{"gene":"YBX2","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":1998,"finding":"MSY2 (YBX2) is a germ cell-specific Y-box protein containing a cold shock domain and four basic/aromatic islands; it is expressed maximally in postmeiotic round spermatids and in diplotene-stage/mature oocytes, and is maternally inherited in the one-cell embryo but degraded by the late two-cell stage coincident with bulk maternal mRNA degradation.","method":"Northern blotting, immunoblotting, in situ analysis of isolated germ cell populations","journal":"Biology of reproduction","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (Northern, Western, cell fractionation), replicated across subsequent studies","pmids":["9780336"],"is_preprint":false},{"year":2000,"finding":"MSY2 (YBX2) forms a sequence-specific RNA-binding complex with MSY4 on non-polysomal mRNPs; the complex co-immunoprecipitates and is associated with translationally repressed mRNAs, consistent with a role in mRNA storage.","method":"Electrophoretic mobility shift assay (EMSA), immunoprecipitation, polysome analysis, yeast three-hybrid system","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — EMSA, co-IP, polysome fractionation in same study; replicated by subsequent work (PMID:11564883)","pmids":["10772793"],"is_preprint":false},{"year":1999,"finding":"In male germ cells, MSY2 is associated on non-polysomal mRNAs with a co-immunoprecipitating kinase activity that phosphorylates MSY2 in vitro; dephosphorylation of MSY2 decreases its RNA-binding affinity, suggesting phosphorylation state regulates mRNA binding. MSY2-bound non-polysomal RNP proteins repress translation of exogenous mRNAs in vitro.","method":"Co-immunoprecipitation, in vitro kinase assay, Northwestern blotting, in vitro translation assay, reconstitution","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro kinase reconstitution, Northwestern, and translation repression assay in one study; single lab","pmids":["10076007"],"is_preprint":false},{"year":2001,"finding":"MSY2 and MSY4 bind a specific 7-8 nucleotide sequence (Y-box recognition site, YRS: U(AC)C(A)CAU(C)CA) in the 3' UTR of the translationally repressed protamine 1 mRNA; single nucleotide mutations abolish binding in vitro, and disruption of the YRS in transgenic mice relieves Prm1-like translational repression in vivo.","method":"EMSA, competition binding, yeast three-hybrid system, transgenic mouse reporter assay","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — mutagenesis in vitro and in vivo validation in transgenic mice; multiple orthogonal methods","pmids":["11564883"],"is_preprint":false},{"year":2001,"finding":"MSY2 protein is primarily cytoplasmic in mouse oocytes (~75% associated with cytoskeletal/Triton-insoluble preparations); it is phosphorylated during oocyte maturation and dephosphorylated following fertilization. MSY2 constitutes ~2% of total oocyte protein.","method":"Immunoblotting, reverse transcription-PCR, microinjection of MSY2-EGFP mRNA, confocal microscopy, cytoskeletal fractionation","journal":"Biology of reproduction","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct localization by imaging and fractionation, phosphorylation by Western, replicated in multiple follow-up studies","pmids":["11566752"],"is_preprint":false},{"year":2002,"finding":"Bacterially expressed recombinant MSY2 binds mRNA with limited sequence specificity (multiple molecules bind one Prm1 mRNA) and represses translation in vitro at protein:mRNA ratios approximating those in oocytes.","method":"Gel shift assay, filter binding assay, in vitro translation/luciferase assay with recombinant protein","journal":"Biology of reproduction","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with recombinant protein, multiple binding and translation assays, single lab","pmids":["12297523"],"is_preprint":false},{"year":2003,"finding":"An intact cold-shock domain (CSD) with its two RNA-binding motifs is required for cytoplasmic localization of MSY2 in oocytes; an additional C-terminal basic/aromatic island is necessary for Triton-insoluble retention. RNase A treatment releases essentially all endogenous MSY2, demonstrating that intact mRNA is required for cytoplasmic retention.","method":"Microinjection of mutant MSY2-EGFP mRNAs, laser-scanning confocal microscopy, Triton extraction, RNase A treatment, RNA EMSA","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — domain mutagenesis coupled with live imaging, fractionation, and in vitro binding; single lab, multiple orthogonal methods","pmids":["12648488"],"is_preprint":false},{"year":2004,"finding":"RNAi-mediated reduction of MSY2 in growing oocytes (~60% knockdown) reduces total mRNA by ~20-25%, impairs protein synthesis, and prevents maturation-associated changes in protein synthesis, directly supporting MSY2's role in stabilizing maternal mRNAs in vivo.","method":"Transgenic RNAi (Zp3 promoter-driven hairpin dsRNA), immunoblotting, microinjection, Ca2+ imaging, total mRNA quantification, protein synthesis assay","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — transgenic knockdown with multiple functional readouts; replicated in subsequent knockout studies","pmids":["15031116"],"is_preprint":false},{"year":2005,"finding":"MSY2 binds a specific subset of germ cell mRNAs enriched for stored/translationally delayed, male gamete-specific transcripts; chromatin precipitation shows most MSY2 target mRNAs are transcribed from promoters containing the Y-box DNA-binding motif; transgenic reporter experiments show Y-box promoters direct mRNAs into the MSY2-bound cytoplasmic fraction, linking nuclear transcription to cytoplasmic mRNA storage.","method":"Immunoprecipitation combined with suppressive subtractive hybridization, chromatin precipitation (ChIP), transgenic mouse GFP reporter assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal IP, ChIP, and in vivo transgenic validation; multiple orthogonal methods in one study","pmids":["15665108"],"is_preprint":false},{"year":2005,"finding":"Genetic deletion of Msy2 in mice causes male and female infertility: males exhibit post-meiotic spermatogenic arrest with multinucleated spermatids and no spermatozoa, accompanied by large reductions in postmeiotic mRNA levels; females show oocyte loss, anovulation, and follicle defects.","method":"Gene targeting/knockout, histology, RT-PCR, apoptosis assays, fertility testing","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — germline knockout with multiple defined phenotypic and molecular readouts; replicated and expanded in follow-up studies","pmids":["15824319"],"is_preprint":false},{"year":2006,"finding":"In Msy2-null male mice, mRNAs are redistributed from RNP storage particles to polysomes and show markedly decreased abundance; transcription, mRNA processing, and intracellular transport are normal, indicating that increased mRNA instability (not transcriptional defects) causes spermatogenic arrest.","method":"Polysome/RNP fractionation, real-time RT-PCR, transcriptional assays, mRNA transport assays","journal":"Biology of reproduction","confidence":"High","confidence_rationale":"Tier 2 / Moderate — polysome fractionation combined with multiple molecular assays in knockout mice; single lab but multiple orthogonal methods","pmids":["17035640"],"is_preprint":false},{"year":2008,"finding":"CDC2A (CDK1)-mediated phosphorylation of MSY2 triggers the maturation-associated degradation of maternal mRNAs during mouse oocyte maturation: CDK1 activation induces MSY2 phosphorylation and mRNA degradation; CDK1 inhibition blocks both; non-phosphorylatable dominant-negative MSY2 prevents mRNA degradation, while constitutively active MSY2 induces degradation in the absence of maturation.","method":"Microinjection of Cdc2a mRNA, CDK1 inhibition with roscovitine, expression of phosphomutant/phosphomimetic MSY2, immunoblotting, mRNA quantification","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — gain-of-function and dominant-negative mutagenesis with pharmacological inhibition; multiple orthogonal approaches in one study","pmids":["18606161"],"is_preprint":false},{"year":2009,"finding":"MSY2 binds a class of small RNAs (~25-31 nt, termed MSY-RNAs) that are MIWI-independent, often initiate with 5' adenine, are expressed in germ and somatic cells, map within annotated genes and to piRNA clusters, and are present in nuclei (enriched in chromatin) and cytoplasm (in both RNPs and polysomes).","method":"RNA immunoprecipitation, small RNA sequencing, fractionation (chromatin, RNP, polysome), analysis in Miwi and Msy2 null mice","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RIP and fractionation in null mice; single lab, functional significance of MSY-RNA binding not fully characterized","pmids":["19597149"],"is_preprint":false},{"year":2011,"finding":"In Msy2-null oocytes, total poly(A)-containing RNA is reduced by ~25%; injection of wild-type MSY2 into mutant oocytes rescues mRNA stability, but