{"gene":"ATXN2L","run_date":"2026-06-09T22:02:44","timeline":{"discoveries":[{"year":2015,"finding":"ATXN2L is asymmetrically dimethylated in vivo, and this arginine methylation is mediated by PRMT1, which physically associates with ATXN2L. Methylation inhibition alters ATXN2L nuclear localization, but mutation of arginine-glycine-rich motifs or methylation inhibition does not alter ATXN2L localization to stress granules.","method":"Co-immunoprecipitation, in vivo methylation analysis, methylation inhibition, site-directed mutagenesis, immunofluorescence localization","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP identifying PRMT1 as the writer, confirmed asymmetric dimethylation in vivo, functional localization consequence shown; single lab, multiple orthogonal methods","pmids":["25748791"],"is_preprint":false},{"year":2020,"finding":"Constitutive deletion of Atxn2l exons 5-8 (encoding Lsm, LsmAD, and PAM2 domains) in mice causes mid-gestational embryonic lethality with brain lamination defects and apoptosis, demonstrating that ATXN2L is essential for embryonic development. ATXN2L-null mouse embryonic fibroblasts show increased multinucleated giant cells. Neither ATXN2L depletion dysregulates ATXN2 nor vice versa.","method":"CRISPR/Cas9 knockout mouse, prenatal histology, brain histological analysis, cell culture phenotyping","journal":"International journal of molecular sciences","confidence":"High","confidence_rationale":"Tier 2 / Strong — constitutive KO mouse with defined embryonic lethal phenotype, histological characterization, and negative cross-regulation result with ortholog; in vivo genetic model","pmids":["32698485"],"is_preprint":false},{"year":2017,"finding":"A chromosomal translocation t(9;13;16) creates an ATXN2L-JAK2 fusion gene encoding a chimeric protein containing all domains of ATXN2L fused to the catalytic (kinase) domain of JAK2, identified in cutaneous CD4+ T-cell lymphoma.","method":"RNA-sequencing, RT-PCR, Sanger sequencing","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — fusion transcript verified by RT-PCR/Sanger in a single patient; constitutive activation is inferred by analogy, not directly demonstrated","pmids":["29262599"],"is_preprint":false},{"year":2019,"finding":"In gastric cancer cells, ATXN2L promotes cell migration and invasion via epithelial-to-mesenchymal transition, confers intrinsic and acquired oxaliplatin resistance (silencing ATXN2L increases ROS and apoptosis in resistant cells), and its expression is upregulated by EGF via PI3K/Akt signaling.","method":"siRNA knockdown, migration/invasion assays, EMT marker analysis, oxaliplatin resistance assays, ROS measurement, apoptosis assay, PI3K/Akt pathway inhibitor experiments","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with multiple functional readouts, pathway inhibitor verification; single lab","pmids":["30787271"],"is_preprint":false},{"year":2022,"finding":"HDAC3 interacts with ATXN2L (confirmed by co-immunoprecipitation and LC-MS/MS) and antagonizes the NRG1-ErbB2-PI3K-AKT signaling axis through this interaction to regulate Schwann cell myelination in diabetic peripheral neuropathy.","method":"Co-immunoprecipitation, liquid chromatography-mass spectrometry (LC-MS/MS), in vivo mouse model (db/db)","journal":"Phytotherapy research : PTR","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP and LC-MS/MS confirm HDAC3-ATXN2L interaction with in vivo functional context; single lab, pathway placement partly inferential","pmids":["36218239"],"is_preprint":false},{"year":2025,"finding":"ATXN2L primarily interacts with a set of RNA-binding proteins including NUFIP2, PABPN1, MCRIP2, RBMS1, LARP1, PTBP1, FMR1, RPS20, FUBP3, MBNL2, ZMAT3, SFPQ, CSDE1, HNRNPK, and HNRNPDL (stronger than established interactors ATXN2, PABPC1, LSM12, and G3BP2), as well as actin complex components SYNE2, LMOD1, ACTA2, FYB, and GOLGA3. Oxidative stress increases HNRNPK but decreases SYNE2 association with ATXN2L. ATXN2L-null fibroblasts show depletion of NUFIP2 and SYNE2 at the proteome level. In the SCA2 mouse model, NUFIP2 and SYNE1 accumulate during ATXN2 aggregation.","method":"Co-immunoprecipitation in wild-type and ATXN2L-null fibroblasts, mass spectrometry proteome profiling, SCA2 KnockIn mouse model tissue analysis","journal":"Neurobiology of disease","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP in null vs. wild-type cells combined with global proteome MS and in vivo SCA2 model validation; multiple orthogonal methods, strong mechanistic depth","pmids":["40220918"],"is_preprint":false},{"year":2025,"finding":"Conditional deletion of ATXN2L LsmAD and PAM2 domains (exons 10-17) in CamK2a+ frontal cortex neurons reduces spontaneous horizontal movement and causes proteome dysregulations enriched in the alternative splicing pathway, suggesting that the Lsm/LsmAD domains of ATXN2L serve a role in splice regulation despite the protein's perinuclear localization.","method":"Conditional