{"gene":"KNL1","run_date":"2026-06-10T02:59:49","timeline":{"discoveries":[{"year":2003,"finding":"KNL-1 is downstream of CeCENP-A and CeCENP-C in a linear kinetochore assembly hierarchy in C. elegans. KNL-1 forms a near-stoichiometric complex with CeNDC-80 and HIM-10 (Ndc80/Nuf2 homologs) and is required to target multiple outer kinetochore components including CeNDC-80 and HIM-10, thereby directing assembly of the microtubule-binding interface.","method":"RNA interference-based genomics, co-immunoprecipitation, epistasis analysis in C. elegans embryos","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP and genetic epistasis with multiple RNAi knockdowns, foundational study replicated by subsequent work","pmids":["14522947"],"is_preprint":false},{"year":2007,"finding":"Human KNL1 (Blinkin/AF15q14) directly interacts via its amino and middle domains with the TPR domains of BubR1 and Bub1, recruiting them to kinetochores. The C-terminal domain of KNL1 associates with the hMis12 complex (c20orf172/hMis13 and DC8/hMis14 subunits). KNL1 RNAi causes spindle checkpoint failure and chromosome misalignment.","method":"Co-immunoprecipitation, domain-mapping pulldowns, RNAi knockdown with live-cell imaging","journal":"Developmental cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP with domain mapping, confirmed by RNAi phenotype, replicated in multiple subsequent studies","pmids":["17981135"],"is_preprint":false},{"year":2007,"finding":"Vertebrate KNL1 is required to localize a subset of outer kinetochore proteins. Unlike in C. elegans, vertebrate KNL1 depletion does not abolish Ndc80 complex kinetochore localization; instead KNL1 and CENP-K coordinately direct Ndc80 complex localization, as simultaneous depletion of both abolishes all kinetochore assembly downstream of centromeric chromatin.","method":"RNAi knockdown (single and double), immunofluorescence, chicken DT40 conditional knockout","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis with double knockdown, multiple orthogonal approaches, replicated across cell types","pmids":["18045986"],"is_preprint":false},{"year":2010,"finding":"A conserved RVSF motif in KNL1 directly interacts with and recruits protein phosphatase 1 (PP1) to the outer kinetochore. PP1 recruitment by KNL1 is required to dephosphorylate Aurora B substrates at kinetochores and stabilize microtubule attachments. Aurora B phosphorylates KNL1 at this motif to disrupt the KNL1-PP1 interaction, creating a positive feedback mechanism by which Aurora B both targets substrates and prevents opposing phosphatase localization.","method":"Direct binding assay (GST pulldown), phospho-specific antibodies, site-directed mutagenesis, immunofluorescence, kinetochore phosphorylation assays","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vitro binding with mutagenesis, phosphorylation assays, multiple orthogonal methods, widely replicated","pmids":["20231380"],"is_preprint":false},{"year":2011,"finding":"Binding of PP1/Glc7 to the conserved RVSF motif of Spc105 (KNL1/Blinkin) in budding yeast is essential for viability by silencing the spindle assembly checkpoint. The amount of PP1 targeted to kinetochores must be finely tuned — neither zero nor one extra copy is tolerated. Persistent PP1-Spc105 interaction without microtubules is insufficient to silence the SAC, indicating dynamic regulation is required.","method":"Rapid gene replacement in budding yeast, genetic analysis, quantitative immunofluorescence","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 2 / Strong — precise gene replacement with multiple alleles, quantitative analysis, functionally validates PP1 binding motif","pmids":["21640906"],"is_preprint":false},{"year":2012,"finding":"MPS1/Mph1 kinase phosphorylates MELT repeat sequences in KNL1/Spc7 (the fission yeast homolog), promoting binding of the Bub1-Bub3 complex. This phosphorylation is required for kinetochore-based SAC activation (Mad1-Mad2-Mad3 localization) and chromosome alignment. Non-phosphorylatable spc7-12A abolishes Bub1-Bub3 kinetochore targeting; phospho-mimetic spc7-12E forces constitutive localization even without Mph1.","method":"In vitro kinase assay, phospho-mimetic/non-phosphorylatable mutants, co-immunoprecipitation, live-cell imaging in fission yeast","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vitro kinase assay with mutagenesis, genetic rescue experiments, replicated independently","pmids":["22660415"],"is_preprint":false},{"year":2012,"finding":"Phosphorylation of conserved MELT motifs in Spc7/KNL1 by Mph1 (Mps1) recruits Bub1 and Bub3 to the kinetochore, which is required to maintain the spindle assembly checkpoint signal. PP1 binding to Spc7 is necessary to stabilize microtubule-kinetochore attachments and silence the SAC.","method":"Phospho-specific antibodies, mutagenesis, co-immunoprecipitation, mass spectrometry, genetic analysis in fission yeast","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods including MS and mutagenesis, independently replicated","pmids":["22521786"],"is_preprint":false},{"year":2012,"finding":"KNL-1 microtubule-binding and bundling activity resides in its extreme N-terminus. Selective perturbation of KNL-1 microtubule binding in C. elegans shows this activity is dispensable for load-bearing attachment and checkpoint activation but contributes independently to checkpoint silencing. Perturbation of both microtubule binding and PP1 docking additively affects checkpoint silencing, indicating these two N-terminal activities make independent contributions.","method":"Domain mutagenesis, in vitro microtubule-binding assays, C. elegans gene replacement, checkpoint reporter assays","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — reconstitution of microtubule binding, mutagenesis, genetic rescue with multiple alleles","pmids":["22331849"],"is_preprint":false},{"year":2012,"finding":"Crystal structure of Bub1 TPR domain in complex with KNL1 KI motif was determined. The interaction develops along the convex surface of the TPR assembly. Point mutations on this surface impaired Bub1/BubR1 interaction with Knl1 in vitro and in vivo. However, a 62-residue segment C-terminal to the TPRs including a Bub3-binding domain was necessary and sufficient for kinetochore recruitment of Bub1, not the TPR-KI interaction alone.","method":"X-ray crystallography, site-directed mutagenesis, co-immunoprecipitation, immunofluorescence","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with mutagenesis validation in vitro and in vivo","pmids":["22331848"],"is_preprint":false},{"year":2013,"finding":"KNL1 contains an extensive array of short linear sequence modules encompassing TxxΩ and MELT motifs that can independently localize BUB1. The number of BUB recruitment modules correlates with kinetochore BUB1 levels and efficiency of chromosome biorientation. A minimal array of generic BUB recruitment modules in KNL1 suffices for accurate chromosome segregation.","method":"KNL1 domain engineering, quantitative immunofluorescence, chromosome alignment assays, SAC functional assays","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — systematic domain engineering with multiple engineered variants, quantitative functional readouts","pmids":["24344183"],"is_preprint":false},{"year":2013,"finding":"KNL1 contains multiple binding sites for Bub proteins, with Mps1-phosphorylated MELT repeats constituting individual docking sites for direct binding of Bub3. A minimum of four active MELT repeats supports chromosome congression and SAC function. PP1 binding to KNL1 during prometaphase reduces Bub protein levels at kinetochores to approximately the level recruited by four active MELT repeats.","method":"MELT repeat deletion analysis, phospho-mimetic mutants, immunofluorescence, SAC assays","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — systematic deletion series with quantitative functional readouts, multiple orthogonal assays","pmids":["24363448"],"is_preprint":false},{"year":2013,"finding":"KI motifs in KNL1 cooperate with neighboring MELT motifs to assemble comprehensive SAC complexes. KI motifs enhance MELT function by providing a more robust mechanism for SAC signaling. A minimal Knl1 fragment (residues 1-250) containing KI and one MELT motif can restore SAC and chromosome alignment when targeted to kinetochores in cells depleted of endogenous Knl1.","method":"Domain truncation/rescue experiments, co-immunoprecipitation, immunofluorescence, SAC functional assays","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 2 / Strong — systematic domain dissection with functional rescue, multiple orthogonal methods","pmids":["24361068"],"is_preprint":false},{"year":2013,"finding":"KNL1 N-terminus is essential for Aurora B kinase activity at kinetochores, likely through promoting Bub1 kinase activity which in turn targets Aurora B. Ectopic targeting of Aurora B to kinetochores does not fully rescue Aurora B activity in KNL1-depleted cells, suggesting KNL1 influences Aurora B through an additional pathway beyond Bub1 recruitment.","method":"RNAi knockdown, phospho-specific antibody staining, ectopic Aurora B targeting constructs, kinetochore-microtubule attachment assays","journal":"The Journal of cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO with defined phosphorylation readouts, single lab, incomplete rescue experiment leaves pathway partially unclear","pmids":["24344188"],"is_preprint":false},{"year":2014,"finding":"BubR1-associated PP2A-B56 is the key phosphatase that removes Mps1-mediated phosphorylations on Knl1 MELT motifs required for Bub1/BubR1 recruitment in mammalian cells, both in vivo and in vitro. This creates a negative feedback loop: Mps1-dependent recruitment of BubR1 brings the phosphatase (PP2A-B56) that opposes Mps1, thereby promoting SAC silencing.","method":"In vitro dephosphorylation assays, co-immunoprecipitation, immunofluorescence, phospho-specific