a RNA-binding-deficient mutant MSY2 does not, directly demonstrating that RNA-binding activity is required for MSY2-mediated mRNA stabilization. Loss of MSY2 also causes failure of transcription quiescence during oocyte growth and aberrant spindle formation.","method":"Knockout mouse analysis, microinjection of wild-type and mutant MSY2 mRNA, mRNA stability assays, spindle imaging, transcriptome profiling","journal":"Biology of reproduction","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — RNA-binding mutant rescue experiment directly links binding activity to mRNA stability function; multiple orthogonal readouts","pmids":["21613634"],"is_preprint":false},{"year":2016,"finding":"YBX2 binding sites positioned near the 3' ends of Prm1 and Smcp mRNA 3'UTRs are required for translational repression in round spermatids; moving the same binding sites to upstream positions produces negligible repression, demonstrating position-dependent cooperative interactions with co-factors. In Ybx2-knockout round spermatids, Prm1 and Smcp mRNAs are prematurely recruited to polysomes.","method":"Transgenic mice with 3'UTR mutations, polysome analysis of Ybx2-knockout mice, transgenic reporter assays","journal":"Molecular reproduction and development","confidence":"High","confidence_rationale":"Tier 2 / Moderate — in vivo transgenic mutagenesis combined with polysome analysis in knockout; single lab but two orthogonal in vivo approaches","pmids":["26773323"],"is_preprint":false},{"year":2016,"finding":"PADI6 is required for anchoring the mRNA-MSY2 complex to oocyte cytoplasmic lattices (CPLs): in Padi6-KO oocytes, the abundance of MSY2 in the Triton-insoluble fraction is markedly decreased; RNase A treatment of permeabilized oocytes releases both PADI6 and MSY2, indicating mRNA bridges the MSY2-CPL interaction.","method":"Padi6 knockout mouse analysis, Triton extraction/fractionation, RNase A treatment, immunostaining","journal":"Cell cycle","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic knockout with fractionation and enzymatic dissection; indirect evidence for PADI6-MSY2-mRNA ternary complex at CPLs","pmids":["27929740"],"is_preprint":false},{"year":2017,"finding":"Ybx2 knockdown in brown adipocytes blocks brown adipogenesis and destabilizes PGC1α mRNA; Ybx2 overexpression promotes brown adipose tissue (BAT) marker expression; RNA immunoprecipitation identifies a set of mRNA targets including Pgc1α that are destabilized upon Ybx2 depletion during cold-induced activation, establishing YBX2 as a regulator of mRNA stability in BAT.","method":"shRNA knockdown, overexpression, Ybx2-knockout mice, RNA-immunoprecipitation, RNA sequencing","journal":"Diabetes","confidence":"High","confidence_rationale":"Tier 2 / Strong — knockout mouse combined with RIP-seq and gain/loss-of-function in cultured adipocytes; multiple orthogonal methods","pmids":["28970281"],"is_preprint":false},{"year":2019,"finding":"YBX2 interacts with PAIP1 (a translation enhancer) in vitro and in vivo in mouse testes; PAIP1 co-localizes with YBX2 in round spermatids; sequential RNA immunoprecipitation identifies spermiogenic mRNAs indirectly bound by PAIP1 through YBX2; translation of YBX2-masked mRNAs is blocked by YBX2 alone but reinitiated when YBX2 is co-expressed with PAIP1 in vitro.","method":"Co-immunoprecipitation (in vitro and in vivo), sequential RNA-IP, in vitro translation assay, immunolocalization","journal":"Biology of reproduction","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — reciprocal co-IP, sequential RIP, and in vitro translation rescue assay; single lab, multiple orthogonal methods","pmids":["30295753"],"is_preprint":false},{"year":2020,"finding":"BNC1 transcription factor directly binds to BNC1 binding elements in the Ybx2 promoter to activate Ybx2 transcription; demonstrated by chromatin immunoprecipitation on mouse testicular tissue and luciferase reporter assays; Bnc1 mutation or knockdown reduces YBX2 protein levels.","method":"Chromatin immunoprecipitation (ChIP), luciferase reporter assay, Bnc1 mutant mouse model, siRNA knockdown, Western blotting","journal":"Reproductive sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and reporter assay orthogonally confirm direct promoter binding; single lab","pmids":["33211273"],"is_preprint":false},{"year":2021,"finding":"YBX2 serves as a mammalian m5C RNA-binding protein; m5C-marked RNA enhances YBX2-dependent liquid-liquid phase separation (LLPS) in vivo and in vitro; crystal structure identifies W100 as the distinct m5C binding site critical for mediating YBX2 phase separation.","method":"Crystal structure determination, m5C RNA-binding assays, LLPS assays in vivo and in vitro, site-directed mutagenesis (W100)","journal":"Fundamental research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure plus mutagenesis plus functional LLPS assay; single lab but multiple orthogonal methods including structural validation","pmids":["38933916"],"is_preprint":false},{"year":2022,"finding":"YBX2 mRNA bearing m5C modification is recognized by ALYREF, which exports it from nucleus to cytoplasm, increasing YBX2 protein expression; elevated YBX2 protein inhibits adipogenesis.","method":"RNA bisulfite sequencing, m5C profiling, in vitro adipogenesis assays, ALYREF knockdown/overexpression, subcellular fractionation","journal":"Cellular and molecular life sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — m5C sequencing combined with functional assays and knockdown; single lab","pmids":["35962235"],"is_preprint":false},{"year":2023,"finding":"YBX2 expressed in endometrial cancer cells forms cytoplasmic granules via its mRNA-binding domain; its cold-shock domain recruits m6A reader YTHDF2 to these granules; YBX2 binding to HSPA6 mRNA reduces its stability, and YTHDF2 knockdown rescues HSPA6 mRNA levels, demonstrating synergistic mRNA destabilization by YBX2 and YTHDF2.","method":"Ectopic expression, transcriptomic analysis, RNA stability assays, co-immunoprecipitation/co-localization, YTHDF2 knockdown, Western blotting","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — co-IP and knockdown rescue with mRNA stability assay; single lab, cancer cell line context","pmids":["37030331"],"is_preprint":false},{"year":2023,"finding":"YBX2 is phosphorylated by AMPK at Thr115 and by Akt2 at Ser137 in brown adipocytes in response to β-adrenergic signaling; these phosphorylations reduce ubiquitination-mediated degradation and stabilize YBX2 protein. Stabilized YBX2 promotes glycolysis by directly binding to 5'-UTRs of glycolytic enzyme mRNAs to modulate their translation.","method":"Phosphorylation assays, site-directed mutagenesis, ubiquitination assays, RNA-binding assays (5'-UTR binding), metabolic assays in brown adipocytes","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mutagenesis of phosphorylation sites with ubiquitination and RNA-binding assays; single lab","pmids":["37860762"],"is_preprint":false},{"year":2006,"finding":"Cell-type-specific expression of dbpC/Contrin (YBX2) in germ cell tumor lines is regulated by N-Myc, which binds a functional E-box element at -272 to -253 relative to the transcription start site; deletion of the C-terminal region causes nuclear translocation of dbpC/Contrin, which is otherwise primarily cytoplasmic.","method":"Promoter deletion/reporter assays, in vivo footprint analysis, co-transfection with Myc expression plasmids, Western blotting, subcellular localization analysis","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo footprinting plus reporter assay; single lab, cell line context","pmids":["16624424"],"is_preprint":false},{"year":2022,"finding":"YBX2 localizes to the axoneme of multi-cilia in Xenopus laevis embryonic epithelium and interacts with RIBC2; knockdown of Ybx2 results in abnormal ciliary beating and reduced cilia-driven fluid flow; Ybx2 axonemal localization is reduced in Ribc2-depleted multi-cilia.","method":"Immunoprecipitation/mass spectrometry, antisense morpholino knockdown, fluorescent bead flow assay, immunostaining, Western blotting in Xenopus","journal":"Genes & genomics","confidence":"Medium","confidence_rationale":"Tier 2-3 / Weak — co-IP/MS identification followed by morpholino knockdown with functional readout; single lab, Xenopus model, non-canonical cellular context for YBX2","pmids":["36508087"],"is_preprint":false},{"year":2025,"finding":"In testicular germ cells, YBX2 forms a complex with STK33 as detected by proximity ligation assay; however, STK33 cannot phosphorylate YBX2 in vitro, and the interaction was not recapitulated in co-transfected cultured cells.","method":"Immunoprecipitation/mass spectrometry, proximity ligation assay, co-transfection, in vitro phosphorylation assay","journal":"Reproductive sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — proximity ligation detected in germ cells but interaction not confirmed in heterologous cells; phosphorylation result is negative; single