{"gene":"INO80","run_date":"2026-04-28T18:06:54","timeline":{"discoveries":[{"year":2004,"finding":"INO80 complex is recruited to DNA double-strand breaks (DSBs) through a specific interaction with phosphorylated histone H2A (γ-H2AX/γH2AX); recruitment requires the Nhp10 HMG-like subunit of INO80 and the H2A phosphoacceptor S129, and loss of INO80 impairs conversion of DSBs into ssDNA (end resection).","method":"Chromatin immunoprecipitation (ChIP) at HO endonuclease-induced DSBs in yeast; genetic analysis of H2A phosphoacceptor and Nhp10 mutants","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 — two independent labs published simultaneously with reciprocal ChIP and genetic epistasis, replicated across studies","pmids":["15607975","15607974"],"is_preprint":false},{"year":2004,"finding":"INO80 complex (containing actin-related proteins Arp5 and Arp8) is required for DNA repair at DSBs; strains lacking INO80, ARP5, or ARP8 are hypersensitive to DNA damaging agents and deficient in processing DSB ends into ssDNA.","method":"Genetic loss-of-function (deletion mutants), sensitivity assays, ChIP","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 — replicated in two simultaneous independent publications with multiple orthogonal methods","pmids":["15607975","15607974"],"is_preprint":false},{"year":2005,"finding":"The human INO80 (hINO80) complex contains orthologs of 8 of 15 yeast INO80 subunits plus at least five metazoan-specific subunits; it exhibits DNA- and nucleosome-activated ATPase activity and catalyzes ATP-dependent nucleosome sliding.","method":"Biochemical purification, mass spectrometry, in vitro ATPase and nucleosome sliding assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution of ATPase and sliding activities with purified human complex","pmids":["16230350"],"is_preprint":false},{"year":2006,"finding":"Ino80 is required for cell cycle checkpoint adaptation following a persistent DSB; loss of Ino80 results in inability to maintain high levels of H2AX phosphorylation and increased incorporation of the Htz1 (H2A.Z) histone variant at the DSB by Swr1; Ino80 and Swr1 function antagonistically at DSB-flanking chromatin.","method":"Genetic epistasis (ino80 swr1 double mutants), ChIP, checkpoint adaptation assays in yeast","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis with multiple chromatin readouts and functional checkpoint assay","pmids":["16951256"],"is_preprint":false},{"year":2007,"finding":"SWR1 is recruited to DSBs in a γH2AX-dependent manner; INO80 (but not SWR1) is responsible for removal of H2A.Z, γH2AX, and core histones near the break; INO80-specific subunits Arp8 and Nhp10 are required for Mre11 nuclease and Mec1 kinase binding at DSBs and for end-resection and checkpoint activation.","method":"ChIP at HO-induced DSBs, genetic analysis of arp8 and nhp10 mutants vs. swr1 mutants","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 — ChIP and genetic epistasis distinguishing INO80 vs. SWR1 functions at DSBs","pmids":["17762868"],"is_preprint":false},{"year":2007,"finding":"YY1 is tightly associated with the human INO80 chromatin-remodeling complex; YY1 recruits INO80 to YY1-activated target genes where INO80 functions as an essential transcriptional coactivator; binding of YY1 to its DNA target sites requires INO80 complex activity.","method":"Co-immunoprecipitation, ChIP, RNAi knockdown with transcriptional readout","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, ChIP, and functional transcription assays across two studies","pmids":["17721549","18026119"],"is_preprint":false},{"year":2007,"finding":"YY1 forms a complex with components of the INO80 chromatin-remodeling complex; both YY1 and INO80 are required for homologous recombination-based DNA repair (HRR) in mammalian cells; YY1 preferentially binds a recombination-intermediate DNA structure in vitro.","method":"Biochemical co-purification, RNAi knockdown, HR functional assays, in vitro DNA binding","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods including biochemical, genetic, and functional assays","pmids":["18026119"],"is_preprint":false},{"year":2007,"finding":"Mec1/Tel1 (ATM/ATR) kinases phosphorylate the Ies4 subunit of the INO80 complex during DNA damage; mutation of Ies4 phosphorylation sites does not affect DNA repair but influences DNA damage checkpoint responses and links INO80 to checkpoint regulators Tof1 and Rad53.","method":"In vivo phosphorylation assays, site-directed mutagenesis of Ies4 phospho-sites, checkpoint assays","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1-2 — phosphorylation mapped by MS and mutagenesis with functional checkpoint readouts","pmids":["17693258"],"is_preprint":false},{"year":2007,"finding":"The Ies3 subunit of yeast INO80 interacts with the tetratricopeptide repeat domain of telomerase subunit Est1p; INO80 subunits localize to telomeres and regulate telomere length, telomere position effect, and recombinational telomere maintenance.","method":"Co-immunoprecipitation, ChIP at telomeres, genetic analysis of IES3 and ARP8 deletions","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP and ChIP with functional telomere assays, single lab","pmids":["17562861"],"is_preprint":false},{"year":2008,"finding":"The Ino80 remodeling enzyme is required for progression of DNA replication forks and for stabilizing the replisome at stalled forks; stalling of replication forks in ino80 mutants is lethal and causes dissociation of replication machinery from stalled forks.","method":"Inducible degradation of Ino80, ChIP at replication origins, DNA fiber analysis, 2D gel electrophoresis","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 2 — inducible depletion with multiple orthogonal replication assays","pmids":["18376411"],"is_preprint":false},{"year":2008,"finding":"INO80 complex binds at replication origins and tRNA genes genome-wide; INO80 enrichment at stalled replication forks increases upon hydroxyurea treatment; ino80 mutants fail to resume DNA replication after HU block and accumulate DSBs during replication restart.","method":"Genome-wide ChIP, hydroxyurea treatment, replication restart assays in yeast","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 2 — genome-wide ChIP with functional replication restart assays","pmids":["18406137"],"is_preprint":false},{"year":2008,"finding":"Uch37 deubiquitinating enzyme is associated with the human INO80 chromatin-remodeling complex in the nucleus, where it is held in an inactive state; Uch37 DUB activity can be activated by transient interaction of the INO80 complex with the proteasome.","method":"Co-immunoprecipitation, DUB activity assays in the presence/absence of INO80 or proteasome","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1-2 — biochemical purification, activity assays, and mechanistic regulation demonstrated","pmids":["18922472"],"is_preprint":false},{"year":2009,"finding":"INO80 acts in the same genetic pathway as nucleotide excision repair (NER); Ino80 interacts with the early NER damage recognition complex Rad4-Rad23; Ino80 is recruited to chromatin by Rad4 in a UV damage-dependent manner and is required for restoration of nucleosome structure after NER, not for chromatin disruption during repair.","method":"Epistasis analysis, Co-immunoprecipitation (Ino80-Rad4-Rad23), modified ChIP assay for nucleosome restoration","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis, Co-IP, and chromatin structure assay with mechanistic resolution","pmids":["21135142"],"is_preprint":false},{"year":2010,"finding":"INO80 has a histone-exchange activity: it can replace nucleosomal H2A.Z/H2B with free H2A/H2B dimers; loss of INO80 causes mislocalization of H2A.Z genome-wide, with reduced responsiveness of H2A.Z at promoters to transcriptional changes.","method":"In vitro histone exchange assay with purified INO80, genome-wide H2A.Z ChIP in ino80 mutants","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 — reconstituted histone exchange activity in vitro combined with genome-wide ChIP","pmids":["21241891"],"is_preprint":false},{"year":2010,"finding":"INO80 promotes nucleosome spacing: it moves nucleosomes to the center of DNA with high precision and requires a minimum of 33-43 bp extranucleosomal DNA; unlike ISWI remodelers, INO80 does not require the H4 tail but is negatively regulated by the H2A tail.","method":"In vitro nucleosome sliding and spacing assays with mononucleosomes and arrays, histone tail deletion mutants","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 — reconstituted in vitro activity assays with defined histone tail requirements","pmids":["21135121"],"is_preprint":false},{"year":2010,"finding":"The mammalian INO80 complex is recruited to laser-induced DNA damage sites in an ARP8-dependent but γH2AX-independent manner, in contrast to yeast INO80 which requires Nhp10 or Arp4 for recruitment.","method":"Live imaging of GFP-tagged subunits at laser-induced damage; ARP8 knockdown","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — direct localization by live imaging with functional subunit requirement, single lab","pmids":["20971067"],"is_preprint":false},{"year":2010,"finding":"INO80 (Ino80 and Arp5 subunits) promotes removal of UV lesions by the nucleotide excision repair (NER) pathway; loss of INO80 abolishes assembly of NER factors at damage; Ino80 and Arp5 are enriched at UV-damaged DNA prior to NER incision, functioning in chromatin relaxation for NER access.","method":"Genetic deletion models, NER factor assembly ChIP, UV photoproduct removal assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — genetic model with ChIP and repair assays demonstrating mechanistic role","pmids":["20855601"],"is_preprint":false},{"year":2011,"finding":"Mammalian Ino80 mediates DSB repair through DNA end strand resection; Ino80 depletion impairs focal recruitment of 53BP1 but not Rad51 focus formation, and reduces BrdU-labeled ssDNA and RPA immunostaining, indicating a role in early 5′-3′ end resection.","method":"siRNA knockdown, comet assay, HR reporter assay, BrdU/RPA immunofluorescence","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods defining resection role in mammalian cells","pmids":["21947284"],"is_preprint":false},{"year":2011,"finding":"The human INO80 complex is organized in three modules assembling with distinct domains of hIno80 ATPase: (i) N-terminal domain with metazoan-specific subunits (dispensable for remodeling); (ii) HSA/PTH domain with Arp4, Arp8, and YY1; (iii) Snf2 ATPase domain with Ies2, Ies6, Arp5, Tip49a, and Tip49b. The evolutionarily conserved core catalyzes ATP-dependent nucleosome remodeling.","method":"Biochemical purification of subassemblies, in vitro ATPase and nucleosome remodeling assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — reconstituted subassemblies with defined activities, multiple modules characterized","pmids":["21303910"],"is_preprint":false},{"year":2011,"finding":"Loss of Ies6 or Ino80 catalytic subunit causes polyploidy and chromosome missegregation; INO80 maintains normal chromatin structure at centromeres (pericentric chromatin) and prevents misincorporation of H2A.Z into pericentric regions.","method":"Genetic deletion, ploidy analysis, chromosome segregation assays, ChIP at centromeres","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 — genetic loss-of-function with multiple phenotypic and chromatin readouts","pmids":["23207916"],"is_preprint":false},{"year":2012,"finding":"Targeting INO80 to a chromatin locus via tethering enhances chromatin mobility in a manner requiring Ino80's ATPase activity; increased chromatin mobility correlates with increased rates of spontaneous gene conversion (homologous recombination).","method":"Live fluorescence microscopy, ATPase-dead mutant analysis, gene conversion assays","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 — ATPase-dead control, live imaging quantification, and functional HR readout","pmids":["22345518"],"is_preprint":false},{"year":2013,"finding":"Nuclear actin exists as a monomer within the yeast INO80 complex; its barbed end is not accessible for polymerization; a mutation in actin subdomain 2 reduces INO80 chromatin remodeling activity in vitro and impairs nuclear functions in vivo; subdomain 2 at the pointed end contributes to INO80's interaction with chromatin.","method":"Biochemical characterization, actin mutagenesis, in vitro chromatin remodeling assays, in vivo genetic assays","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 — mutagenesis with in vitro and in vivo functional validation","pmids":["23524535"],"is_preprint":false},{"year":2013,"finding":"Arp8 of INO80 interacts with nucleosomes principally via H3 and H4 histones through an insertion in the actin fold; Arp8 forms dimers that