antibodies","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vitro and in vivo demonstration with multiple orthogonal methods","pmids":["25246613"],"is_preprint":false},{"year":2015,"finding":"Human KNL1 MELT-containing repeats contain a vertebrate-specific SHT motif C-terminal to the MELT sequence. MPS1 phosphorylates SHT motifs in a manner requiring prior MELT phosphorylation (sequential multisite regulation). Phospho-SHT (SHpT) synergizes with phospho-MELT (MELpT) in BUB3/BUB1 binding in vitro and in cells. BUB3 mutated in a predicted SHpT-binding surface cannot localize to kinetochores.","method":"Systematic phospho-mutant screening, in vitro binding assays, BUB3 mutagenesis, immunofluorescence","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vitro reconstitution with mutagenesis combined with cell-based validation, mechanistic detail","pmids":["25661489"],"is_preprint":false},{"year":2015,"finding":"The RZZ complex localizes to the N-terminus of KNL1, downstream of Bub1, to mediate robust Mad1/Mad2 kinetochore localization. The RZZ complex is the primary mediator for Mad1/Mad2 kinetochore localization in human cells, with a KNL1/Bub1-independent mechanism also existing for RZZ recruitment.","method":"RNAi knockdown, domain targeting experiments, immunofluorescence, FRAP","journal":"Open biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple knockdown conditions, domain targeting, single lab","pmids":["26581576"],"is_preprint":false},{"year":2015,"finding":"The KNL1-Bub3-Bub1 (KBB) pathway is required during normal mitotic progression when kinetochores are misaligned but is nonessential for SAC activation when kinetochores are fully unattached from microtubules. The RZZ complex provides a separate, KBB-independent pathway to recruit Mad1:Mad2 to unattached kinetochores.","method":"siRNA knockdown, genome editing, immunofluorescence, live-cell imaging in non-transformed diploid human cells","journal":"Developmental cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic dissection with multiple complementary knockdown experiments, non-transformed cell model, clear epistasis","pmids":["26651294"],"is_preprint":false},{"year":2016,"finding":"Multisite binding of Bub3 to the Spc7/KNL1 MELT array is required for Mph1(Mps1)-dependent interaction of Bub1 with Mad1-Mad2 in fission yeast, thus toggling the spindle checkpoint switch. The Spc7 MELT array licenses Bub1-Mad1-Mad2 interaction.","method":"Genetic epistasis, co-immunoprecipitation, phospho-mutant analysis, fission yeast genetics","journal":"Current biology : CB","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with phospho-mutants in yeast, single lab","pmids":["27618268"],"is_preprint":false},{"year":2018,"finding":"X-ray crystallography, NMR spectroscopy, and biochemical co-sedimentation assays demonstrate that PP1 and microtubules bind KNL1 via overlapping binding sites, making their interactions mutually exclusive. Aurora B kinase phosphorylation causes distinct patterns of KNL1 complex disruption, and preferential formation of the KNL1:PP1 holoenzyme occurs in the presence of PP1.","method":"X-ray crystallography, NMR spectroscopy, co-sedimentation assays, in vitro kinase assays","journal":"Structure (London, England : 1993)","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic-resolution structure combined with NMR and biochemical assays, multiple orthogonal methods in single study","pmids":["30100357"],"is_preprint":false},{"year":2018,"finding":"Genome editing to eliminate KNL1 in human cells shows that Bub1 and KNL1 activate kinetochore-bound Mad1-Mad2 to produce a 'wait anaphase' signal but are not required for fibrous corona formation. RZZ complex's sole role in SAC activation is to tether Mad1-Mad2 to kinetochores. Mps1 kinase triggers fibrous corona formation by phosphorylating two N-terminal sites on Rod, not KNL1.","method":"CRISPR genome editing, immunofluorescence, live-cell imaging","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean genome editing with multiple complementary knockouts, functional dissection of SAC components","pmids":["30415700"],"is_preprint":false},{"year":2014,"finding":"C. elegans KNL-1 exists as an oligomer. A specific N-terminal domain forms a decameric assembly visible by electron microscopy, with a small hydrophobic region responsible for oligomerization. However, mutations that precisely disrupt KNL-1 oligomerization did not alter KNL-1 localization or embryonic viability in C. elegans gene replacements.","method":"Biochemical oligomerization assays, electron microscopy, site-directed mutagenesis, C. elegans gene replacement","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — structural characterization by EM with mutagenesis and genetic validation, but oligomerization found dispensable for function","pmids":["25411336"],"is_preprint":false},{"year":2024,"finding":"In postmitotic C. elegans PVD neurons, KNL-1 (along with KMN network partners) controls dendrite branching and contact-dependent repulsion. Loss of KNL-1 causes significant F-actin cytoskeleton alterations and changes in microtubule dynamics within dendrites. The KNL-1 N-terminus can initiate F-actin assembly, and KNL-1 modulates F-actin dynamics to generate proper dendrite architecture.","method":"C. elegans genetics (neuronal-specific knockdown/knockout), live imaging, F-actin staining, domain rescue experiments","journal":"The Journal of cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO with defined cellular phenotype and domain rescue, novel postmitotic function, single lab","pmids":["39625434"],"is_preprint":false},{"year":2024,"finding":"In C. elegans, the signaling motifs within KNL-1 responsible for recruiting PP1 and activating the SAC are required for postmitotic neurodevelopment. Microtubule-binding activity of KMN is crucial for neuronal function, while NDC-80 microtubule-binding mutants display defects in axon bundling during nerve ring formation.","method":"C. elegans gene-replacement approaches, conditional KNL-1 degradation, neurodevelopmental phenotype analysis","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — gene replacement with domain-specific mutations, multiple neuronal phenotype readouts, single lab","pmids":["38656792"],"is_preprint":false},{"year":2026,"finding":"Proteomics of purified KNL1 from HEK293T cells treated with microtubule-disrupting compounds identified 111 phosphorylation sites on KNL1, including several that may be attachment-state specific, demonstrating extensive phosphoregulation of KNL1 beyond the known MELT motifs.","method":"KNL1 purification followed by mass spectrometry-based phosphoproteomics","journal":"microPublication biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — quantitative MS with multiple drug conditions, identifies extensive phosphosites but functional characterization of individual sites not yet established","pmids":["42058159","41959482"],"is_preprint":false}],"current_model":"KNL1 is a large scaffold protein at the outer kinetochore that acts as a central hub for chromosome segregation: its RVSF/SILK motifs recruit PP1 phosphatase (to counter Aurora B and silence the SAC), its Mps1-phosphorylated MELT (and vertebrate SHT) repeats recruit the Bub1/Bub3 and BubR1/Bub3 complexes (which in turn scaffold Mad1-Mad2 for SAC activation), its KI motifs enhance Bub1/BubR1 binding, and its N-terminus harbors microtubule-binding activity that contributes to SAC silencing; Aurora B phosphorylation of KNL1 disrupts PP1 binding (creating a positive feedback loop amplifying Aurora B activity), BubR1-associated PP2A-B56 dephosphorylates MELT motifs to silence the SAC, and KNL1-PP1 and KNL1-microtubule interactions are mutually exclusive due to overlapping binding sites; beyond mitosis, KNL1 is also repurposed postmitotically in neurons to regulate F-actin dynamics and dendrite architecture."},"narrative":{"mechanistic_narrative":"KNL1 is a large outer-kinetochore scaffold protein that serves as the central signaling hub coordinating kinetochore assembly, microtubule attachment, and the spindle assembly checkpoint (SAC) during chromosome segregation [PMID:14522947, PMID:17981135]. Within the kinetochore assembly hierarchy it acts downstream of centromeric chromatin: in C. elegans it forms a near-stoichiometric complex with the Ndc80/Nuf2 microtubule-binding module and directs its kinetochore targeting, while in vertebrates it cooperates with CENP-K to localize the Ndc80 complex and binds the Mis12 complex through its C-terminus [PMID:14522947, PMID:17981135, PMID:18045986]. KNL1 integrates opposing kinase–phosphatase signals through distinct sequence modules. Its conserved RVSF motif recruits protein phosphatase 1 (PP1), which dephosphorylates Aurora B substrates to stabilize microtubule attachments and silence the SAC; Aurora B phosphorylation of this motif disrupts PP1 binding, generating positive feedback that sustains its own activity [PMID:20231380, PMID:21640906]. Its array of MELT repeats, phosphorylated by Mps1/Mph1 kinase, creates docking sites for the Bub3–Bub1 and Bub3–BubR1 complexes that scaffold downstream SAC signaling, with the number of active recruitment modules tuning Bub1 levels and biorientation fidelity [PMID:22660415, PMID:24344183, PMID:24363448]. In vertebrates a sequential SHT motif phosphorylated after the MELT synergizes in BUB3/BUB1 binding, and KI motifs cooperate with neighboring MELT repeats to enhance SAC complex assembly [PMID:25661489, PMID:24361068]. SAC silencing is enforced by a negative feedback loop in which BubR1-associated PP2A-B56 dephosphorylates the MELT motifs [PMID:25246613]. The KNL1 N-terminus additionally binds and bundles microtubules through a site overlapping the PP1-docking site, rendering the two interactions mutually exclusive, and contributes independently to checkpoint silencing [PMID:22331849, PMID:30100357]. KNL1-recruited Bub1 licenses kinetochore Mad1-Mad2 for the 'wait anaphase' signal, operating in parallel with an RZZ-dependent pathway [PMID:26651294, PMID:30415700]. Beyond mitosis, KNL1 is repurposed in postmitotic C. elegans neurons, where its N-terminus initiates F-actin assembly and its PP1/SAC signaling motifs are required to shape dendrite branching and architecture [PMID:39625434, PMID:38656792].","teleology":[{"year":2003,"claim":"Established that KNL1 sits within a defined kinetochore assembly hierarchy and physically scaffolds the microtubule-binding machinery, answering where in kinetochore construction it acts.","evidence":"RNAi genomics, reciprocal co-IP, and epistasis in C. elegans embryos","pmids":["14522947"],"confidence":"High","gaps":["Hierarchy defined in C. elegans; vertebrate dependencies later found to differ","Did not resolve the molecular interfaces with Ndc80/Mis12"]},{"year":2007,"claim":"Defined KNL1's bipartite architecture in human cells — N/middle domains binding Bub1/BubR1 TPR domains and the C-terminus binding the Mis12 complex — explaining how it bridges checkpoint kinases to the kinetochore core.","evidence":"Domain-mapping co-IP/pulldowns and RNAi with live imaging in human cells; double-depletion epistasis in DT40","pmids":["17981135","18045986"],"confidence":"High","gaps":["TPR-binding motif identity not yet resolved","Vertebrate KNL1 only partially required for Ndc80 localization, unlike worm"]},{"year":2010,"claim":"Identified the RVSF motif as the PP1-docking site and showed Aurora B phosphorylation toggles it, establishing how KNL1 balances opposing kinase/phosphatase activity to control attachment stability.","evidence":"GST pulldown binding, phospho-antibodies, mutagenesis, kinetochore phosphorylation assays","pmids":["20231380"],"confidence":"High","gaps":["Did not address competition with other N-terminal activities","Quantitative tuning of PP1 levels unresolved"]},{"year":2011,"claim":"Showed PP1-RVSF binding is essential for viability via SAC silencing and must be precisely dosed, establishing that phosphatase recruitment is dynamically, not statically, regulated.","evidence":"Rapid gene replacement with allelic series and quantitative immunofluorescence in budding yeast","pmids":["21640906"],"confidence":"High","gaps":["Mechanism of dynamic regulation not defined","Microtubule-dependence of silencing not mechanistically resolved here"]},{"year":2012,"claim":"Identified MELT repeats as the Mps1-phosphorylated docking platform for Bub1/Bub3 and mapped the KI motif–Bub1 TPR interface, defining the core mechanism by which KNL1 builds the SAC signal and how its N-terminal microtubule/PP1 activities silence it.","evidence":"In vitro kinase assays, phospho-mutants, co-IP, MS, crystallography of Bub1 TPR–KI, and microtubule-binding reconstitution across fission yeast, C. elegans, and human cells","pmids":["22660415","22521786","22331849","22331848","24344188"],"confidence":"High","gaps":["TPR-KI interaction shown insufficient alone for Bub1 recruitment (Bub3-binding segment required)","Aurora B activation via KNL1 only partially explained by Bub1 (Medium-confidence #12)"]},{"year":2013,"claim":"Quantified the modular logic of the MELT/KI array, showing recruitment-module number sets Bub1 levels and that a minimum of ~four active MELT repeats supports congression and SAC, explaining how scaffold output is tunable.","evidence":"Systematic domain engineering, MELT deletion series, phospho-mimetic mutants, and rescue assays in human cells","pmids":["24344183","24363448","24361068"],"confidence":"High","gaps":["Functional redundancy among individual MELTs not fully parsed","How PP1 lowers Bub levels to the four-MELT setpoint not mechanistically resolved"]},{"year":2014,"claim":"Identified BubR1-associated PP2A-B56 as the phosphatase that removes Mps1-dependent MELT phosphorylation, defining the negative feedback loop that silences the SAC.","evidence":"In vitro and in vivo dephosphorylation assays, co-IP, phospho-antibodies in mammalian cells","pmids":["25246613"],"confidence":"High","gaps":["Spatiotemporal coordination with PP1-mediated silencing unresolved","Did not address SHT-motif dephosphorylation"]},{"year":2015,"claim":"Refined vertebrate SAC signaling by identifying the sequential SHT motif that synergizes with MELT in BUB3/BUB1 binding and showing KNL1/Bub1 acts in parallel with RZZ to localize Mad1-Mad2.","evidence":"Phospho-mutant screening, in vitro binding, BUB3 mutagenesis, RNAi/genome editing and imaging in human cells","pmids":["25661489","26581576","26651294"],"confidence":"High","gaps":["Relative contributions of KBB vs RZZ pathways context-dependent","RZZ recruitment mechanism partly KNL1-independent and undefined"]},{"year":2016,"claim":"Showed the MELT array licenses the Bub1–Mad1–Mad2 interaction, connecting Bub3 multisite binding to the actual checkpoint switch.","evidence":"Genetic epistasis, co-IP, phospho-mutant analysis in fission yeast","pmids":["27618268"],"confidence":"Medium","gaps":["Single-lab yeast study","Structural basis of Bub1–Mad1 licensing not resolved"]},{"year":2018,"claim":"Resolved at atomic level that PP1 and microtubule binding use overlapping KNL1 sites, establishing them as mutually exclusive and clarifying that KNL1's sole SAC-activating role downstream is tethering Mad1-Mad2, not corona formation.","evidence":"X-ray crystallography, NMR, co-sedimentation, kinase assays; CRISPR knockout with imaging in human cells","pmids":["30100357","30415700"],"confidence":"High","gaps":["Physiological switching between PP1- and microtubule-bound states not directly observed in cells","Fibrous corona formation shown to depend on Rod, not KNL1"]},{"year":2024,"claim":"Revealed a postmitotic moonlighting role: KNL1 and its mitotic PP1/SAC and microtubule-binding motifs, plus an N-terminal F-actin-initiating activity, shape dendrite branching and neuronal architecture.","evidence":"Neuronal-specific knockdown/knockout, gene replacement with domain-specific mutants, live imaging and F-actin staining in C. elegans PVD neurons","pmids":["39625434","38656792"],"confidence":"Medium","gaps":["Demonstrated in C. elegans neurons only","Direct biochemistry of F-actin initiation by the N-terminus not reconstituted","Single lab"]},{"year":2026,"claim":"Mapped extensive attachment-state-associated phosphorylation, indicating KNL1 phosphoregulation extends well beyond the MELT motifs.","evidence":"KNL1 purification and MS phosphoproteomics under microtubule-disrupting conditions in HEK293T cells","pmids":["42058159","41959482"],"confidence":"Medium","gaps":["Functional roles of the 111 sites not established","Responsible kinases for most sites unknown"]},{"year":null,"claim":"How KNL1 dynamically switches between PP1-bound (silencing) and microtubule-bound states in real time, and the functional logic of its broad non-MELT phosphorylation, remain open.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No in-cell measurement of PP1/microtubule occupancy switching","Most newly identified phosphosites uncharacterized","Mechanism of postmitotic neuronal repurposing only beginning to be defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,3,5,9,10]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[7,18,21]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1,2]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3,13]}],"localization":[{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,3,9]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[7,21]}],"pathway":[{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0,1,3,5,9]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[21,22]}],"complexes":["KMN network (KNL1-Mis12-Ndc80)","kinetochore"],"partners":["PP1","BUB1","BUBR1","BUB3","MPS1","MIS12 COMPLEX","NDC80","PP2A-B56"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8NG31","full_name":"Outer kinetochore KNL1 complex subunit KNL1","aliases":["ALL1-fused gene from chromosome 15q14 protein","AF15q14","Bub-linking kinetochore protein","Blinkin","Cancer susceptibility candidate gene 5 protein","Cancer/testis antigen 29","CT29","Kinetochore scaffold 1","Kinetochore-null protein 1","Protein CASC5","Protein D40/AF15q14"],"length_aa":2342,"mass_kda":265.4,"function":"Acts as a component of the outer kinetochore KNL1 complex that serves as a docking point for spindle assembly checkpoint components and mediates microtubule-kinetochore interactions (PubMed:15502821, PubMed:17981135, PubMed:18045986, PubMed:19893618, PubMed:21199919, PubMed:22000412, PubMed:22331848, PubMed:27881301, PubMed:30100357). Kinetochores, consisting of a centromere-associated inner segment and a microtubule-contacting outer segment, play a crucial role in chromosome segregation by mediating the physical connection between centromeric DNA and spindle microtubules (PubMed:18045986, PubMed:19893618, PubMed:27881301). The outer kinetochore is made up of the ten-subunit KMN network, comprising the MIS12, NDC80 and KNL1 complexes, and auxiliary microtubule-associated components; together they connect the outer kinetochore with the inner kinetochore, bind microtubules, and mediate interactions with mitotic checkpoint proteins that delay anaphase until chromosomes are bioriented on the spindle (PubMed:17981135, PubMed:19893618, PubMed:22000412, PubMed:38459127, PubMed:38459128). Required for kinetochore binding by a distinct subset of kMAPs (kinetochore-bound microtubule-associated proteins) and motors (PubMed:19893618). Acts in coordination with CENPK to recruit the NDC80 complex to the outer kinetochore (PubMed:18045986, PubMed:27881301). Can bind either to microtubules or to the protein phosphatase 1 (PP1) catalytic subunits PPP1CA and PPP1CC (via overlapping binding sites), it has higher affinity for PP1 (PubMed:30100357). Recruits MAD2L1 to the kinetochore and also directly links BUB1 and BUB1B to