CamK2a-CreERT2 knockout mouse, tamoxifen induction, behavioral locomotion assay, global proteome profiling of frontal cortex","journal":"Cells","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional KO with behavioral readout and proteome profiling; pathway enrichment analysis supports splicing role; single lab, indirect evidence for splicing mechanism","pmids":["41090760"],"is_preprint":false},{"year":2025,"finding":"ATXN2L undergoes liquid-liquid phase separation (LLPS) to form granules that recruit eukaryotic initiation factors (eIFs) and promote mRNA translation of downstream targets such as ADAM9; co-localization with stress granules further enhances ADAM9 translation. Knockdown or knockout of ATXN2L suppresses HCC progression.","method":"LLPS assays, ATXN2L knockdown/knockout (HCC cells and mice), eIF co-localization, ADAM9 translation assays, stress granule co-localization imaging","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — LLPS characterization with functional translational readout and in vivo KO model; single lab, mechanism supported by multiple assays","pmids":["41273724"],"is_preprint":false},{"year":2025,"finding":"FOXL1 (delivered via BMSC exosomes) acts as an RNA-binding protein that stabilizes METTL3, which in turn increases ATXN2L mRNA expression through m6A methylation, thereby protecting retinal microvascular endothelial cells against high glucose-induced inflammation, apoptosis, and oxidative stress.","method":"Dual-luciferase reporter assay, RNA immunoprecipitation (RIP), siRNA/overexpression, Western blotting, ELISA, flow cytometry","journal":"Diabetology & metabolic syndrome","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, co-IP and reporter assays establish pathway placement but ATXN2L's own mechanism is not directly interrogated beyond being a downstream target","pmids":["40533826"],"is_preprint":false},{"year":2025,"finding":"Cytoplasmic HSATIII RNA-translated MEWNG-rich proteins form complexes with stress granule proteins including ATXN2L, as detected during thermal stress recovery.","method":"Immunofluorescence co-localization, co-immunoprecipitation (inferred from abstract description of complex formation)","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, ATXN2L listed as a stress granule complex component but is not the primary focus; single method, limited mechanistic detail about ATXN2L itself","pmids":["bio_10.1101_2025.11.12.688122"],"is_preprint":true}],"current_model":"ATXN2L is a perinuclear/cytoplasmic RNA-binding protein with Lsm, LsmAD, and PAM2 domains that is essential for embryonic development; it undergoes liquid-liquid phase separation to form granules that recruit eIF translation factors and promote mRNA translation, associates with a broad network of RNA-binding proteins (most prominently NUFIP2) and actin complex components, is asymmetrically dimethylated by PRMT1 (which controls its nuclear localization), is regulated by HDAC3 interaction to modulate NRG1-ErbB2-PI3K-AKT signaling, and contributes to alternative splicing regulation via its Lsm/LsmAD domains in neurons."},"narrative":{"mechanistic_narrative":"ATXN2L is a perinuclear/cytoplasmic RNA-binding protein that organizes ribonucleoprotein assemblies controlling mRNA translation and is essential for embryonic development [PMID:32698485, PMID:40220918, PMID:41273724]. Through liquid-liquid phase separation it forms granules that recruit eukaryotic initiation factors and promote translation of target mRNAs such as ADAM9, an activity augmented by co-localization with stress granules [PMID:41273724]. It associates with a broad network of RNA-binding proteins—most prominently NUFIP2, along with PABPN1, LARP1, PTBP1, FMR1, HNRNPK and others—and with actin-complex components including SYNE2; oxidative stress remodels these associations, and loss of ATXN2L depletes NUFIP2 and SYNE2 at the proteome level [PMID:40220918]. ATXN2L is asymmetrically dimethylated by PRMT1, which physically associates with it and controls its nuclear localization independently of its stress-granule recruitment [PMID:25748791]. Its Lsm/LsmAD and PAM2 domains contribute to alternative splicing regulation and neuronal locomotor behavior despite the protein's perinuclear distribution [PMID:41090760], and its interaction with HDAC3 modulates the NRG1-ErbB2-PI3K-AKT axis in the context of Schwann cell myelination [PMID:36218239]. In cancer settings ATXN2L promotes migration, EMT and chemoresistance downstream of EGF-driven PI3K/Akt signaling, and supports tumor progression [PMID:30787271, PMID:41273724]. Notably, ATXN2L acts independently of its paralog ATXN2, as neither protein cross-regulates the other [PMID:32698485].","teleology":[{"year":2015,"claim":"Established a post-translational regulatory input on ATXN2L by identifying its arginine methylation writer and linking that modification to subcellular partitioning.","evidence":"Co-immunoprecipitation, in vivo methylation