonstrated"]},{"year":2006,"claim":"NFIL3 was shown to directly repress Per2 through a novel D-box-like B-site in the Per2 promoter, and to interact physically with PER2 and CRY2, integrating it into the negative limb of the circadian feedback loop.","evidence":"siRNA knockdown, ChIP, luciferase reporter with promoter mutations (Per2 regulation); co-immunoprecipitation and domain mapping (PER2/CRY2 interaction)","pmids":["17182630","17274955"],"confidence":"High","gaps":["Functional consequence of PER2/CRY2 interaction on NFIL3 activity was not resolved","PER2/CRY2 interactions were from single-lab co-IP"]},{"year":2009,"claim":"A landmark finding demonstrated that NFIL3 is cell-intrinsically essential for NK cell development: Nfil3⁻/⁻ mice specifically lack mature NK cells, and NFIL3 acts downstream of IL-15R signaling and upstream of Id2, establishing it as a master regulator of NK lineage commitment.","evidence":"Two independent Nfil3⁻/⁻ mouse models, mixed bone marrow chimeras, NK cytotoxicity and IFN-γ assays, in vivo rejection assays","pmids":["19749763","19995955"],"confidence":"High","gaps":["Direct transcriptional targets driving the NK commitment block were not yet identified","Whether NFIL3 is continuously required for mature NK cell maintenance was unclear"]},{"year":2009,"claim":"NFIL3 was shown to function in adaptive immunity beyond NK cells: it is induced by IL-4/STAT6 in B cells, binds the Iε promoter in vivo, and is required for germline ε transcription and IgE class switching.","evidence":"Nfil3⁻/⁻ mice, ChIP at Iε promoter, enforced NFIL3 expression rescue, cycloheximide experiments","pmids":["20080759"],"confidence":"High","gaps":["Whether NFIL3 cooperates with other bZIP factors at the Iε promoter was not determined"]},{"year":2011,"claim":"Multiple studies revealed NFIL3's broad immunoregulatory scope: it directly represses IL-12p40 production in macrophages (via binding the Il12b promoter/enhancer), controls TH2 cytokine balance by repressing IL-13 while promoting IL-10 and IL-4, and is required for CD8α⁺ cDC development.","evidence":"Nfil3⁻/⁻ mice and myeloid/T cell assays, ChIP at Il12b and Il13 loci, enforced expression/knockdown, cross-priming assays, Flt3L bone marrow cultures","pmids":["21474667","21499227","21566115","21383239","21460847"],"confidence":"High","gaps":["How NFIL3 switches between activator and repressor at different cytokine loci was mechanistically unclear","Genome-wide binding landscape in immune cells was not determined"]},{"year":2013,"claim":"The epigenetic mechanism of NFIL3-mediated repression was elucidated: E4BP4 recruits the histone methyltransferase G9a, increasing H3K9me2 at target promoters such as Fgf21, establishing a chromatin-level repression mechanism beyond Dr1 recruitment.","evidence":"Co-immunoprecipitation (E4BP4–G9a), G9a catalytic inhibitor and SET domain deletion mutant, ChIP for H3K9me2, adenoviral shRNA knockdown in vivo","pmids":["23283977"],"confidence":"High","gaps":["Whether G9a is recruited to all NFIL3-repressed targets or only a subset was unknown","Relative contributions of G9a vs. Dr1 vs. other co-repressors were not compared"]},{"year":2014,"claim":"The direct transcriptional targets of NFIL3 in NK/ILC development were defined: NFIL3 binds regulatory regions of Eomes and Id2 to drive their expression at the CLP stage, and separately drives TOX expression to specify a committed ILC precursor; Eomes/Id2 overexpression rescues Nfil3⁻/⁻ NK/ILC defects.","evidence":"Conditional/stage-specific E4bp4 deletion, ChIP at Eomes, Id2, and TOX loci, retroviral rescue experiments, clonal ILC differentiation assays","pmids":["24663216","25310240","25801035","24532575"],"confidence":"High","gaps":["Whether NFIL3 maintains expression of these targets beyond the commitment stage was unclear","Genome-wide binding in progenitors was not performed"]},{"year":2015,"claim":"The upstream signaling pathway to NFIL3 in NK development was mapped: PDK1 connects IL-15 signaling to NFIL3 induction via mTOR, with mTORC1 primarily controlling NFIL3 expression and mTORC2 controlling T-bet, defining branching pathways for NK cell maturation.","evidence":"Conditional PDK1, Raptor, and Rictor KO mice, ectopic E4BP4/mTOR rescue, stage-specific NK flow cytometry","pmids":["25624444","33462410"],"confidence":"High","gaps":["Direct mechanism by which mTORC1 induces NFIL3 transcription or stability was not identified","Whether mTORC1 regulates NFIL3 protein translation or transcription was not resolved"]},{"year":2017,"claim":"NFIL3's metabolic functions were expanded: it represses hepatic gluconeogenesis by competing with CREB for CRE elements in Pepck/G6pc promoters, and the intestinal microbiota controls NFIL3 circadian oscillation in epithelial cells via ILC3/STAT3 to regulate a lipid metabolic program.","evidence":"ChIP at CRE elements, reporter mutagenesis, adenoviral gain/loss of function, glucose tolerance tests; germ-free vs. colonized mice, ILC3 depletion, Nfil3⁻/⁻ mice, lipid absorption assays","pmids":["29132537","28860383"],"confidence":"High","gaps":["Whether NFIL3 and CREB physically interact or simply compete for DNA was unclear","The full set of metabolic genes regulated by microbiota-tuned NFIL3 was not identified"]},{"year":2017,"claim":"IRES-mediated cap-independent translation was identified as a key post-transcriptional control: hnRNP A1 binds the Nfil3 5′-UTR IRES and drives circadian NFIL3 protein oscillation even when mRNA levels are constant.","evidence":"IRES reporter assay, RNA pulldown, hnRNP A1 siRNA knockdown, bioluminescent protein oscillation tracking","pmids":["28220845"],"confidence":"Medium","gaps":["Single-lab finding; independent confirmation needed","Whether IRES-dependent translation is relevant in immune cell contexts was not tested"]},{"year":2018,"claim":"NFIL3's epigenetic co-repressor repertoire was broadened: it recruits HDAC1 and EZH2 to repress Bcl6, inhibiting Tfh differentiation in a phosphorylation-dependent manner; separately, it interacts with REV-ERBα to regulate carboxylesterase expression and drug metabolism.","evidence":"Conditional KO/knockin mice, co-IP/ChIP for HDAC1 and EZH2 at Bcl6, phosphorylation mutant analysis; co-IP (E4BP4–REV-ERBα), EMSA, reporter, E4bp4⁻/⁻ pharmacokinetics","pmids":["32190636","29653076"],"confidence":"High","gaps":["Whether the same phosphorylation events control G9a vs. HDAC1/EZH2 recruitment was unknown","Structural basis of co-repressor selectivity at different loci was not addressed"]},{"year":2019,"claim":"An Nfil3-Zeb2-Id2 transcriptional circuit was shown to control dendritic cell progenitor specification by enabling a switch in Irf8 enhancer usage, defining NFIL3's role in cDC1 lineage commitment at single-cell resolution.","evidence":"Single-cell RNA-seq of CDPs, multi-gene epistasis (Nfil3, Zeb2, Id2 KO combinations), Irf8 enhancer reporter","pmids":["31406377"],"confidence":"High","gaps":["Whether NFIL3 directly binds Zeb2 regulatory elements was not demonstrated","Upstream signals controlling NFIL3 in DC progenitors were not defined"]},{"year":2023,"claim":"NFIL3's role in hepatic lipid metabolism was further specified: it activates Fsp27/CIDEC expression (cooperating with CREBH) to promote lipid droplet biogenesis, and high-fat diet-induced deSUMOylation of NFIL3 at five lysine residues activates this lipogenic program.","evidence":"Liver-specific E4bp4 KO and overexpression, Fsp27 rescue, co-IP (E4BP4–CREBH), SUMOylation site mutagenesis","pmids":["36508222"],"confidence":"High","gaps":["Identity of the SUMO E3 ligase and the deSUMOylation enzyme acting on NFIL3 was not determined","How SUMOylation and CK1ε phosphorylation are coordinated was not addressed"]},{"year":2024,"claim":"NFIL3 was linked to liver fibrosis through a non-canonical mechanism: hepatocyte NFIL3 stabilizes YAP protein, which activates OPN expression, and secreted OPN acts in a paracrine manner to activate hepatic stellate cells.","evidence":"Hepatocyte-specific E4bp4 KO, conditioned medium transfer, co-IP (E4BP4–YAP), OPN neutralization/shRNA, in vivo fibrosis model","pmids":["39473081"],"confidence":"High","gaps":["Mechanism by which NFIL3 stabilizes YAP (direct binding vs. indirect regulation) needs dissection","Whether this pathway is active in other fibrotic organs was not tested"]},{"year":null,"claim":"Key open questions remain: the structural basis for NFIL3's context-dependent switching between activation and repression, the genome-wide binding landscape across immune and metabolic cell types, and how post-translational modifications (phosphorylation, SUMOylation) are integrated to select co-repressor partners at specific loci.","evidence":"","pmids":[],"confidence":"Low","gaps":["No crystal structure or cryo-EM structure of NFIL3 with co-repressors","Genome-wide ChIP-seq across multiple cell types is lacking","Integration of CK1ε phosphorylation, SUMOylation, and IRES-dependent translation into a unified regulatory model is not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0,3,9,14,30]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,1,3,9,14,16,17,21,30,32]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,8,9]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[11,12,13,15,16,17,19,22,23,34]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[1,3,14,17,21,30]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[14,27,29,30,43]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[5,6,26]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[5,6,12]}],"complexes":[],"partners":["PER2","CRY2","G9A","HDAC1","EZH2","SREBP1","YAP1","CREBH"],"other_free_text":[]},"mechanistic_narrative":"NFIL3 (E4BP4) is a basic leucine zipper (bZIP) transcription factor that acts as both a transcriptional repressor and activator to integrate circadian clock regulation, immune cell development, and hepatic metabolic programs. It binds D-box and related cis-elements in target promoters, competing with PAR-family activators (DBP, HLF, TEF) to generate antiphase oscillatory gene expression in the suprachiasmatic nucleus and liver, and its repression activity is mediated by a C-terminal minimal repression domain that recruits co-repressors including Dr1, G9a (depositing H3K9me2), HDAC1, and EZH2 [PMID:11316793, PMID:8127655, PMID:23283977, PMID:32190636]. NFIL3 is essential for NK cell, innate lymphoid cell (ILC), and CD8α⁺ dendritic cell lineage commitment, acting downstream of IL-15/PDK1/mTOR signaling to directly activate Eomes, Id2, and TOX transcription, and it further modulates adaptive immunity by regulating IgE class switching, TH2 cytokine balance, Tfh differentiation, and IL-12 repression [PMID:19749763, PMID:24663216, PMID:25310240, PMID:20080759, PMID:21499227, PMID:32190636, PMID:21566115]. In hepatocytes, NFIL3 represses FGF21 and gluconeogenic genes, stabilizes SREBP-1c to amplify lipogenesis, promotes lipid droplet biogenesis via Fsp27/CIDEC, and drives liver fibrosis through YAP stabilization and OPN-mediated hepatic stellate cell activation; its protein abundance is controlled post-translationally by CK1ε-mediated phosphorylation targeting it for proteasomal degradation, by SUMOylation that modulates its transcriptional output, and by IRES-dependent translational regulation via hnRNP A1 [PMID:20851878, PMID:29132537, PMID:36508222, PMID:39473081, PMID:15182670, PMID:28220845]."