the kinetochore (PubMed:17981135, PubMed:19893618, PubMed:22000412, PubMed:22331848, PubMed:25308863). In addition to orienting mitotic chromosomes, it is also essential for alignment of homologous chromosomes during meiotic metaphase I (By similarity). In meiosis I, required to activate the spindle assembly checkpoint at unattached kinetochores to correct erroneous kinetochore-microtubule attachments (By similarity)","subcellular_location":"Nucleus; Chromosome, centromere, kinetochore; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q8NG31/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/KNL1","classification":"Common Essential","n_dependent_lines":987,"n_total_lines":1208,"dependency_fraction":0.8170529801324503},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"MIS12","stoichiometry":10.0},{"gene":"DNAJC7","stoichiometry":0.2},{"gene":"HSPA4","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/KNL1","total_profiled":1310},"omim":[{"mim_id":"619635","title":"ZINC FINGER FYVE DOMAIN-CONTAINING PROTEIN 19; ZFYVE19","url":"https://www.omim.org/entry/619635"},{"mim_id":"615128","title":"CENTROMERIC PROTEIN X; CENPX","url":"https://www.omim.org/entry/615128"},{"mim_id":"609173","title":"KINETOCHORE SCAFFOLD 1; KNL1","url":"https://www.omim.org/entry/609173"},{"mim_id":"609130","title":"CENTROMERIC PROTEIN S; CENPS","url":"https://www.omim.org/entry/609130"},{"mim_id":"608046","title":"SYNOVIAL APOPTOSIS INHIBITOR 1; SYVN1","url":"https://www.omim.org/entry/608046"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nuclear bodies","reliability":"Additional"}],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"bone marrow","ntpm":4.9},{"tissue":"lymphoid tissue","ntpm":6.9},{"tissue":"testis","ntpm":15.8}],"url":"https://www.proteinatlas.org/search/KNL1"},"hgnc":{"alias_symbol":["D40","AF15Q14","CT29","KIAA1570","hKNL-1","hSpc105","PPP1R55","Spc7"],"prev_symbol":["MCPH4","CASC5"]},"alphafold":{"accession":"Q8NG31","domains":[{"cath_id":"-","chopping":"1879-1910_1928-2063","consensus_level":"medium","plddt":82.3636,"start":1879,"end":2063},{"cath_id":"-","chopping":"2134-2240","consensus_level":"medium","plddt":79.6173,"start":2134,"end":2240},{"cath_id":"-","chopping":"2255-2342","consensus_level":"medium","plddt":82.8157,"start":2255,"end":2342},{"cath_id":"1.20.5","chopping":"2081-2130","consensus_level":"medium","plddt":81.4106,"start":2081,"end":2130}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8NG31","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8NG31-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8NG31-F1-predicted_aligned_error_v6.png","plddt_mean":39.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=KNL1","jax_strain_url":"https://www.jax.org/strain/search?query=KNL1"},"sequence":{"accession":"Q8NG31","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8NG31.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8NG31/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8NG31"}},"corpus_meta":[{"pmid":"20231380","id":"PMC_20231380","title":"Regulated targeting of protein phosphatase 1 to the outer kinetochore by KNL1 opposes Aurora B kinase.","date":"2010","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/20231380","citation_count":307,"is_preprint":false},{"pmid":"22660415","id":"PMC_22660415","title":"MPS1/Mph1 phosphorylates the kinetochore protein KNL1/Spc7 to recruit SAC components.","date":"2012","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/22660415","citation_count":291,"is_preprint":false},{"pmid":"17981135","id":"PMC_17981135","title":"Human Blinkin/AF15q14 is required for chromosome alignment and the mitotic checkpoint through direct interaction with Bub1 and BubR1.","date":"2007","source":"Developmental cell","url":"https://pubmed.ncbi.nlm.nih.gov/17981135","citation_count":250,"is_preprint":false},{"pmid":"22521786","id":"PMC_22521786","title":"Phosphodependent recruitment of Bub1 and Bub3 to Spc7/KNL1 by Mph1 kinase maintains the spindle checkpoint.","date":"2012","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/22521786","citation_count":242,"is_preprint":false},{"pmid":"14522947","id":"PMC_14522947","title":"KNL-1 directs assembly of the microtubule-binding interface of the kinetochore in C. elegans.","date":"2003","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/14522947","citation_count":201,"is_preprint":false},{"pmid":"21640906","id":"PMC_21640906","title":"KNL1/Spc105 recruits PP1 to silence the spindle assembly checkpoint.","date":"2011","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/21640906","citation_count":185,"is_preprint":false},{"pmid":"18045986","id":"PMC_18045986","title":"KNL1 and the CENP-H/I/K complex coordinately direct kinetochore assembly in vertebrates.","date":"2007","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/18045986","citation_count":163,"is_preprint":false},{"pmid":"22331849","id":"PMC_22331849","title":"Microtubule binding by KNL-1 contributes to spindle checkpoint silencing at the kinetochore.","date":"2012","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/22331849","citation_count":125,"is_preprint":false},{"pmid":"22331848","id":"PMC_22331848","title":"Structural analysis reveals features of the spindle checkpoint kinase Bub1-kinetochore subunit Knl1 interaction.","date":"2012","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/22331848","citation_count":114,"is_preprint":false},{"pmid":"24344183","id":"PMC_24344183","title":"Arrayed BUB recruitment modules in the kinetochore scaffold KNL1 promote accurate chromosome segregation.","date":"2013","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/24344183","citation_count":114,"is_preprint":false},{"pmid":"25246613","id":"PMC_25246613","title":"PP2A-B56 opposes Mps1 phosphorylation of Knl1 and thereby promotes spindle assembly checkpoint silencing.","date":"2014","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/25246613","citation_count":108,"is_preprint":false},{"pmid":"24363448","id":"PMC_24363448","title":"A minimal number of MELT repeats supports all the functions of KNL1 in chromosome segregation.","date":"2013","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/24363448","citation_count":97,"is_preprint":false},{"pmid":"25661489","id":"PMC_25661489","title":"Sequential multisite phospho-regulation of KNL1-BUB3 interfaces at mitotic kinetochores.","date":"2015","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/25661489","citation_count":95,"is_preprint":false},{"pmid":"24361068","id":"PMC_24361068","title":"KI motifs of human Knl1 enhance assembly of comprehensive spindle checkpoint complexes around MELT repeats.","date":"2013","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/24361068","citation_count":92,"is_preprint":false},{"pmid":"30415700","id":"PMC_30415700","title":"Distinct Roles of RZZ and Bub1-KNL1 in Mitotic Checkpoint Signaling and Kinetochore Expansion.","date":"2018","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/30415700","citation_count":89,"is_preprint":false},{"pmid":"26651294","id":"PMC_26651294","title":"KNL1-Bubs and RZZ Provide Two Separable Pathways for Checkpoint Activation at Human Kinetochores.","date":"2015","source":"Developmental cell","url":"https://pubmed.ncbi.nlm.nih.gov/26651294","citation_count":78,"is_preprint":false},{"pmid":"24831118","id":"PMC_24831118","title":"Cotton KNL1, encoding a class II KNOX transcription factor, is involved in regulation of fibre development.","date":"2014","source":"Journal of experimental botany","url":"https://pubmed.ncbi.nlm.nih.gov/24831118","citation_count":69,"is_preprint":false},{"pmid":"24344188","id":"PMC_24344188","title":"KNL1 facilitates phosphorylation of outer kinetochore proteins by promoting Aurora B kinase activity.","date":"2013","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/24344188","citation_count":63,"is_preprint":false},{"pmid":"30390708","id":"PMC_30390708","title":"Dysregulation of NCAPG, KNL1, miR-148a-3p, miR-193b-3p, and miR-1179 may contribute to the progression of gastric cancer.","date":"2018","source":"Biological research","url":"https://pubmed.ncbi.nlm.nih.gov/30390708","citation_count":57,"is_preprint":false},{"pmid":"24310619","id":"PMC_24310619","title":"KNL1: bringing order to the kinetochore.","date":"2013","source":"Chromosoma","url":"https://pubmed.ncbi.nlm.nih.gov/24310619","citation_count":56,"is_preprint":false},{"pmid":"26581576","id":"PMC_26581576","title":"The RZZ complex requires the N-terminus of KNL1 to mediate optimal Mad1 kinetochore localization in human cells.","date":"2015","source":"Open biology","url":"https://pubmed.ncbi.nlm.nih.gov/26581576","citation_count":49,"is_preprint":false},{"pmid":"30100357","id":"PMC_30100357","title":"KNL1 Binding to PP1 and Microtubules Is Mutually Exclusive.","date":"2018","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/30100357","citation_count":42,"is_preprint":false},{"pmid":"25052095","id":"PMC_25052095","title":"The dynamic protein Knl1 - a kinetochore rendezvous.","date":"2014","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/25052095","citation_count":41,"is_preprint":false},{"pmid":"31197172","id":"PMC_31197172","title":"Robust elimination of genome-damaged cells safeguards against brain somatic aneuploidy following Knl1 deletion.","date":"2019","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/31197172","citation_count":38,"is_preprint":false},{"pmid":"27618268","id":"PMC_27618268","title":"Bub3-Bub1 Binding to Spc7/KNL1 Toggles the Spindle Checkpoint Switch by Licensing the Interaction of Bub1 with Mad1-Mad2.","date":"2016","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/27618268","citation_count":38,"is_preprint":false},{"pmid":"26254484","id":"PMC_26254484","title":"Widespread Recurrent Patterns of Rapid Repeat Evolution in the Kinetochore Scaffold KNL1.","date":"2015","source":"Genome biology