analysis, methylation inhibition and arginine-motif mutagenesis with immunofluorescence in cells","pmids":["25748791"],"confidence":"Medium","gaps":["Functional consequence of nuclear vs cytoplasmic ATXN2L on RNA metabolism not defined","Specific methylated arginine residues not mapped","Why methylation controls nuclear but not stress-granule localization is unexplained"]},{"year":2017,"claim":"Showed ATXN2L can be structurally co-opted in disease through a chromosomal fusion linking its domains to a kinase catalytic domain.","evidence":"RNA-sequencing, RT-PCR and Sanger sequencing of a cutaneous CD4+ T-cell lymphoma patient","pmids":["29262599"],"confidence":"Medium","gaps":["Constitutive kinase activation inferred by analogy, not demonstrated","Single patient, no functional oncogenic assay","Role of the ATXN2L portion in the fusion unknown"]},{"year":2019,"claim":"Placed ATXN2L downstream of EGF-PI3K/Akt signaling and assigned it pro-migratory, pro-EMT, and chemoresistance functions in cancer cells.","evidence":"siRNA knockdown with migration/invasion, EMT marker, oxaliplatin resistance, ROS and apoptosis assays plus PI3K/Akt inhibitor experiments in gastric cancer cells","pmids":["30787271"],"confidence":"Medium","gaps":["Direct molecular mechanism linking ATXN2L to EMT not defined","Whether RNA-binding/translation activity drives the phenotype unclear","Single cell-line/lab context"]},{"year":2020,"claim":"Demonstrated ATXN2L is essential for development and acts independently of its paralog ATXN2, resolving whether the two proteins are functionally redundant.","evidence":"Constitutive CRISPR/Cas9 Atxn2l knockout mouse with prenatal and brain histology and MEF phenotyping","pmids":["32698485"],"confidence":"High","gaps":["Molecular cause of mid-gestational lethality not pinpointed","Mechanism of multinucleation in null MEFs unknown","Which domains drive the essential function not dissected here"]},{"year":2022,"claim":"Identified HDAC3 as an ATXN2L interactor and connected this interaction to NRG1-ErbB2-PI3K-AKT signaling in a myelination/neuropathy context.","evidence":"Co-immunoprecipitation and LC-MS/MS with a db/db diabetic mouse model","pmids":["36218239"],"confidence":"Medium","gaps":["Pathway placement partly inferential","Direct vs indirect HDAC3-ATXN2L effect on signaling not resolved","Whether ATXN2L is an HDAC3 substrate or scaffold unknown"]},{"year":2025,"claim":"Defined the ATXN2L interactome, showing it preferentially binds a network of RNA-binding proteins and actin-complex components that are remodeled by oxidative stress and dependent on ATXN2L for their abundance.","evidence":"Reciprocal co-IP in wild-type vs ATXN2L-null fibroblasts, global proteome mass spectrometry, and SCA2 knock-in mouse tissue analysis","pmids":["40220918"],"confidence":"High","gaps":["Direct vs RNA-bridged nature of individual interactions not separated","Functional consequence of NUFIP2/SYNE2 depletion not mechanistically resolved","Stoichiometry of a defined complex not established"]},{"year":2025,"claim":"Assigned ATXN2L's Lsm/LsmAD and PAM2 domains a role in alternative splicing regulation and neuronal behavior, linking domain architecture to function in vivo.","evidence":"Conditional CamK2a-CreERT2 domain-deletion mouse with behavioral locomotion assay and frontal cortex proteome profiling","pmids":["41090760"],"confidence":"Medium","gaps":["Splicing role inferred from proteome enrichment, no direct splice-event mapping","How a perinuclear protein influences splicing unresolved","Causal link between splicing changes and behavior not established"]},{"year":2025,"claim":"Provided a molecular mechanism for ATXN2L in translation, showing it phase-separates into granules that recruit eIFs to promote target mRNA translation and tumor progression.","evidence":"LLPS assays, eIF co-localization, ADAM9 translation readouts, stress granule imaging, and ATXN2L knockdown/knockout in HCC cells and mice","pmids":["41273724"],"confidence":"Medium","gaps":["Determinants of LLPS within ATXN2L not mapped","Breadth of translationally regulated targets beyond ADAM9 unknown","Single tumor context"]},{"year":2025,"claim":"Positioned ATXN2L as a downstream target of an m6A-mediated regulatory axis protecting endothelial cells from hyperglycemic stress.","evidence":"Dual-luciferase reporter, RNA immunoprecipitation, knockdown/overexpression, Western blot, ELISA and flow cytometry in retinal microvascular endothelial cells","pmids":["40533826"],"confidence":"Low","gaps":["ATXN2L's own mechanism not interrogated beyond being a target","Direct m6A site on ATXN2L mRNA not mapped","Single lab, indirect pathway placement"]},{"year":2025,"claim":"Listed ATXN2L as a component of stress-granule complexes containing aberrantly translated HSATIII-derived proteins during thermal stress recovery.","evidence":"Immunofluorescence co-localization and co-IP in a preprint focused on HSATIII