lab","pmids":["39909973"],"is_preprint":false},{"year":2026,"finding":"YBX2 acts as an m5C reader for SCD1 mRNA: NSUN5-installed m5C on SCD1 mRNA is bound by YBX2, which prolongs SCD1 mRNA half-life and enhances its stability, thereby suppressing ferroptosis in renal tubular epithelial cells.","method":"Bisulfite sequencing, RNA immunoprecipitation, mRNA stability (half-life) assays, YBX2 binding assays, NSUN5 overexpression/knockdown, ferroptosis assays","journal":"Advanced science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RIP and mRNA stability assays with genetic perturbation; single lab, disease model context","pmids":["42011916"],"is_preprint":false}],"current_model":"YBX2 (MSY2/Contrin) is a germ cell-enriched Y-box protein that functions primarily as a global stabilizer and translational repressor of stored mRNAs: it binds mRNA through its cold-shock domain (and auxiliary C-terminal basic/aromatic islands) with limited sequence specificity to package mRNAs into translationally silent RNPs, but can also recognize a specific 7-8 nt Y-box recognition site (YRS) in 3'UTRs with MSY4 to repress specific transcripts (e.g., Prm1) in a position-dependent manner; CDK1-mediated phosphorylation of YBX2 during oocyte maturation triggers a switch from mRNA stabilization to mRNA degradation; in brown adipose tissue YBX2 is stabilized by AMPK/Akt2 phosphorylation to promote PGC1α mRNA stability and glycolytic gene translation; YBX2 also acts as an m5C RNA reader (via W100) that promotes mRNA stability and can undergo liquid-liquid phase separation, and interacts with PAIP1 to enable translational reactivation of stored spermatogenic mRNAs and with YTHDF2 to destabilize specific mRNAs; transcription of Ybx2 itself is driven by BNC1 binding to its promoter and by N-Myc in germ cell contexts."},"narrative":{"mechanistic_narrative":"YBX2 (MSY2/Contrin) is a germ cell-enriched Y-box protein that serves as a global stabilizer and translational repressor of stored mRNAs, packaging them into translationally silent cytoplasmic ribonucleoprotein particles during gametogenesis [PMID:9780336, PMID:10772793, PMID:15031116]. It binds mRNA through its cold-shock domain together with C-terminal basic/aromatic islands, with the intact CSD required for cytoplasmic localization and an additional C-terminal island needed for cytoskeletal/Triton-insoluble retention; intact mRNA bridges YBX2 to these cytoplasmic structures [PMID:12297523, PMID:12648488]. Binding occurs largely with limited sequence specificity, allowing multiple YBX2 molecules to coat a single transcript, but YBX2 with MSY4 can also recognize a defined 7-8 nt Y-box recognition site in 3'UTRs to repress specific transcripts such as Prm1 in a position-dependent manner [PMID:11564883, PMID:12297523, PMID:26773323]. RNA-binding activity is mechanistically required for its stabilizing function: knockout reduces postmeiotic and maternal mRNA pools, and wild-type but not RNA-binding-deficient YBX2 rescues mRNA stability in null oocytes [PMID:17035640, PMID:21613634]. Genetic deletion causes male and female infertility, with postmeiotic spermatogenic arrest and oocyte/follicle defects driven by mRNA destabilization rather than transcriptional failure [PMID:15824319, PMID:17035640]. YBX2 function is switched by phosphorylation: CDK1-mediated phosphorylation during oocyte maturation converts it from a stabilizer to a trigger of maternal mRNA degradation [PMID:18606161]. Beyond germ cells, YBX2 acts as an m5C RNA reader via W100 that promotes target mRNA stability and undergoes liquid-liquid phase separation [PMID:38933916, PMID:42011916], partners with PAIP1 to reactivate translation of masked spermatogenic mRNAs [PMID:30295753], and cooperates with the m6A reader YTHDF2 to destabilize specific transcripts [PMID:37030331]. In brown adipose tissue, AMPK/Akt2 phosphorylation stabilizes YBX2 to promote PGC1α mRNA stability and translation of glycolytic enzyme mRNAs [PMID:28970281, PMID:37860762]. Transcription of Ybx2 itself is driven by BNC1 and by N-Myc binding to its promoter [PMID:33211273, PMID:16624424].","teleology":[{"year":1998,"claim":"Establishing that YBX2 is a germ cell-specific Y-box protein with defined developmental expression set the stage for a gamete-specific RNA-handling function.","evidence":"Northern, immunoblot, and in situ analysis of isolated germ cell populations","pmids":["9780336"],"confidence":"High","gaps":["Molecular function not yet defined","No direct RNA target identified at this stage"]},{"year":2000,"claim":"Identifying that YBX2 forms a complex with MSY4 on non-polysomal mRNPs linked the protein to translationally repressed, stored mRNAs.","evidence":"EMSA, co-IP, polysome analysis, yeast three-hybrid","pmids":["10772793"],"confidence":"High","gaps":["Specific RNA sequence target not yet mapped","Mechanism of repression unresolved"]},{"year":1999,"claim":"Showing that an associated kinase phosphorylates YBX2 and that dephosphorylation reduces RNA binding introduced phosphorylation as a regulator of its mRNA-binding state.","evidence":"Co-IP, in vitro kinase assay, Northwestern, in vitro translation repression","pmids":["10076007"],"confidence":"High","gaps":["Identity of the kinase not established","In vivo relevance of phosphoregulation not yet shown"]},{"year":2001,"claim":"Defining the 7-8 nt Y-box recognition site in the Prm1 3'UTR, with in vitro mutagenesis and transgenic validation, established sequence-specific repression alongside general binding.","evidence":"EMSA, competition binding, yeast three-hybrid, transgenic mouse reporter","pmids":["11564883"],"confidence":"High","gaps":["Generality of YRS across the transcriptome unclear","Co-factor requirement not yet defined"]},{"year":2001,"claim":"Localizing YBX2 to the oocyte cytoplasm/cytoskeletal fraction and documenting maturation-coupled phosphorylation tied its activity to oocyte developmental transitions.","evidence":"Immunoblot, RT-PCR, MSY2-EGFP microinjection, confocal imaging, cytoskeletal fractionation","pmids":["11566752"],"confidence":"High","gaps":["Functional consequence of maturation phosphorylation not yet established","Kinase responsible unidentified"]},{"year":2002,"claim":"Demonstrating that recombinant YBX2 binds mRNA with limited sequence specificity and represses translation at physiological ratios established its capacity as a global mRNA-coating repressor.","evidence":"Gel shift, filter binding, in vitro translation/luciferase with recombinant protein","pmids":["12297523"],"confidence":"High","gaps":["In vivo target spectrum not addressed","Reconciliation of sequence-specific vs non-specific binding modes incomplete"]},{"year":2003,"claim":"Mapping the CSD requirement for cytoplasmic localization and the C-terminal island for insoluble retention, with RNase release of YBX2, established that mRNA binding underpins its cytoplasmic anchoring.","evidence":"Domain-mutant MSY2-EGFP microinjection, confocal imaging, Triton extraction, RNase A treatment, RNA EMSA","pmids":["12648488"],"confidence":"High","gaps":["Identity of cytoskeletal anchoring structures not defined here","Structural basis of CSD binding not resolved"]},{"year":2004,"claim":"RNAi knockdown reducing total mRNA and impairing protein synthesis provided the first in vivo functional evidence that YBX2 stabilizes maternal mRNAs.","evidence":"Transgenic Zp3-driven RNAi, immunoblot, microinjection, Ca2+ imaging, mRNA and protein synthesis assays","pmids":["15031116"],"confidence":"High","gaps":["Residual protein from partial knockdown","Direct vs indirect effect on individual targets not separated"]},{"year":2005,"claim":"Defining the YBX2-bound germ cell mRNA subset and linking Y-box promoters to cytoplasmic storage connected nuclear transcription to cytoplasmic mRNA masking.","evidence":"IP plus suppressive subtractive hybridization, ChIP, transgenic GFP reporter","pmids":["15665108"],"confidence":"High","gaps":["Mechanism coupling transcription to storage not biochemically defined","Direct vs indirect target distinction limited"]},{"year":2005,"claim":"Germline knockout producing male and female infertility with reduced postmeiotic mRNA established YBX2 as essential for gametogenesis.","evidence":"Gene targeting, histology, RT-PCR, apoptosis and fertility assays","pmids":["15824319"],"confidence":"High","gaps":["Causal chain from mRNA loss to arrest not yet dissected","Stage-specific requirements not separated"]},{"year":2006,"claim":"Showing that in null testes mRNAs shift from RNP storage to polysomes and decline established mRNA instability, not transcriptional defects, as the cause of arrest.","evidence":"Polysome/RNP fractionation, real-time RT-PCR, transcription and transport assays in knockout","pmids":["17035640"],"confidence":"High","gaps":["Degradation machinery engaged not identified","Selectivity among targets not fully mapped"]},{"year":2006,"claim":"Identifying N-Myc-driven transcription via an E-box and a C-terminal