and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/26254484","citation_count":37,"is_preprint":false},{"pmid":"10980622","id":"PMC_10980622","title":"AF15q14, a novel partner gene fused to the MLL gene in an acute myeloid leukaemia with a t(11;15)(q23;q14).","date":"2000","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/10980622","citation_count":36,"is_preprint":false},{"pmid":"12087463","id":"PMC_12087463","title":"Frequent expression of new cancer/testis gene D40/AF15q14 in lung cancers of smokers.","date":"2002","source":"British journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/12087463","citation_count":28,"is_preprint":false},{"pmid":"33990465","id":"PMC_33990465","title":"Knl1 participates in spindle assembly checkpoint signaling in maize.","date":"2021","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/33990465","citation_count":28,"is_preprint":false},{"pmid":"31315522","id":"PMC_31315522","title":"Effect of KNL1 on the proliferation and apoptosis of colorectal cancer cells.","date":"2019","source":"Technology in cancer research & treatment","url":"https://pubmed.ncbi.nlm.nih.gov/31315522","citation_count":17,"is_preprint":false},{"pmid":"26348410","id":"PMC_26348410","title":"Targeted Knockdown of the Kinetochore Protein D40/Knl-1 Inhibits Human Cancer in a p53 Status-Independent Manner.","date":"2015","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/26348410","citation_count":16,"is_preprint":false},{"pmid":"12618766","id":"PMC_12618766","title":"A t(11;15) fuses MLL to two different genes, AF15q14 and a novel gene MPFYVE on chromosome 15.","date":"2003","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/12618766","citation_count":15,"is_preprint":false},{"pmid":"38857680","id":"PMC_38857680","title":"Kaempferol from Alpinia officinarum hance induces G2/M cell cycle arrest in hepatocellular carcinoma cells by regulating the ATM/CHEK2/KNL1 pathway.","date":"2024","source":"Journal of ethnopharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/38857680","citation_count":15,"is_preprint":false},{"pmid":"32795273","id":"PMC_32795273","title":"LINC02418 promotes malignant behaviors in lung adenocarcinoma cells by sponging miR-4677-3p to upregulate KNL1 expression.","date":"2020","source":"BMC pulmonary medicine","url":"https://pubmed.ncbi.nlm.nih.gov/32795273","citation_count":15,"is_preprint":false},{"pmid":"12618768","id":"PMC_12618768","title":"Characterization of the MLL partner gene AF15q14 involved in t(11;15)(q23;q14).","date":"2003","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/12618768","citation_count":13,"is_preprint":false},{"pmid":"15579588","id":"PMC_15579588","title":"The protein encoded by cancer/testis gene D40/AF15q14 is localized in spermatocytes, acrosomes of spermatids and ejaculated spermatozoa.","date":"2004","source":"Reproduction (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/15579588","citation_count":9,"is_preprint":false},{"pmid":"25411336","id":"PMC_25411336","title":"The outer kinetochore protein KNL-1 contains a defined oligomerization domain in nematodes.","date":"2014","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/25411336","citation_count":9,"is_preprint":false},{"pmid":"10780384","id":"PMC_10780384","title":"Chromosomal assignment of a novel human gene D40.","date":"1999","source":"Nucleic acids symposium series","url":"https://pubmed.ncbi.nlm.nih.gov/10780384","citation_count":9,"is_preprint":false},{"pmid":"38403686","id":"PMC_38403686","title":"KNL1 and NDC80 represent new universal markers for the detection of functional centromeres in plants.","date":"2024","source":"Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology","url":"https://pubmed.ncbi.nlm.nih.gov/38403686","citation_count":8,"is_preprint":false},{"pmid":"18771174","id":"PMC_18771174","title":"[The involvement of c-Abl and D40 (AF15q14/CASC5) proteins in the regulation of cell proliferation and cancer].","date":"2008","source":"Tsitologiia","url":"https://pubmed.ncbi.nlm.nih.gov/18771174","citation_count":6,"is_preprint":false},{"pmid":"39625434","id":"PMC_39625434","title":"The kinetochore protein KNL-1 regulates the actin cytoskeleton to control dendrite branching.","date":"2024","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/39625434","citation_count":5,"is_preprint":false},{"pmid":"28901661","id":"PMC_28901661","title":"D40/KNL1/CASC5 and autosomal recessive primary microcephaly.","date":"2017","source":"Congenital anomalies","url":"https://pubmed.ncbi.nlm.nih.gov/28901661","citation_count":4,"is_preprint":false},{"pmid":"24456977","id":"PMC_24456977","title":"Kinetochore signalling: the KIss that MELTs Knl1.","date":"2014","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/24456977","citation_count":4,"is_preprint":false},{"pmid":"37928953","id":"PMC_37928953","title":"Role of Kinetochore Scaffold 1 (KNL1) in Tumorigenesis and Tumor Immune Microenvironment in Pan-Cancer: Bioinformatics Analyses and Validation of Expression.","date":"2023","source":"International journal of general medicine","url":"https://pubmed.ncbi.nlm.nih.gov/37928953","citation_count":3,"is_preprint":false},{"pmid":"38656792","id":"PMC_38656792","title":"The outer kinetochore components KNL-1 and Ndc80 complex regulate axon and neuronal cell body positioning in the C. elegans nervous system.","date":"2024","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/38656792","citation_count":3,"is_preprint":false},{"pmid":"37937525","id":"PMC_37937525","title":"A novel KNL1 intronic splicing variant likely destabilizes the KMN complex, causing primary microcephaly.","date":"2023","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/37937525","citation_count":2,"is_preprint":false},{"pmid":"21272090","id":"PMC_21272090","title":"Testis cancer gene D40 expression and its relationship with clinicopathological features in infertile men.","date":"2011","source":"International journal of urology : official journal of the Japanese Urological Association","url":"https://pubmed.ncbi.nlm.nih.gov/21272090","citation_count":1,"is_preprint":false},{"pmid":"39820668","id":"PMC_39820668","title":"The KNL-1/Knl1 outer kinetochore protein caught regulating F-actin.","date":"2025","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/39820668","citation_count":0,"is_preprint":false},{"pmid":"41930176","id":"PMC_41930176","title":"KNL1 Regulates Ferroptosis Resistance and Migration in Lung Adenocarcinoma Cells via AMPK-mTOR Signaling.","date":"2026","source":"Oncology research","url":"https://pubmed.ncbi.nlm.nih.gov/41930176","citation_count":0,"is_preprint":false},{"pmid":"41959482","id":"PMC_41959482","title":"Proteomics reveals extensive phosphoregulation of outer kinetochore protein KNL1.","date":"2026","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/41959482","citation_count":0,"is_preprint":false},{"pmid":"42058159","id":"PMC_42058159","title":"Proteomics reveals extensive phosphoregulation of outer kinetochore protein KNL1.","date":"2026","source":"microPublication biology","url":"https://pubmed.ncbi.nlm.nih.gov/42058159","citation_count":0,"is_preprint":false},{"pmid":"10780383","id":"PMC_10780383","title":"Isolation of cDNAs that cover the entire coding region of a novel human protein D40.","date":"1999","source":"Nucleic acids symposium series","url":"https://pubmed.ncbi.nlm.nih.gov/10780383","citation_count":0,"is_preprint":false},{"pmid":"11857474","id":"PMC_11857474","title":"Isolation of the peri-acrosomal plasma membrane protein D40 enriched fraction from guinea pig spermatozoa using a monoclonal antibody.","date":"2002","source":"The Journal of experimental zoology","url":"https://pubmed.ncbi.nlm.nih.gov/11857474","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.10.23.684222","title":"Trophoblast stem cells and syncytiotrophoblasts lack inflammatory responses to LPS but retain robust interferon-mediated antiviral immunity","date":"2025-10-24","source":"bioRxiv","url":"https://doi.org/10.1101/2025.10.23.684222","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.05.23.655733","title":"Single kinetochores execute an ordered series of molecular events as the Spindle Assembly Checkpoint is silenced","date":"2025-05-23","source":"bioRxiv","url":"https://doi.org/10.1101/2025.05.23.655733","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.07.25.666731","title":"hSpindly’s dynamic controls SAC activity independently of the KBB pathway at unattached kinetochores","date":"2025-07-25","source":"bioRxiv","url":"https://doi.org/10.1101/2025.07.25.666731","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.03.21.25324295","title":"A Prospective Pilot Clinical Study reveals a promising non-toxic anti-biofilm activity of Gentamicin-EDTA-Na₂ Central Venous Catheter Lock Solution","date":"2025-03-21","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.21.25324295","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.05.19.654957","title":"A periplasmic metallochaperone (PmcY) couples Zn  <sup>2+</sup>  -transport to sensing in  <i>Pseudomonas aeruginosa</i>","date":"2025-05-20","source":"bioRxiv","url":"https://doi.org/10.1101/2025.05.19.654957","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.02.27.640699","title":"Computational elucidation of possible contributors to formation and stabilization of ATP-lid down-conformation in the N-terminal domain of Hsp90","date":"2025-03-03","source":"bioRxiv","url":"https://doi.org/10.1101/2025.02.27.640699","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.09.10.612026","title":"Revisiting the cytogenetics of  <i>Vellozia</i>  Vand.: immunolocalization of KLN1 elucidates the chromosome number for the genus","date":"2024-09-13","source":"bioRxiv","url":"https://doi.org/10.1101/2024.09.10.612026","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.11.04.686612","title":"<i>Cryptococcus neoformans</i>  employs both PP1 and PP2A phosphatases to silence the spindle checkpoint","date":"2025-11-06","source":"bioRxiv","url":"https://doi.org/10.1101/2025.11.04.686612","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.06.03.657598","title":"Assembly and phospho-regulatory mechanisms of the budding yeast outer kinetochore KMN complex","date":"2025-06-04","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.03.657598","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":29499,"output_tokens":6070,"usd":0.089774,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":14719,"output_tokens":4499,"usd":0.093035,"stage2_stop_reason":"end_turn"},"total_usd":0.182809,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2003,\n      \"finding\": \"KNL-1 is downstream of CeCENP-A and CeCENP-C in a linear kinetochore assembly hierarchy in C. elegans. KNL-1 forms a near-stoichiometric complex with CeNDC-80 and HIM-10 (Ndc80/Nuf2 homologs) and is required to target multiple outer kinetochore components including CeNDC-80 and HIM-10, thereby directing assembly of the microtubule-binding interface.