exploit the twofold symmetry of the nucleosome core for stable histone binding.","method":"Crystal structure of yArp8CTD, biochemical binding assays, electron microscopy","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 — crystal structure combined with biochemical binding validation","pmids":["23213201"],"is_preprint":false},{"year":2013,"finding":"Ies2 is a potent activator of the intrinsic catalytic ATPase activity of the human Ino80 SNF2 ATPase; Ies6 and Arp5 together promote binding of the Ino80 ATPase to nucleosomes.","method":"In vitro ATPase assays with purified subassemblies, nucleosome binding assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 — reconstituted in vitro assays with defined subunit requirements","pmids":["24297934"],"is_preprint":false},{"year":2014,"finding":"INO80 is recruited to replication forks in human cells through interaction with ubiquitinated H2A, aided by BAP1 (a nuclear deubiquitinase that also stabilizes Ino80 protein); Ino80 promotes fork progression under normal conditions; Ino80 is essential for mouse embryonic DNA replication.","method":"Co-immunoprecipitation, ChIP at replication forks (iPOND), DNA fiber assay, mouse knockout","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods including molecular interaction, functional replication assays, and in vivo KO","pmids":["25283999"],"is_preprint":false},{"year":2014,"finding":"INO80 co-occupies pluripotency gene promoters with OCT4 and WDR5; its occupancy is dependent on OCT4 and WDR5; INO80 maintains open chromatin at pluripotency genes and licenses Mediator and RNA polymerase II recruitment for gene activation.","method":"ChIP-seq, ChIP-qPCR, RNAi depletion, ATAC/DNaseI accessibility assays, co-IP","journal":"Cell stem cell","confidence":"High","confidence_rationale":"Tier 2 — genome-wide and targeted ChIP with dependency mapping and functional transcription assays","pmids":["24792115"],"is_preprint":false},{"year":2014,"finding":"INO80 is required for DSB relocation to the inner nuclear membrane (Mps3) in S and G2 phases, requiring both INO80 activity and Rad51; this is distinct from DSB relocation to nuclear pores which is INO80-independent; SWR1-dependent H2A.Z incorporation is necessary for break relocation to either perinuclear site.","method":"Live-cell fluorescence microscopy, genetic epistasis with ino80, rad51, swr1 mutants","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 — live imaging with multiple genetic controls defining pathway position","pmids":["25066231"],"is_preprint":false},{"year":2015,"finding":"Mammalian INO80 removes H2A.Z from chromatin flanking DNA damage; the histone chaperone ANP32E similarly promotes HR and acts in the same pathway as INO80; HR defects in INO80- or ANP32E-depleted cells are rescued by co-depletion of H2A.Z, demonstrating that H2A.Z removal is the primary function of INO80 in promoting HR.","method":"RNAi depletion, ChIP, HR reporter assays, epistasis via H2A.Z co-depletion","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis with rescue experiment and chromatin assays","pmids":["26142279"],"is_preprint":false},{"year":2015,"finding":"INO80 complex interacts physically and functionally with Cdc48/p97/VCP to form a ternary complex with RNAPII; INO80 is required for turnover (degradation) of chromatin-bound ubiquitinated Rpb1 (largest RNAPII subunit) during transcriptional stress; cells lacking INO80 accumulate ubiquitinated Rpb1 on chromatin.","method":"Co-immunoprecipitation (Ino80-Cdc48-RNAPII), RNAPII ubiquitination and degradation assays, chromatin fractionation","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 — ternary complex identified by Co-IP, functional assays for RNAPII degradation","pmids":["26656161"],"is_preprint":false},{"year":2015,"finding":"The Arp5-Ies6 subcomplex forms an abundant distinct module in vivo that stimulates INO80-mediated ATPase and nucleosome sliding activity in vitro; Ies2 is required for Arp5-Ies6 association with the catalytic INO80 components; Arp5 insertion domains are required to couple ATP hydrolysis to nucleosome movement.","method":"Purification of Arp5-Ies6 subcomplex, in vitro ATPase and sliding assays, genetic and biochemical assembly analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — reconstituted subcomplex with mechanistic mutagenesis and in vitro assays","pmids":["26306040"],"is_preprint":false},{"year":2015,"finding":"The Ino80 complex directly prevents euchromatin invasion into silent chromatin; Ino80C blocks H3K79 methylation by Dot1 in vitro; heterochromatin stimulates Ino80C binding in vitro and in vivo.","method":"In vitro H3K79 methylation blocking assay with purified Ino80C and Dot1, ChIP at heterochromatin borders, genetic analysis","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 — in vitro enzymatic blocking assay with in vivo corroboration","pmids":["25691465"],"is_preprint":false},{"year":2016,"finding":"Inositol hexaphosphate (IP6) is a non-competitive inhibitor of the human INO80 complex that blocks the stimulatory effect of nucleosomes on ATPase activity; the IP6 binding site resides in the C-terminal region of the Ino80 subunit; Ies2 and Arp5/Ies6 regulate coupling of ATP hydrolysis to nucleosome sliding synergistically.","method":"In vitro ATPase and nucleosome sliding assays with purified recombinant hINO80; IP6 inhibition kinetics; subunit deletion analysis","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 — reconstituted system with mechanistic inhibitor characterization and domain mapping","pmids":["27257055"],"is_preprint":false},{"year":2016,"finding":"INO80 occupies >90% of superenhancers in melanoma; Ino80 binding reduces nucleosome occupancy and facilitates Mediator recruitment at superenhancers; occupancy is dependent on transcription factors MITF and Sox9.","method":"ChIP-seq, ATAC-seq, Co-IP, RNAi knockdown with transcriptional and tumor growth readouts","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 — genome-wide ChIP combined with mechanistic Mediator recruitment and TF dependency assays","pmids":["27340176"],"is_preprint":false},{"year":2016,"finding":"Mec1, INO80, and PAF1 complexes cooperate to degrade chromatin-bound RNAPII under replication stress; Mec1 triggers removal of PAF1C and RNAPII from transcribed genes near early firing origins during hydroxyurea treatment; failure to evict RNAPII correlates with replication fork restart defects.","method":"Genetic and proteomic analyses, ChIP of RNAPII/PAF1 in ino80 and mec1 mutants, replication restart assays","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 — multiple genetic and biochemical approaches establishing pathway relationships","pmids":["26798134"],"is_preprint":false},{"year":2017,"finding":"INO80 translocates along DNA at the H2A-H2B interface of nucleosomes (not at the H3-H4 interface as other remodelers), creating persistent DNA displacement and torsional strain near the nucleosome entry site; this mechanism promotes both nucleosome mobilization and selective exchange of H2A.Z-H2B dimers for H2A-H2B without additional histone chaperones; INO80 mobilizes H2A.Z-containing nucleosomes more efficiently than H2A-containing ones.","method":"Site-directed protein-DNA crosslinking to map translocation site, in vitro histone exchange assay without chaperones, nucleosome sliding assays comparing H2A and H2A.Z substrates","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — mechanistic mapping of translocation site by crosslinking, reconstituted exchange without chaperones","pmids":["28604691"],"is_preprint":false},{"year":2017,"finding":"INO80 complex has at least two distinct functions during homologous recombination: DNA end resection and presynaptic filament formation; the second function is linked to H2A.Z—in the absence of H2A.Z, presynaptic filament formation and HR are restored in INO80-deficient cells.","method":"High-resolution HR assay in yeast, genetic epistasis with H2A.Z deletion, fluorescence microscopy of Rad51 foci","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis with mechanistic resolution of two distinct INO80 functions in HR","pmids":["28514650"],"is_preprint":false},{"year":2017,"finding":"Cryo-EM structure of human INO80 shows the complex is assembled around a single RUVBL1/RUVBL2 AAA+ heterohexamer; a spoked-wheel structural domain of Ino80 is engulfed by this heterohexamer; a cleft in RUVBL1/RUVBL2 forms a major interaction site for partner proteins.","method":"Cryo-EM structural analysis at 9.6 Å (portions at 4.1 Å)","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 — cryo-EM structure of human complex revealing architectural mechanism","pmids":["29323271"],"is_preprint":false},{"year":2017,"finding":"Two INO80 complexes cooperate during nucleosome spacing via dimerization of the Ino80CTD; a single active ATPase motor within the dimer is sufficient for sliding; ATPase activity is not regulated per se but becomes uncoupled as sliding reaches an endpoint, controlled by Ino80CTD.","method":"Biochemical reconstitution of dimer, ATPase assays, nucleosome sliding assays with wild-type vs. dead ATPase mutants","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1 — reconstitution with mechanistic ATPase-dead mutant analysis","pmids":["28585918"],"is_preprint":false},{"year":2017,"finding":"A domain in Ino80 ATPase subunit (Ino80INS) stimulates Rvb1/Rvb2 ATPase activity 16-fold and promotes their dodecamerization; Ino80INS binds asymmetrically along the dodecamerization interface; ATP addition collapses dodecamers into hexamers, suggesting Rvbs act as protein assembly chaperones.","method":"In vitro ATPase stimulation assay, cryo-EM, mass spectrometry, integrative modeling","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 — in vitro biochemical assay combined with cryo-EM structural validation","pmids":["28591576"],"is_preprint":false},{"year":2018,"finding":"Cryo-EM structure of the evolutionarily conserved INO80 core from Chaetomium thermophilum bound to a nucleosome at 3.7-4.3 Å reveals: Rvb1/Rvb2 heterohexamer acts as a stator scaffold; the Swi2/Snf2 ATPase motor binds nucleosomal DNA at SHL -6, unwraps ~15 bp, and disrupts H2A-DNA contacts; Arp5 and Ies6 bind SHL -2/-3 as a counter-grip; the Arp5 insertion domain (grappler) connects Arp5 actin-fold and entry DNA to pack against H2A-H2B acidic patch.","method":"Cryo-EM structure at 3.7-4.3 Å resolution with functional biochemical validation","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 — near-atomic cryo-EM structure with mechanistic biochemical data","pmids":["29643509"],"is_preprint":false},{"year":2018,"finding":"Cryo-EM structure of human INO80 with bound nucleosome reveals that the motor domains are located on entry DNA rather than at SHL2 (as in other remodelers); the ARP5-IES6 module contacts the opposite side of the nucleosome; H3 histone tails regulate INO80 motor domain activity (unlike other remodelers regulated by H4 tails).","method":"Cryo-EM structural analysis at 9.6 Å with 4.1 Å local resolution; functional ATPase assays with H3 tail mutants","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 — cryo-EM structure with functional validation of H3 tail regulatory mechanism","pmids":["29643506"],"is_preprint":false},{"year":2018,"finding":"Crystal structure of the 180-kDa Arp8 module of yeast INO80 shows Arp8 engages nuclear actin distinctly from other actin-fold proteins; the HSA domain of Ino80 (spanning >120 Å) recruits the Arp4-N-actin heterodimer and provides an extended platform for extranucleosomal entry DNA required for nucleosome sliding and genome-wide nucleosome positioning.","method":"Crystal structure of Arp8 module; biochemical DNA binding assays; genome-wide nucleosome mapping in Arp8 mutants","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 — crystal structure with biochemical and genomic functional validation","pmids":["30177756"],"is_preprint":false},{"year":2018,"finding":"INO80 acts as a DNA length-sensitive switch: nucleosome sliding rate increases ~100-fold when flanking DNA increases from 40 to 60 bp; the Nhp10 module plays an auto-inhibitory role tuning this switch-like response; once initiated, INO80 moves nucleosomes processively at least 20 bp and can change direction without dissociation.","method":"Ensemble and single-molecule enzymology (FRET, single-molecule imaging), ATPase assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 — single-molecule and ensemble assays with mechanistic mutagenesis of Nhp10 module","pmids":["29452642"],"is_preprint":false},{"year":2018,"finding":"The Arp8 N-terminus, Arp4 C-terminus, and Ino80 HSA domain bind extranucleosomal DNA 37-51 bp from the nucleosome edge, acting as a DNA-length sensor; disruption of Arp8/Arp4 DNA binding uncouples ATP hydrolysis from