},"prefetch_data":{"uniprot":{"accession":"Q16649","full_name":"Nuclear factor interleukin-3-regulated protein","aliases":["E4 promoter-binding protein 4","Interleukin-3 promoter transcriptional activator","Interleukin-3-binding protein 1","Transcriptional activator NF-IL3A"],"length_aa":462,"mass_kda":51.5,"function":"Acts as a transcriptional regulator that recognizes and binds to the sequence 5'-[GA]TTA[CT]GTAA[CT]-3', a sequence present in many cellular and viral promoters. Represses transcription from promoters with activating transcription factor (ATF) sites. Represses promoter activity in osteoblasts (By similarity). Represses transcriptional activity of PER1 (By similarity). Represses transcriptional activity of PER2 via the B-site on the promoter (By similarity). Activates transcription from the interleukin-3 promoter in T-cells. Competes for the same consensus-binding site with PAR DNA-binding factors (DBP, HLF and TEF) (By similarity). Component of the circadian clock that acts as a negative regulator for the circadian expression of PER2 oscillation in the cell-autonomous core clock (By similarity). Protects pro-B cells from programmed cell death (By similarity). Represses the transcription of CYP2A5 (By similarity). Positively regulates the expression and activity of CES2 by antagonizing the repressive action of NR1D1 on CES2 (By similarity). Required for the development of natural killer cell precursors (By similarity)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q16649/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NFIL3","classification":"Not Classified","n_dependent_lines":6,"n_total_lines":1208,"dependency_fraction":0.004966887417218543},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/NFIL3","total_profiled":1310},"omim":[{"mim_id":"618795","title":"JUVENILE ARTHRITIS; JUVAR","url":"https://www.omim.org/entry/618795"},{"mim_id":"606200","title":"BASIC HELIX-LOOP-HELIX FAMILY, MEMBER E41; BHLHE41","url":"https://www.omim.org/entry/606200"},{"mim_id":"605802","title":"ZINC FINGER E BOX-BINDING HOMEOBOX 2; ZEB2","url":"https://www.omim.org/entry/605802"},{"mim_id":"605327","title":"NUCLEAR FACTOR, INTERLEUKIN 3-REGULATED; NFIL3","url":"https://www.omim.org/entry/605327"},{"mim_id":"604256","title":"BASIC HELIX-LOOP-HELIX FAMILY, MEMBER E40; BHLHE40","url":"https://www.omim.org/entry/604256"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nuclear bodies","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NFIL3"},"hgnc":{"alias_symbol":["E4BP4","NFIL3A","NF-IL3A"],"prev_symbol":["IL3BP1"]},"alphafold":{"accession":"Q16649","domains":[{"cath_id":"1.10.287","chopping":"73-154","consensus_level":"medium","plddt":93.1076,"start":73,"end":154}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q16649","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q16649-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q16649-F1-predicted_aligned_error_v6.png","plddt_mean":57.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NFIL3","jax_strain_url":"https://www.jax.org/strain/search?query=NFIL3"},"sequence":{"accession":"Q16649","fasta_url":"https://rest.uniprot.org/uniprotkb/Q16649.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q16649/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q16649"}},"corpus_meta":[{"pmid":"19749763","id":"PMC_19749763","title":"The basic leucine zipper transcription factor E4BP4 is essential for natural killer cell development.","date":"2009","source":"Nature immunology","url":"https://pubmed.ncbi.nlm.nih.gov/19749763","citation_count":364,"is_preprint":false},{"pmid":"28860383","id":"PMC_28860383","title":"The intestinal microbiota regulates body composition through NFIL3 and the circadian clock.","date":"2017","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/28860383","citation_count":351,"is_preprint":false},{"pmid":"11316793","id":"PMC_11316793","title":"Antagonistic role of E4BP4 and PAR proteins in the circadian oscillatory mechanism.","date":"2001","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/11316793","citation_count":332,"is_preprint":false},{"pmid":"19995955","id":"PMC_19995955","title":"Nfil3/E4bp4 is required for the development and maturation of NK cells in vivo.","date":"2009","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/19995955","citation_count":280,"is_preprint":false},{"pmid":"25113970","id":"PMC_25113970","title":"Nfil3 is crucial for development of innate lymphoid cells and host protection against intestinal pathogens.","date":"2014","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/25113970","citation_count":218,"is_preprint":false},{"pmid":"25310240","id":"PMC_25310240","title":"The basic leucine zipper transcription factor NFIL3 directs the development of a common innate lymphoid cell precursor.","date":"2014","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/25310240","citation_count":206,"is_preprint":false},{"pmid":"25092873","id":"PMC_25092873","title":"Nfil3 is required for the development of all innate lymphoid cell subsets.","date":"2014","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/25092873","citation_count":203,"is_preprint":false},{"pmid":"25614966","id":"PMC_25614966","title":"An IL-27/NFIL3 signalling axis drives Tim-3 and IL-10 expression and T-cell dysfunction.","date":"2015","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/25614966","citation_count":177,"is_preprint":false},{"pmid":"21460847","id":"PMC_21460847","title":"The transcription factor E4BP4 regulates the production of IL-10 and IL-13 in CD4+ T cells.","date":"2011","source":"Nature immunology","url":"https://pubmed.ncbi.nlm.nih.gov/21460847","citation_count":169,"is_preprint":false},{"pmid":"24663216","id":"PMC_24663216","title":"The transcription factor E4bp4/Nfil3 controls commitment to the NK lineage and directly regulates Eomes and Id2 expression.","date":"2014","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/24663216","citation_count":159,"is_preprint":false},{"pmid":"28262747","id":"PMC_28262747","title":"Smad3 promotes cancer progression by inhibiting E4BP4-mediated NK cell development.","date":"2017","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/28262747","citation_count":156,"is_preprint":false},{"pmid":"25801035","id":"PMC_25801035","title":"NFIL3 orchestrates the emergence of common helper innate lymphoid cell precursors.","date":"2015","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/25801035","citation_count":155,"is_preprint":false},{"pmid":"24740507","id":"PMC_24740507","title":"Cutting edge: Salivary gland NK cells develop independently of Nfil3 in steady-state.","date":"2014","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/24740507","citation_count":151,"is_preprint":false},{"pmid":"21474667","id":"PMC_21474667","title":"NFIL3/E4BP4 is a key transcription factor for CD8α⁺ dendritic cell development.","date":"2011","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/21474667","citation_count":146,"is_preprint":false},{"pmid":"20080759","id":"PMC_20080759","title":"IL-4-induced transcription factor NFIL3/E4BP4 controls IgE class switching.","date":"2009","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/20080759","citation_count":138,"is_preprint":false},{"pmid":"9122243","id":"PMC_9122243","title":"Pivotal role for the NFIL3/E4BP4 transcription factor in interleukin 3-mediated survival of pro-B lymphocytes.","date":"1997","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/9122243","citation_count":127,"is_preprint":false},{"pmid":"12386933","id":"PMC_12386933","title":"E4BP4/NFIL3, a PAR-related bZIP factor with many roles.","date":"2002","source":"BioEssays : news and reviews in molecular, cellular and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/12386933","citation_count":120,"is_preprint":false},{"pmid":"24277151","id":"PMC_24277151","title":"Nfil3-independent lineage maintenance and antiviral response of natural killer cells.","date":"2013","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/24277151","citation_count":119,"is_preprint":false},{"pmid":"7565758","id":"PMC_7565758","title":"Molecular cloning and characterization of NF-IL3A, a transcriptional activator of the human interleukin-3 promoter.","date":"1995","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/7565758","citation_count":116,"is_preprint":false},{"pmid":"24532575","id":"PMC_24532575","title":"Differential requirement for Nfil3 during NK cell development.","date":"2014","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/24532575","citation_count":106,"is_preprint":false},{"pmid":"31406377","id":"PMC_31406377","title":"An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development.","date":"2019","source":"Nature immunology","url":"https://pubmed.ncbi.nlm.nih.gov/31406377","citation_count":95,"is_preprint":false},{"pmid":"23297132","id":"PMC_23297132","title":"CD8α+ DCs can be induced in the absence of transcription factors Id2, Nfil3, and Batf3.","date":"2013","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/23297132","citation_count":93,"is_preprint":false},{"pmid":"21383239","id":"PMC_21383239","title":"NFIL3 is a regulator of IL-12 p40 in macrophages and mucosal immunity.","date":"2011","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/21383239","citation_count":92,"is_preprint":false},{"pmid":"20851878","id":"PMC_20851878","title":"Transcriptional repressor E4-binding protein 4 (E4BP4) regulates metabolic hormone fibroblast growth factor 21 (FGF21) during circadian cycles and feeding.