\",\n      \"method\": \"RNA interference-based genomics, co-immunoprecipitation, epistasis analysis in C. elegans embryos\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP and genetic epistasis with multiple RNAi knockdowns, foundational study replicated by subsequent work\",\n      \"pmids\": [\"14522947\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Human KNL1 (Blinkin/AF15q14) directly interacts via its amino and middle domains with the TPR domains of BubR1 and Bub1, recruiting them to kinetochores. The C-terminal domain of KNL1 associates with the hMis12 complex (c20orf172/hMis13 and DC8/hMis14 subunits). KNL1 RNAi causes spindle checkpoint failure and chromosome misalignment.\",\n      \"method\": \"Co-immunoprecipitation, domain-mapping pulldowns, RNAi knockdown with live-cell imaging\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP with domain mapping, confirmed by RNAi phenotype, replicated in multiple subsequent studies\",\n      \"pmids\": [\"17981135\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Vertebrate KNL1 is required to localize a subset of outer kinetochore proteins. Unlike in C. elegans, vertebrate KNL1 depletion does not abolish Ndc80 complex kinetochore localization; instead KNL1 and CENP-K coordinately direct Ndc80 complex localization, as simultaneous depletion of both abolishes all kinetochore assembly downstream of centromeric chromatin.\",\n      \"method\": \"RNAi knockdown (single and double), immunofluorescence, chicken DT40 conditional knockout\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis with double knockdown, multiple orthogonal approaches, replicated across cell types\",\n      \"pmids\": [\"18045986\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"A conserved RVSF motif in KNL1 directly interacts with and recruits protein phosphatase 1 (PP1) to the outer kinetochore. PP1 recruitment by KNL1 is required to dephosphorylate Aurora B substrates at kinetochores and stabilize microtubule attachments. Aurora B phosphorylates KNL1 at this motif to disrupt the KNL1-PP1 interaction, creating a positive feedback mechanism by which Aurora B both targets substrates and prevents opposing phosphatase localization.\",\n      \"method\": \"Direct binding assay (GST pulldown), phospho-specific antibodies, site-directed mutagenesis, immunofluorescence, kinetochore phosphorylation assays\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vitro binding with mutagenesis, phosphorylation assays, multiple orthogonal methods, widely replicated\",\n      \"pmids\": [\"20231380\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Binding of PP1/Glc7 to the conserved RVSF motif of Spc105 (KNL1/Blinkin) in budding yeast is essential for viability by silencing the spindle assembly checkpoint. The amount of PP1 targeted to kinetochores must be finely tuned — neither zero nor one extra copy is tolerated. Persistent PP1-Spc105 interaction without microtubules is insufficient to silence the SAC, indicating dynamic regulation is required.\",\n      \"method\": \"Rapid gene replacement in budding yeast, genetic analysis, quantitative immunofluorescence\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — precise gene replacement with multiple alleles, quantitative analysis, functionally validates PP1 binding motif\",\n      \"pmids\": [\"21640906\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"MPS1/Mph1 kinase phosphorylates MELT repeat sequences in KNL1/Spc7 (the fission yeast homolog), promoting binding of the Bub1-Bub3 complex. This phosphorylation is required for kinetochore-based SAC activation (Mad1-Mad2-Mad3 localization) and chromosome alignment. Non-phosphorylatable spc7-12A abolishes Bub1-Bub3 kinetochore targeting; phospho-mimetic spc7-12E forces constitutive localization even without Mph1.\",\n      \"method\": \"In vitro kinase assay, phospho-mimetic/non-phosphorylatable mutants, co-immunoprecipitation, live-cell imaging in fission yeast\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vitro kinase assay with mutagenesis, genetic rescue experiments, replicated independently\",\n      \"pmids\": [\"22660415\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Phosphorylation of conserved MELT motifs in Spc7/KNL1 by Mph1 (Mps1) recruits Bub1 and Bub3 to the kinetochore, which is required to maintain the spindle assembly checkpoint signal. PP1 binding to Spc7 is necessary to stabilize microtubule-kinetochore attachments and silence the SAC.\",\n      \"method\": \"Phospho-specific antibodies, mutagenesis, co-immunoprecipitation, mass spectrometry, genetic analysis in fission yeast\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods including MS and mutagenesis, independently replicated\",\n      \"pmids\": [\"22521786\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"KNL-1 microtubule-binding and bundling activity resides in its extreme N-terminus. Selective perturbation of KNL-1 microtubule binding in C. elegans shows this activity is dispensable for load-bearing attachment and checkpoint activation but contributes independently to checkpoint silencing. Perturbation of both microtubule binding and PP1 docking additively affects checkpoint silencing, indicating these two N-terminal activities make independent contributions.\",\n      \"method\": \"Domain mutagenesis, in vitro microtubule-binding assays, C. elegans gene replacement, checkpoint reporter assays\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — reconstitution of microtubule binding, mutagenesis, genetic rescue with multiple alleles\",\n      \"pmids\": [\"22331849\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Crystal structure of Bub1 TPR domain in complex with KNL1 KI motif was determined. The interaction develops along the convex surface of the TPR assembly. Point mutations on this surface impaired Bub1/BubR1 interaction with Knl1 in vitro and in vivo. However, a 62-residue segment C-terminal to the TPRs including a Bub3-binding domain was necessary and sufficient for kinetochore recruitment of Bub1, not the TPR-KI interaction alone.\",\n      \"method\": \"X-ray crystallography, site-directed mutagenesis, co-immunoprecipitation, immunofluorescence\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with mutagenesis validation in vitro and in vivo\",\n      \"pmids\": [\"22331848\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"KNL1 contains an extensive array of short linear sequence modules encompassing TxxΩ and MELT motifs that can independently localize BUB1. The number of BUB recruitment modules correlates with kinetochore BUB1 levels and efficiency of chromosome biorientation. A minimal array of generic BUB recruitment modules in KNL1 suffices for accurate chromosome segregation.\",\n      \"method\": \"KNL1 domain engineering, quantitative immunofluorescence, chromosome alignment assays, SAC functional assays\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — systematic domain engineering with multiple engineered variants, quantitative functional readouts\",\n      \"pmids\": [\"24344183\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"KNL1 contains multiple binding sites for Bub proteins, with Mps1-phosphorylated MELT repeats constituting individual docking sites for direct binding of Bub3. A minimum of four active MELT repeats supports chromosome congression and SAC function. PP1 binding to KNL1 during prometaphase reduces Bub protein levels at kinetochores to approximately the level recruited by four active MELT repeats.\",\n      \"method\": \"MELT repeat deletion analysis, phospho-mimetic mutants, immunofluorescence, SAC assays\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — systematic deletion series with quantitative functional readouts, multiple orthogonal assays\",\n      \"pmids\": [\"24363448\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"KI motifs in KNL1 cooperate with neighboring MELT motifs to assemble comprehensive SAC complexes. KI motifs enhance MELT function by providing a more robust mechanism for SAC signaling. A minimal Knl1 fragment (residues 1-250) containing KI and one MELT motif can restore SAC and chromosome alignment when targeted to kinetochores in cells depleted of endogenous Knl1.\",\n      \"method\": \"Domain truncation/rescue experiments, co-immunoprecipitation, immunofluorescence, SAC functional assays\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — systematic domain dissection with functional rescue, multiple orthogonal methods\",\n      \"pmids\": [\"24361068\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"KNL1 N-terminus is essential for Aurora B kinase activity at kinetochores, likely through promoting Bub1 kinase activity which in turn targets Aurora B. Ectopic targeting of Aurora B to kinetochores does not fully rescue Aurora B activity in KNL1-depleted cells, suggesting KNL1 influences Aurora B through an additional pathway beyond Bub1 recruitment.