nucleosome mobilization by disengaging Arp5 from the H2A-H2B acidic patch and the Ino80-ATPase from SHL-6.","method":"Protein-DNA crosslinking, mutagenesis of DNA-binding interfaces, in vitro nucleosome sliding and ATPase assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — mechanistic mapping with mutagenesis and reconstituted biochemical assays","pmids":["30120252"],"is_preprint":false},{"year":2019,"finding":"TRIM3 E3 ubiquitin ligase mediates degradation of INO80 in the nucleus accumbens; TRIM3-INO80 interaction is reduced during cocaine abstinence (day 30), leading to increased INO80 protein levels that regulate transcriptional programs associated with cocaine craving.","method":"Co-immunoprecipitation (TRIM3-INO80), viral gene transfer, ChIP-seq","journal":"Science advances","confidence":"Medium","confidence_rationale":"Tier 3 — Co-IP for interaction and functional behavioral assays but limited mechanistic biochemistry","pmids":["31633032"],"is_preprint":false},{"year":2019,"finding":"BAP1 promotes restart of hydroxyurea-induced stalled replication forks by stabilizing Ino80 and recruiting INO80 to stalled forks; ectopic INO80 expression rescues the fork restart defect of BAP1-depleted cells.","method":"RNAi depletion, DNA fiber assay, ChIP at stalled forks, rescue by INO80 overexpression","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 2 — mechanistic rescue experiment with ChIP and fiber assays","pmids":["31657441"],"is_preprint":false},{"year":2020,"finding":"INO80 promotes resolution of R-loops to prevent replication-associated DNA damage in cancer cells; INO80 depletion increases R-loops; overexpression of RNase H1 rescues DNA synthesis defects from INO80 depletion; R-loops co-localize with and promote INO80 recruitment; artificial INO80 tethering enables R-loop turnover in cis.","method":"siRNA depletion, R-loop immunofluorescence (S9.6 antibody), DNA fiber assay, RNase H1 rescue, LacO tethering assay","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods including RNase H1 rescue and tethering","pmids":["32913330"],"is_preprint":false},{"year":2020,"finding":"Linc-MYH lncRNA regulates the composition of the INO80 complex in muscle stem cells, preventing interaction of INO80 with WDR5 and YY1, selectively inhibiting the pro-proliferative function of INO80 without affecting its role in genome stability.","method":"RNA immunoprecipitation, Co-IP showing INO80-WDR5-YY1 interaction is blocked by linc-MYH, genetic deletion","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 3 — Co-IP and RIP with functional genetic data, single lab","pmids":["32960481"],"is_preprint":false},{"year":2021,"finding":"INO80 reads genomic information through DNA shape/mechanics encoded motifs, processing this through allosteric interplay between its core and Arp8 modules to position nucleosomes; at promoters, INO80 integrates DNA shape readout with general regulatory factor binding for +1 nucleosome positioning.","method":"Whole-genome chromatin reconstitution assays, biochemical analysis of allosteric module communication","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — genome-scale reconstitution with mechanistic dissection of allosteric regulation","pmids":["34050142"],"is_preprint":false},{"year":2021,"finding":"In primed pluripotent stem cells, INO80 promotes H2A.Z occupancy (deposition) at bivalent promoters and facilitates H3K27me3 installation and maintenance, leading to repression of developmental genes—an unexpected function opposite to INO80's known H2A.Z removal activity.","method":"Conditional Ino80 deletion, ChIP-seq for H2A.Z, H3K4me3, H3K27me3, gene expression analysis","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 — conditional KO with genome-wide chromatin and transcriptional analysis","pmids":["34139016"],"is_preprint":false},{"year":2022,"finding":"Cryo-EM structures reveal how INO80 binds and is regulated by extranucleosomal DNA: the A-module (Arp8 regulatory module) binds linker DNA and is connected to the motor via an HSA/post-HSA lever that chemomechanically couples motor activity to linker DNA sensing; two sites of curved DNA recognition coordinate sliding regulation by extranucleosomal DNA; YY1/Ies4 subunit recruitment mechanism is revealed.","method":"Cryo-EM structural analysis of multiple INO80 states; functional sliding assays","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1 — cryo-EM structures with functional validation","pmids":["36490333"],"is_preprint":false},{"year":2022,"finding":"INO80 prefers hexasomes (nucleosomes lacking one H2A-H2B dimer) as substrates over full nucleosomes by up to ~60-fold when flanking DNA approaches ~18-bp linkers; INO80 affects hexasome positioning within yeast genes in vivo; INO80 may promote nucleosome sliding by transiently dislodging H2A-H2B to make nucleosomes resemble hexasomes.","method":"In vitro sliding assays comparing nucleosome and hexasome substrates; in vivo MNase-seq in ino80 mutants","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 — reconstituted in vitro assays with in vivo genomic corroboration","pmids":["35597239"],"is_preprint":false},{"year":2023,"finding":"Cryo-EM structure of INO80-hexasome complex reveals that INO80 recognizes hexasome-specific DNA and histone features; loss of H2A-H2B triggers a large structural rearrangement (spin-rotated catalytic core) while the nuclear actin module remains tethered to unwrapped linker DNA; exposed H3-H4 interface directly activates INO80 independently of the H2A-H2B acidic patch.","method":"Cryo-EM structure of INO80-hexasome complex; functional ATPase and sliding assays","journal":"Science (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1 — near-atomic cryo-EM structure with mechanistic biochemical validation","pmids":["37384673"],"is_preprint":false},{"year":2023,"finding":"TORC1 activates Rpd3L histone deacetylase complex to deacetylate Ino80 at K929, protecting Ino80 from autophagy-mediated degradation; stabilized Ino80 then promotes H2A.Z eviction from autophagy-related gene promoters to repress their transcription; Rpd3L also deacetylates H2A.Z to block its chromatin deposition.","method":"Mass spectrometry identification of acetylation site, site-directed mutagenesis, ChIP, autophagy assays, rapamycin treatment","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1-2 — PTM site mapped by MS, mutagenesis confirms function, downstream chromatin and transcriptional consequences measured","pmids":["36888706"],"is_preprint":false},{"year":2014,"finding":"The mammalian INO80 complex is required for replication stress recovery: INO80 is specifically needed for replication elongation (not initiation); Ino80 or Arp8 depletion impairs replication restart after hydroxyurea treatment and causes DSB accumulation; INO80 protects stalled forks from collapse.","method":"siRNA depletion, DNA fiber labeling, γH2AX and Rad51 focus formation assays, comet assay","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods in mammalian cells","pmids":["25016522"],"is_preprint":false},{"year":2007,"finding":"INO80 functions in sister chromatid cohesion: Arp8 mutant cells defective in INO80 chromatin remodeling show sister chromatid cohesion defects; Ino80 directly associates with centromeres and cohesin-associated regions; in early S phase, Ino80 is recruited to replication forks with Ctf18 and PCNA; arp8 mutation impairs Ctf18 and PCNA association with forks.","method":"ChIP at centromeres and cohesin sites, cohesion assay, co-localization with Ctf18 and PCNA by ChIP","journal":"Cell cycle (Georgetown, Tex.)","confidence":"Medium","confidence_rationale":"Tier 2 — ChIP and genetic analysis, single lab","pmids":["17471029"],"is_preprint":false}],"current_model":"INO80 is a conserved, multisubunit ATP-dependent chromatin remodeling complex whose SNF2-family ATPase motor engages nucleosomal DNA at SHL-6, while the Arp5-Ies6 counter-grip module contacts the opposite face of the nucleosome at SHL-2/-3 and the Arp8-Arp4-actin regulatory module senses extranucleosomal linker DNA length to allosterically control remodeling; together these activities enable INO80 to slide nucleosomes, preferentially exchange H2A.Z/H2B dimers for H2A/H2B (and vice versa in context-dependent manner), and remodel hexasomes, thereby regulating promoter architecture, transcription, DNA damage repair (via γH2AX-dependent recruitment, end resection, and homologous recombination), replication fork progression and restart, and genome stability through control of H2A.Z distribution."},"narrative":{"teleology":[{"year":2004,"claim":"Establishing that INO80 is a DNA damage-responsive complex: it was unknown how chromatin remodelers participated in DSB repair until INO80 was shown to be recruited to breaks via γH2AX and shown to be required for end resection, placing chromatin remodeling upstream of DSB processing.","evidence":"ChIP at HO-induced DSBs in yeast with H2A-S129 and Nhp10 mutants, DNA damage sensitivity assays","pmids":["15607975","15607974"],"confidence":"High","gaps":["Mechanism of INO80-mediated resection was undefined","Whether mammalian INO80 uses the same recruitment mechanism was unknown","Direct biochemical connection between remodeling activity and resection not established"]},{"year":2005,"claim":"Demonstrating conservation of core biochemical activities: human INO80 was purified and shown to possess nucleosome-stimulated ATPase and ATP-dependent nucleosome sliding activity, establishing that the remodeling mechanism is conserved from yeast to mammals.","evidence":"Biochemical purification, mass spectrometry, in vitro ATPase and sliding assays with human INO80","pmids":["16230350"],"confidence":"High","gaps":["Histone exchange activity not yet detected","Subunit contributions to catalysis unresolved","Structural basis of sliding unknown"]},{"year":2006,"claim":"Revealing antagonism between INO80 and SWR1 at DSBs: the functional relationship between INO80 and H2A.Z was unclear until genetic epistasis showed that INO80 opposes SWR1-dependent H2A.Z incorporation at damage sites and is required for checkpoint adaptation.","evidence":"Genetic epistasis with ino80/swr1 double mutants, ChIP for H2A.Z at DSBs, checkpoint adaptation assays","pmids":["16951256"],"confidence":"High","gaps":["Whether INO80 directly removes H2A.Z biochemically was unknown","Molecular basis of INO80–SWR1 antagonism unresolved"]},{"year":2007,"claim":"Expanding INO80 functions beyond DSB repair: INO80 was linked to transcription via YY1-dependent recruitment to target genes, to homologous recombination in mammalian cells, to checkpoint signaling via Ies4 phosphorylation by Mec1/Tel1, to telomere maintenance, and to sister chromatid cohesion, revealing the complex as a multifunctional genome maintenance machine.","evidence":"Co-IP of YY1–INO80, ChIP at YY1 targets and telomeres, HR reporter assays, Ies4 phospho-site mutagenesis, cohesion assays","pmids":["17721549","18026119","17693258","17562861","17762868","17471029"],"confidence":"High","gaps":["YY1 structural role within INO80 architecture not resolved","How Ies4 phosphorylation mechanistically affects checkpoint undefined","Telomere function single-lab finding"]},{"year":2008,"claim":"Establishing INO80 as a replication fork factor: it was unknown whether chromatin remodelers directly support DNA replication until INO80 was shown to stabilize replisomes at stalled forks and to be essential for replication restart, with genome-wide enrichment at origins and stalled forks.","evidence":"Inducible Ino80 degradation, ChIP at origins, DNA fiber analysis, genome-wide ChIP, HU restart assays","pmids":["18376411","18406137"],"confidence":"High","gaps":["Mechanism of replisome stabilization unknown","Whether INO80 remodels chromatin ahead of or behind forks not determined"]},{"year":2010,"claim":"Discovering INO80's histone exchange and spacing activities: INO80 was shown to catalyze ATP-dependent replacement of H2A.Z/H2B with H2A/H2B dimers and to center nucleosomes on DNA with precise spacing rules, establishing its dual biochemical outputs and revealing it requires extranucleosomal DNA but not the H4 tail.","evidence":"In vitro histone exchange with purified INO80, genome-wide H2A.Z ChIP in ino80 mutants, nucleosome sliding/spacing with tail deletions","pmids":["21241891","21135121"],"confidence":"High","gaps":["How the same complex performs both sliding and exchange was unclear","Structural basis of H2A.Z selectivity unknown"]},{"year":2011,"claim":"Defining modular architecture and mammalian DNA repair function: the human INO80 complex was shown to comprise three functionally distinct modules assembled on different Ino80 ATPase domains, and mammalian INO80 was directly implicated in DSB end resection.","evidence":"Purification of