translation","pmids":["bio_10.1101_2025.11.12.688122"],"confidence":"Low","gaps":["Preprint, not peer-reviewed","ATXN2L not the focus; its functional role in these complexes unaddressed","Single method with limited ATXN2L-specific detail"]},{"year":null,"claim":"How ATXN2L's RNA-binding, phase-separation, and translation-promoting activities mechanistically converge to produce its essential developmental function remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model linking domains to LLPS and eIF recruitment","The mRNA targets that account for embryonic essentiality are unidentified","Whether splicing, translation, or cytoskeletal roles are primary in vivo is unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[5,7]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[7]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[5,7]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[5,7]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[5,7]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[7]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[5,7]}],"complexes":["stress granule"],"partners":["NUFIP2","PRMT1","HDAC3","SYNE2","HNRNPK","PABPN1","LARP1","PTBP1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8WWM7","full_name":"Ataxin-2-like protein","aliases":["Ataxin-2 domain protein","Ataxin-2-related protein"],"length_aa":1075,"mass_kda":113.4,"function":"Involved in the regulation of stress granule and P-body formation","subcellular_location":"Membrane; Cytoplasm; Nucleus speckle; Cytoplasmic granule","url":"https://www.uniprot.org/uniprotkb/Q8WWM7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ATXN2L","classification":"Not Classified","n_dependent_lines":57,"n_total_lines":1208,"dependency_fraction":0.04718543046357616},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000168488","cell_line_id":"CID001509","localizations":[{"compartment":"cytoplasmic","grade":3}],"interactors":[{"gene":"FAM195B","stoichiometry":10.0},{"gene":"DDX6","stoichiometry":10.0},{"gene":"LSM12","stoichiometry":0.2},{"gene":"NUFIP2","stoichiometry":0.2},{"gene":"SLMAP","stoichiometry":0.2},{"gene":"PABPC4","stoichiometry":0.2},{"gene":"PABPC1;PABPC3","stoichiometry":0.2},{"gene":"RCBTB2","stoichiometry":0.2},{"gene":"CAPZB","stoichiometry":0.2},{"gene":"G3BP2","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001509","total_profiled":1310},"omim":[{"mim_id":"607931","title":"ATAXIN 2-LIKE; ATXN2L","url":"https://www.omim.org/entry/607931"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Cytosol","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ATXN2L"},"hgnc":{"alias_symbol":["A2lp","A2D"],"prev_symbol":[]},"alphafold":{"accession":"Q8WWM7","domains":[{"cath_id":"2.30.30.100","chopping":"117-206","consensus_level":"high","plddt":88.2149,"start":117,"end":206},{"cath_id":"-","chopping":"250-281","consensus_level":"medium","plddt":85.9928,"start":250,"end":281},{"cath_id":"-","chopping":"285-317","consensus_level":"medium","plddt":88.0,"start":285,"end":317}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8WWM7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8WWM7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8WWM7-F1-predicted_aligned_error_v6.png","plddt_mean":48.53},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ATXN2L","jax_strain_url":"https://www.jax.org/strain/search?query=ATXN2L"},"sequence":{"accession":"Q8WWM7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8WWM7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8WWM7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8WWM7"}},"corpus_meta":[{"pmid":"30787271","id":"PMC_30787271","title":"ATXN2L upregulated by epidermal growth factor promotes gastric cancer cell invasiveness and oxaliplatin resistance.","date":"2019","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/30787271","citation_count":61,"is_preprint":false},{"pmid":"32698485","id":"PMC_32698485","title":"Mid-Gestation lethality of Atxn2l-Ablated Mice.","date":"2020","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/32698485","citation_count":23,"is_preprint":false},{"pmid":"29262599","id":"PMC_29262599","title":"Fusion of the genes ataxin 2 like, ATXN2L, and Janus kinase 2, JAK2, in cutaneous CD4 positive T-cell lymphoma.","date":"2017","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/29262599","citation_count":22,"is_preprint":false},{"pmid":"25748791","id":"PMC_25748791","title":"PRMT1-mediated arginine methylation controls ATXN2L localization.","date":"2015","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/25748791","citation_count":17,"is_preprint":false},{"pmid":"36218239","id":"PMC_36218239","title":"Jatrorrhizine ameliorates Schwann cell myelination via inhibiting HDAC3 ability to recruit Atxn2l for regulating the NRG1-ErbB2-PI3K-AKT pathway in diabetic peripheral neuropathy mice.","date":"2022","source":"Phytotherapy research : PTR","url":"https://pubmed.ncbi.nlm.nih.gov/36218239","citation_count":14,"is_preprint":false},{"pmid":"40220918","id":"PMC_40220918","title":"ATXN2L