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20851878","citation_count":92,"is_preprint":false},{"pmid":"17182630","id":"PMC_17182630","title":"A novel E4BP4 element drives circadian expression of mPeriod2.","date":"2006","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/17182630","citation_count":87,"is_preprint":false},{"pmid":"22075207","id":"PMC_22075207","title":"E4BP4: an unexpected player in the immune response.","date":"2011","source":"Trends in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/22075207","citation_count":85,"is_preprint":false},{"pmid":"25624444","id":"PMC_25624444","title":"PDK1 orchestrates early NK cell development through induction of E4BP4 expression and maintenance of IL-15 responsiveness.","date":"2015","source":"The Journal of experimental medicine","url":"https://pubmed.ncbi.nlm.nih.gov/25624444","citation_count":84,"is_preprint":false},{"pmid":"21499227","id":"PMC_21499227","title":"NFIL3/E4BP4 controls type 2 T helper cell cytokine expression.","date":"2011","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/21499227","citation_count":83,"is_preprint":false},{"pmid":"8127655","id":"PMC_8127655","title":"Transcriptional repression by the human bZIP factor E4BP4: definition of a minimal repression domain.","date":"1994","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/8127655","citation_count":81,"is_preprint":false},{"pmid":"10082541","id":"PMC_10082541","title":"Two distinct interleukin-3-mediated signal pathways, Ras-NFIL3 (E4BP4) and Bcl-xL, regulate the survival of murine pro-B lymphocytes.","date":"1999","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/10082541","citation_count":73,"is_preprint":false},{"pmid":"21566115","id":"PMC_21566115","title":"A distal enhancer in Il12b is the target of transcriptional repression by the STAT3 pathway and requires the basic leucine zipper (B-ZIP) protein NFIL3.","date":"2011","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21566115","citation_count":59,"is_preprint":false},{"pmid":"21635892","id":"PMC_21635892","title":"Cellular DBP and E4BP4 proteins are critical for determining the period length of the circadian oscillator.","date":"2011","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/21635892","citation_count":58,"is_preprint":false},{"pmid":"35036997","id":"PMC_35036997","title":"Circadian REV-ERBs repress E4bp4 to activate NAMPT-dependent NAD+ biosynthesis and sustain cardiac function.","date":"2021","source":"Nature cardiovascular research","url":"https://pubmed.ncbi.nlm.nih.gov/35036997","citation_count":56,"is_preprint":false},{"pmid":"31311918","id":"PMC_31311918","title":"The transcription factor NFIL3 controls regulatory T-cell function and stability.","date":"2019","source":"Experimental & molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/31311918","citation_count":51,"is_preprint":false},{"pmid":"35180863","id":"PMC_35180863","title":"Elevated expression of the rhythm gene NFIL3 promotes the progression of TNBC by activating NF-κB signaling through suppression of NFKBIA transcription.","date":"2022","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/35180863","citation_count":50,"is_preprint":false},{"pmid":"24534532","id":"PMC_24534532","title":"The transcription factor E4BP4 is not required for extramedullary pathways of NK cell development.","date":"2014","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/24534532","citation_count":49,"is_preprint":false},{"pmid":"10627534","id":"PMC_10627534","title":"Identification of multiple transcription factors, HLF, FTF, and E4BP4, controlling hepatitis B virus enhancer II.","date":"2000","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/10627534","citation_count":49,"is_preprint":false},{"pmid":"32191636","id":"PMC_32191636","title":"E4BP4-mediated inhibition of T follicular helper cell differentiation is compromised in autoimmune diseases.","date":"2020","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/32191636","citation_count":47,"is_preprint":false},{"pmid":"15306565","id":"PMC_15306565","title":"The CES-2-related transcription factor E4BP4 is an intrinsic regulator of motoneuron growth and survival.","date":"2004","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/15306565","citation_count":43,"is_preprint":false},{"pmid":"26880402","id":"PMC_26880402","title":"Eosinophil resistance to glucocorticoid-induced apoptosis is mediated by the transcription factor NFIL3.","date":"2016","source":"Apoptosis : an international journal on programmed cell death","url":"https://pubmed.ncbi.nlm.nih.gov/26880402","citation_count":42,"is_preprint":false},{"pmid":"17274955","id":"PMC_17274955","title":"The negative transcription factor E4BP4 is associated with circadian clock protein PERIOD2.","date":"2007","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/17274955","citation_count":41,"is_preprint":false},{"pmid":"23340290","id":"PMC_23340290","title":"E4BP4 overexpression: a protective mechanism in CD4+ T cells from SLE patients.","date":"2013","source":"Journal of autoimmunity","url":"https://pubmed.ncbi.nlm.nih.gov/23340290","citation_count":41,"is_preprint":false},{"pmid":"24442434","id":"PMC_24442434","title":"NFIL3-deficient mice develop microbiota-dependent, IL-12/23-driven spontaneous colitis.","date":"2014","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/24442434","citation_count":40,"is_preprint":false},{"pmid":"30250199","id":"PMC_30250199","title":"E4BP4 promotes thyroid cancer proliferation by modulating iron homeostasis through repression of hepcidin.","date":"2018","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/30250199","citation_count":40,"is_preprint":false},{"pmid":"9125190","id":"PMC_9125190","title":"Inducibility of E4BP4 suggests a novel mechanism of negative gene regulation by glucocorticoids.","date":"1997","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/9125190","citation_count":39,"is_preprint":false},{"pmid":"15182670","id":"PMC_15182670","title":"Negative control of circadian clock regulator E4BP4 by casein kinase Iepsilon-mediated phosphorylation.","date":"2004","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/15182670","citation_count":37,"is_preprint":false},{"pmid":"31477838","id":"PMC_31477838","title":"Cellular prion protein transcriptionally regulated by NFIL3 enhances lung cancer cell lamellipodium formation and migration through JNK signaling.","date":"2019","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/31477838","citation_count":36,"is_preprint":false},{"pmid":"26539561","id":"PMC_26539561","title":"New Frontiers for the NFIL3 bZIP Transcription Factor in Cancer, Metabolism and Beyond.","date":"2014","source":"Discoveries (Craiova, Romania)","url":"https://pubmed.ncbi.nlm.nih.gov/26539561","citation_count":35,"is_preprint":false},{"pmid":"32781006","id":"PMC_32781006","title":"LncRNA GAS5 suppresses CD4+ T cell activation by upregulating E4BP4 via inhibiting miR-92a-3p in systemic lupus erythematosus.","date":"2020","source":"Immunology letters","url":"https://pubmed.ncbi.nlm.nih.gov/32781006","citation_count":35,"is_preprint":false},{"pmid":"8836190","id":"PMC_8836190","title":"Protein-protein interaction between the transcriptional repressor E4BP4 and the TBP-binding protein Dr1.","date":"1996","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/8836190","citation_count":35,"is_preprint":false},{"pmid":"23283977","id":"PMC_23283977","title":"Recruitment of histone methyltransferase G9a mediates transcriptional repression of Fgf21 gene by E4BP4 protein.","date":"2013","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/23283977","citation_count":34,"is_preprint":false},{"pmid":"27521341","id":"PMC_27521341","title":"NFIL3 Expression Distinguishes Tissue-Resident NK Cells and Conventional NK-like Cells in the Mouse Submandibular Glands.","date":"2016","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/27521341","citation_count":34,"is_preprint":false},{"pmid":"20854132","id":"PMC_20854132","title":"Multiple PAR and E4BP4 bZIP transcription factors in zebrafish: diverse spatial and temporal expression patterns.","date":"2010","source":"Chronobiology international","url":"https://pubmed.ncbi.nlm.nih.gov/20854132","citation_count":34,"is_preprint":false},{"pmid":"10074173","id":"PMC_10074173","title":"Transcriptional repression of human hepatitis B virus genes by a bZIP family member, E4BP4.","date":"1999","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/10074173","citation_count":32,"is_preprint":false},{"pmid":"18829486","id":"PMC_18829486","title":"Negative regulation of the osteoblast function in multiple myeloma through the repressor gene E4BP4 activated by malignant plasma cells.","date":"2008","source":"Clinical cancer research : an official journal of the American Association for Cancer Research","url":"https://pubmed.ncbi.nlm.nih.gov/18829486","citation_count":31,"is_preprint":false},{"pmid":"29215740","id":"PMC_29215740","title":"The STAT3/NFIL3 signaling axis-mediated chemotherapy resistance is reversed by Raddeanin A via inducing apoptosis in choriocarcinoma cells.","date":"2018","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/29215740","citation_count":30,"is_preprint":false},{"pmid":"33462410","id":"PMC_33462410","title":"mTORC1 and mTORC2 coordinate early NK cell development by differentially inducing E4BP4 and T-bet.","date":"2021","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/33462410","citation_count":30,"is_preprint":false},{"pmid":"12743120","id":"PMC_12743120","title":"Parathyroid hormone-induced E4BP4/NFIL3 down-regulates transcription in osteoblasts.","date":"2003","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12743120","citation_count":29,"is_preprint":false},{"pmid":"29653076","id":"PMC_29653076","title":"E4bp4 regulates carboxylesterase 2 enzymes through repression of the nuclear receptor Rev-erbα in mice.","date":"2018","source":"Biochemical pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/29653076","citation_count":29,"is_preprint":false},{"pmid":"30484891","id":"PMC_30484891","title":"miR-203 accelerates apoptosis and inflammation induced by LPS via targeting NFIL3 in cardiomyocytes.","date":"2018","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/30484891","citation_count":29,"is_preprint":false},{"pmid":"12023274","id":"PMC_12023274","title":"GATA factors are essential for transcription of the survival gene E4bp4 and the viability response of interleukin-3 in Ba/F3 hematopoietic cells.","date":"2002","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12023274","citation_count":29,"is_preprint":false},{"pmid":"24794868","id":"PMC_24794868","title":"α1-adrenergic receptor signaling in osteoblasts regulates clock genes and bone morphogenetic protein 4 expression through up-regulation of the transcriptional factor nuclear factor IL-3 (Nfil3)/E4 promoter-binding protein 4 (E4BP4).","date":"2014","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/24794868","citation_count":29,"is_preprint":false},{"pmid":"30552177","id":"PMC_30552177","title":"NFIL3 mutations alter immune homeostasis and sensitise for arthritis pathology.","date":"2018","source":"Annals of the rheumatic diseases","url":"https://pubmed.ncbi.nlm.nih.gov/30552177","citation_count":28,"is_preprint":false},{"pmid":"26985000","id":"PMC_26985000","title":"The Transcription Factor NFIL3 Is Essential for Normal Placental and Embryonic Development but Not for Uterine Natural Killer (UNK) Cell Differentiation in Mice.","date":"2016","source":"Biology of reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/26985000","citation_count":28,"is_preprint":false},{"pmid":"35713240","id":"PMC_35713240","title":"E4BP4 Coordinates Circadian Control of Cognition in Delirium.","date":"2022","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/35713240","citation_count":27,"is_preprint":false},{"pmid":"29311361","id":"PMC_29311361","title":"Multiple Levels of Control Determine How E4bp4/Nfil3 Regulates NK Cell Development.","date":"2018","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/29311361","citation_count":26,"is_preprint":false},{"pmid":"25338303","id":"PMC_25338303","title":"E4BP4 is a repressor of epigenetically regulated SOSTDC1 expression in breast cancer cells.","date":"2014","source":"Cellular oncology (Dordrecht, Netherlands)","url":"https://pubmed.ncbi.nlm.nih.gov/25338303","citation_count":25,"is_preprint":false},{"pmid":"24658772","id":"PMC_24658772","title":"Glucocorticoid