subassemblies with in vitro ATPase assays; siRNA, comet, HR reporter, and ssDNA assays in mammalian cells","pmids":["21303910","21947284"],"confidence":"High","gaps":["How modules communicate allosterically during remodeling was not resolved","Structural architecture of nucleosome-bound complex unknown"]},{"year":2013,"claim":"Characterizing the Arp8 histone-binding and actin regulatory mechanisms: crystal structure of Arp8 revealed how it contacts H3–H4 via an actin-fold insertion, and nuclear actin was shown to function as a monomer within INO80 with subdomain 2 contributing to chromatin interaction.","evidence":"Crystal structure of Arp8CTD, actin mutagenesis with in vitro remodeling assays","pmids":["23213201","23524535","24297934"],"confidence":"High","gaps":["How Arp8 senses linker DNA was unknown","Role of nuclear actin in allosteric communication not resolved"]},{"year":2014,"claim":"Connecting INO80 to replication fork recruitment via ubiquitinated H2A/BAP1 and to pluripotency gene regulation: INO80 was shown to be recruited to forks through ubiquitinated H2A with BAP1-dependent stabilization, and to co-occupy pluripotency promoters with OCT4/WDR5 maintaining open chromatin for Mediator/Pol II recruitment.","evidence":"iPOND-ChIP, DNA fiber assays, mouse KO, ChIP-seq at pluripotency loci with RNAi dependency mapping","pmids":["25283999","25016522","24792115"],"confidence":"High","gaps":["Whether H2A ubiquitination directly regulates INO80 remodeling activity was untested","Structural basis of OCT4/WDR5-mediated recruitment unknown"]},{"year":2015,"claim":"Demonstrating that H2A.Z removal is INO80's primary HR-promoting activity and discovering new functions in heterochromatin boundary maintenance and RNAPII turnover: rescue of INO80-depleted HR defects by H2A.Z co-depletion proved that H2A.Z eviction is the critical step; separately, INO80 was shown to block Dot1-mediated H3K79 methylation at heterochromatin borders and to form a ternary complex with Cdc48/VCP for degradation of ubiquitinated Rpb1.","evidence":"H2A.Z co-depletion rescue of HR, in vitro Dot1 blocking assay, Ino80-Cdc48-RNAPII co-IP and degradation assays","pmids":["26142279","25691465","26656161","26306040"],"confidence":"High","gaps":["How INO80 physically blocks Dot1 access was structurally unresolved","Whether RNAPII degradation is coupled to remodeling activity unclear"]},{"year":2017,"claim":"Revealing the translocation mechanism and structural architecture: INO80 was shown to translocate DNA at the H2A–H2B interface (not H3–H4 as other remodelers), explaining its unique ability to exchange H2A.Z–H2B without chaperones; cryo-EM revealed assembly around a RUVBL1/2 heterohexamer stator, and dimerization via Ino80CTD was shown to enable cooperative nucleosome spacing.","evidence":"Site-directed crosslinking, chaperone-free exchange assays, cryo-EM at 9.6/4.1 Å, ATPase-dead dimer reconstitution","pmids":["28604691","29323271","28585918","28591576","28514650"],"confidence":"High","gaps":["Near-atomic resolution of nucleosome-engaged complex not yet achieved","How dimerization is regulated in vivo was unknown"]},{"year":2018,"claim":"Achieving near-atomic structural understanding of the INO80–nucleosome complex and its DNA-length sensing mechanism: cryo-EM structures at 3.7–4.3 Å revealed the motor at SHL −6 with Arp5–Ies6 counter-grip at SHL −2/−3; the Arp8 module was crystallized showing it senses linker DNA 37–51 bp from the nucleosome edge, allosterically coupling motor engagement to linker length with ~100-fold rate modulation.","evidence":"Cryo-EM of Chaetomium and human INO80–nucleosome complexes, crystal structure of Arp8 module, single-molecule FRET, protein–DNA crosslinking","pmids":["29643509","29643506","30177756","29452642","30120252"],"confidence":"High","gaps":["Structural basis for H2A.Z selectivity during exchange not resolved","How the Nhp10 auto-inhibitory mechanism couples to the structural rearrangement was not visualized"]},{"year":2020,"claim":"Discovering INO80's role in R-loop resolution: INO80 depletion increased R-loops and caused replication-associated DNA damage; RNase H1 overexpression rescued the replication defect, and artificial INO80 tethering resolved R-loops in cis, establishing a direct mechanistic link between chromatin remodeling and R-loop turnover.","evidence":"S9.6 immunofluorescence, DNA fiber assays, RNase H1 rescue, LacO tethering in cancer cells","pmids":["32913330"],"confidence":"High","gaps":["Whether INO80 displaces RNA or remodels nucleosomes to expose R-loops for resolution is unknown","Generality beyond cancer cell lines not established"]},{"year":2021,"claim":"Revealing context-dependent directionality of H2A.Z regulation and DNA-shape readout: in primed pluripotent stem cells INO80 unexpectedly promotes H2A.Z deposition and H3K27me3 at bivalent promoters; genome-wide reconstitution showed INO80 reads DNA shape/mechanics through allosteric interplay between core and Arp8 modules for +1 nucleosome positioning.","evidence":"Conditional Ino80 KO with ChIP-seq for H2A.Z/H3K27me3, whole-genome chromatin reconstitution assays","pmids":["34139016","34050142"],"confidence":"High","gaps":["Mechanism by which INO80 switches between H2A.Z removal and deposition modes is unknown","Whether DNA-shape readout contributes to damage-site targeting is untested"]},{"year":2022,"claim":"Structural elucidation of linker DNA sensing and hexasome preference: cryo-EM revealed the HSA/post-HSA lever connecting the Arp8 module to the motor for chemomechanical coupling; INO80 was shown to prefer hexasomes over nucleosomes by ~60-fold at short linkers, suggesting it remodels through transient H2A–H2B dislodgement.","evidence":"Cryo-EM of multiple INO80 conformational states, in vitro hexasome vs. nucleosome sliding assays, MNase-seq in ino80 mutants","pmids":["36490333","35597239"],"confidence":"High","gaps":["Whether hexasome intermediates form during sliding in vivo is not demonstrated","Structural basis for YY1 recruitment clarified but functional role in remodeling regulation unclear"]},{"year":2023,"claim":"Resolving hexasome recognition and post-translational regulation of Ino80 stability: cryo-EM of INO80–hexasome showed that loss of one H2A–H2B triggers a spin-rotated catalytic core activated by exposed H3–H4; TORC1-Rpd3L-mediated deacetylation of Ino80-K929 protects it from autophagic degradation, linking metabolic signaling to chromatin remodeling output.","evidence":"Cryo-EM of INO80–hexasome, ATPase/sliding assays; MS-identified acetylation site mutagenesis, rapamycin treatment, autophagy assays","pmids":["37384673","36888706"],"confidence":"High","gaps":["Whether the spin-rotation mechanism applies to full nucleosome sliding is unknown","How TORC1 regulation of Ino80 stability interfaces with other degradation pathways (e.g. TRIM3) is not integrated"]},{"year":null,"claim":"The molecular basis by which INO80 switches between H2A.Z removal and H2A.Z deposition in different genomic and cellular contexts remains unresolved, as does the structural mechanism of R-loop resolution and the in vivo relevance of hexasome intermediates during processive sliding.","evidence":"","pmids":[],"confidence":"High","gaps":["No structural or reconstitution data for context-dependent H2A.Z deposition vs. removal switch","Mechanism of R-loop resolution (direct RNA displacement vs. nucleosome remodeling) undefined","In vivo evidence for hexasome intermediates during INO80-mediated sliding lacking"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[2,14,23,29,31,34,37,39,42]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[13,34,51,52]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[41,43,48]}],"localization":[{"term_id":"GO:0005694","term_label":"chromosome","supporting_discovery_ids":[0,1,4,10,19,39,40,55]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[5,11,15,25,44]}],"pathway":[{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[2,13,14,30,34,48,51]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[0,1,3,4,12,16,17,27,35]},{"term_id":"R-HSA-69306","term_label":"DNA Replication","supporting_discovery_ids":[9,10,24,45,54]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[5,25,32,49]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[7,19,55]}],"complexes":["INO80 chromatin remodeling complex","Arp5-Ies6 subcomplex","Arp8-Arp4-actin module"],"partners":["ARP5","ARP8","IES6","RUVBL1","RUVBL2","YY1","BAP1","ACTIN"],"other_free_text":[]},"mechanistic_narrative":"INO80 is a conserved, multisubunit ATP-dependent chromatin remodeling complex that integrates nucleosome sliding, histone variant (H2A.Z) exchange, and hexasome remodeling to regulate transcription, DNA repair, replication fork stability, and genome integrity. The SNF2-family ATPase motor engages nucleosomal DNA at superhelical location −6 while the Arp5–Ies6 counter-grip module contacts SHL −2/−3, and the Arp8–Arp4–actin regulatory module senses extranucleosomal linker DNA length to allosterically gate remodeling activity, producing a DNA-length-sensitive switch with ~100-fold rate increase as flanking DNA extends from 40 to 60 bp [PMID:29452642, PMID:29643509, PMID:30120252, PMID:36490333]. INO80 is recruited to DNA double-strand breaks via γH2AX interaction and promotes end resection, H2A.Z removal, presynaptic filament formation, and DSB relocation to the nuclear periphery for homologous recombination; it similarly facilitates nucleotide excision repair by restoring nucleosome structure after lesion removal and resolves R-loops to prevent replication-associated damage [PMID:15607975, PMID:26142279, PMID:28514650, PMID:21135142, PMID:32913330]. At replication forks, INO80 stabilizes the replisome, promotes fork progression and restart after stalling—recruited via ubiquitinated H2A and stabilized by BAP1—while at gene promoters it positions the +1 nucleosome through DNA-shape readout, maintains open chromatin at pluripotency and superenhancer loci via Mediator recruitment, and context-dependently either removes or promotes H2A.Z occupancy to regulate transcriptional programs [PMID:18376411, PMID:25283999, PMID:24792115, PMID:27340176, PMID:34139016, PMID:34050142]."},"prefetch_data":{"uniprot":{"accession":"Q9ULG1","full_name":"Chromatin-remodeling ATPase INO80","aliases":["DNA helicase-related INO80 complex homolog 1","DNA helicase-related protein INO80","INO80 complex subunit A"],"length_aa":1556,"mass_kda":176.8,"function":"ATPase component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and DNA repair (PubMed:16230350, PubMed:16298340, PubMed:17721549, PubMed:20237820, PubMed:20855601). Binds DNA (PubMed:16298340, PubMed:21303910). As part of the INO80 complex, remodels chromatin by shifting nucleosomes (PubMed:16230350, PubMed:21303910). Regulates transcription upon recruitment by YY1 to YY1-activated genes, where it acts as an essential coactivator (PubMed:17721549). Involved in UV-damage excision DNA repair (PubMed:20855601). The contribution to DNA double-strand break repair appears to be largely indirect through transcriptional regulation (PubMed:20687897). Involved in DNA replication (PubMed:20237820). Required for microtubule assembly during mitosis thereby regulating chromosome segregation cycle (PubMed:20237820)","subcellular_location":"Cytoplasm; Nucleus; Cytoplasm, cytoskeleton, spindle; Chromosome","url":"https://www.uniprot.org/uniprotkb/Q9ULG1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/INO80","classification":"Common Essential","n_dependent_lines":951,"n_total_lines":1208,"dependency_fraction":0.7872516556291391},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000128908","cell_line_id":"CID001667","localizations":[{"compartment":"chromatin","grade":3}],"interactors":[{"gene":"NFRKB","stoichiometry":10.0},{"gene":"ACTR5","stoichiometry":4.0},{"gene":"RUVBL2","stoichiometry":0.2},{"gene":"RACK1","stoichiometry":0.2},{"gene":"RUVBL1","stoichiometry":0.2},{"gene":"YY1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001667","total_profiled":1310},"omim":[{"mim_id":"619730","title":"ACTIN-RELATED PROTEIN 5; ACTR5","url":"https://www.omim.org/entry/619730"},{"mim_id":"619716","title":"ACTIN-RELATED PROTEIN 8; ACTR8","url":"https://www.omim.org/entry/619716"},{"mim_id":"619207","title":"INO80 COMPLEX, SUBUNIT D; INO80D","url":"https://www.omim.org/entry/619207"},{"mim_id":"616456","title":"INO80 COMPLEX, SUBUNIT B; INO80B","url":"https://www.omim.org/entry/616456"},{"mim_id":"611421","title":"SNF2-RELATED CBP ACTIVATOR PROTEIN; SRCAP","url":"https://www.omim.org/entry/611421"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"},{"location":"Nuclear bodies","reliability":"Enhanced"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/INO80"},"hgnc":{"alias_symbol":["KIAA1259","hINO80","INO80A"],"prev_symbol":["INOC1"]},"alphafold":{"accession":"Q9ULG1","domains":[{"cath_id":"3.40.50.10810","chopping":"519-750","consensus_level":"high","plddt":82.2175,"start":519,"end":750},{"cath_id":"3.40.50.300","chopping":"771-827_1103-1271","consensus_level":"medium","plddt":82.0959,"start":771,"end":1271},{"cath_id":"1.20.5","chopping":"1272-1300","consensus_level":"medium","plddt":71.9883,"start":1272,"end":1300}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9ULG1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9ULG1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9ULG1-F1-predicted_aligned_error_v6.png","plddt_mean":65.