primarily interacts with NUFIP2, the absence of ATXN2L results in NUFIP2 depletion, and the ATXN2-polyQ expansion triggers NUFIP2 accumulation.","date":"2025","source":"Neurobiology of disease","url":"https://pubmed.ncbi.nlm.nih.gov/40220918","citation_count":8,"is_preprint":false},{"pmid":"35513260","id":"PMC_35513260","title":"From the comparative study of a circRNA originating from an mammalian ATXN2L intron to understanding the genesis of intron lariat-derived circRNAs.","date":"2022","source":"Biochimica et biophysica acta. Gene regulatory mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/35513260","citation_count":7,"is_preprint":false},{"pmid":"40533826","id":"PMC_40533826","title":"Exosomal FOXL1 from bone marrow mesenchymal stem cells activates the METTL3/ATXN2L pathway to ameliorate high glucose-induced human retinal microvascular endothelial cell injury.","date":"2025","source":"Diabetology & metabolic syndrome","url":"https://pubmed.ncbi.nlm.nih.gov/40533826","citation_count":5,"is_preprint":false},{"pmid":"41090760","id":"PMC_41090760","title":"Conditional ATXN2L-Null in Adult Frontal Cortex CamK2a+ Neurons Does Not Cause Cell Death but Restricts Spontaneous Mobility and Affects the Alternative Splicing Pathway.","date":"2025","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/41090760","citation_count":3,"is_preprint":false},{"pmid":"41273724","id":"PMC_41273724","title":"Liquid-liquid phase separation of ATXN2L enhances mRNA translation in hepatocellular carcinoma.","date":"2025","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/41273724","citation_count":1,"is_preprint":false},{"pmid":"39820928","id":"PMC_39820928","title":"Circ-NMNAT1 Drives Tumor Progression in Bladder Cancer by Modulating the miR-370-3p/ATXN2L Axis.","date":"2025","source":"Applied biochemistry and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/39820928","citation_count":0,"is_preprint":false},{"pmid":"41688673","id":"PMC_41688673","title":"Complete remission of relapsed ATXN2L::JAK2 fusion positive anaplastic large cell lymphoma following ruxolitinib monotherapy in a child.","date":"2026","source":"NPJ precision oncology","url":"https://pubmed.ncbi.nlm.nih.gov/41688673","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.11.12.688122","title":"Cytoplasmic roles of HSATIII RNAs in RNA granule assembly and production of actin cytoskeleton-associated repeat-containing proteins","date":"2025-11-13","source":"bioRxiv","url":"https://doi.org/10.1101/2025.11.12.688122","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9187,"output_tokens":2785,"usd":0.034668,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10011,"output_tokens":3656,"usd":0.070727,"stage2_stop_reason":"end_turn"},"total_usd":0.105395,"stage1_batch_id":"msgbatch_0179Z2pxRYBsXi2xADneafRw","stage2_batch_id":"msgbatch_01LaY9ZaVdgjWArcZo9eqQE5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"ATXN2L is asymmetrically dimethylated in vivo, and this arginine methylation is mediated by PRMT1, which physically associates with ATXN2L. Methylation inhibition alters ATXN2L nuclear localization, but mutation of arginine-glycine-rich motifs or methylation inhibition does not alter ATXN2L localization to stress granules.\",\n      \"method\": \"Co-immunoprecipitation, in vivo methylation analysis, methylation inhibition, site-directed mutagenesis, immunofluorescence localization\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP identifying PRMT1 as the writer, confirmed asymmetric dimethylation in vivo, functional localization consequence shown; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"25748791\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Constitutive deletion of Atxn2l exons 5-8 (encoding Lsm, LsmAD, and PAM2 domains) in mice causes mid-gestational embryonic lethality with brain lamination defects and apoptosis, demonstrating that ATXN2L is essential for embryonic development. ATXN2L-null mouse embryonic fibroblasts show increased multinucleated giant cells. Neither ATXN2L depletion dysregulates ATXN2 nor vice versa.\",\n      \"method\": \"CRISPR/Cas9 knockout mouse, prenatal histology, brain histological analysis, cell culture phenotyping\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — constitutive KO mouse with defined embryonic lethal phenotype, histological characterization, and negative cross-regulation result with ortholog; in vivo genetic model\",\n      \"pmids\": [\"32698485\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"A chromosomal translocation t(9;13;16) creates an ATXN2L-JAK2 fusion gene encoding a chimeric protein containing all domains of ATXN2L fused to the catalytic (kinase) domain of JAK2, identified in cutaneous CD4+ T-cell lymphoma.