\",\n      \"method\": \"RNAi knockdown, phospho-specific antibody staining, ectopic Aurora B targeting constructs, kinetochore-microtubule attachment assays\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with defined phosphorylation readouts, single lab, incomplete rescue experiment leaves pathway partially unclear\",\n      \"pmids\": [\"24344188\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"BubR1-associated PP2A-B56 is the key phosphatase that removes Mps1-mediated phosphorylations on Knl1 MELT motifs required for Bub1/BubR1 recruitment in mammalian cells, both in vivo and in vitro. This creates a negative feedback loop: Mps1-dependent recruitment of BubR1 brings the phosphatase (PP2A-B56) that opposes Mps1, thereby promoting SAC silencing.\",\n      \"method\": \"In vitro dephosphorylation assays, co-immunoprecipitation, immunofluorescence, phospho-specific antibodies\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vitro and in vivo demonstration with multiple orthogonal methods\",\n      \"pmids\": [\"25246613\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Human KNL1 MELT-containing repeats contain a vertebrate-specific SHT motif C-terminal to the MELT sequence. MPS1 phosphorylates SHT motifs in a manner requiring prior MELT phosphorylation (sequential multisite regulation). Phospho-SHT (SHpT) synergizes with phospho-MELT (MELpT) in BUB3/BUB1 binding in vitro and in cells. BUB3 mutated in a predicted SHpT-binding surface cannot localize to kinetochores.\",\n      \"method\": \"Systematic phospho-mutant screening, in vitro binding assays, BUB3 mutagenesis, immunofluorescence\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vitro reconstitution with mutagenesis combined with cell-based validation, mechanistic detail\",\n      \"pmids\": [\"25661489\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The RZZ complex localizes to the N-terminus of KNL1, downstream of Bub1, to mediate robust Mad1/Mad2 kinetochore localization. The RZZ complex is the primary mediator for Mad1/Mad2 kinetochore localization in human cells, with a KNL1/Bub1-independent mechanism also existing for RZZ recruitment.\",\n      \"method\": \"RNAi knockdown, domain targeting experiments, immunofluorescence, FRAP\",\n      \"journal\": \"Open biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple knockdown conditions, domain targeting, single lab\",\n      \"pmids\": [\"26581576\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The KNL1-Bub3-Bub1 (KBB) pathway is required during normal mitotic progression when kinetochores are misaligned but is nonessential for SAC activation when kinetochores are fully unattached from microtubules. The RZZ complex provides a separate, KBB-independent pathway to recruit Mad1:Mad2 to unattached kinetochores.\",\n      \"method\": \"siRNA knockdown, genome editing, immunofluorescence, live-cell imaging in non-transformed diploid human cells\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic dissection with multiple complementary knockdown experiments, non-transformed cell model, clear epistasis\",\n      \"pmids\": [\"26651294\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Multisite binding of Bub3 to the Spc7/KNL1 MELT array is required for Mph1(Mps1)-dependent interaction of Bub1 with Mad1-Mad2 in fission yeast, thus toggling the spindle checkpoint switch. The Spc7 MELT array licenses Bub1-Mad1-Mad2 interaction.\",\n      \"method\": \"Genetic epistasis, co-immunoprecipitation, phospho-mutant analysis, fission yeast genetics\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with phospho-mutants in yeast, single lab\",\n      \"pmids\": [\"27618268\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"X-ray crystallography, NMR spectroscopy, and biochemical co-sedimentation assays demonstrate that PP1 and microtubules bind KNL1 via overlapping binding sites, making their interactions mutually exclusive. Aurora B kinase phosphorylation causes distinct patterns of KNL1 complex disruption, and preferential formation of the KNL1:PP1 holoenzyme occurs in the presence of PP1.\",\n      \"method\": \"X-ray crystallography, NMR spectroscopy, co-sedimentation assays, in vitro kinase assays\",\n      \"journal\": \"Structure (London, England : 1993)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic-resolution structure combined with NMR and biochemical assays, multiple orthogonal methods in single study\",\n      \"pmids\": [\"30100357\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Genome editing to eliminate KNL1 in human cells shows that Bub1 and KNL1 activate kinetochore-bound Mad1-Mad2 to produce a 'wait anaphase' signal but are not required for fibrous corona formation. RZZ complex's sole role in SAC activation is to tether Mad1-Mad2 to kinetochores. Mps1 kinase triggers fibrous corona formation by phosphorylating two N-terminal sites on Rod, not KNL1.\",\n      \"method\": \"CRISPR genome editing, immunofluorescence, live-cell imaging\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean genome editing with multiple complementary knockouts, functional dissection of SAC components\",\n      \"pmids\": [\"30415700\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"C. elegans KNL-1 exists as an oligomer. A specific N-terminal domain forms a decameric assembly visible by electron microscopy, with a small hydrophobic region responsible for oligomerization. However, mutations that precisely disrupt KNL-1 oligomerization did not alter KNL-1 localization or embryonic viability in C. elegans gene replacements.\",\n      \"method\": \"Biochemical oligomerization assays, electron microscopy, site-directed mutagenesis, C. elegans gene replacement\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — structural characterization by EM with mutagenesis and genetic validation, but oligomerization found dispensable for function\",\n      \"pmids\": [\"25411336\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In postmitotic C. elegans PVD neurons, KNL-1 (along with KMN network partners) controls dendrite branching and contact-dependent repulsion. Loss of KNL-1 causes significant F-actin cytoskeleton alterations and changes in microtubule dynamics within dendrites. The KNL-1 N-terminus can initiate F-actin assembly, and KNL-1 modulates F-actin dynamics to generate proper dendrite architecture.\",\n      \"method\": \"C. elegans genetics (neuronal-specific knockdown/knockout), live imaging, F-actin staining, domain rescue experiments\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with defined cellular phenotype and domain rescue, novel postmitotic function, single lab\",\n      \"pmids\": [\"39625434\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In C. elegans, the signaling motifs within KNL-1 responsible for recruiting PP1 and activating the SAC are required for postmitotic neurodevelopment. Microtubule-binding activity of KMN is crucial for neuronal function, while NDC-80 microtubule-binding mutants display defects in axon bundling during nerve ring formation.\",\n      \"method\": \"C. elegans gene-replacement approaches, conditional KNL-1 degradation, neurodevelopmental phenotype analysis\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — gene replacement with domain-specific mutations, multiple neuronal phenotype readouts, single lab\",\n      \"pmids\": [\"38656792\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Proteomics of purified KNL1 from HEK293T cells treated with microtubule-disrupting compounds identified 111 phosphorylation sites on KNL1, including several that may be attachment-state specific, demonstrating extensive phosphoregulation of KNL1 beyond the known MELT motifs.\",\n      \"method\": \"KNL1 purification followed by mass spectrometry-based phosphoproteomics\",\n      \"journal\": \"microPublication biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — quantitative MS with multiple drug conditions, identifies extensive phosphosites but functional characterization of individual sites not yet established\",\n      \"pmids\": [\"42058159\", \"41959482\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"KNL1 is a large scaffold protein at the outer kinetochore that acts as a central hub for chromosome segregation: its RVSF/SILK motifs recruit PP1 phosphatase (to counter Aurora B and silence the SAC), its Mps1-phosphorylated MELT (and vertebrate SHT) repeats recruit the Bub1/Bub3 and BubR1/Bub3 complexes (which in turn scaffold Mad1-Mad2 for SAC activation), its KI motifs enhance Bub1/BubR1 binding, and its N-terminus harbors microtubule-binding activity that contributes to SAC silencing; Aurora B phosphorylation of KNL1 disrupts PP1 binding (creating a positive feedback loop amplifying Aurora B activity), BubR1-associated PP2A-B56 dephosphorylates MELT motifs to silence the SAC, and KNL1-PP1 and KNL1-microtubule interactions are mutually exclusive due to overlapping binding sites; beyond mitosis, KNL1 is also repurposed postmitotically in neurons to regulate F-actin dynamics and dendrite architecture.