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=INO80","jax_strain_url":"https://www.jax.org/strain/search?query=INO80"},"sequence":{"accession":"Q9ULG1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9ULG1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9ULG1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9ULG1"}},"corpus_meta":[{"pmid":"15607975","id":"PMC_15607975","title":"Recruitment of the INO80 complex by H2A phosphorylation links ATP-dependent chromatin remodeling with DNA double-strand break repair.","date":"2004","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/15607975","citation_count":484,"is_preprint":false},{"pmid":"15607974","id":"PMC_15607974","title":"INO80 and gamma-H2AX interaction links ATP-dependent chromatin remodeling to DNA damage repair.","date":"2004","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/15607974","citation_count":448,"is_preprint":false},{"pmid":"21241891","id":"PMC_21241891","title":"Global regulation of H2A.Z localization by the INO80 chromatin-remodeling enzyme is essential for genome integrity.","date":"2011","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/21241891","citation_count":337,"is_preprint":false},{"pmid":"17762868","id":"PMC_17762868","title":"Distinct roles for SWR1 and INO80 chromatin remodeling complexes at chromosomal double-strand breaks.","date":"2007","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/17762868","citation_count":253,"is_preprint":false},{"pmid":"19424290","id":"PMC_19424290","title":"Chromatin remodelling beyond transcription: the INO80 and SWR1 complexes.","date":"2009","source":"Nature reviews. 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recruitment requires the Nhp10 HMG-like subunit of INO80 and the H2A phosphoacceptor S129, and loss of INO80 impairs conversion of DSBs into ssDNA (end resection).\",\n      \"method\": \"Chromatin immunoprecipitation (ChIP) at HO endonuclease-induced DSBs in yeast; genetic analysis of H2A phosphoacceptor and Nhp10 mutants\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — two independent labs published simultaneously with reciprocal ChIP and genetic epistasis, replicated across studies\",\n      \"pmids\": [\"15607975\", \"15607974\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"INO80 complex (containing actin-related proteins Arp5 and Arp8) is required for DNA repair at DSBs; strains lacking INO80, ARP5, or ARP8 are hypersensitive to DNA damaging agents and deficient in processing DSB ends into ssDNA.\",\n      \"method\": \"Genetic loss-of-function (deletion mutants), sensitivity assays, ChIP\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — replicated in two simultaneous independent publications with multiple orthogonal methods\",\n      \"pmids\": [\"15607975\", \"15607974\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"The human INO80 (hINO80) complex contains orthologs of 8 of 15 yeast INO80 subunits plus at least five metazoan-specific subunits; it exhibits DNA- and nucleosome-activated ATPase activity and catalyzes ATP-dependent nucleosome sliding.\",\n      \"method\": \"Biochemical purification, mass spectrometry, in vitro ATPase and nucleosome sliding assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution of ATPase and sliding activities with purified human complex\",\n      \"pmids\": [\"16230350\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Ino80 is required for cell cycle checkpoint adaptation following a persistent DSB; loss of Ino80 results in inability to maintain high levels of H2AX phosphorylation and increased incorporation of the Htz1 (H2A.Z) histone variant at the DSB by Swr1; Ino80 and Swr1 function antagonistically at DSB-flanking chromatin.\",\n      \"method\": \"Genetic epistasis (ino80 swr1 double mutants), ChIP, checkpoint adaptation assays in yeast\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis with multiple chromatin readouts and functional checkpoint assay\",\n      \"pmids\": [\"16951256\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"SWR1 is recruited to DSBs in a γH2AX-dependent manner; INO80 (but not SWR1) is responsible for removal of H2A.Z, γH2AX, and core histones near the break; INO80-specific subunits Arp8 and Nhp10 are required for Mre11 nuclease and Mec1 kinase binding at DSBs and for end-resection and checkpoint activation.\",\n      \"method\": \"ChIP at HO-induced DSBs, genetic analysis of arp8 and nhp10 mutants vs. swr1 mutants\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — ChIP and genetic epistasis distinguishing INO80 vs. SWR1 functions at DSBs\",\n      \"pmids\": [\"17762868\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"YY1 is tightly associated with the human INO80 chromatin-remodeling complex; YY1 recruits INO80 to YY1-activated target genes where INO80 functions as an essential transcriptional coactivator; binding of YY1 to its DNA target sites requires INO80 complex activity.\",\n      \"method\": \"Co-immunoprecipitation, ChIP, RNAi knockdown with transcriptional readout\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, ChIP, and functional transcription assays across two studies\",\n      \"pmids\": [\"17721549\", \"18026119\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"YY1 forms a complex with components of the INO80 chromatin-remodeling complex; both YY1 and INO80 are required for homologous recombination-based DNA repair (HRR) in mammalian cells; YY1 preferentially binds a recombination-intermediate DNA structure in vitro.\",\n      \"method\": \"Biochemical co-purification, RNAi knockdown, HR functional assays, in vitro DNA binding\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods including biochemical, genetic, and functional assays\",\n      \"pmids\": [\"18026119\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Mec1/Tel1 (ATM/ATR) kinases phosphorylate the Ies4 subunit of the INO80 complex during DNA damage; mutation of Ies4 phosphorylation sites does not affect DNA repair but influences DNA damage checkpoint responses and links INO80 to checkpoint regulators Tof1 and Rad53.\",\n      \"method\": \"In vivo phosphorylation assays, site-directed mutagenesis of Ies4 phospho-sites, checkpoint assays\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — phosphorylation mapped by MS and mutagenesis with functional checkpoint readouts\",\n      \"pmids\": [\"17693258\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"The Ies3 subunit of yeast INO80 interacts with the tetratricopeptide repeat domain of telomerase subunit Est1p; INO80 subunits localize to telomeres and regulate telomere length, telomere position effect, and recombinational telomere maintenance.\",\n      \"method\": \"Co-immunoprecipitation, ChIP at telomeres, genetic analysis of IES3 and ARP8 deletions\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP and ChIP with functional telomere assays, single lab\",\n      \"pmids\": [\"17562861\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"The Ino80 remodeling enzyme is required for progression of DNA replication forks and for stabilizing the replisome at stalled forks; stalling of replication forks in ino80 mutants is lethal and causes dissociation of replication machinery from stalled forks.\",\n      \"method\": \"Inducible degradation of Ino80, ChIP at replication origins, DNA fiber analysis, 2D gel electrophoresis\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — inducible depletion with multiple orthogonal replication assays\",\n      \"pmids\": [\"18376411\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"INO80 complex binds at replication origins and tRNA genes genome-wide; INO80 enrichment at stalled replication forks increases upon hydroxyurea treatment; ino80 mutants fail to resume DNA replication after HU block and accumulate DSBs during replication restart.\",\n      \"method\": \"Genome-wide ChIP, hydroxyurea treatment, replication restart assays in yeast\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genome-wide ChIP with functional replication restart assays\",\n      \"pmids\": [\"18406137\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Uch37 deubiquitinating enzyme is associated with the human INO80 chromatin-remodeling complex in the nucleus, where it is held in an inactive state; Uch37 DUB activity can be activated by transient interaction of the INO80 complex with the proteasome.\",\n      \"method\": \"Co-immunoprecipitation, DUB activity assays in the presence/absence of INO80 or proteasome\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — biochemical purification, activity assays, and mechanistic regulation demonstrated\",\n      \"pmids\": [\"18922472\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"INO80 acts in the same genetic pathway as nucleotide excision repair (NER); Ino80 interacts with the early NER damage recognition complex Rad4-Rad23; Ino80 is recruited to chromatin by Rad4 in a UV damage-dependent manner and is required for restoration of nucleosome structure after NER, not for chromatin disruption during repair.\",\n      \"method\": \"Epistasis analysis, Co-immunoprecipitation (Ino80-Rad4-Rad23), modified ChIP assay for nucleosome restoration\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis, Co-IP, and chromatin structure assay with mechanistic resolution\",\n      \"pmids\": [\"21135142\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"INO80 has a histone-exchange activity: it can replace nucleosomal H2A.Z/H2B with free H2A/H2B dimers; loss of INO80 causes mislocalization of H2A.Z genome-wide, with reduced responsiveness of H2A.Z at promoters to transcriptional changes.\",\n      \"method\": \"In vitro histone exchange assay with purified INO80, genome-wide H2A.Z ChIP in ino80 mutants\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted histone exchange activity in vitro combined with genome-wide ChIP\",\n      \"pmids\": [\"21241891\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"INO80 promotes nucleosome spacing: it moves nucleosomes to the center of DNA with high precision and requires a minimum of 33-43 bp extranucleosomal DNA; unlike ISWI remodelers, INO80 does not require the H4 tail but is negatively regulated by the H2A tail.\",\n      \"method\": \"In vitro nucleosome sliding and spacing assays with mononucleosomes and arrays, histone tail deletion mutants\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted in vitro activity assays with defined histone tail requirements\",\n      \"pmids\": [\"21135121\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The mammalian INO80 complex is recruited to laser-induced DNA damage sites in an ARP8-dependent but γH2AX-independent manner, in contrast to yeast INO80 which requires Nhp10 or Arp4 for recruitment.\",\n      \"method\": \"Live imaging of GFP-tagged subunits at laser-induced damage; ARP8 knockdown\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct localization by live imaging with functional subunit requirement, single lab\",\n      \"pmids\": [\"20971067\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"INO80 (Ino80 and Arp5 subunits) promotes removal of UV lesions by the nucleotide excision repair (NER) pathway; loss of INO80 abolishes assembly of NER factors at damage; Ino80 and Arp5 are enriched at UV-damaged DNA prior to NER incision, functioning in chromatin relaxation for NER access.\",\n      \"method\": \"Genetic deletion models, NER factor assembly ChIP, UV photoproduct removal assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic model with ChIP and repair assays demonstrating mechanistic role\",\n      \"pmids\": [\"20855601\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Mammalian Ino80 mediates DSB repair through DNA end strand resection; Ino80 depletion impairs focal recruitment of 53BP1 but not Rad51 focus formation, and reduces BrdU-labeled ssDNA and RPA immunostaining, indicating a role in early 5′-3′ end resection.