region controlling cytoplasmic retention added upstream regulation and a nuclear-exclusion determinant.","evidence":"Promoter deletion/reporter, in vivo footprinting, Myc co-transfection, localization analysis in germ cell tumor lines","pmids":["16624424"],"confidence":"Medium","gaps":["Cell line context may not reflect normal germ cells","Physiological role of nuclear translocation unclear"]},{"year":2008,"claim":"Demonstrating that CDK1 phosphorylation triggers maturation-associated maternal mRNA degradation defined a phospho-switch converting YBX2 from stabilizer to destabilizer.","evidence":"Cdc2a microinjection, roscovitine inhibition, phosphomutant/phosphomimetic MSY2, immunoblot, mRNA quantification","pmids":["18606161"],"confidence":"High","gaps":["Mechanism linking phosphorylation to degradation machinery unknown","Which targets are selected for degradation not defined"]},{"year":2009,"claim":"Discovering YBX2 association with a class of MIWI-independent small RNAs broadened its RNA-binding repertoire beyond mRNA.","evidence":"RNA-IP, small RNA-seq, fractionation, analysis in Miwi and Msy2 null mice","pmids":["19597149"],"confidence":"Medium","gaps":["Functional significance of MSY-RNA binding not established","Single lab"]},{"year":2011,"claim":"Rescue with wild-type but not RNA-binding-deficient YBX2 in null oocytes directly proved RNA-binding activity is required for mRNA stabilization.","evidence":"Knockout analysis, WT and mutant MSY2 microinjection, mRNA stability assays, spindle imaging, transcriptome profiling","pmids":["21613634"],"confidence":"High","gaps":["Stabilization mechanism (sequestration vs decay protection) not resolved","Link to spindle defect not mechanistically defined"]},{"year":2016,"claim":"Showing that 3'UTR binding-site position dictates repression and that targets are prematurely polysome-loaded in knockouts established position-dependent cooperative repression.","evidence":"Transgenic 3'UTR mutants, polysome analysis in knockout, reporter assays","pmids":["26773323"],"confidence":"High","gaps":["Identity of position-dependent co-factors not defined","Single lab"]},{"year":2016,"claim":"Identifying PADI6 as required to anchor the mRNA-YBX2 complex to cytoplasmic lattices placed YBX2 storage in a defined oocyte structure.","evidence":"Padi6 knockout, Triton fractionation, RNase A treatment, immunostaining","pmids":["27929740"],"confidence":"Medium","gaps":["Ternary complex inferred indirectly","Direct PADI6-YBX2 contact not shown"]},{"year":2017,"claim":"Extending YBX2 function to brown adipocytes, where it stabilizes PGC1α mRNA and drives adipogenesis, established a somatic mRNA-stability role.","evidence":"shRNA, overexpression, knockout mice, RIP-seq","pmids":["28970281"],"confidence":"High","gaps":["Mechanism of selective stabilization unclear","Direct vs indirect targets not fully separated"]},{"year":2019,"claim":"Demonstrating that PAIP1 partnership reactivates translation of YBX2-masked mRNAs defined how stored transcripts are switched on for spermiogenesis.","evidence":"Reciprocal co-IP, sequential RNA-IP, in vitro translation rescue, immunolocalization","pmids":["30295753"],"confidence":"High","gaps":["In vivo requirement of PAIP1 for reactivation not tested","Single lab"]},{"year":2021,"claim":"Crystal structure identifying W100 as the m5C-binding site and linking m5C RNA to phase separation defined YBX2 as an m5C reader driving LLPS.","evidence":"Crystal structure, m5C RNA-binding assays, in vivo/in vitro LLPS, W100 mutagenesis","pmids":["38933916"],"confidence":"High","gaps":["Physiological consequence of m5C-driven LLPS in vivo not established","Single lab"]},{"year":2022,"claim":"Showing ALYREF exports m5C-marked YBX2 mRNA to increase YBX2 protein, which inhibits adipogenesis, added a post-transcriptional layer to YBX2 regulation.","evidence":"Bisulfite/m5C sequencing, adipogenesis assays, ALYREF perturbation, fractionation","pmids":["35962235"],"confidence":"Medium","gaps":["Mechanism by which YBX2 inhibits adipogenesis not defined","Single lab"]},{"year":2022,"claim":"Detecting YBX2 at the multi-cilia axoneme interacting with RIBC2, with ciliary defects on knockdown, raised a non-canonical structural/ciliary role.","evidence":"IP/MS, morpholino knockdown, bead flow assay, immunostaining in Xenopus","pmids":["36508087"],"confidence":"Medium","gaps":["Non-canonical context for YBX2; mechanism unclear","Mammalian relevance not tested"]},{"year":2023,"claim":"Showing YBX2 recruits YTHDF2 to cytoplasmic granules and cooperatively destabilizes HSPA6 mRNA defined a co-reader destabilization mechanism in cancer cells.","evidence":"Ectopic expression, transcriptomics, RNA stability assays, co-IP/co-localization, YTHDF2 knockdown","pmids":["37030331"],"confidence":"Medium","gaps":["Cancer cell line context","Endogenous relevance not established"]},{"year":2023,"claim":"Identifying AMPK/Akt2 phosphorylation sites that block YBX2 ubiquitination and showing 5'-UTR binding to glycolytic mRNAs defined how β-adrenergic signaling stabilizes YBX2 to drive glycolysis.","evidence":"Phosphosite mutagenesis, ubiquitination assays, 5'-UTR RNA-binding, metabolic assays in brown adipocytes","pmids":["37860762"],"confidence":"Medium","gaps":["In vivo contribution of each phosphosite not separated","Single lab"]},{"year":2026,"claim":"Demonstrating YBX2 reads NSUN5-installed m5C on SCD1 mRNA to prolong its half-life and suppress ferroptosis extended the m5C-reader stabilizing function to a disease context.","evidence":"Bisulfite sequencing, RIP, mRNA half-life assays, NSUN5 perturbation, ferroptosis assays","pmids":["42011916"],"confidence":"Medium","gaps":["Generality of m5C-stabilization across targets unclear","Single lab, disease model"]},{"year":null,"claim":"How phosphorylation, m5C/m6A reader cooperation, and phase separation are integrated to switch individual transcripts between storage, stabilization, and degradation remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model of transcript-selective fate control","Degradation machinery downstream of CDK1 phosphorylation unidentified","Structural basis of cooperative position-dependent repression undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[1,3,5,6,13,16]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[2,5,14,17]},{"term_id":"GO:0140313","term_label":"molecular sequestering activity","supporting_discovery_ids":[7,10,13]},{"term_id":"GO:0003677","term_label":"DNA 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Involved in the regulation of the stability and/or translation of germ cell mRNAs. Binds to Y-box consensus promoter element. Binds to full-length mRNA with high affinity in a sequence-independent manner. Binds to short RNA sequences containing the consensus site 5'-UCCAUCA-3' with low affinity and limited sequence specificity. Its binding with maternal mRNAs is necessary for its cytoplasmic retention. May mark specific mRNAs (those transcribed from Y-box promoters) in the nucleus for cytoplasmic storage, thereby linking transcription and mRNA storage/translational delay (By similarity)","subcellular_location":"Cytoplasm; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9Y2T7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/YBX2","classification":"Not Classified","n_dependent_lines":3,"n_total_lines":1208,"dependency_fraction":0.0024834437086092716},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/YBX2","total_profiled":1310},"omim":[{"mim_id":"620424","title":"ZYGOTE ARREST 1-LIKE; ZAR1L","url":"https://www.omim.org/entry/620424"},{"mim_id":"611447","title":"Y BOX-BINDING PROTEIN 2; YBX2","url":"https://www.omim.org/entry/611447"},{"mim_id":"610224","title":"SPERMATOGENESIS- AND OOGENESIS-SPECIFIC BASIC HELIX-LOOP-HELIX PROTEIN 1; SOHLH1","url":"https://www.omim.org/entry/610224"},{"mim_id":"607520","title":"ZYGOTE ARREST 1; ZAR1","url":"https://www.omim.org/entry/607520"},{"mim_id":"601930","title":"BASONUCLIN 1; BNC1","url":"https://www.omim.org/entry/601930"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"testis","ntpm":493.0}],"url":"https://www.proteinatlas.org/search/YBX2"},"hgnc":{"alias_symbol":["MSY2","CSDA3","Contrin"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y2T7","domains":[{"cath_id":"2.40.50.140","chopping":"88-164","consensus_level":"high","plddt":92.8094,"start":88,"end":164}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2T7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2T7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2T7-F1-predicted_aligned_error_v6.png","plddt_mean":62.