induced osteoblast apoptosis by increasing E4BP4 expression via up-regulation of Bim.","date":"2014","source":"Calcified tissue international","url":"https://pubmed.ncbi.nlm.nih.gov/24658772","citation_count":25,"is_preprint":false},{"pmid":"8547328","id":"PMC_8547328","title":"Characterization of human E4BP4, a phosphorylated bZIP factor.","date":"1995","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/8547328","citation_count":25,"is_preprint":false},{"pmid":"20186462","id":"PMC_20186462","title":"E4BP4 is a cardiac survival factor and essential for embryonic heart development.","date":"2010","source":"Molecular and cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20186462","citation_count":23,"is_preprint":false},{"pmid":"27252523","id":"PMC_27252523","title":"E4BP4 is an insulin-induced stabilizer of nuclear SREBP-1c and promotes SREBP-1c-mediated lipogenesis.","date":"2016","source":"Journal of lipid research","url":"https://pubmed.ncbi.nlm.nih.gov/27252523","citation_count":23,"is_preprint":false},{"pmid":"39097582","id":"PMC_39097582","title":"Ferroptosis and inflammation are modulated by the NFIL3-ACSL4 axis in sepsis associated-acute kidney injury.","date":"2024","source":"Cell death discovery","url":"https://pubmed.ncbi.nlm.nih.gov/39097582","citation_count":22,"is_preprint":false},{"pmid":"25536374","id":"PMC_25536374","title":"NFIL3 suppresses hypoxia-induced apoptotic cell death by targeting the insulin-like growth factor 2 receptor.","date":"2015","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/25536374","citation_count":22,"is_preprint":false},{"pmid":"32780887","id":"PMC_32780887","title":"Hepatic E4BP4 induction promotes lipid accumulation by suppressing AMPK signaling in response to chemical or diet-induced ER stress.","date":"2020","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/32780887","citation_count":22,"is_preprint":false},{"pmid":"29132537","id":"PMC_29132537","title":"NFIL3 is a negative regulator of hepatic gluconeogenesis.","date":"2017","source":"Metabolism: clinical and experimental","url":"https://pubmed.ncbi.nlm.nih.gov/29132537","citation_count":22,"is_preprint":false},{"pmid":"32190943","id":"PMC_32190943","title":"PBX1 promotes development of natural killer cells by binding directly to the Nfil3 promoter.","date":"2020","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/32190943","citation_count":21,"is_preprint":false},{"pmid":"33013924","id":"PMC_33013924","title":"Diurnal Rhythmicity Programs of Microbiota and Transcriptional Oscillation of Circadian Regulator, NFIL3.","date":"2020","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/33013924","citation_count":20,"is_preprint":false},{"pmid":"20697558","id":"PMC_20697558","title":"The transcriptional regulator NFIL3 controls IgE production.","date":"2010","source":"Transactions of the American Clinical and Climatological Association","url":"https://pubmed.ncbi.nlm.nih.gov/20697558","citation_count":20,"is_preprint":false},{"pmid":"23425966","id":"PMC_23425966","title":"Nfil3 is a glucocorticoid-regulated gene required for glucocorticoid-induced apoptosis in male murine T cells.","date":"2013","source":"Endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/23425966","citation_count":20,"is_preprint":false},{"pmid":"33434146","id":"PMC_33434146","title":"Hepatic metabolic regulation by nuclear factor E4BP4.","date":"2021","source":"Journal of molecular endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/33434146","citation_count":19,"is_preprint":false},{"pmid":"28220845","id":"PMC_28220845","title":"Heterogeneous nuclear ribonucleoprotein A1 regulates rhythmic synthesis of mouse Nfil3 protein via IRES-mediated translation.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/28220845","citation_count":19,"is_preprint":false},{"pmid":"36439145","id":"PMC_36439145","title":"NFIL3 and its immunoregulatory role in rheumatoid arthritis patients.","date":"2022","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/36439145","citation_count":19,"is_preprint":false},{"pmid":"21975218","id":"PMC_21975218","title":"E4BP4 facilitates glucocorticoid-evoked apoptosis of human leukemic CEM cells via upregulation of Bim.","date":"2011","source":"Journal of molecular signaling","url":"https://pubmed.ncbi.nlm.nih.gov/21975218","citation_count":19,"is_preprint":false},{"pmid":"25083807","id":"PMC_25083807","title":"Molecular cloning and functional characterization of the NFIL3/E4BP4 transcription factor of grass carp, Ctenopharyngodon idella.","date":"2014","source":"Developmental and comparative immunology","url":"https://pubmed.ncbi.nlm.nih.gov/25083807","citation_count":18,"is_preprint":false},{"pmid":"15498853","id":"PMC_15498853","title":"Cell type-specific regulation of von Willebrand factor expression by the E4BP4 transcriptional repressor.","date":"2004","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/15498853","citation_count":18,"is_preprint":false},{"pmid":"15087429","id":"PMC_15087429","title":"Parathyroid hormone induces E4bp4 messenger ribonucleic acid expression primarily through cyclic adenosine 3',5'-monophosphate signaling in osteoblasts.","date":"2004","source":"Endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/15087429","citation_count":18,"is_preprint":false},{"pmid":"34660620","id":"PMC_34660620","title":"NFIL3 Facilitates Neutrophil Autophagy, Neutrophil Extracellular Trap Formation and Inflammation During Gout via REDD1-Dependent mTOR Inactivation.","date":"2021","source":"Frontiers in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34660620","citation_count":18,"is_preprint":false},{"pmid":"16630563","id":"PMC_16630563","title":"Calcium-dependent upregulation of E4BP4 expression correlates with glucocorticoid-evoked apoptosis of human leukemic CEM cells.","date":"2006","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/16630563","citation_count":18,"is_preprint":false},{"pmid":"39473081","id":"PMC_39473081","title":"OPN-Mediated Crosstalk Between Hepatocyte E4BP4 and Hepatic Stellate Cells Promotes MASH-Associated Liver Fibrosis.","date":"2024","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/39473081","citation_count":17,"is_preprint":false},{"pmid":"31319087","id":"PMC_31319087","title":"The nuclear factor interleukin 3-regulated (NFIL3) transcription factor involved in innate immunity by activating NF-κB pathway in mud crab Scylla paramamosain.","date":"2019","source":"Developmental and comparative immunology","url":"https://pubmed.ncbi.nlm.nih.gov/31319087","citation_count":17,"is_preprint":false},{"pmid":"17996471","id":"PMC_17996471","title":"Ontogeny of melatonin, Per2 and E4bp4 light responsiveness in the chicken embryonic pineal gland.","date":"2007","source":"Comparative biochemistry and physiology. Part A, Molecular & integrative physiology","url":"https://pubmed.ncbi.nlm.nih.gov/17996471","citation_count":17,"is_preprint":false},{"pmid":"24280221","id":"PMC_24280221","title":"Neuroprotective role of the basic leucine zipper transcription factor NFIL3 in models of amyotrophic lateral sclerosis.","date":"2013","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/24280221","citation_count":17,"is_preprint":false},{"pmid":"36508222","id":"PMC_36508222","title":"High-Fat Diet-Induced DeSUMOylation of E4BP4 Promotes Lipid Droplet Biogenesis and Liver Steatosis in Mice.","date":"2023","source":"Diabetes","url":"https://pubmed.ncbi.nlm.nih.gov/36508222","citation_count":15,"is_preprint":false},{"pmid":"30796914","id":"PMC_30796914","title":"The transcription factor E4bp4 regulates the expression and activity of Cyp3a11 in mice.","date":"2019","source":"Biochemical pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/30796914","citation_count":14,"is_preprint":false},{"pmid":"29856483","id":"PMC_29856483","title":"A minireview of E4BP4/NFIL3 in heart failure.","date":"2018","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/29856483","citation_count":13,"is_preprint":false},{"pmid":"35777910","id":"PMC_35777910","title":"NFIL3 deficiency alleviates EAE through regulating different immune cell subsets.","date":"2021","source":"Journal of advanced research","url":"https://pubmed.ncbi.nlm.nih.gov/35777910","citation_count":12,"is_preprint":false},{"pmid":"19129193","id":"PMC_19129193","title":"Identification of adjacent binding sites for the YY1 and E4BP4 transcription factors in the ovine PrP (Prion) gene promoter.","date":"2009","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19129193","citation_count":12,"is_preprint":false},{"pmid":"28416324","id":"PMC_28416324","title":"E4BP4 mediates glucocorticoid-regulated adipogenesis through COX2.","date":"2017","source":"Molecular and cellular endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/28416324","citation_count":12,"is_preprint":false},{"pmid":"18242748","id":"PMC_18242748","title":"Identification of negative transcriptional factor E4BP4-binding site in the mouse circadian-regulated gene Mdr2.","date":"2007","source":"Neuroscience research","url":"https://pubmed.ncbi.nlm.nih.gov/18242748","citation_count":12,"is_preprint":false},{"pmid":"36403704","id":"PMC_36403704","title":"Nuclear factor interleukin 3 (NFIL3) participates in regulation of the NF-κB-mediated inflammation and antioxidant system in Litopenaeus vannamei under ammonia-N stress.","date":"2022","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/36403704","citation_count":11,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":47573,"output_tokens":10493,"usd":0.150057},"stage2":{"model":"claude-opus-4-6","input_tokens":14767,"output_tokens":5055,"usd":0.300315},"total_usd":0.450372,"stage1_batch_id":"msgbatch_012ZiiCUBfB62NCTQd4Bk1Jo","stage2_batch_id":"msgbatch_01Xuqq9aUHoQouS7UVGZNStZ","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2001,\n      \"finding\": \"E4BP4/NFIL3 functions as a transcriptional repressor that competes with PAR family proteins (DBP, HLF, TEF) for the same DNA binding sites but cannot heterodimerize with them; E4BP4 and PAR proteins oscillate in antiphase in the SCN and liver, forming a reciprocating on/off switch for target gene transcription.\",\n      \"method\": \"Transcriptional reporter assays in vitro, electrophoretic mobility shift assay (EMSA), mRNA rhythm profiling in SCN and liver, analysis of mCry-deficient mice\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — multiple orthogonal methods (EMSA, reporter assay, in vivo expression profiling, genetic model) in a single well-cited study\",\n      \"pmids\": [\"11316793\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"E4BP4 contains a 65-amino-acid minimal repression domain near its C-terminus that is sufficient to repress transcription when fused to the GAL4 DNA-binding domain; a charge-configuration mutation in this domain abolishes repressor activity, and the mechanism involves interaction with a component of the general transcription machinery rather than resembling known repression domains.