\",\n      \"method\": \"siRNA knockdown, comet assay, HR reporter assay, BrdU/RPA immunofluorescence\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods defining resection role in mammalian cells\",\n      \"pmids\": [\"21947284\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"The human INO80 complex is organized in three modules assembling with distinct domains of hIno80 ATPase: (i) N-terminal domain with metazoan-specific subunits (dispensable for remodeling); (ii) HSA/PTH domain with Arp4, Arp8, and YY1; (iii) Snf2 ATPase domain with Ies2, Ies6, Arp5, Tip49a, and Tip49b. The evolutionarily conserved core catalyzes ATP-dependent nucleosome remodeling.\",\n      \"method\": \"Biochemical purification of subassemblies, in vitro ATPase and nucleosome remodeling assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted subassemblies with defined activities, multiple modules characterized\",\n      \"pmids\": [\"21303910\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Loss of Ies6 or Ino80 catalytic subunit causes polyploidy and chromosome missegregation; INO80 maintains normal chromatin structure at centromeres (pericentric chromatin) and prevents misincorporation of H2A.Z into pericentric regions.\",\n      \"method\": \"Genetic deletion, ploidy analysis, chromosome segregation assays, ChIP at centromeres\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic loss-of-function with multiple phenotypic and chromatin readouts\",\n      \"pmids\": [\"23207916\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Targeting INO80 to a chromatin locus via tethering enhances chromatin mobility in a manner requiring Ino80's ATPase activity; increased chromatin mobility correlates with increased rates of spontaneous gene conversion (homologous recombination).\",\n      \"method\": \"Live fluorescence microscopy, ATPase-dead mutant analysis, gene conversion assays\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — ATPase-dead control, live imaging quantification, and functional HR readout\",\n      \"pmids\": [\"22345518\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Nuclear actin exists as a monomer within the yeast INO80 complex; its barbed end is not accessible for polymerization; a mutation in actin subdomain 2 reduces INO80 chromatin remodeling activity in vitro and impairs nuclear functions in vivo; subdomain 2 at the pointed end contributes to INO80's interaction with chromatin.\",\n      \"method\": \"Biochemical characterization, actin mutagenesis, in vitro chromatin remodeling assays, in vivo genetic assays\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — mutagenesis with in vitro and in vivo functional validation\",\n      \"pmids\": [\"23524535\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Arp8 of INO80 interacts with nucleosomes principally via H3 and H4 histones through an insertion in the actin fold; Arp8 forms dimers that exploit the twofold symmetry of the nucleosome core for stable histone binding.\",\n      \"method\": \"Crystal structure of yArp8CTD, biochemical binding assays, electron microscopy\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure combined with biochemical binding validation\",\n      \"pmids\": [\"23213201\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Ies2 is a potent activator of the intrinsic catalytic ATPase activity of the human Ino80 SNF2 ATPase; Ies6 and Arp5 together promote binding of the Ino80 ATPase to nucleosomes.\",\n      \"method\": \"In vitro ATPase assays with purified subassemblies, nucleosome binding assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted in vitro assays with defined subunit requirements\",\n      \"pmids\": [\"24297934\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"INO80 is recruited to replication forks in human cells through interaction with ubiquitinated H2A, aided by BAP1 (a nuclear deubiquitinase that also stabilizes Ino80 protein); Ino80 promotes fork progression under normal conditions; Ino80 is essential for mouse embryonic DNA replication.\",\n      \"method\": \"Co-immunoprecipitation, ChIP at replication forks (iPOND), DNA fiber assay, mouse knockout\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods including molecular interaction, functional replication assays, and in vivo KO\",\n      \"pmids\": [\"25283999\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"INO80 co-occupies pluripotency gene promoters with OCT4 and WDR5; its occupancy is dependent on OCT4 and WDR5; INO80 maintains open chromatin at pluripotency genes and licenses Mediator and RNA polymerase II recruitment for gene activation.\",\n      \"method\": \"ChIP-seq, ChIP-qPCR, RNAi depletion, ATAC/DNaseI accessibility assays, co-IP\",\n      \"journal\": \"Cell stem cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genome-wide and targeted ChIP with dependency mapping and functional transcription assays\",\n      \"pmids\": [\"24792115\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"INO80 is required for DSB relocation to the inner nuclear membrane (Mps3) in S and G2 phases, requiring both INO80 activity and Rad51; this is distinct from DSB relocation to nuclear pores which is INO80-independent; SWR1-dependent H2A.Z incorporation is necessary for break relocation to either perinuclear site.\",\n      \"method\": \"Live-cell fluorescence microscopy, genetic epistasis with ino80, rad51, swr1 mutants\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — live imaging with multiple genetic controls defining pathway position\",\n      \"pmids\": [\"25066231\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Mammalian INO80 removes H2A.Z from chromatin flanking DNA damage; the histone chaperone ANP32E similarly promotes HR and acts in the same pathway as INO80; HR defects in INO80- or ANP32E-depleted cells are rescued by co-depletion of H2A.Z, demonstrating that H2A.Z removal is the primary function of INO80 in promoting HR.\",\n      \"method\": \"RNAi depletion, ChIP, HR reporter assays, epistasis via H2A.Z co-depletion\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis with rescue experiment and chromatin assays\",\n      \"pmids\": [\"26142279\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"INO80 complex interacts physically and functionally with Cdc48/p97/VCP to form a ternary complex with RNAPII; INO80 is required for turnover (degradation) of chromatin-bound ubiquitinated Rpb1 (largest RNAPII subunit) during transcriptional stress; cells lacking INO80 accumulate ubiquitinated Rpb1 on chromatin.\",\n      \"method\": \"Co-immunoprecipitation (Ino80-Cdc48-RNAPII), RNAPII ubiquitination and degradation assays, chromatin fractionation\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — ternary complex identified by Co-IP, functional assays for RNAPII degradation\",\n      \"pmids\": [\"26656161\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The Arp5-Ies6 subcomplex forms an abundant distinct module in vivo that stimulates INO80-mediated ATPase and nucleosome sliding activity in vitro; Ies2 is required for Arp5-Ies6 association with the catalytic INO80 components; Arp5 insertion domains are required to couple ATP hydrolysis to nucleosome movement.\",\n      \"method\": \"Purification of Arp5-Ies6 subcomplex, in vitro ATPase and sliding assays, genetic and biochemical assembly analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted subcomplex with mechanistic mutagenesis and in vitro assays\",\n      \"pmids\": [\"26306040\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The Ino80 complex directly prevents euchromatin invasion into silent chromatin; Ino80C blocks H3K79 methylation by Dot1 in vitro; heterochromatin stimulates Ino80C binding in vitro and in vivo.\",\n      \"method\": \"In vitro H3K79 methylation blocking assay with purified Ino80C and Dot1, ChIP at heterochromatin borders, genetic analysis\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro enzymatic blocking assay with in vivo corroboration\",\n      \"pmids\": [\"25691465\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Inositol hexaphosphate (IP6) is a non-competitive inhibitor of the human INO80 complex that blocks the stimulatory effect of nucleosomes on ATPase activity; the IP6 binding site resides in the C-terminal region of the Ino80 subunit; Ies2 and Arp5/Ies6 regulate coupling of ATP hydrolysis to nucleosome sliding synergistically.\",\n      \"method\": \"In vitro ATPase and nucleosome sliding assays with purified recombinant hINO80; IP6 inhibition kinetics; subunit deletion analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted system with mechanistic inhibitor characterization and domain mapping\",\n      \"pmids\": [\"27257055\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"INO80 occupies >90% of superenhancers in melanoma; Ino80 binding reduces nucleosome occupancy and facilitates Mediator recruitment at superenhancers; occupancy is dependent on transcription factors MITF and Sox9.\",\n      \"method\": \"ChIP-seq, ATAC-seq, Co-IP, RNAi knockdown with transcriptional and tumor growth readouts\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genome-wide ChIP combined with mechanistic Mediator recruitment and TF dependency assays\",\n      \"pmids\": [\"27340176\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Mec1, INO80, and PAF1 complexes cooperate to degrade chromatin-bound RNAPII under replication stress; Mec1 triggers removal of PAF1C and RNAPII from transcribed genes near early firing origins during hydroxyurea treatment; failure to evict RNAPII correlates with replication fork restart defects.\",\n      \"method\": \"Genetic and proteomic analyses, ChIP of RNAPII/PAF1 in ino80 and mec1 mutants, replication restart assays\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple genetic and biochemical approaches establishing pathway relationships\",\n      \"pmids\": [\"26798134\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"INO80 translocates along DNA at the H2A-H2B interface of nucleosomes (not at the H3-H4 interface as other remodelers), creating persistent DNA displacement and torsional strain near the nucleosome entry site; this mechanism promotes both nucleosome mobilization and selective exchange of H2A.Z-H2B dimers for H2A-H2B without additional histone chaperones; INO80 mobilizes H2A.Z-containing nucleosomes more efficiently than H2A-containing ones.\",\n      \"method\": \"Site-directed protein-DNA crosslinking to map translocation site, in vitro histone exchange assay without chaperones, nucleosome sliding assays comparing H2A and H2A.Z substrates\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — mechanistic mapping of translocation site by crosslinking, reconstituted exchange without chaperones\",\n      \"pmids\": [\"28604691\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"INO80 complex has at least two distinct functions during homologous recombination: DNA end resection and presynaptic filament formation; the second function is linked to H2A.Z—in the absence of H2A.Z, presynaptic filament formation and HR are restored in INO80-deficient cells.\",\n      \"method\": \"High-resolution HR assay in yeast, genetic epistasis with H2A.Z deletion, fluorescence microscopy of Rad51 foci\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis with mechanistic resolution of two distinct INO80 functions in HR\",\n      \"pmids\": [\"28514650\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Cryo-EM structure of human INO80 shows the complex is assembled around a single RUVBL1/RUVBL2 AAA+ heterohexamer; a spoked-wheel structural domain of Ino80 is engulfed by this heterohexamer; a cleft in RUVBL1/RUVBL2 forms a major interaction site for partner proteins.\",\n      \"method\": \"Cryo-EM structural analysis at 9.6 Å (portions at 4.1 Å)\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structure of human complex revealing architectural mechanism\",\n      \"pmids\": [\"29323271\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Two INO80 complexes cooperate during nucleosome spacing via dimerization of the Ino80CTD; a single active ATPase motor within the dimer is sufficient for sliding; ATPase activity is not regulated per se but becomes uncoupled as sliding reaches an endpoint, controlled by Ino80CTD.\",\n      \"method\": \"Biochemical reconstitution of dimer, ATPase assays, nucleosome sliding assays with wild-type vs. dead ATPase mutants\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstitution with mechanistic ATPase-dead mutant analysis\",\n      \"pmids\": [\"28585918\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"A domain in Ino80 ATPase subunit (Ino80INS) stimulates Rvb1/Rvb2 ATPase activity 16-fold and promotes their dodecamerization; Ino80INS binds asymmetrically along the dodecamerization interface; ATP addition collapses dodecamers into hexamers, suggesting Rvbs act as protein assembly chaperones.