\",\n      \"method\": \"RNA-sequencing, RT-PCR, Sanger sequencing\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — fusion transcript verified by RT-PCR/Sanger in a single patient; constitutive activation is inferred by analogy, not directly demonstrated\",\n      \"pmids\": [\"29262599\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In gastric cancer cells, ATXN2L promotes cell migration and invasion via epithelial-to-mesenchymal transition, confers intrinsic and acquired oxaliplatin resistance (silencing ATXN2L increases ROS and apoptosis in resistant cells), and its expression is upregulated by EGF via PI3K/Akt signaling.\",\n      \"method\": \"siRNA knockdown, migration/invasion assays, EMT marker analysis, oxaliplatin resistance assays, ROS measurement, apoptosis assay, PI3K/Akt pathway inhibitor experiments\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with multiple functional readouts, pathway inhibitor verification; single lab\",\n      \"pmids\": [\"30787271\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"HDAC3 interacts with ATXN2L (confirmed by co-immunoprecipitation and LC-MS/MS) and antagonizes the NRG1-ErbB2-PI3K-AKT signaling axis through this interaction to regulate Schwann cell myelination in diabetic peripheral neuropathy.\",\n      \"method\": \"Co-immunoprecipitation, liquid chromatography-mass spectrometry (LC-MS/MS), in vivo mouse model (db/db)\",\n      \"journal\": \"Phytotherapy research : PTR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP and LC-MS/MS confirm HDAC3-ATXN2L interaction with in vivo functional context; single lab, pathway placement partly inferential\",\n      \"pmids\": [\"36218239\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ATXN2L primarily interacts with a set of RNA-binding proteins including NUFIP2, PABPN1, MCRIP2, RBMS1, LARP1, PTBP1, FMR1, RPS20, FUBP3, MBNL2, ZMAT3, SFPQ, CSDE1, HNRNPK, and HNRNPDL (stronger than established interactors ATXN2, PABPC1, LSM12, and G3BP2), as well as actin complex components SYNE2, LMOD1, ACTA2, FYB, and GOLGA3. Oxidative stress increases HNRNPK but decreases SYNE2 association with ATXN2L. ATXN2L-null fibroblasts show depletion of NUFIP2 and SYNE2 at the proteome level. In the SCA2 mouse model, NUFIP2 and SYNE1 accumulate during ATXN2 aggregation.\",\n      \"method\": \"Co-immunoprecipitation in wild-type and ATXN2L-null fibroblasts, mass spectrometry proteome profiling, SCA2 KnockIn mouse model tissue analysis\",\n      \"journal\": \"Neurobiology of disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP in null vs. wild-type cells combined with global proteome MS and in vivo SCA2 model validation; multiple orthogonal methods, strong mechanistic depth\",\n      \"pmids\": [\"40220918\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Conditional deletion of ATXN2L LsmAD and PAM2 domains (exons 10-17) in CamK2a+ frontal cortex neurons reduces spontaneous horizontal movement and causes proteome dysregulations enriched in the alternative splicing pathway, suggesting that the Lsm/LsmAD domains of ATXN2L serve a role in splice regulation despite the protein's perinuclear localization.\",\n      \"method\": \"Conditional CamK2a-CreERT2 knockout mouse, tamoxifen induction, behavioral locomotion assay, global proteome profiling of frontal cortex\",\n      \"journal\": \"Cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional KO with behavioral readout and proteome profiling; pathway enrichment analysis supports splicing role; single lab, indirect evidence for splicing mechanism\",\n      \"pmids\": [\"41090760\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ATXN2L undergoes liquid-liquid phase separation (LLPS) to form granules that recruit eukaryotic initiation factors (eIFs) and promote mRNA translation of downstream targets such as ADAM9; co-localization with stress granules further enhances ADAM9 translation. Knockdown or knockout of ATXN2L suppresses HCC progression.\",\n      \"method\": \"LLPS assays, ATXN2L knockdown/knockout (HCC cells and mice), eIF co-localization, ADAM9 translation assays, stress granule co-localization imaging\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — LLPS characterization with functional translational readout and in vivo KO model; single lab, mechanism supported by multiple assays\",\n      \"pmids\": [\"41273724\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"FOXL1 (delivered via BMSC exosomes) acts as an RNA-binding protein that stabilizes METTL3, which in turn increases ATXN2L mRNA expression through m6A methylation, thereby protecting retinal microvascular endothelial cells against high glucose-induced inflammation, apoptosis, and oxidative stress.\",\n      \"method\": \"Dual-luciferase reporter assay, RNA immunoprecipitation (RIP), siRNA/overexpression, Western blotting, ELISA, flow cytometry\",\n      \"journal\": \"Diabetology & metabolic syndrome\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, co-IP and reporter assays establish pathway placement but ATXN2L's own mechanism is not directly interrogated beyond being a downstream target\",\n      \"pmids\": [\"40533826\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cytoplasmic HSATIII RNA-translated MEWNG-rich proteins form complexes with stress granule proteins including ATXN2L, as detected during thermal stress recovery.