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=YBX2","jax_strain_url":"https://www.jax.org/strain/search?query=YBX2"},"sequence":{"accession":"Q9Y2T7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y2T7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y2T7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2T7"}},"corpus_meta":[{"pmid":"9780336","id":"PMC_9780336","title":"Mammalian 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\"method\": \"Northern blotting, immunoblotting, in situ analysis of isolated germ cell populations\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (Northern, Western, cell fractionation), replicated across subsequent studies\",\n      \"pmids\": [\"9780336\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"MSY2 (YBX2) forms a sequence-specific RNA-binding complex with MSY4 on non-polysomal mRNPs; the complex co-immunoprecipitates and is associated with translationally repressed mRNAs, consistent with a role in mRNA storage.\",\n      \"method\": \"Electrophoretic mobility shift assay (EMSA), immunoprecipitation, polysome analysis, yeast three-hybrid system\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — EMSA, co-IP, polysome fractionation in same study; replicated by subsequent work (PMID:11564883)\",\n      \"pmids\": [\"10772793\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"In male germ cells, MSY2 is associated on non-polysomal mRNAs with a co-immunoprecipitating kinase activity that phosphorylates MSY2 in vitro; dephosphorylation of MSY2 decreases its RNA-binding affinity, suggesting phosphorylation state regulates mRNA binding. MSY2-bound non-polysomal RNP proteins repress translation of exogenous mRNAs in vitro.\",\n      \"method\": \"Co-immunoprecipitation, in vitro kinase assay, Northwestern blotting, in vitro translation assay, reconstitution\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro kinase reconstitution, Northwestern, and translation repression assay in one study; single lab\",\n      \"pmids\": [\"10076007\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"MSY2 and MSY4 bind a specific 7-8 nucleotide sequence (Y-box recognition site, YRS: U(AC)C(A)CAU(C)CA) in the 3' UTR of the translationally repressed protamine 1 mRNA; single nucleotide mutations abolish binding in vitro, and disruption of the YRS in transgenic mice relieves Prm1-like translational repression in vivo.\",\n      \"method\": \"EMSA, competition binding, yeast three-hybrid system, transgenic mouse reporter assay\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — mutagenesis in vitro and in vivo validation in transgenic mice; multiple orthogonal methods\",\n      \"pmids\": [\"11564883\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"MSY2 protein is primarily cytoplasmic in mouse oocytes (~75% associated with cytoskeletal/Triton-insoluble preparations); it is phosphorylated during oocyte maturation and dephosphorylated following fertilization. MSY2 constitutes ~2% of total oocyte protein.\",\n      \"method\": \"Immunoblotting, reverse transcription-PCR, microinjection of MSY2-EGFP mRNA, confocal microscopy, cytoskeletal fractionation\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct localization by imaging and fractionation, phosphorylation by Western, replicated in multiple follow-up studies\",\n      \"pmids\": [\"11566752\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Bacterially expressed recombinant MSY2 binds mRNA with limited sequence specificity (multiple molecules bind one Prm1 mRNA) and represses translation in vitro at protein:mRNA ratios approximating those in oocytes.\",\n      \"method\": \"Gel shift assay, filter binding assay, in vitro translation/luciferase assay with recombinant protein\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with recombinant protein, multiple binding and translation assays, single lab\",\n      \"pmids\": [\"12297523\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"An intact cold-shock domain (CSD) with its two RNA-binding motifs is required for cytoplasmic localization of MSY2 in oocytes; an additional C-terminal basic/aromatic island is necessary for Triton-insoluble retention. RNase A treatment releases essentially all endogenous MSY2, demonstrating that intact mRNA is required for cytoplasmic retention.\",\n      \"method\": \"Microinjection of mutant MSY2-EGFP mRNAs, laser-scanning confocal microscopy, Triton extraction, RNase A treatment, RNA EMSA\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — domain mutagenesis coupled with live imaging, fractionation, and in vitro binding; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"12648488\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"RNAi-mediated reduction of MSY2 in growing oocytes (~60% knockdown) reduces total mRNA by ~20-25%, impairs protein synthesis, and prevents maturation-associated changes in protein synthesis, directly supporting MSY2's role in stabilizing maternal mRNAs in vivo.\",\n      \"method\": \"Transgenic RNAi (Zp3 promoter-driven hairpin dsRNA), immunoblotting, microinjection, Ca2+ imaging, total mRNA quantification, protein synthesis assay\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — transgenic knockdown with multiple functional readouts; replicated in subsequent knockout studies\",\n      \"pmids\": [\"15031116\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"MSY2 binds a specific subset of germ cell mRNAs enriched for stored/translationally delayed, male gamete-specific transcripts; chromatin precipitation shows most MSY2 target mRNAs are transcribed from promoters containing the Y-box DNA-binding motif; transgenic reporter experiments show Y-box promoters direct mRNAs into the MSY2-bound cytoplasmic fraction, linking nuclear transcription to cytoplasmic mRNA storage.\",\n      \"method\": \"Immunoprecipitation combined with suppressive subtractive hybridization, chromatin precipitation (ChIP), transgenic mouse GFP reporter assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal IP, ChIP, and in vivo transgenic validation; multiple orthogonal methods in one study\",\n      \"pmids\": [\"15665108\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Genetic deletion of Msy2 in mice causes male and female infertility: males exhibit post-meiotic spermatogenic arrest with multinucleated spermatids and no spermatozoa, accompanied by large reductions in postmeiotic mRNA levels; females show oocyte loss, anovulation, and follicle defects.\",\n      \"method\": \"Gene targeting/knockout, histology, RT-PCR, apoptosis assays, fertility testing\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — germline knockout with multiple defined phenotypic and molecular readouts; replicated and expanded in follow-up studies\",\n      \"pmids\": [\"15824319\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"In Msy2-null male mice, mRNAs are redistributed from RNP storage particles to polysomes and show markedly decreased abundance; transcription, mRNA processing, and intracellular transport are normal, indicating that increased mRNA instability (not transcriptional defects) causes spermatogenic arrest.\",\n      \"method\": \"Polysome/RNP fractionation, real-time RT-PCR, transcriptional assays, mRNA transport assays\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — polysome fractionation combined with multiple molecular assays in knockout mice; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"17035640\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"CDC2A (CDK1)-mediated phosphorylation of MSY2 triggers the maturation-associated degradation of maternal mRNAs during mouse oocyte maturation: CDK1 activation induces MSY2 phosphorylation and mRNA degradation; CDK1 inhibition blocks both; non-phosphorylatable dominant-negative MSY2 prevents mRNA degradation, while constitutively active MSY2 induces degradation in the absence of maturation.\",\n      \"method\": \"Microinjection of Cdc2a mRNA, CDK1 inhibition with roscovitine, expression of phosphomutant/phosphomimetic MSY2, immunoblotting, mRNA quantification\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — gain-of-function and dominant-negative mutagenesis with pharmacological inhibition; multiple orthogonal approaches in one study\",\n      \"pmids\": [\"18606161\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"MSY2 binds a class of small RNAs (~25-31 nt, termed MSY-RNAs) that are MIWI-independent, often initiate with 5' adenine, are expressed in germ and somatic cells, map within annotated genes and to piRNA clusters, and are present in nuclei (enriched in chromatin) and cytoplasm (in both RNPs and polysomes).\",\n      \"method\": \"RNA immunoprecipitation, small RNA sequencing, fractionation (chromatin, RNP, polysome), analysis in Miwi and Msy2 null mice\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RIP and fractionation in null mice; single lab, functional significance of MSY-RNA binding not fully characterized\",\n      \"pmids\": [\"19597149\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"In Msy2-null oocytes, total poly(A)-containing RNA is reduced by ~25%; injection of wild-type MSY2 into mutant oocytes rescues mRNA stability, but a RNA-binding-deficient mutant MSY2 does not, directly demonstrating that RNA-binding activity is required for MSY2-mediated mRNA stabilization. Loss of MSY2 also causes failure of transcription quiescence during oocyte growth and aberrant spindle formation.