\",\n      \"method\": \"In vitro ATPase stimulation assay, cryo-EM, mass spectrometry, integrative modeling\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro biochemical assay combined with cryo-EM structural validation\",\n      \"pmids\": [\"28591576\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Cryo-EM structure of the evolutionarily conserved INO80 core from Chaetomium thermophilum bound to a nucleosome at 3.7-4.3 Å reveals: Rvb1/Rvb2 heterohexamer acts as a stator scaffold; the Swi2/Snf2 ATPase motor binds nucleosomal DNA at SHL -6, unwraps ~15 bp, and disrupts H2A-DNA contacts; Arp5 and Ies6 bind SHL -2/-3 as a counter-grip; the Arp5 insertion domain (grappler) connects Arp5 actin-fold and entry DNA to pack against H2A-H2B acidic patch.\",\n      \"method\": \"Cryo-EM structure at 3.7-4.3 Å resolution with functional biochemical validation\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — near-atomic cryo-EM structure with mechanistic biochemical data\",\n      \"pmids\": [\"29643509\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Cryo-EM structure of human INO80 with bound nucleosome reveals that the motor domains are located on entry DNA rather than at SHL2 (as in other remodelers); the ARP5-IES6 module contacts the opposite side of the nucleosome; H3 histone tails regulate INO80 motor domain activity (unlike other remodelers regulated by H4 tails).\",\n      \"method\": \"Cryo-EM structural analysis at 9.6 Å with 4.1 Å local resolution; functional ATPase assays with H3 tail mutants\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structure with functional validation of H3 tail regulatory mechanism\",\n      \"pmids\": [\"29643506\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Crystal structure of the 180-kDa Arp8 module of yeast INO80 shows Arp8 engages nuclear actin distinctly from other actin-fold proteins; the HSA domain of Ino80 (spanning >120 Å) recruits the Arp4-N-actin heterodimer and provides an extended platform for extranucleosomal entry DNA required for nucleosome sliding and genome-wide nucleosome positioning.\",\n      \"method\": \"Crystal structure of Arp8 module; biochemical DNA binding assays; genome-wide nucleosome mapping in Arp8 mutants\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure with biochemical and genomic functional validation\",\n      \"pmids\": [\"30177756\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"INO80 acts as a DNA length-sensitive switch: nucleosome sliding rate increases ~100-fold when flanking DNA increases from 40 to 60 bp; the Nhp10 module plays an auto-inhibitory role tuning this switch-like response; once initiated, INO80 moves nucleosomes processively at least 20 bp and can change direction without dissociation.\",\n      \"method\": \"Ensemble and single-molecule enzymology (FRET, single-molecule imaging), ATPase assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — single-molecule and ensemble assays with mechanistic mutagenesis of Nhp10 module\",\n      \"pmids\": [\"29452642\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The Arp8 N-terminus, Arp4 C-terminus, and Ino80 HSA domain bind extranucleosomal DNA 37-51 bp from the nucleosome edge, acting as a DNA-length sensor; disruption of Arp8/Arp4 DNA binding uncouples ATP hydrolysis from nucleosome mobilization by disengaging Arp5 from the H2A-H2B acidic patch and the Ino80-ATPase from SHL-6.\",\n      \"method\": \"Protein-DNA crosslinking, mutagenesis of DNA-binding interfaces, in vitro nucleosome sliding and ATPase assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — mechanistic mapping with mutagenesis and reconstituted biochemical assays\",\n      \"pmids\": [\"30120252\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TRIM3 E3 ubiquitin ligase mediates degradation of INO80 in the nucleus accumbens; TRIM3-INO80 interaction is reduced during cocaine abstinence (day 30), leading to increased INO80 protein levels that regulate transcriptional programs associated with cocaine craving.\",\n      \"method\": \"Co-immunoprecipitation (TRIM3-INO80), viral gene transfer, ChIP-seq\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — Co-IP for interaction and functional behavioral assays but limited mechanistic biochemistry\",\n      \"pmids\": [\"31633032\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"BAP1 promotes restart of hydroxyurea-induced stalled replication forks by stabilizing Ino80 and recruiting INO80 to stalled forks; ectopic INO80 expression rescues the fork restart defect of BAP1-depleted cells.\",\n      \"method\": \"RNAi depletion, DNA fiber assay, ChIP at stalled forks, rescue by INO80 overexpression\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — mechanistic rescue experiment with ChIP and fiber assays\",\n      \"pmids\": [\"31657441\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"INO80 promotes resolution of R-loops to prevent replication-associated DNA damage in cancer cells; INO80 depletion increases R-loops; overexpression of RNase H1 rescues DNA synthesis defects from INO80 depletion; R-loops co-localize with and promote INO80 recruitment; artificial INO80 tethering enables R-loop turnover in cis.\",\n      \"method\": \"siRNA depletion, R-loop immunofluorescence (S9.6 antibody), DNA fiber assay, RNase H1 rescue, LacO tethering assay\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods including RNase H1 rescue and tethering\",\n      \"pmids\": [\"32913330\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Linc-MYH lncRNA regulates the composition of the INO80 complex in muscle stem cells, preventing interaction of INO80 with WDR5 and YY1, selectively inhibiting the pro-proliferative function of INO80 without affecting its role in genome stability.\",\n      \"method\": \"RNA immunoprecipitation, Co-IP showing INO80-WDR5-YY1 interaction is blocked by linc-MYH, genetic deletion\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — Co-IP and RIP with functional genetic data, single lab\",\n      \"pmids\": [\"32960481\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"INO80 reads genomic information through DNA shape/mechanics encoded motifs, processing this through allosteric interplay between its core and Arp8 modules to position nucleosomes; at promoters, INO80 integrates DNA shape readout with general regulatory factor binding for +1 nucleosome positioning.\",\n      \"method\": \"Whole-genome chromatin reconstitution assays, biochemical analysis of allosteric module communication\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — genome-scale reconstitution with mechanistic dissection of allosteric regulation\",\n      \"pmids\": [\"34050142\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In primed pluripotent stem cells, INO80 promotes H2A.Z occupancy (deposition) at bivalent promoters and facilitates H3K27me3 installation and maintenance, leading to repression of developmental genes—an unexpected function opposite to INO80's known H2A.Z removal activity.\",\n      \"method\": \"Conditional Ino80 deletion, ChIP-seq for H2A.Z, H3K4me3, H3K27me3, gene expression analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — conditional KO with genome-wide chromatin and transcriptional analysis\",\n      \"pmids\": [\"34139016\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Cryo-EM structures reveal how INO80 binds and is regulated by extranucleosomal DNA: the A-module (Arp8 regulatory module) binds linker DNA and is connected to the motor via an HSA/post-HSA lever that chemomechanically couples motor activity to linker DNA sensing; two sites of curved DNA recognition coordinate sliding regulation by extranucleosomal DNA; YY1/Ies4 subunit recruitment mechanism is revealed.\",\n      \"method\": \"Cryo-EM structural analysis of multiple INO80 states; functional sliding assays\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structures with functional validation\",\n      \"pmids\": [\"36490333\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"INO80 prefers hexasomes (nucleosomes lacking one H2A-H2B dimer) as substrates over full nucleosomes by up to ~60-fold when flanking DNA approaches ~18-bp linkers; INO80 affects hexasome positioning within yeast genes in vivo; INO80 may promote nucleosome sliding by transiently dislodging H2A-H2B to make nucleosomes resemble hexasomes.\",\n      \"method\": \"In vitro sliding assays comparing nucleosome and hexasome substrates; in vivo MNase-seq in ino80 mutants\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted in vitro assays with in vivo genomic corroboration\",\n      \"pmids\": [\"35597239\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Cryo-EM structure of INO80-hexasome complex reveals that INO80 recognizes hexasome-specific DNA and histone features; loss of H2A-H2B triggers a large structural rearrangement (spin-rotated catalytic core) while the nuclear actin module remains tethered to unwrapped linker DNA; exposed H3-H4 interface directly activates INO80 independently of the H2A-H2B acidic patch.\",\n      \"method\": \"Cryo-EM structure of INO80-hexasome complex; functional ATPase and sliding assays\",\n      \"journal\": \"Science (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — near-atomic cryo-EM structure with mechanistic biochemical validation\",\n      \"pmids\": [\"37384673\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TORC1 activates Rpd3L histone deacetylase complex to deacetylate Ino80 at K929, protecting Ino80 from autophagy-mediated degradation; stabilized Ino80 then promotes H2A.Z eviction from autophagy-related gene promoters to repress their transcription; Rpd3L also deacetylates H2A.Z to block its chromatin deposition.\",\n      \"method\": \"Mass spectrometry identification of acetylation site, site-directed mutagenesis, ChIP, autophagy assays, rapamycin treatment\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — PTM site mapped by MS, mutagenesis confirms function, downstream chromatin and transcriptional consequences measured\",\n      \"pmids\": [\"36888706\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"The mammalian INO80 complex is required for replication stress recovery: INO80 is specifically needed for replication elongation (not initiation); Ino80 or Arp8 depletion impairs replication restart after hydroxyurea treatment and causes DSB accumulation; INO80 protects stalled forks from collapse.\",\n      \"method\": \"siRNA depletion, DNA fiber labeling, γH2AX and Rad51 focus formation assays, comet assay\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods in mammalian cells\",\n      \"pmids\": [\"25016522\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"INO80 functions in sister chromatid cohesion: Arp8 mutant cells defective in INO80 chromatin remodeling show sister chromatid cohesion defects; Ino80 directly associates with centromeres and cohesin-associated regions; in early S phase, Ino80 is recruited to replication forks with Ctf18 and PCNA; arp8 mutation impairs Ctf18 and PCNA association with forks.\",\n      \"method\": \"ChIP at centromeres and cohesin sites, cohesion assay, co-localization with Ctf18 and PCNA by ChIP\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — ChIP and genetic analysis, single lab\",\n      \"pmids\": [\"17471029\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"INO80 is a conserved, multisubunit ATP-dependent chromatin remodeling complex whose SNF2-family ATPase motor engages nucleosomal DNA at SHL-6, while the Arp5-Ies6 counter-grip module contacts the opposite face of the nucleosome at SHL-2/-3 and the Arp8-Arp4-actin regulatory module senses extranucleosomal linker DNA length to allosterically control remodeling; together these activities enable INO80 to slide nucleosomes, preferentially exchange H2A.Z/H2B dimers for H2A/H2B (and vice versa in context-dependent manner), and remodel hexasomes, thereby regulating promoter architecture, transcription, DNA damage repair (via γH2AX-dependent recruitment, end resection, and homologous recombination), replication fork progression and restart, and genome stability through control of H2A.Z distribution.