\",\n      \"method\": \"Immunofluorescence co-localization, co-immunoprecipitation (inferred from abstract description of complex formation)\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, ATXN2L listed as a stress granule complex component but is not the primary focus; single method, limited mechanistic detail about ATXN2L itself\",\n      \"pmids\": [\"bio_10.1101_2025.11.12.688122\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"ATXN2L is a perinuclear/cytoplasmic RNA-binding protein with Lsm, LsmAD, and PAM2 domains that is essential for embryonic development; it undergoes liquid-liquid phase separation to form granules that recruit eIF translation factors and promote mRNA translation, associates with a broad network of RNA-binding proteins (most prominently NUFIP2) and actin complex components, is asymmetrically dimethylated by PRMT1 (which controls its nuclear localization), is regulated by HDAC3 interaction to modulate NRG1-ErbB2-PI3K-AKT signaling, and contributes to alternative splicing regulation via its Lsm/LsmAD domains in neurons.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ATXN2L is a perinuclear/cytoplasmic RNA-binding protein that organizes ribonucleoprotein assemblies controlling mRNA translation and is essential for embryonic development [#1, #5, #7]. Through liquid-liquid phase separation it forms granules that recruit eukaryotic initiation factors and promote translation of target mRNAs such as ADAM9, an activity augmented by co-localization with stress granules [#7]. It associates with a broad network of RNA-binding proteins—most prominently NUFIP2, along with PABPN1, LARP1, PTBP1, FMR1, HNRNPK and others—and with actin-complex components including SYNE2; oxidative stress remodels these associations, and loss of ATXN2L depletes NUFIP2 and SYNE2 at the proteome level [#5]. ATXN2L is asymmetrically dimethylated by PRMT1, which physically associates with it and controls its nuclear localization independently of its stress-granule recruitment [#0]. Its Lsm/LsmAD and PAM2 domains contribute to alternative splicing regulation and neuronal locomotor behavior despite the protein's perinuclear distribution [#6], and its interaction with HDAC3 modulates the NRG1-ErbB2-PI3K-AKT axis in the context of Schwann cell myelination [#4]. In cancer settings ATXN2L promotes migration, EMT and chemoresistance downstream of EGF-driven PI3K/Akt signaling, and supports tumor progression [#3, #7]. Notably, ATXN2L acts independently of its paralog ATXN2, as neither protein cross-regulates the other [#1].\",\n  \"teleology\": [\n    {\n      \"year\": 2015,\n      \"claim\": \"Established a post-translational regulatory input on ATXN2L by identifying its arginine methylation writer and linking that modification to subcellular partitioning.\",\n      \"evidence\": \"Co-immunoprecipitation, in vivo methylation analysis, methylation inhibition and arginine-motif mutagenesis with immunofluorescence in cells\",\n      \"pmids\": [\"25748791\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of nuclear vs cytoplasmic ATXN2L on RNA metabolism not defined\", \"Specific methylated arginine residues not mapped\", \"Why methylation controls nuclear but not stress-granule localization is unexplained\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Showed ATXN2L can be structurally co-opted in disease through a chromosomal fusion linking its domains to a kinase catalytic domain.\",\n      \"evidence\": \"RNA-sequencing, RT-PCR and Sanger sequencing of a cutaneous CD4+ T-cell lymphoma patient\",\n      \"pmids\": [\"29262599\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Constitutive kinase activation inferred by analogy, not demonstrated\", \"Single patient, no functional oncogenic assay\", \"Role of the ATXN2L portion in the fusion unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Placed ATXN2L downstream of EGF-PI3K/Akt signaling and assigned it pro-migratory, pro-EMT, and chemoresistance functions in cancer cells.\",\n      \"evidence\": \"siRNA knockdown with migration/invasion, EMT marker, oxaliplatin resistance, ROS and apoptosis assays plus PI3K/Akt inhibitor experiments in gastric cancer cells\",\n      \"pmids\": [\"30787271\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular mechanism linking ATXN2L to EMT not defined\", \"Whether RNA-binding/translation activity drives the phenotype unclear\", \"Single cell-line/lab context\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Demonstrated ATXN2L is essential for development and acts independently of its paralog ATXN2, resolving whether the two proteins are functionally redundant.