\",\n      \"method\": \"Knockout mouse analysis, microinjection of wild-type and mutant MSY2 mRNA, mRNA stability assays, spindle imaging, transcriptome profiling\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — RNA-binding mutant rescue experiment directly links binding activity to mRNA stability function; multiple orthogonal readouts\",\n      \"pmids\": [\"21613634\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"YBX2 binding sites positioned near the 3' ends of Prm1 and Smcp mRNA 3'UTRs are required for translational repression in round spermatids; moving the same binding sites to upstream positions produces negligible repression, demonstrating position-dependent cooperative interactions with co-factors. In Ybx2-knockout round spermatids, Prm1 and Smcp mRNAs are prematurely recruited to polysomes.\",\n      \"method\": \"Transgenic mice with 3'UTR mutations, polysome analysis of Ybx2-knockout mice, transgenic reporter assays\",\n      \"journal\": \"Molecular reproduction and development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo transgenic mutagenesis combined with polysome analysis in knockout; single lab but two orthogonal in vivo approaches\",\n      \"pmids\": [\"26773323\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"PADI6 is required for anchoring the mRNA-MSY2 complex to oocyte cytoplasmic lattices (CPLs): in Padi6-KO oocytes, the abundance of MSY2 in the Triton-insoluble fraction is markedly decreased; RNase A treatment of permeabilized oocytes releases both PADI6 and MSY2, indicating mRNA bridges the MSY2-CPL interaction.\",\n      \"method\": \"Padi6 knockout mouse analysis, Triton extraction/fractionation, RNase A treatment, immunostaining\",\n      \"journal\": \"Cell cycle\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic knockout with fractionation and enzymatic dissection; indirect evidence for PADI6-MSY2-mRNA ternary complex at CPLs\",\n      \"pmids\": [\"27929740\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Ybx2 knockdown in brown adipocytes blocks brown adipogenesis and destabilizes PGC1α mRNA; Ybx2 overexpression promotes brown adipose tissue (BAT) marker expression; RNA immunoprecipitation identifies a set of mRNA targets including Pgc1α that are destabilized upon Ybx2 depletion during cold-induced activation, establishing YBX2 as a regulator of mRNA stability in BAT.\",\n      \"method\": \"shRNA knockdown, overexpression, Ybx2-knockout mice, RNA-immunoprecipitation, RNA sequencing\",\n      \"journal\": \"Diabetes\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — knockout mouse combined with RIP-seq and gain/loss-of-function in cultured adipocytes; multiple orthogonal methods\",\n      \"pmids\": [\"28970281\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"YBX2 interacts with PAIP1 (a translation enhancer) in vitro and in vivo in mouse testes; PAIP1 co-localizes with YBX2 in round spermatids; sequential RNA immunoprecipitation identifies spermiogenic mRNAs indirectly bound by PAIP1 through YBX2; translation of YBX2-masked mRNAs is blocked by YBX2 alone but reinitiated when YBX2 is co-expressed with PAIP1 in vitro.\",\n      \"method\": \"Co-immunoprecipitation (in vitro and in vivo), sequential RNA-IP, in vitro translation assay, immunolocalization\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — reciprocal co-IP, sequential RIP, and in vitro translation rescue assay; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"30295753\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"BNC1 transcription factor directly binds to BNC1 binding elements in the Ybx2 promoter to activate Ybx2 transcription; demonstrated by chromatin immunoprecipitation on mouse testicular tissue and luciferase reporter assays; Bnc1 mutation or knockdown reduces YBX2 protein levels.\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP), luciferase reporter assay, Bnc1 mutant mouse model, siRNA knockdown, Western blotting\",\n      \"journal\": \"Reproductive sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and reporter assay orthogonally confirm direct promoter binding; single lab\",\n      \"pmids\": [\"33211273\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"YBX2 serves as a mammalian m5C RNA-binding protein; m5C-marked RNA enhances YBX2-dependent liquid-liquid phase separation (LLPS) in vivo and in vitro; crystal structure identifies W100 as the distinct m5C binding site critical for mediating YBX2 phase separation.\",\n      \"method\": \"Crystal structure determination, m5C RNA-binding assays, LLPS assays in vivo and in vitro, site-directed mutagenesis (W100)\",\n      \"journal\": \"Fundamental research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure plus mutagenesis plus functional LLPS assay; single lab but multiple orthogonal methods including structural validation\",\n      \"pmids\": [\"38933916\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"YBX2 mRNA bearing m5C modification is recognized by ALYREF, which exports it from nucleus to cytoplasm, increasing YBX2 protein expression; elevated YBX2 protein inhibits adipogenesis.\",\n      \"method\": \"RNA bisulfite sequencing, m5C profiling, in vitro adipogenesis assays, ALYREF knockdown/overexpression, subcellular fractionation\",\n      \"journal\": \"Cellular and molecular life sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — m5C sequencing combined with functional assays and knockdown; single lab\",\n      \"pmids\": [\"35962235\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"YBX2 expressed in endometrial cancer cells forms cytoplasmic granules via its mRNA-binding domain; its cold-shock domain recruits m6A reader YTHDF2 to these granules; YBX2 binding to HSPA6 mRNA reduces its stability, and YTHDF2 knockdown rescues HSPA6 mRNA levels, demonstrating synergistic mRNA destabilization by YBX2 and YTHDF2.\",\n      \"method\": \"Ectopic expression, transcriptomic analysis, RNA stability assays, co-immunoprecipitation/co-localization, YTHDF2 knockdown, Western blotting\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — co-IP and knockdown rescue with mRNA stability assay; single lab, cancer cell line context\",\n      \"pmids\": [\"37030331\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"YBX2 is phosphorylated by AMPK at Thr115 and by Akt2 at Ser137 in brown adipocytes in response to β-adrenergic signaling; these phosphorylations reduce ubiquitination-mediated degradation and stabilize YBX2 protein. Stabilized YBX2 promotes glycolysis by directly binding to 5'-UTRs of glycolytic enzyme mRNAs to modulate their translation.\",\n      \"method\": \"Phosphorylation assays, site-directed mutagenesis, ubiquitination assays, RNA-binding assays (5'-UTR binding), metabolic assays in brown adipocytes\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mutagenesis of phosphorylation sites with ubiquitination and RNA-binding assays; single lab\",\n      \"pmids\": [\"37860762\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Cell-type-specific expression of dbpC/Contrin (YBX2) in germ cell tumor lines is regulated by N-Myc, which binds a functional E-box element at -272 to -253 relative to the transcription start site; deletion of the C-terminal region causes nuclear translocation of dbpC/Contrin, which is otherwise primarily cytoplasmic.\",\n      \"method\": \"Promoter deletion/reporter assays, in vivo footprint analysis, co-transfection with Myc expression plasmids, Western blotting, subcellular localization analysis\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo footprinting plus reporter assay; single lab, cell line context\",\n      \"pmids\": [\"16624424\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"YBX2 localizes to the axoneme of multi-cilia in Xenopus laevis embryonic epithelium and interacts with RIBC2; knockdown of Ybx2 results in abnormal ciliary beating and reduced cilia-driven fluid flow; Ybx2 axonemal localization is reduced in Ribc2-depleted multi-cilia.\",\n      \"method\": \"Immunoprecipitation/mass spectrometry, antisense morpholino knockdown, fluorescent bead flow assay, immunostaining, Western blotting in Xenopus\",\n      \"journal\": \"Genes & genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Weak — co-IP/MS identification followed by morpholino knockdown with functional readout; single lab, Xenopus model, non-canonical cellular context for YBX2\",\n      \"pmids\": [\"36508087\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In testicular germ cells, YBX2 forms a complex with STK33 as detected by proximity ligation assay; however, STK33 cannot phosphorylate YBX2 in vitro, and the interaction was not recapitulated in co-transfected cultured cells.