\",\n      \"method\": \"Domain mapping by GAL4 fusion reporter assays, site-directed mutagenesis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstitution and mutagenesis of repression domain with functional readout\",\n      \"pmids\": [\"8127655\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"The E4BP4 repression domain interacts specifically with the TBP-binding repressor protein Dr1; E4BP4 mutants deficient in repression are also deficient in Dr1 binding, suggesting that recruitment of Dr1 mediates transcriptional repression by E4BP4.\",\n      \"method\": \"Protein-protein interaction mapping, pulldown assays, correlation of repression-defective mutants with Dr1 binding\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single-lab protein interaction study with functional mutant correlation\",\n      \"pmids\": [\"8836190\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"NFIL3/NF-IL3A binds the sequence TAATTACGTCTG (minimal: ATTACG) in the IL-3 promoter and transactivates IL-3 promoter-reporter constructs in resting T cells in a binding-site-dependent manner, establishing it as a transcriptional activator of the human IL-3 gene.\",\n      \"method\": \"DNase I footprinting, gel shift assay, cotransfection reporter assays with mutant promoters\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro binding assays plus functional reporter assays with site-specific mutations\",\n      \"pmids\": [\"7565758\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"E4BP4 is a phosphoprotein; phosphorylation produced in baculovirus-infected Sf9 cells (but not in E. coli) enhances its DNA-binding activity, and the leucine heptad repeat domain is required for both DNA binding and repression activity.\",\n      \"method\": \"Comparison of bacterially vs. baculovirus-produced protein by gel shift assay, mutagenesis of leucine zipper, post-translational modification analysis\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 method (in vitro biochemistry + mutagenesis) but single lab, limited follow-up\",\n      \"pmids\": [\"8547328\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"NFIL3/E4BP4 is a delayed-early IL-3-responsive gene in pro-B lymphocytes regulated through the Ras signaling pathway; enforced expression of NFIL3 promotes survival but not proliferation of IL-3-deprived pro-B cells, identifying it as a downstream mediator of IL-3 survival signaling.\",\n      \"method\": \"Northern blot, enforced cDNA expression in IL-3-dependent pro-B cell lines (Baf-3, FL5.12), survival assays upon growth factor withdrawal\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — gain-of-function with defined survival phenotype, replicated across two cell lines\",\n      \"pmids\": [\"9122243\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"NFIL3 expression is regulated by oncogenic Ras through both the Raf-MAPK and PI3K pathways; NFIL3 inhibits apoptosis independently of Bcl-xL, defining two distinct IL-3 survival pathways.\",\n      \"method\": \"Constitutively active Ras mutant expression, pathway inhibitors, cell survival assays in IL-3-dependent pro-B cells\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — epistasis via pathway inhibitors and genetic mutants with defined survival readout\",\n      \"pmids\": [\"10082541\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"GATA-1 and GATA-2 bind the E4bp4 promoter GATA motif in vitro and in vivo; GATA-1 overexpression transactivates the E4bp4 reporter and modulates IL-3-withdrawal apoptosis, placing GATA factors upstream of NFIL3 in the IL-3 survival pathway.\",\n      \"method\": \"Promoter deletion analysis, gel shift assay, chromatin immunoprecipitation (ChIP), stable overexpression of GATA-1 and GATA-1 DNA-binding mutant, apoptosis assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — ChIP confirming in vivo binding plus functional genetic epistasis with defined apoptosis readout\",\n      \"pmids\": [\"12023274\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Casein kinase 1ε (CK1ε) physically associates with E4BP4, phosphorylates it at Ser182, and promotes proteasomal degradation of E4BP4 protein; CK1ε also attenuates E4BP4 nuclear accumulation independently of its kinase activity, thereby reducing E4BP4-mediated repression of cPer2.\",\n      \"method\": \"Co-immunoprecipitation, in vitro kinase assay, site-directed mutagenesis (Ser182), proteasome inhibitor rescue, nuclear localization assay\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — physical association, in vitro phosphorylation, mutagenesis, and proteasomal mechanism all demonstrated\",\n      \"pmids\": [\"15182670\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"E4BP4 binds a novel D-box-like element (B-site) in the Per2 promoter and negatively regulates Per2 mRNA oscillation; the B-site together with the E2 enhancer is required for robust circadian Per2 expression in cell-autonomous clocks.\",\n      \"method\": \"siRNA knockdown, luciferase reporter assays with promoter deletion/mutation constructs, chromatin immunoprecipitation (ChIP)\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal methods (siRNA KD, mutagenesis, ChIP) in a single study\",\n      \"pmids\": [\"17182630\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"E4BP4 physically interacts with PER2 (via E4BP4's C-terminal repression domain) and with CRY2, placing E4BP4 within the negative regulator complex of the mammalian circadian clock.\",\n      \"method\": \"Co-immunoprecipitation, deletion mapping of interaction domain\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single-lab co-IP with domain mapping\",\n      \"pmids\": [\"17274955\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"E4BP4/NFIL3 is essential for NK cell development in a cell-intrinsic manner, acting downstream of the IL-15 receptor and upstream of the transcription factor Id2; Nfil3−/− mice specifically lack NK cells but retain B, T, and NKT cells, and NK cell-mediated cytotoxicity is severely impaired.\",\n      \"method\": \"Gene-targeted Nfil3−/− mice, mixed bone marrow chimeras (cell-intrinsic test), hematopoietic progenitor overexpression, NK cytotoxicity assays\",\n      \"journal\": \"Nature immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — independently generated KO mouse with defined cellular phenotype, cell-intrinsic rescue, replicated across multiple labs\",\n      \"pmids\": [\"19749763\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"NFIL3 is an anti-apoptotic transcription factor in NK cells; Nfil3−/− mice show a specific NK cell intrinsic developmental block with severely reduced mature NK cells, impaired IFN-γ production and cytolytic activity, and failure to reject MHC-I-deficient cells in vivo.\",\n      \"method\": \"Gene-targeted Nfil3−/− mice, NK cell-intrinsic bone marrow transfer, in vitro cytotoxicity and IFN-γ assays, in vivo rejection assay\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — independent KO mouse replication confirming NK-intrinsic requirement\",\n      \"pmids\": [\"19995955\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"NFIL3 is induced by IL-4 in B cells in a STAT6-dependent manner, binds the Iε promoter in vivo, and is required for IL-4-induced germline epsilon (GLε) transcription and IgE class switching in a B-cell-intrinsic manner.\",\n      \"method\": \"Nfil3−/− mice, ChIP (in vivo binding to Iε promoter), enforced NFIL3 expression rescue, cycloheximide experiment to show direct induction of GLε\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — ChIP, genetic KO, gain-of-function rescue, multiple orthogonal methods\",\n      \"pmids\": [\"20080759\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"E4BP4 binds a D-box element in the distal Fgf21 promoter and suppresses FGF21 transcription; insulin increases E4BP4 expression and promoter binding via AKT activation, linking E4BP4 to circadian and feeding-state repression of FGF21.\",\n      \"method\": \"E4BP4 overexpression/depletion in hepatocytes, luciferase reporter with D-box mutation, ChIP, FGF21 secretion assay, AKT inhibitor experiments\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal methods (ChIP, reporter, KD, OE, secretion assay) in a single study\",\n      \"pmids\": [\"20851878\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"NFIL3/E4BP4 is essential for development of CD8α+ conventional DCs in a cell-intrinsic manner, in part through regulation of Batf3 expression; Nfil3−/− mice lack CD8α+ cDCs, show impaired cross-priming of CD8+ T cells and reduced IL-12 production after TLR3 stimulation.\",\n      \"method\": \"Nfil3−/− mice, Flt3L bone marrow cultures, cross-priming assay, IL-12 production assay\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse with cell-intrinsic test and defined functional readouts\",\n      \"pmids\": [\"21474667\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"E4BP4 directly binds to and negatively regulates the Il13 gene in TH2 cells, while positively regulating IL-4 production; E4BP4 controls TH2 cytokine balance in a T-cell-intrinsic manner.\",\n      \"method\": \"Nfil3−/− mice, enforced E4BP4 expression, ChIP, cytokine assays in TH2 cells\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — ChIP demonstrating direct binding, KO and OE with defined cytokine phenotype\",\n      \"pmids\": [\"21499227\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"NFIL3 is induced by IL-10 via STAT3 in myeloid cells and binds a single 10-bp site in a distal enhancer 10 kb upstream of the Il12b transcription start site, mediating transcriptional repression of IL-12p40 as part of a negative feedback loop.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP), enhancer deletion analysis, NFIL3-deficient myeloid cells, IL-10/STAT3 pathway analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — ChIP, site-specific mutagenesis, genetic KO cells with defined cytokine readout\",\n      \"pmids\": [\"21566115\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"NFIL3 binds the Il12b promoter and represses IL-12p40 production in macrophages induced by bacterial products; repression requires a C-terminal minimal repression domain of NFIL3 and is IL-10-independent.\",\n      \"method\": \"ChIP, Il12b-BAC-GFP reporter macrophage line with NFIL3 overexpression/shRNA knockdown, Nfil3−/− macrophages\",\n      \"journal\": \"Journal of immunology (Baltimore, Md. : 1950)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — ChIP, reporter assay, KO/KD, domain requirement all demonstrated\",\n      \"pmids\": [\"21383239\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"E4BP4 controls IL-10 and IL-13 production in CD4+ T cells; enforced E4bp4 expression induces IL-10 and IL-13 in TH1 cells, and E4bp4−/− TH1, Treg, and NKT cells show attenuated IL-10 and IL-13 expression.\",\n      \"method\": \"Nfil3−/− mice, enforced expression vectors, cytokine measurement in multiple T cell subsets\",\n      \"journal\": \"Nature immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO with gain-of-function validation across multiple cell types\",\n      \"pmids\": [\"21460847\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"E4BP4 interacts with histone methyltransferase G9a; E4BP4-dependent repression of Fgf21 requires G9a catalytic activity (SET domain), and E4BP4 overexpression increases H3K9me2 at the Fgf21 promoter, defining an epigenetic repression mechanism.