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"KNL1 is a large outer-kinetochore scaffold protein that serves as the central signaling hub coordinating kinetochore assembly, microtubule attachment, and the spindle assembly checkpoint (SAC) during chromosome segregation [#0, #1]. Within the kinetochore assembly hierarchy it acts downstream of centromeric chromatin: in C. elegans it forms a near-stoichiometric complex with the Ndc80/Nuf2 microtubule-binding module and directs its kinetochore targeting, while in vertebrates it cooperates with CENP-K to localize the Ndc80 complex and binds the Mis12 complex through its C-terminus [#0, #1, #2]. KNL1 integrates opposing kinase–phosphatase signals through distinct sequence modules. Its conserved RVSF motif recruits protein phosphatase 1 (PP1), which dephosphorylates Aurora B substrates to stabilize microtubule attachments and silence the SAC; Aurora B phosphorylation of this motif disrupts PP1 binding, generating positive feedback that sustains its own activity [#3, #4]. Its array of MELT repeats, phosphorylated by Mps1/Mph1 kinase, creates docking sites for the Bub3–Bub1 and Bub3–BubR1 complexes that scaffold downstream SAC signaling, with the number of active recruitment modules tuning Bub1 levels and biorientation fidelity [#5, #9, #10]. In vertebrates a sequential SHT motif phosphorylated after the MELT synergizes in BUB3/BUB1 binding, and KI motifs cooperate with neighboring MELT repeats to enhance SAC complex assembly [#14, #11]. SAC silencing is enforced by a negative feedback loop in which BubR1-associated PP2A-B56 dephosphorylates the MELT motifs [#13]. The KNL1 N-terminus additionally binds and bundles microtubules through a site overlapping the PP1-docking site, rendering the two interactions mutually exclusive, and contributes independently to checkpoint silencing [#7, #18]. KNL1-recruited Bub1 licenses kinetochore Mad1-Mad2 for the 'wait anaphase' signal, operating in parallel with an RZZ-dependent pathway [#16, #19]. Beyond mitosis, KNL1 is repurposed in postmitotic C. elegans neurons, where its N-terminus initiates F-actin assembly and its PP1/SAC signaling motifs are required to shape dendrite branching and architecture [#21, #22].\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Established that KNL1 sits within a defined kinetochore assembly hierarchy and physically scaffolds the microtubule-binding machinery, answering where in kinetochore construction it acts.\",\n      \"evidence\": \"RNAi genomics, reciprocal co-IP, and epistasis in C. elegans embryos\",\n      \"pmids\": [\"14522947\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Hierarchy defined in C. elegans; vertebrate dependencies later found to differ\", \"Did not resolve the molecular interfaces with Ndc80/Mis12\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Defined KNL1's bipartite architecture in human cells \\u2014 N/middle domains binding Bub1/BubR1 TPR domains and the C-terminus binding the Mis12 complex \\u2014 explaining how it bridges checkpoint kinases to the kinetochore core.\",\n      \"evidence\": \"Domain-mapping co-IP/pulldowns and RNAi with live imaging in human cells; double-depletion epistasis in DT40\",\n      \"pmids\": [\"17981135\", \"18045986\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"TPR-binding motif identity not yet resolved\", \"Vertebrate KNL1 only partially required for Ndc80 localization, unlike worm\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Identified the RVSF motif as the PP1-docking site and showed Aurora B phosphorylation toggles it, establishing how KNL1 balances opposing kinase/phosphatase activity to control attachment stability.\",\n      \"evidence\": \"GST pulldown binding, phospho-antibodies, mutagenesis, kinetochore phosphorylation assays\",\n      \"pmids\": [\"20231380\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not address competition with other N-terminal activities\", \"Quantitative tuning of PP1 levels unresolved\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Showed PP1-RVSF binding is essential for viability via SAC silencing and must be precisely dosed, establishing that phosphatase recruitment is dynamically, not statically, regulated.\",\n      \"evidence\": \"Rapid gene replacement with allelic series and quantitative immunofluorescence in budding yeast\",\n      \"pmids\": [\"21640906\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of dynamic regulation not defined\", \"Microtubule-dependence of silencing not mechanistically resolved here\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identified MELT repeats as the Mps1-phosphorylated docking platform for Bub1/Bub3 and mapped the KI motif\\u2013Bub1 TPR interface, defining the core mechanism by which KNL1 builds the SAC signal and how its N-terminal microtubule/PP1 activities silence it.\",\n      \"evidence\": \"In vitro kinase assays, phospho-mutants, co-IP, MS, crystallography of Bub1 TPR\\u2013KI, and microtubule-binding reconstitution across fission yeast, C. elegans, and human cells\",\n      \"pmids\": [\"22660415\", \"22521786\", \"22331849\", \"22331848\", \"24344188\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"TPR-KI interaction shown insufficient alone for Bub1 recruitment (Bub3-binding segment required)\", \"Aurora B activation via KNL1 only partially explained by Bub1 (Medium-confidence #12)\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Quantified the modular logic of the MELT/KI array, showing recruitment-module number sets Bub1 levels and that a minimum of ~four active MELT repeats supports congression and SAC, explaining how scaffold output is tunable.\",\n      \"evidence\": \"Systematic domain engineering, MELT deletion series, phospho-mimetic mutants, and rescue assays in human cells\",\n      \"pmids\": [\"24344183\", \"24363448\", \"24361068\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional redundancy among individual MELTs not fully parsed\", \"How PP1 lowers Bub levels to the four-MELT setpoint not mechanistically resolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identified BubR1-associated PP2A-B56 as the phosphatase that removes Mps1-dependent MELT phosphorylation, defining the negative feedback loop that silences the SAC.\",\n      \"evidence\": \"In vitro and in vivo dephosphorylation assays, co-IP, phospho-antibodies in mammalian cells\",\n      \"pmids\": [\"25246613\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Spatiotemporal coordination with PP1-mediated silencing unresolved\", \"Did not address SHT-motif dephosphorylation\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Refined vertebrate SAC signaling by identifying the sequential SHT motif that synergizes with MELT in BUB3/BUB1 binding and showing KNL1/Bub1 acts in parallel with RZZ to localize Mad1-Mad2.\",\n      \"evidence\": \"Phospho-mutant screening, in vitro binding, BUB3 mutagenesis, RNAi/genome editing and imaging in human cells\",\n      \"pmids\": [\"25661489\", \"26581576\", \"26651294\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contributions of KBB vs RZZ pathways context-dependent\", \"RZZ recruitment mechanism partly KNL1-independent and undefined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Showed the MELT array licenses the Bub1\\u2013Mad1\\u2013Mad2 interaction, connecting Bub3 multisite binding to the actual checkpoint switch.\",\n      \"evidence\": \"Genetic epistasis, co-IP, phospho-mutant analysis in fission yeast\",\n      \"pmids\": [\"27618268\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab yeast study\", \"Structural basis of Bub1\\u2013Mad1 licensing not resolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Resolved at atomic level that PP1 and microtubule binding use overlapping KNL1 sites, establishing them as mutually exclusive and clarifying that KNL1's sole SAC-activating role downstream is tethering Mad1-Mad2, not corona formation.\",\n      \"evidence\": \"X-ray crystallography, NMR, co-sedimentation, kinase assays; CRISPR knockout with imaging in human cells\",\n      \"pmids\": [\"30100357\", \"30415700\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological switching between PP1- and microtubule-bound states not directly observed in cells\", \"Fibrous corona formation shown to depend on Rod, not KNL1\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Revealed a postmitotic moonlighting role: KNL1 and its mitotic PP1/SAC and microtubule-binding motifs, plus an N-terminal F-actin-initiating activity, shape dendrite branching and neuronal architecture.\",\n      \"evidence\": \"Neuronal-specific knockdown/knockout, gene replacement with domain-specific mutants, live imaging and F-actin staining in C. elegans PVD neurons\",\n      \"pmids\": [\"39625434\", \"38656792\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Demonstrated in C. elegans neurons only\", \"Direct biochemistry of F-actin initiation by the N-terminus not reconstituted\", \"Single lab\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Mapped extensive attachment-state-associated phosphorylation, indicating KNL1 phosphoregulation extends well beyond the MELT motifs.\",\n      \"evidence\": \"KNL1 purification and MS phosphoproteomics under microtubule-disrupting conditions in HEK293T cells\",\n      \"pmids\": [\"42058159\", \"41959482\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional roles of the 111 sites not established\", \"Responsible kinases for most sites unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How KNL1 dynamically switches between PP1-bound (silencing) and microtubule-bound states in real time, and the functional logic of its broad non-MELT phosphorylation, remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No in-cell measurement of PP1/microtubule occupancy switching\", \"Most newly identified phosphosites uncharacterized\", \"Mechanism of postmitotic neuronal repurposing only beginning to be defined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 3, 5, 9, 10]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [7, 18, 21]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3, 13]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 3, 9]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [7, 21]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0, 1, 3, 5, 9]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [21, 22]}\n    ],\n    \"complexes\": [\"KMN network (KNL1-Mis12-Ndc80)\", \"kinetochore\"],\n    \"partners\": [\"PP1\", \"BUB1\", \"BUBR1\", \"BUB3\", \"MPS1\", \"Mis12 complex\", \"NDC80\", \"PP2A-B56\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":9,"faith_total":9,"faith_pct":100.0}}