\",\n      \"evidence\": \"Constitutive CRISPR/Cas9 Atxn2l knockout mouse with prenatal and brain histology and MEF phenotyping\",\n      \"pmids\": [\"32698485\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular cause of mid-gestational lethality not pinpointed\", \"Mechanism of multinucleation in null MEFs unknown\", \"Which domains drive the essential function not dissected here\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identified HDAC3 as an ATXN2L interactor and connected this interaction to NRG1-ErbB2-PI3K-AKT signaling in a myelination/neuropathy context.\",\n      \"evidence\": \"Co-immunoprecipitation and LC-MS/MS with a db/db diabetic mouse model\",\n      \"pmids\": [\"36218239\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Pathway placement partly inferential\", \"Direct vs indirect HDAC3-ATXN2L effect on signaling not resolved\", \"Whether ATXN2L is an HDAC3 substrate or scaffold unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined the ATXN2L interactome, showing it preferentially binds a network of RNA-binding proteins and actin-complex components that are remodeled by oxidative stress and dependent on ATXN2L for their abundance.\",\n      \"evidence\": \"Reciprocal co-IP in wild-type vs ATXN2L-null fibroblasts, global proteome mass spectrometry, and SCA2 knock-in mouse tissue analysis\",\n      \"pmids\": [\"40220918\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct vs RNA-bridged nature of individual interactions not separated\", \"Functional consequence of NUFIP2/SYNE2 depletion not mechanistically resolved\", \"Stoichiometry of a defined complex not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Assigned ATXN2L's Lsm/LsmAD and PAM2 domains a role in alternative splicing regulation and neuronal behavior, linking domain architecture to function in vivo.\",\n      \"evidence\": \"Conditional CamK2a-CreERT2 domain-deletion mouse with behavioral locomotion assay and frontal cortex proteome profiling\",\n      \"pmids\": [\"41090760\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Splicing role inferred from proteome enrichment, no direct splice-event mapping\", \"How a perinuclear protein influences splicing unresolved\", \"Causal link between splicing changes and behavior not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Provided a molecular mechanism for ATXN2L in translation, showing it phase-separates into granules that recruit eIFs to promote target mRNA translation and tumor progression.\",\n      \"evidence\": \"LLPS assays, eIF co-localization, ADAM9 translation readouts, stress granule imaging, and ATXN2L knockdown/knockout in HCC cells and mice\",\n      \"pmids\": [\"41273724\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Determinants of LLPS within ATXN2L not mapped\", \"Breadth of translationally regulated targets beyond ADAM9 unknown\", \"Single tumor context\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Positioned ATXN2L as a downstream target of an m6A-mediated regulatory axis protecting endothelial cells from hyperglycemic stress.\",\n      \"evidence\": \"Dual-luciferase reporter, RNA immunoprecipitation, knockdown/overexpression, Western blot, ELISA and flow cytometry in retinal microvascular endothelial cells\",\n      \"pmids\": [\"40533826\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"ATXN2L's own mechanism not interrogated beyond being a target\", \"Direct m6A site on ATXN2L mRNA not mapped\", \"Single lab, indirect pathway placement\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Listed ATXN2L as a component of stress-granule complexes containing aberrantly translated HSATIII-derived proteins during thermal stress recovery.\",\n      \"evidence\": \"Immunofluorescence co-localization and co-IP in a preprint focused on HSATIII translation\",\n      \"pmids\": [\"bio_10.1101_2025.11.12.688122\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Preprint, not peer-reviewed\", \"ATXN2L not the focus; its functional role in these complexes unaddressed\", \"Single method with limited ATXN2L-specific detail\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ATXN2L's RNA-binding, phase-separation, and translation-promoting activities mechanistically converge to produce its essential developmental function remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model linking domains to LLPS and eIF recruitment\", \"The mRNA targets that account for embryonic essentiality are unidentified\", \"Whether splicing, translation, or cytoskeletal roles are primary in vivo is unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [5, 7]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [5, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [5, 7]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [5, 7]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [5, 7]}\n    ],\n    \"complexes\": [\"stress granule\"],\n    \"partners\": [\"NUFIP2\", \"PRMT1\", \"HDAC3\", \"SYNE2\", \"HNRNPK\", \"PABPN1\", \"LARP1\", \"PTBP1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":7,"faith_pct":85.71428571428571}}