\",\n      \"method\": \"Co-immunoprecipitation (E4BP4–G9a interaction), G9a inhibitor (BIX01294), SET domain deletion mutant, ChIP for H3K9me2, adenoviral shRNA knockdown in vivo\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — physical interaction, catalytic mutant, ChIP for histone mark, and in vivo KD all demonstrated\",\n      \"pmids\": [\"23283977\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"E4BP4 is required at the CLP stage for NK lineage commitment and directly binds the regulatory regions of Eomes and Id2, promoting their transcription; Eomes and Id2 overexpression rescues NK production from E4bp4−/− progenitors.\",\n      \"method\": \"Conditional/stage-specific E4bp4 deletion, ChIP (E4BP4 binding to Eomes and Id2 loci), rescue experiments with Eomes/Id2 overexpression\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — ChIP plus genetic epistasis (rescue) defining direct transcriptional targets\",\n      \"pmids\": [\"24663216\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"NFIL3 directs differentiation of a committed ILC precursor (αLP/CXCR6+ cells) that gives rise to all ILC lineages; NFIL3 governs ILC development by directly regulating expression of the transcription factor TOX.\",\n      \"method\": \"Nfil3−/− mice, clonal differentiation assays, bone marrow precursor identification, ChIP/reporter for TOX regulation\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic KO with clonal assays and identification of direct downstream target\",\n      \"pmids\": [\"25310240\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"NFIL3 is required for the CHILP (common helper innate lymphoid cell progenitor) and acts via direct Id2 regulation; NFIL3 expression in lymphoid progenitors is controlled by IL-7, and ectopic Id2 expression rescues defective ILC lineage development in Nfil3-null precursors in vivo.\",\n      \"method\": \"Conditional Nfil3 targeting, mixed bone marrow chimeras, Id2 rescue experiments in vivo, promoter binding assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — conditional KO, cell-intrinsic demonstration, genetic rescue defining direct pathway\",\n      \"pmids\": [\"25801035\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Nfil3 is required for Eomes-expressing conventional NK cells but not for TRAIL+Eomes− NK cells; restoration of Eomes in Nfil3−/− progenitors rescues NK cell development, placing Eomes as the key downstream effector of Nfil3 in NK commitment.\",\n      \"method\": \"Nfil3−/− mice, Eomes reporter/flow cytometry, retroviral Eomes overexpression rescue in Nfil3−/− progenitors\",\n      \"journal\": \"Journal of immunology (Baltimore, Md. : 1950)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic KO plus gain-of-function rescue defining Eomes as direct downstream effector\",\n      \"pmids\": [\"24532575\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"IL-27 induces NFIL3, which promotes permissive chromatin remodeling at the Tim-3 locus and drives Tim-3 and IL-10 expression in T cells; the inhibitory effect of IL-27-conditioned TH1 cells is NFIL3-dependent.\",\n      \"method\": \"NFIL3 KO/KD, chromatin remodeling assays (ATAC/accessibility), Tim-3 and IL-10 expression assays, IL-27R−/− mice\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic KO in vitro and in vivo with chromatin remodeling and functional readouts\",\n      \"pmids\": [\"25614966\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"PDK1 connects IL-15 signaling to E4BP4 induction via mTOR during early NK cell development; PDK1-deficient NK cells show reduced mTOR activation and E4BP4 induction, and ectopic E4BP4 expression or mTOR activation partially rescues NK cell development.\",\n      \"method\": \"Conditional PDK1 KO, E4BP4 ectopic expression rescue, mTOR activation bypass, IL-15/CD122 signaling assays\",\n      \"journal\": \"The Journal of experimental medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — conditional KO with genetic epistasis rescue, defining PDK1-mTOR-E4BP4-CD122 pathway\",\n      \"pmids\": [\"25624444\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"E4BP4 binds the Fgf21 promoter D-box element and represses FGF21 expression; E4bp4 knockout mice show upregulated hepatic Fgf21. E4BP4 interacts with nuclear SREBP-1c to preserve its acetylation and protect it from ubiquitination-dependent degradation, thereby amplifying lipogenesis.\",\n      \"method\": \"E4bp4−/− mice, co-immunoprecipitation (E4BP4–SREBP-1c), ubiquitination assay, adenoviral shRNA in vivo, lipogenic enzyme expression assays\",\n      \"journal\": \"Journal of lipid research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — KO mice, co-IP for protein interaction, ubiquitination assay with in vivo validation\",\n      \"pmids\": [\"27252523\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Smad3 directly suppresses E4BP4/NFIL3 transcription; deletion of Smad3 expands NK cells and enhances their anti-tumor functions via E4BP4, and Smad3 suppresses IFN-γ production via E4BP4 in a T-bet-independent manner.\",\n      \"method\": \"Smad3−/− bone marrow transfer, ChIP (Smad3 binding to E4BP4 locus), E4BP4 rescue in Smad3−/− cells, tumor models, SIS3 inhibitor\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — ChIP establishing direct transcriptional regulation, genetic KO with functional rescue\",\n      \"pmids\": [\"28262747\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The intestinal microbiota controls the amplitude of NFIL3 circadian oscillation in intestinal epithelial cells via group 3 ILCs, STAT3, and the epithelial cell circadian clock; NFIL3 in turn regulates a circadian lipid metabolic program controlling lipid absorption and export.\",\n      \"method\": \"Germ-free vs. colonized mice, ILC3 depletion, STAT3 inhibition, Nfil3−/− mice, lipid absorption/export assays\",\n      \"journal\": \"Science (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple genetic and pharmacological manipulations with defined metabolic phenotype and signaling pathway\",\n      \"pmids\": [\"28860383\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"NFIL3 represses hepatic gluconeogenesis by competing with CREB for binding to cAMP response elements in gluconeogenic gene promoters (e.g., Pepck, G6pc); the repression requires the bZIP DNA-binding domain, and hepatic NFIL3 overexpression ameliorates hyperglycemia in insulin-resistant mice.\",\n      \"method\": \"ChIP (NFIL3 binding to CRE elements), luciferase reporter with CRE mutations, adenoviral overexpression/knockdown in mice, glucose tolerance tests\",\n      \"journal\": \"Metabolism: clinical and experimental\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — ChIP, mutagenesis of binding site, gain/loss of function in vivo\",\n      \"pmids\": [\"29132537\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"E4BP4 regulates carboxylesterase 2 (Ces) enzymes by physically interacting with REV-ERBα and antagonizing its trans-repressive activity on Ces2b promoter; E4bp4−/− mice show reduced Ces expression and altered pharmacokinetics of CPT-11.\",\n      \"method\": \"Co-immunoprecipitation (E4BP4–REV-ERBα), luciferase reporter, EMSA (REV-ERBα binding site), E4bp4−/− mice, pharmacokinetic study\",\n      \"journal\": \"Biochemical pharmacology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — co-IP, EMSA, reporter, and in vivo pharmacokinetics in KO mice\",\n      \"pmids\": [\"29653076\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"E4BP4 mediates transcriptional inhibition of Bcl6 by recruiting the repressive epigenetic modifiers HDAC1 and EZH2, thereby inhibiting T follicular helper (Tfh) cell differentiation; E4BP4 phosphorylation site mutants cannot inhibit Tfh differentiation.\",\n      \"method\": \"Conditional E4bp4 KO and knockin mice, co-IP/ChIP (HDAC1, EZH2 recruitment), phosphorylation mutant analysis, Tfh differentiation assays\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — conditional KO/KI, co-IP for epigenetic complex, mutagenesis of phosphorylation sites\",\n      \"pmids\": [\"32191636\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"E4BP4 interacts with G9a to form a multi-molecular complex that silences SOSTDC1 through G9a-mediated epigenetic modification, thereby regulating hepcidin expression and iron homeostasis in thyroid cancer cells.\",\n      \"method\": \"Co-immunoprecipitation (E4BP4–G9a), ChIP, E4BP4/G9a siRNA knockdown, in vivo xenograft\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — co-IP and ChIP but single lab, cancer context\",\n      \"pmids\": [\"30250199\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"An Nfil3-Zeb2-Id2 transcriptional circuit is required for cDC1 progenitor development; Nfil3 drives the transition from Zeb2hi/Id2lo CDPs to Zeb2lo/Id2hi committed cDC1 progenitors, enabling the switch in Irf8 enhancer usage from the +41-kb to the +32-kb element.\",\n      \"method\": \"Single-cell RNA-seq of CDPs, genetic epistasis (Nfil3, Zeb2, Id2 KO combinations), Irf8 enhancer reporter\",\n      \"journal\": \"Nature immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — scRNA-seq plus multi-gene epistasis defining transcriptional circuit\",\n      \"pmids\": [\"31406377\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"NFIL3 directly binds the PRNP promoter and acts as a transcriptional activator of PrPc expression; NFIL3-driven PrPc upregulation promotes lung cancer cell lamellipodium formation and migration through JNK signaling.\",\n      \"method\": \"NFIL3 KD, luciferase reporter with PRNP promoter, ChIP (NFIL3 binding to PRNP promoter), JNK inhibitor, migration/invasion assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — ChIP and reporter for direct binding, KD with defined phenotype, but single lab\",\n      \"pmids\": [\"31477838\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"NFIL3 directly binds and negatively regulates Foxp3 expression, and induces methylation at Foxp3 regulatory CpG sites, thereby impairing Treg cell function and stability.\",\n      \"method\": \"ChIP (NFIL3 binding to Foxp3 locus), bisulfite sequencing for CpG methylation, NFIL3 overexpression in Treg cells, suppression assays in vitro and in vivo\",\n      \"journal\": \"Experimental & molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP, methylation assay, functional suppression assay in single study\",\n      \"pmids\": [\"31311918\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"E4BP4 directly binds to the Notch1 locus and regulates its expression; SUMOylation and phosphorylation of E4BP4 modulate its activity and NK cell development; brief Notch ligand exposure completely rescues NK cell development from E4bp4−/− progenitors.