\",\n      \"method\": \"Immunoprecipitation/mass spectrometry, proximity ligation assay, co-transfection, in vitro phosphorylation assay\",\n      \"journal\": \"Reproductive sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — proximity ligation detected in germ cells but interaction not confirmed in heterologous cells; phosphorylation result is negative; single lab\",\n      \"pmids\": [\"39909973\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"YBX2 acts as an m5C reader for SCD1 mRNA: NSUN5-installed m5C on SCD1 mRNA is bound by YBX2, which prolongs SCD1 mRNA half-life and enhances its stability, thereby suppressing ferroptosis in renal tubular epithelial cells.\",\n      \"method\": \"Bisulfite sequencing, RNA immunoprecipitation, mRNA stability (half-life) assays, YBX2 binding assays, NSUN5 overexpression/knockdown, ferroptosis assays\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RIP and mRNA stability assays with genetic perturbation; single lab, disease model context\",\n      \"pmids\": [\"42011916\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"YBX2 (MSY2/Contrin) is a germ cell-enriched Y-box protein that functions primarily as a global stabilizer and translational repressor of stored mRNAs: it binds mRNA through its cold-shock domain (and auxiliary C-terminal basic/aromatic islands) with limited sequence specificity to package mRNAs into translationally silent RNPs, but can also recognize a specific 7-8 nt Y-box recognition site (YRS) in 3'UTRs with MSY4 to repress specific transcripts (e.g., Prm1) in a position-dependent manner; CDK1-mediated phosphorylation of YBX2 during oocyte maturation triggers a switch from mRNA stabilization to mRNA degradation; in brown adipose tissue YBX2 is stabilized by AMPK/Akt2 phosphorylation to promote PGC1α mRNA stability and glycolytic gene translation; YBX2 also acts as an m5C RNA reader (via W100) that promotes mRNA stability and can undergo liquid-liquid phase separation, and interacts with PAIP1 to enable translational reactivation of stored spermatogenic mRNAs and with YTHDF2 to destabilize specific mRNAs; transcription of Ybx2 itself is driven by BNC1 binding to its promoter and by N-Myc in germ cell contexts.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"YBX2 (MSY2/Contrin) is a germ cell-enriched Y-box protein that serves as a global stabilizer and translational repressor of stored mRNAs, packaging them into translationally silent cytoplasmic ribonucleoprotein particles during gametogenesis [#0, #1, #7]. It binds mRNA through its cold-shock domain together with C-terminal basic/aromatic islands, with the intact CSD required for cytoplasmic localization and an additional C-terminal island needed for cytoskeletal/Triton-insoluble retention; intact mRNA bridges YBX2 to these cytoplasmic structures [#5, #6]. Binding occurs largely with limited sequence specificity, allowing multiple YBX2 molecules to coat a single transcript, but YBX2 with MSY4 can also recognize a defined 7-8 nt Y-box recognition site in 3'UTRs to repress specific transcripts such as Prm1 in a position-dependent manner [#3, #5, #14]. RNA-binding activity is mechanistically required for its stabilizing function: knockout reduces postmeiotic and maternal mRNA pools, and wild-type but not RNA-binding-deficient YBX2 rescues mRNA stability in null oocytes [#10, #13]. Genetic deletion causes male and female infertility, with postmeiotic spermatogenic arrest and oocyte/follicle defects driven by mRNA destabilization rather than transcriptional failure [#9, #10]. YBX2 function is switched by phosphorylation: CDK1-mediated phosphorylation during oocyte maturation converts it from a stabilizer to a trigger of maternal mRNA degradation [#11]. Beyond germ cells, YBX2 acts as an m5C RNA reader via W100 that promotes target mRNA stability and undergoes liquid-liquid phase separation [#19, #26], partners with PAIP1 to reactivate translation of masked spermatogenic mRNAs [#17], and cooperates with the m6A reader YTHDF2 to destabilize specific transcripts [#21]. In brown adipose tissue, AMPK/Akt2 phosphorylation stabilizes YBX2 to promote PGC1\\u03b1 mRNA stability and translation of glycolytic enzyme mRNAs [#16, #22]. Transcription of Ybx2 itself is driven by BNC1 and by N-Myc binding to its promoter [#18, #23].\",\n  \"teleology\": [\n    {\n      \"year\": 1998,\n      \"claim\": \"Establishing that YBX2 is a germ cell-specific Y-box protein with defined developmental expression set the stage for a gamete-specific RNA-handling function.\",\n      \"evidence\": \"Northern, immunoblot, and in situ analysis of isolated germ cell populations\",\n      \"pmids\": [\"9780336\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular function not yet defined\", \"No direct RNA target identified at this stage\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Identifying that YBX2 forms a complex with MSY4 on non-polysomal mRNPs linked the protein to translationally repressed, stored mRNAs.\",\n      \"evidence\": \"EMSA, co-IP, polysome analysis, yeast three-hybrid\",\n      \"pmids\": [\"10772793\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific RNA sequence target not yet mapped\", \"Mechanism of repression unresolved\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Showing that an associated kinase phosphorylates YBX2 and that dephosphorylation reduces RNA binding introduced phosphorylation as a regulator of its mRNA-binding state.\",\n      \"evidence\": \"Co-IP, in vitro kinase assay, Northwestern, in vitro translation repression\",\n      \"pmids\": [\"10076007\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the kinase not established\", \"In vivo relevance of phosphoregulation not yet shown\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Defining the 7-8 nt Y-box recognition site in the Prm1 3'UTR, with in vitro mutagenesis and transgenic validation, established sequence-specific repression alongside general binding.\",\n      \"evidence\": \"EMSA, competition binding, yeast three-hybrid, transgenic mouse reporter\",\n      \"pmids\": [\"11564883\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Generality of YRS across the transcriptome unclear\", \"Co-factor requirement not yet defined\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Localizing YBX2 to the oocyte cytoplasm/cytoskeletal fraction and documenting maturation-coupled phosphorylation tied its activity to oocyte developmental transitions.\",\n      \"evidence\": \"Immunoblot, RT-PCR, MSY2-EGFP microinjection, confocal imaging, cytoskeletal fractionation\",\n      \"pmids\": [\"11566752\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of maturation phosphorylation not yet established\", \"Kinase responsible unidentified\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Demonstrating that recombinant YBX2 binds mRNA with limited sequence specificity and represses translation at physiological ratios established its capacity as a global mRNA-coating repressor.\",\n      \"evidence\": \"Gel shift, filter binding, in vitro translation/luciferase with recombinant protein\",\n      \"pmids\": [\"12297523\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo target spectrum not addressed\", \"Reconciliation of sequence-specific vs non-specific binding modes incomplete\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Mapping the CSD requirement for cytoplasmic localization and the C-terminal island for insoluble retention, with RNase release of YBX2, established that mRNA binding underpins its cytoplasmic anchoring.\",\n      \"evidence\": \"Domain-mutant MSY2-EGFP microinjection, confocal imaging, Triton extraction, RNase A treatment, RNA EMSA\",\n      \"pmids\": [\"12648488\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of cytoskeletal anchoring structures not defined here\", \"Structural basis of CSD binding not resolved\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"RNAi knockdown reducing total mRNA and impairing protein synthesis provided the first in vivo functional evidence that YBX2 stabilizes maternal mRNAs.\",\n      \"evidence\": \"Transgenic Zp3-driven RNAi, immunoblot, microinjection, Ca2+ imaging, mRNA and protein synthesis assays\",\n      \"pmids\": [\"15031116\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Residual protein from partial knockdown\", \"Direct vs indirect effect on individual targets not separated\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Defining the YBX2-bound germ cell mRNA subset and linking Y-box promoters to cytoplasmic storage connected nuclear transcription to cytoplasmic mRNA masking.\",\n      \"evidence\": \"IP plus suppressive subtractive hybridization, ChIP, transgenic GFP reporter\",\n      \"pmids\": [\"15665108\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism coupling transcription to storage not biochemically defined\", \"Direct vs indirect target distinction limited\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Germline knockout producing male and female infertility with reduced postmeiotic mRNA established YBX2 as essential for gametogenesis.