\",\n      \"method\": \"E4BP4 PTM mutants, ChIP (E4BP4 at Notch1 locus), Notch inhibition/rescue experiments, NK cell development assays\",\n      \"journal\": \"Journal of immunology (Baltimore, Md. : 1950)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — ChIP for novel target, PTM mutant analysis, genetic rescue; single lab\",\n      \"pmids\": [\"29311361\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"PBX1 directly binds the Nfil3 promoter and upregulates NFIL3 expression to promote NK cell development; knockout of the PBX1 binding site in the Nfil3 promoter reduces NK precursor and NK cell numbers analogously to Nfil3 KO.\",\n      \"method\": \"PBX1 conditional KO, ChIP/EMSA (PBX1 binding to Nfil3 promoter), CRISPR deletion of binding site, NK progenitor flow cytometry\",\n      \"journal\": \"FASEB journal : official publication of the Federation of American Societies for Experimental Biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — ChIP, CRISPR binding site deletion, and conditional KO all converge on same conclusion\",\n      \"pmids\": [\"32190943\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"REV-ERBα and REV-ERBβ directly repress E4bp4 expression in cardiomyocytes; loss of Rev-erbs induces E4BP4, which in turn directly represses Nampt via D-box elements, reducing NAD+ biosynthesis and causing cardiomyopathy.\",\n      \"method\": \"Cardiomyocyte-specific Rev-erb double KO mice, ChIP (REV-ERB binding to E4bp4; E4BP4 binding to Nampt), NAD+ measurement, cardiac function assessment\",\n      \"journal\": \"Nature cardiovascular research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — conditional double KO, ChIP for both regulatory steps, metabolite measurement\",\n      \"pmids\": [\"35036997\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"mTORC1 mainly promotes E4BP4 expression during early NK cell development, while mTORC2 controls T-bet expression; this differential regulation by the two mTOR complexes coordinates sequential stages of NK cell differentiation.\",\n      \"method\": \"CD122-Cre and Ncr1-Cre conditional KO of Raptor (mTORC1) and Rictor (mTORC2), E4BP4/T-bet protein measurement, NK cell stage-specific flow cytometry\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — conditional KO with stage-specific phenotype and molecular readout; single lab\",\n      \"pmids\": [\"33462410\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"NFIL3 directly suppresses NFKBIA transcription, thereby enhancing NF-κB signaling and promoting proliferation and metastasis of triple-negative breast cancer cells.\",\n      \"method\": \"ChIP (NFIL3 binding to NFKBIA promoter), luciferase reporter, gain/loss of function, in vivo xenograft, NF-κB activity assays\",\n      \"journal\": \"Journal of experimental & clinical cancer research : CR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP, reporter with functional rescue in vivo; single lab\",\n      \"pmids\": [\"35180863\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"E4BP4 restrains microglial activation by directly binding a D-box element in the Mapk1/3 promoter and trans-repressing ERK1/2 (Mapk1/3) expression; microglial-specific E4bp4 deletion exacerbates delirium-associated cognitive decline.\",\n      \"method\": \"Global and microglial-specific E4bp4 KO, ChIP (E4BP4 at Mapk1/3 promoter), single-cell RNA-seq, LTP measurement, cognitive assays\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — ChIP, cell-type-specific KO, scRNA-seq, multiple functional readouts\",\n      \"pmids\": [\"35713240\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"E4BP4 promotes lipid droplet biogenesis and liver steatosis by activating Fsp27 (CIDEC) expression; E4BP4 enhances Fsp27 transactivation by CREBH. E4BP4 is SUMOylated on five lysine residues, and HFD-induced deSUMOylation of E4BP4 activates Fsp27 and lipid droplet formation.\",\n      \"method\": \"E4bp4 liver-specific KO and overexpression, Fsp27 rescue, co-IP (E4BP4–CREBH interaction), SUMOylation site mutagenesis, cAMP signaling experiments\",\n      \"journal\": \"Diabetes\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — LKO, OE, rescue, co-IP, and SUMOylation mutagenesis all in one study\",\n      \"pmids\": [\"36508222\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Hepatocyte E4BP4 promotes liver fibrosis by stabilizing YAP, which activates OPN (osteopontin) expression; OPN secreted from hepatocytes activates hepatic stellate cells (HSCs). Antibody neutralization or shRNA depletion of OPN abrogates E4BP4-induced HSC activation.\",\n      \"method\": \"Hepatocyte-specific E4bp4 KO, medium transfer experiment, RNA-Seq, co-IP (E4BP4–YAP), OPN neutralization, shRNA, in vivo fibrosis model\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — LKO, medium transfer for paracrine mechanism, co-IP, rescue with OPN neutralization\",\n      \"pmids\": [\"39473081\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"hnRNP A1 binds a specific region of the Nfil3 5'-UTR IRES and regulates cap-independent, IRES-mediated translation of Nfil3 mRNA in a phase-dependent manner; hnRNP A1 knockdown abolishes NFIL3 protein oscillation without affecting mRNA oscillation.\",\n      \"method\": \"IRES reporter assay, RNA pulldown of hnRNP A1, hnRNP A1 siRNA knockdown, bioluminescent protein oscillation tracking\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — functional IRES reporter, RNA-protein interaction, KD phenotype; single lab\",\n      \"pmids\": [\"28220845\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NFIL3/E4BP4 is a bZIP transcription factor that functions primarily as a transcriptional repressor (via a C-terminal repression domain that recruits Dr1 and epigenetic co-repressors such as G9a, HDAC1, and EZH2) but can also activate transcription; it binds D-box/EBPRE elements in target gene promoters to regulate circadian gene expression (competing antagonistically with PAR-family activators DBP/HLF/TEF), immune cell development (acting downstream of IL-15/PDK1/mTOR to drive Eomes and Id2 expression, thereby being essential for NK cell, ILC, and CD8α+ DC lineage commitment), and metabolic programs (repressing FGF21, gluconeogenic genes, and drug-metabolizing enzymes while stabilizing SREBP-1c); its activity is controlled post-translationally by CK1ε-mediated phosphorylation (leading to proteasomal degradation), SUMOylation, and protein–protein interactions with PER2, CRY2, REV-ERB, and YAP.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"NFIL3 (E4BP4) is a basic leucine zipper (bZIP) transcription factor that acts as both a transcriptional repressor and activator to integrate circadian clock regulation, immune cell development, and hepatic metabolic programs. It binds D-box and related cis-elements in target promoters, competing with PAR-family activators (DBP, HLF, TEF) to generate antiphase oscillatory gene expression in the suprachiasmatic nucleus and liver, and its repression activity is mediated by a C-terminal minimal repression domain that recruits co-repressors including Dr1, G9a (depositing H3K9me2), HDAC1, and EZH2 [PMID:11316793, PMID:8127655, PMID:23283977, PMID:32190636]. NFIL3 is essential for NK cell, innate lymphoid cell (ILC), and CD8α⁺ dendritic cell lineage commitment, acting downstream of IL-15/PDK1/mTOR signaling to directly activate Eomes, Id2, and TOX transcription, and it further modulates adaptive immunity by regulating IgE class switching, TH2 cytokine balance, Tfh differentiation, and IL-12 repression [PMID:19749763, PMID:24663216, PMID:25310240, PMID:20080759, PMID:21499227, PMID:32190636, PMID:21566115]. In hepatocytes, NFIL3 represses FGF21 and gluconeogenic genes, stabilizes SREBP-1c to amplify lipogenesis, promotes lipid droplet biogenesis via Fsp27/CIDEC, and drives liver fibrosis through YAP stabilization and OPN-mediated hepatic stellate cell activation; its protein abundance is controlled post-translationally by CK1ε-mediated phosphorylation targeting it for proteasomal degradation, by SUMOylation that modulates its transcriptional output, and by IRES-dependent translational regulation via hnRNP A1 [PMID:20851878, PMID:29132537, PMID:36508222, PMID:39473081, PMID:15182670, PMID:28220845].\",\n  \"teleology\": [\n    {\n      \"year\": 1994,\n      \"claim\": \"Identification of how NFIL3 represses transcription resolved a basic mechanistic question: a 65-amino-acid C-terminal minimal repression domain was mapped and shown to function through interaction with general transcription machinery rather than through known silencing motifs.\",\n      \"evidence\": \"GAL4 fusion reporter assays and site-directed mutagenesis in cell lines\",\n      \"pmids\": [\"8127655\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The specific general transcription factor target was not identified in this study\", \"Whether the repression domain is sufficient in chromatin context was untested\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"The mechanism of NFIL3-mediated repression was refined by demonstrating that the repression domain physically recruits Dr1, a TBP-associated repressor, and that repression-defective mutants lose Dr1 binding.\",\n      \"evidence\": \"Pulldown assays and correlation of repression-defective mutants with Dr1 binding\",\n      \"pmids\": [\"8836190\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab protein interaction without reciprocal validation\", \"Whether Dr1 recruitment is the sole or primary repression mechanism in vivo was not tested\"]\n    },\n    {\n      \"year\": 1997,\n      \"claim\": \"NFIL3 was established as a survival factor downstream of IL-3/Ras signaling in pro-B lymphocytes, showing that its function extends beyond transcriptional repression to anti-apoptotic activity in hematopoietic cells.\",\n      \"evidence\": \"Enforced NFIL3 expression in IL-3-dependent pro-B cell lines (Baf-3, FL5.12) with survival assays upon growth factor withdrawal\",\n      \"pmids\": [\"9122243\", \"10082541\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct transcriptional targets mediating survival were not identified\", \"Whether NFIL3 survival function is relevant in vivo was not addressed\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"The circadian role of NFIL3 was defined: it competes with PAR-family activators (DBP, HLF, TEF) for D-box binding sites, and their antiphase oscillation in the SCN and liver establishes a reciprocating transcriptional switch that shapes circadian gene expression.\",\n      \"evidence\": \"EMSA, transcriptional reporter assays, mRNA rhythm profiling in SCN and liver, mCry-deficient mice\",\n      \"pmids\": [\"11316793\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Genome-wide identification of shared D-box target genes was not performed\", \"Whether NFIL3 loss alone disrupts circadian behavior was not tested\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"The post-translational control of NFIL3 protein abundance was established: CK1ε phosphorylates Ser182, promoting proteasomal degradation and reducing nuclear accumulation, thereby linking the core clock kinase to NFIL3 turnover.\",\n      \"evidence\": \"Co-immunoprecipitation, in vitro kinase assay, Ser182 mutagenesis, proteasome inhibitor rescue, nuclear localization assay\",\n      \"pmids\": [\"15182670\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether other CK1 family members contribute was not tested\", \"In vivo relevance of CK1ε-NFIL3 axis for circadian phenotype was not demonstrated\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"NFIL3 was shown to directly repress Per2 through a novel D-box-like B-site in the Per2 promoter, and to interact physically with PER2 and CRY2, integrating it into the negative limb of the circadian feedback loop.\",\n      \"evidence\": \"siRNA knockdown, ChIP, luciferase reporter with promoter mutations (Per2 regulation); co-immunoprecipitation and domain mapping (PER2/CRY2 interaction)\",\n      \"pmids\": [\"17182630\", \"17274955\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of PER2/CRY2 interaction on NFIL3 activity was not resolved\", \"PER2/CRY2 interactions were from single-lab co-IP\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"A landmark finding demonstrated that NFIL3 is cell-intrinsically essential for NK cell development: Nfil3⁻/⁻ mice specifically lack mature NK cells, and NFIL3 acts downstream of IL-15R signaling and upstream of Id2, establishing it as a master regulator of NK lineage commitment.\",\n      \"evidence\": \"Two independent Nfil3⁻/⁻ mouse models, mixed bone marrow chimeras, NK cytotoxicity and IFN-γ assays, in vivo rejection assays\",\n      \"pmids\": [\"19749763\", \"19995955\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct transcriptional targets driving the NK commitment block were not yet identified\", \"Whether NFIL3 is continuously required for mature NK cell maintenance was unclear\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"NFIL3 was shown to function in adaptive immunity beyond NK cells: it is induced by IL-4/STAT6 in B cells, binds the Iε promoter in vivo, and is required for germline ε transcription and IgE class switching.\",\n      \"evidence\": \"Nfil3⁻/⁻ mice, ChIP at Iε promoter, enforced NFIL3 expression rescue, cycloheximide experiments\",\n      \"pmids\": [\"20080759\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether NFIL3 cooperates with other bZIP factors at the Iε promoter was not determined\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Multiple studies revealed NFIL3's broad immunoregulatory scope: it directly represses IL-12p40 production in macrophages (via binding the Il12b promoter/enhancer), controls TH2 cytokine balance by repressing IL-13 while promoting IL-10 and IL-4, and is required for CD8α⁺ cDC development.\",\n      \"evidence\": \"Nfil3⁻/⁻ mice and myeloid/T cell assays, ChIP at Il12b and Il13 loci, enforced expression/knockdown, cross-priming assays, Flt3L bone marrow cultures\",\n      \"pmids\": [\"21474667\", \"21499227\", \"21566115\", \"21383239\", \"21460847\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How NFIL3 switches between activator and repressor at different cytokine loci was mechanistically unclear\", \"Genome-wide binding landscape in immune cells was not determined\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"The epigenetic mechanism of NFIL3-mediated repression was elucidated: E4BP4 recruits the histone methyltransferase G9a, increasing H3K9me2 at target promoters such as Fgf21, establishing a chromatin-level repression mechanism beyond Dr1 recruitment.\",\n      \"evidence\": \"Co-immunoprecipitation (E4BP4–G9a), G9a catalytic inhibitor and SET domain deletion mutant, ChIP for H3K9me2, adenoviral shRNA knockdown in vivo\",\n      \"pmids\": [\"23283977\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether G9a is recruited to all NFIL3-repressed targets or only a subset was unknown\", \"Relative contributions of G9a vs. Dr1 vs. other co-repressors were not compared\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"The direct transcriptional targets of NFIL3 in NK/ILC development were defined: NFIL3 binds regulatory regions of Eomes and Id2 to drive their expression at the CLP stage, and separately drives TOX expression to specify a committed ILC precursor; Eomes/Id2 overexpression rescues Nfil3⁻/⁻ NK/ILC defects.\",\n      \"evidence\": \"Conditional/stage-specific E4bp4 deletion, ChIP at Eomes, Id2, and TOX loci, retroviral rescue experiments, clonal ILC differentiation assays\",\n      \"pmids\": [\"24663216\", \"25310240\", \"25801035\", \"24532575\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether NFIL3 maintains expression of these targets beyond the commitment stage was unclear\", \"Genome-wide binding in progenitors was not performed\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"The upstream signaling pathway to NFIL3 in NK development was mapped: PDK1 connects IL-15 signaling to NFIL3 induction via mTOR, with mTORC1 primarily controlling NFIL3 expression and mTORC2 controlling T-bet, defining branching pathways for NK cell maturation.\",\n      \"evidence\": \"Conditional PDK1, Raptor, and Rictor KO mice, ectopic E4BP4/mTOR rescue, stage-specific NK flow cytometry\",\n      \"pmids\": [\"25624444\", \"33462410\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct mechanism by which mTORC1 induces NFIL3 transcription or stability was not identified\", \"Whether mTORC1 regulates NFIL3 protein translation or transcription was not resolved\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"NFIL3's metabolic functions were expanded: it represses hepatic gluconeogenesis by competing with CREB for CRE elements in Pepck/G6pc promoters, and the intestinal microbiota controls NFIL3 circadian oscillation in epithelial cells via ILC3/STAT3 to regulate a lipid metabolic program.\",\n      \"evidence\": \"ChIP at CRE elements, reporter mutagenesis, adenoviral gain/loss of function, glucose tolerance tests; germ-free vs. colonized mice, ILC3 depletion, Nfil3⁻/⁻ mice, lipid absorption assays\",\n      \"pmids\": [\"29132537\", \"28860383\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether NFIL3 and CREB physically interact or simply compete for DNA was unclear\", \"The full set of metabolic genes regulated by microbiota-tuned NFIL3 was not identified\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"IRES-mediated cap-independent translation was identified as a key post-transcriptional control: hnRNP A1 binds the Nfil3 5′-UTR IRES and drives circadian NFIL3 protein oscillation even when mRNA levels are constant.\",\n      \"evidence\": \"IRES reporter assay, RNA pulldown, hnRNP A1 siRNA knockdown, bioluminescent protein oscillation tracking\",\n      \"pmids\": [\"28220845\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab finding; independent confirmation needed\", \"Whether IRES-dependent translation is relevant in immune cell contexts was not tested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"NFIL3's epigenetic co-repressor repertoire was broadened: it recruits HDAC1 and EZH2 to repress Bcl6, inhibiting Tfh differentiation in a phosphorylation-dependent manner; separately, it interacts with REV-ERBα to regulate carboxylesterase expression and drug metabolism.\",\n      \"evidence\": \"Conditional KO/knockin mice, co-IP/ChIP for HDAC1 and EZH2 at Bcl6, phosphorylation mutant analysis; co-IP (E4BP4–REV-ERBα), EMSA, reporter, E4bp4⁻/⁻ pharmacokinetics\",\n      \"pmids\": [\"32190636\", \"29653076\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the same phosphorylation events control G9a vs. HDAC1/EZH2 recruitment was unknown\", \"Structural basis of co-repressor selectivity at different loci was not addressed\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"An Nfil3-Zeb2-Id2 transcriptional circuit was shown to control dendritic cell progenitor specification by enabling a switch in Irf8 enhancer usage, defining NFIL3's role in cDC1 lineage commitment at single-cell resolution.\",\n      \"evidence\": \"Single-cell RNA-seq of CDPs, multi-gene epistasis (Nfil3, Zeb2, Id2 KO combinations), Irf8 enhancer reporter\",\n      \"pmids\": [\"31406377\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether NFIL3 directly binds Zeb2 regulatory elements was not demonstrated\", \"Upstream signals controlling NFIL3 in DC progenitors were not defined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"NFIL3's role in hepatic lipid metabolism was further specified: it activates Fsp27/CIDEC expression (cooperating with CREBH) to promote lipid droplet biogenesis, and high-fat diet-induced deSUMOylation of NFIL3 at five lysine residues activates this lipogenic program.\",\n      \"evidence\": \"Liver-specific E4bp4 KO and overexpression, Fsp27 rescue, co-IP (E4BP4–CREBH), SUMOylation site mutagenesis\",\n      \"pmids\": [\"36508222\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the SUMO E3 ligase and the deSUMOylation enzyme acting on NFIL3 was not determined\", \"How SUMOylation and CK1ε phosphorylation are coordinated was not addressed\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"NFIL3 was linked to liver fibrosis through a non-canonical mechanism: hepatocyte NFIL3 stabilizes YAP protein, which activates OPN expression, and secreted OPN acts in a paracrine manner to activate hepatic stellate cells.\",\n      \"evidence\": \"Hepatocyte-specific E4bp4 KO, conditioned medium transfer, co-IP (E4BP4–YAP), OPN neutralization/shRNA, in vivo fibrosis model\",\n      \"pmids\": [\"39473081\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which NFIL3 stabilizes YAP (direct binding vs. indirect regulation) needs dissection\", \"Whether this pathway is active in other fibrotic organs was not tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions remain: the structural basis for NFIL3's context-dependent switching between activation and repression, the genome-wide binding landscape across immune and metabolic cell types, and how post-translational modifications (phosphorylation, SUMOylation) are integrated to select co-repressor partners at specific loci.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No crystal structure or cryo-EM structure of NFIL3 with co-repressors\", \"Genome-wide ChIP-seq across multiple cell types is lacking\", \"Integration of CK1ε phosphorylation, SUMOylation, and IRES-dependent translation into a unified regulatory model is not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0, 3, 9, 14, 30]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 1, 3, 9, 14, 16, 17, 21, 30, 32]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 8, 9]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0009909396\", \"supporting_discovery_ids\": [0, 8, 9, 10]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [11, 12, 13, 15, 16, 17, 19, 22, 23, 34]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [1, 3, 14, 17, 21, 30]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [14, 27, 29, 30, 43]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [5, 6, 26]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [5, 6, 12]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"PER2\", \"CRY2\", \"G9a\", \"HDAC1\", \"EZH2\", \"SREBP1\", \"YAP1\", \"CREBH\"],\n    \"other_free_text\": []\n  }\n}\n```"}