\",\n      \"evidence\": \"Gene targeting, histology, RT-PCR, apoptosis and fertility assays\",\n      \"pmids\": [\"15824319\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Causal chain from mRNA loss to arrest not yet dissected\", \"Stage-specific requirements not separated\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Showing that in null testes mRNAs shift from RNP storage to polysomes and decline established mRNA instability, not transcriptional defects, as the cause of arrest.\",\n      \"evidence\": \"Polysome/RNP fractionation, real-time RT-PCR, transcription and transport assays in knockout\",\n      \"pmids\": [\"17035640\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Degradation machinery engaged not identified\", \"Selectivity among targets not fully mapped\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Identifying N-Myc-driven transcription via an E-box and a C-terminal region controlling cytoplasmic retention added upstream regulation and a nuclear-exclusion determinant.\",\n      \"evidence\": \"Promoter deletion/reporter, in vivo footprinting, Myc co-transfection, localization analysis in germ cell tumor lines\",\n      \"pmids\": [\"16624424\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cell line context may not reflect normal germ cells\", \"Physiological role of nuclear translocation unclear\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Demonstrating that CDK1 phosphorylation triggers maturation-associated maternal mRNA degradation defined a phospho-switch converting YBX2 from stabilizer to destabilizer.\",\n      \"evidence\": \"Cdc2a microinjection, roscovitine inhibition, phosphomutant/phosphomimetic MSY2, immunoblot, mRNA quantification\",\n      \"pmids\": [\"18606161\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism linking phosphorylation to degradation machinery unknown\", \"Which targets are selected for degradation not defined\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Discovering YBX2 association with a class of MIWI-independent small RNAs broadened its RNA-binding repertoire beyond mRNA.\",\n      \"evidence\": \"RNA-IP, small RNA-seq, fractionation, analysis in Miwi and Msy2 null mice\",\n      \"pmids\": [\"19597149\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional significance of MSY-RNA binding not established\", \"Single lab\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Rescue with wild-type but not RNA-binding-deficient YBX2 in null oocytes directly proved RNA-binding activity is required for mRNA stabilization.\",\n      \"evidence\": \"Knockout analysis, WT and mutant MSY2 microinjection, mRNA stability assays, spindle imaging, transcriptome profiling\",\n      \"pmids\": [\"21613634\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stabilization mechanism (sequestration vs decay protection) not resolved\", \"Link to spindle defect not mechanistically defined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Showing that 3'UTR binding-site position dictates repression and that targets are prematurely polysome-loaded in knockouts established position-dependent cooperative repression.\",\n      \"evidence\": \"Transgenic 3'UTR mutants, polysome analysis in knockout, reporter assays\",\n      \"pmids\": [\"26773323\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of position-dependent co-factors not defined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Identifying PADI6 as required to anchor the mRNA-YBX2 complex to cytoplasmic lattices placed YBX2 storage in a defined oocyte structure.\",\n      \"evidence\": \"Padi6 knockout, Triton fractionation, RNase A treatment, immunostaining\",\n      \"pmids\": [\"27929740\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ternary complex inferred indirectly\", \"Direct PADI6-YBX2 contact not shown\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Extending YBX2 function to brown adipocytes, where it stabilizes PGC1\\u03b1 mRNA and drives adipogenesis, established a somatic mRNA-stability role.\",\n      \"evidence\": \"shRNA, overexpression, knockout mice, RIP-seq\",\n      \"pmids\": [\"28970281\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of selective stabilization unclear\", \"Direct vs indirect targets not fully separated\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrating that PAIP1 partnership reactivates translation of YBX2-masked mRNAs defined how stored transcripts are switched on for spermiogenesis.\",\n      \"evidence\": \"Reciprocal co-IP, sequential RNA-IP, in vitro translation rescue, immunolocalization\",\n      \"pmids\": [\"30295753\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo requirement of PAIP1 for reactivation not tested\", \"Single lab\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Crystal structure identifying W100 as the m5C-binding site and linking m5C RNA to phase separation defined YBX2 as an m5C reader driving LLPS.\",\n      \"evidence\": \"Crystal structure, m5C RNA-binding assays, in vivo/in vitro LLPS, W100 mutagenesis\",\n      \"pmids\": [\"38933916\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological consequence of m5C-driven LLPS in vivo not established\", \"Single lab\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Showing ALYREF exports m5C-marked YBX2 mRNA to increase YBX2 protein, which inhibits adipogenesis, added a post-transcriptional layer to YBX2 regulation.\",\n      \"evidence\": \"Bisulfite/m5C sequencing, adipogenesis assays, ALYREF perturbation, fractionation\",\n      \"pmids\": [\"35962235\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which YBX2 inhibits adipogenesis not defined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Detecting YBX2 at the multi-cilia axoneme interacting with RIBC2, with ciliary defects on knockdown, raised a non-canonical structural/ciliary role.\",\n      \"evidence\": \"IP/MS, morpholino knockdown, bead flow assay, immunostaining in Xenopus\",\n      \"pmids\": [\"36508087\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Non-canonical context for YBX2; mechanism unclear\", \"Mammalian relevance not tested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Showing YBX2 recruits YTHDF2 to cytoplasmic granules and cooperatively destabilizes HSPA6 mRNA defined a co-reader destabilization mechanism in cancer cells.\",\n      \"evidence\": \"Ectopic expression, transcriptomics, RNA stability assays, co-IP/co-localization, YTHDF2 knockdown\",\n      \"pmids\": [\"37030331\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cancer cell line context\", \"Endogenous relevance not established\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identifying AMPK/Akt2 phosphorylation sites that block YBX2 ubiquitination and showing 5'-UTR binding to glycolytic mRNAs defined how \\u03b2-adrenergic signaling stabilizes YBX2 to drive glycolysis.\",\n      \"evidence\": \"Phosphosite mutagenesis, ubiquitination assays, 5'-UTR RNA-binding, metabolic assays in brown adipocytes\",\n      \"pmids\": [\"37860762\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo contribution of each phosphosite not separated\", \"Single lab\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Demonstrating YBX2 reads NSUN5-installed m5C on SCD1 mRNA to prolong its half-life and suppress ferroptosis extended the m5C-reader stabilizing function to a disease context.\",\n      \"evidence\": \"Bisulfite sequencing, RIP, mRNA half-life assays, NSUN5 perturbation, ferroptosis assays\",\n      \"pmids\": [\"42011916\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Generality of m5C-stabilization across targets unclear\", \"Single lab, disease model\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How phosphorylation, m5C/m6A reader cooperation, and phase separation are integrated to switch individual transcripts between storage, stabilization, and degradation remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model of transcript-selective fate control\", \"Degradation machinery downstream of CDK1 phosphorylation unidentified\", \"Structural basis of cooperative position-dependent repression undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [1, 3, 5, 6, 13, 16]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [2, 5, 14, 17]},\n      {\"term_id\": \"GO:0140313\", \"supporting_discovery_ids\": [7, 10, 13]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [4, 6, 10]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [4, 6, 15]},\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [24]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [1, 10, 13, 16]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [9, 14, 17]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [2, 5, 14, 17]}\n    ],\n    \"complexes\": [\"YBX2-MSY4 mRNP\", \"cytoplasmic lattice mRNP (with PADI6)\"],\n    \"partners\": [\"MSY4\", \"PAIP1\", \"YTHDF2\", \"PADI6\", \"ALYREF\", \"RIBC2\", \"BNC1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":9,"faith_pct":88.88888888888889}}