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"INO80 is a conserved, multisubunit ATP-dependent chromatin remodeling complex that integrates nucleosome sliding, histone variant (H2A.Z) exchange, and hexasome remodeling to regulate transcription, DNA repair, replication fork stability, and genome integrity. The SNF2-family ATPase motor engages nucleosomal DNA at superhelical location −6 while the Arp5–Ies6 counter-grip module contacts SHL −2/−3, and the Arp8–Arp4–actin regulatory module senses extranucleosomal linker DNA length to allosterically gate remodeling activity, producing a DNA-length-sensitive switch with ~100-fold rate increase as flanking DNA extends from 40 to 60 bp [PMID:29452642, PMID:29643509, PMID:30120252, PMID:36490333]. INO80 is recruited to DNA double-strand breaks via γH2AX interaction and promotes end resection, H2A.Z removal, presynaptic filament formation, and DSB relocation to the nuclear periphery for homologous recombination; it similarly facilitates nucleotide excision repair by restoring nucleosome structure after lesion removal and resolves R-loops to prevent replication-associated damage [PMID:15607975, PMID:26142279, PMID:28514650, PMID:21135142, PMID:32913330]. At replication forks, INO80 stabilizes the replisome, promotes fork progression and restart after stalling—recruited via ubiquitinated H2A and stabilized by BAP1—while at gene promoters it positions the +1 nucleosome through DNA-shape readout, maintains open chromatin at pluripotency and superenhancer loci via Mediator recruitment, and context-dependently either removes or promotes H2A.Z occupancy to regulate transcriptional programs [PMID:18376411, PMID:25283999, PMID:24792115, PMID:27340176, PMID:34139016, PMID:34050142].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Establishing that INO80 is a DNA damage-responsive complex: it was unknown how chromatin remodelers participated in DSB repair until INO80 was shown to be recruited to breaks via γH2AX and shown to be required for end resection, placing chromatin remodeling upstream of DSB processing.\",\n      \"evidence\": \"ChIP at HO-induced DSBs in yeast with H2A-S129 and Nhp10 mutants, DNA damage sensitivity assays\",\n      \"pmids\": [\"15607975\", \"15607974\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of INO80-mediated resection was undefined\", \"Whether mammalian INO80 uses the same recruitment mechanism was unknown\", \"Direct biochemical connection between remodeling activity and resection not established\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Demonstrating conservation of core biochemical activities: human INO80 was purified and shown to possess nucleosome-stimulated ATPase and ATP-dependent nucleosome sliding activity, establishing that the remodeling mechanism is conserved from yeast to mammals.\",\n      \"evidence\": \"Biochemical purification, mass spectrometry, in vitro ATPase and sliding assays with human INO80\",\n      \"pmids\": [\"16230350\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Histone exchange activity not yet detected\", \"Subunit contributions to catalysis unresolved\", \"Structural basis of sliding unknown\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Revealing antagonism between INO80 and SWR1 at DSBs: the functional relationship between INO80 and H2A.Z was unclear until genetic epistasis showed that INO80 opposes SWR1-dependent H2A.Z incorporation at damage sites and is required for checkpoint adaptation.\",\n      \"evidence\": \"Genetic epistasis with ino80/swr1 double mutants, ChIP for H2A.Z at DSBs, checkpoint adaptation assays\",\n      \"pmids\": [\"16951256\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether INO80 directly removes H2A.Z biochemically was unknown\", \"Molecular basis of INO80–SWR1 antagonism unresolved\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Expanding INO80 functions beyond DSB repair: INO80 was linked to transcription via YY1-dependent recruitment to target genes, to homologous recombination in mammalian cells, to checkpoint signaling via Ies4 phosphorylation by Mec1/Tel1, to telomere maintenance, and to sister chromatid cohesion, revealing the complex as a multifunctional genome maintenance machine.\",\n      \"evidence\": \"Co-IP of YY1–INO80, ChIP at YY1 targets and telomeres, HR reporter assays, Ies4 phospho-site mutagenesis, cohesion assays\",\n      \"pmids\": [\"17721549\", \"18026119\", \"17693258\", \"17562861\", \"17762868\", \"17471029\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"YY1 structural role within INO80 architecture not resolved\", \"How Ies4 phosphorylation mechanistically affects checkpoint undefined\", \"Telomere function single-lab finding\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Establishing INO80 as a replication fork factor: it was unknown whether chromatin remodelers directly support DNA replication until INO80 was shown to stabilize replisomes at stalled forks and to be essential for replication restart, with genome-wide enrichment at origins and stalled forks.\",\n      \"evidence\": \"Inducible Ino80 degradation, ChIP at origins, DNA fiber analysis, genome-wide ChIP, HU restart assays\",\n      \"pmids\": [\"18376411\", \"18406137\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of replisome stabilization unknown\", \"Whether INO80 remodels chromatin ahead of or behind forks not determined\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Discovering INO80's histone exchange and spacing activities: INO80 was shown to catalyze ATP-dependent replacement of H2A.Z/H2B with H2A/H2B dimers and to center nucleosomes on DNA with precise spacing rules, establishing its dual biochemical outputs and revealing it requires extranucleosomal DNA but not the H4 tail.\",\n      \"evidence\": \"In vitro histone exchange with purified INO80, genome-wide H2A.Z ChIP in ino80 mutants, nucleosome sliding/spacing with tail deletions\",\n      \"pmids\": [\"21241891\", \"21135121\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How the same complex performs both sliding and exchange was unclear\", \"Structural basis of H2A.Z selectivity unknown\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Defining modular architecture and mammalian DNA repair function: the human INO80 complex was shown to comprise three functionally distinct modules assembled on different Ino80 ATPase domains, and mammalian INO80 was directly implicated in DSB end resection.\",\n      \"evidence\": \"Purification of subassemblies with in vitro ATPase assays; siRNA, comet, HR reporter, and ssDNA assays in mammalian cells\",\n      \"pmids\": [\"21303910\", \"21947284\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How modules communicate allosterically during remodeling was not resolved\", \"Structural architecture of nucleosome-bound complex unknown\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Characterizing the Arp8 histone-binding and actin regulatory mechanisms: crystal structure of Arp8 revealed how it contacts H3–H4 via an actin-fold insertion, and nuclear actin was shown to function as a monomer within INO80 with subdomain 2 contributing to chromatin interaction.\",\n      \"evidence\": \"Crystal structure of Arp8CTD, actin mutagenesis with in vitro remodeling assays\",\n      \"pmids\": [\"23213201\", \"23524535\", \"24297934\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How Arp8 senses linker DNA was unknown\", \"Role of nuclear actin in allosteric communication not resolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Connecting INO80 to replication fork recruitment via ubiquitinated H2A/BAP1 and to pluripotency gene regulation: INO80 was shown to be recruited to forks through ubiquitinated H2A with BAP1-dependent stabilization, and to co-occupy pluripotency promoters with OCT4/WDR5 maintaining open chromatin for Mediator/Pol II recruitment.\",\n      \"evidence\": \"iPOND-ChIP, DNA fiber assays, mouse KO, ChIP-seq at pluripotency loci with RNAi dependency mapping\",\n      \"pmids\": [\"25283999\", \"25016522\", \"24792115\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether H2A ubiquitination directly regulates INO80 remodeling activity was untested\", \"Structural basis of OCT4/WDR5-mediated recruitment unknown\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Demonstrating that H2A.Z removal is INO80's primary HR-promoting activity and discovering new functions in heterochromatin boundary maintenance and RNAPII turnover: rescue of INO80-depleted HR defects by H2A.Z co-depletion proved that H2A.Z eviction is the critical step; separately, INO80 was shown to block Dot1-mediated H3K79 methylation at heterochromatin borders and to form a ternary complex with Cdc48/VCP for degradation of ubiquitinated Rpb1.\",\n      \"evidence\": \"H2A.Z co-depletion rescue of HR, in vitro Dot1 blocking assay, Ino80-Cdc48-RNAPII co-IP and degradation assays\",\n      \"pmids\": [\"26142279\", \"25691465\", \"26656161\", \"26306040\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How INO80 physically blocks Dot1 access was structurally unresolved\", \"Whether RNAPII degradation is coupled to remodeling activity unclear\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Revealing the translocation mechanism and structural architecture: INO80 was shown to translocate DNA at the H2A–H2B interface (not H3–H4 as other remodelers), explaining its unique ability to exchange H2A.Z–H2B without chaperones; cryo-EM revealed assembly around a RUVBL1/2 heterohexamer stator, and dimerization via Ino80CTD was shown to enable cooperative nucleosome spacing.\",\n      \"evidence\": \"Site-directed crosslinking, chaperone-free exchange assays, cryo-EM at 9.6/4.1 Å, ATPase-dead dimer reconstitution\",\n      \"pmids\": [\"28604691\", \"29323271\", \"28585918\", \"28591576\", \"28514650\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Near-atomic resolution of nucleosome-engaged complex not yet achieved\", \"How dimerization is regulated in vivo was unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Achieving near-atomic structural understanding of the INO80–nucleosome complex and its DNA-length sensing mechanism: cryo-EM structures at 3.7–4.3 Å revealed the motor at SHL −6 with Arp5–Ies6 counter-grip at SHL −2/−3; the Arp8 module was crystallized showing it senses linker DNA 37–51 bp from the nucleosome edge, allosterically coupling motor engagement to linker length with ~100-fold rate modulation.\",\n      \"evidence\": \"Cryo-EM of Chaetomium and human INO80–nucleosome complexes, crystal structure of Arp8 module, single-molecule FRET, protein–DNA crosslinking\",\n      \"pmids\": [\"29643509\", \"29643506\", \"30177756\", \"29452642\", \"30120252\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis for H2A.Z selectivity during exchange not resolved\", \"How the Nhp10 auto-inhibitory mechanism couples to the structural rearrangement was not visualized\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Discovering INO80's role in R-loop resolution: INO80 depletion increased R-loops and caused replication-associated DNA damage; RNase H1 overexpression rescued the replication defect, and artificial INO80 tethering resolved R-loops in cis, establishing a direct mechanistic link between chromatin remodeling and R-loop turnover.\",\n      \"evidence\": \"S9.6 immunofluorescence, DNA fiber assays, RNase H1 rescue, LacO tethering in cancer cells\",\n      \"pmids\": [\"32913330\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether INO80 displaces RNA or remodels nucleosomes to expose R-loops for resolution is unknown\", \"Generality beyond cancer cell lines not established\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Revealing context-dependent directionality of H2A.Z regulation and DNA-shape readout: in primed pluripotent stem cells INO80 unexpectedly promotes H2A.Z deposition and H3K27me3 at bivalent promoters; genome-wide reconstitution showed INO80 reads DNA shape/mechanics through allosteric interplay between core and Arp8 modules for +1 nucleosome positioning.\",\n      \"evidence\": \"Conditional Ino80 KO with ChIP-seq for H2A.Z/H3K27me3, whole-genome chromatin reconstitution assays\",\n      \"pmids\": [\"34139016\", \"34050142\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which INO80 switches between H2A.Z removal and deposition modes is unknown\", \"Whether DNA-shape readout contributes to damage-site targeting is untested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Structural elucidation of linker DNA sensing and hexasome preference: cryo-EM revealed the HSA/post-HSA lever connecting the Arp8 module to the motor for chemomechanical coupling; INO80 was shown to prefer hexasomes over nucleosomes by ~60-fold at short linkers, suggesting it remodels through transient H2A–H2B dislodgement.\",\n      \"evidence\": \"Cryo-EM of multiple INO80 conformational states, in vitro hexasome vs. nucleosome sliding assays, MNase-seq in ino80 mutants\",\n      \"pmids\": [\"36490333\", \"35597239\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether hexasome intermediates form during sliding in vivo is not demonstrated\", \"Structural basis for YY1 recruitment clarified but functional role in remodeling regulation unclear\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Resolving hexasome recognition and post-translational regulation of Ino80 stability: cryo-EM of INO80–hexasome showed that loss of one H2A–H2B triggers a spin-rotated catalytic core activated by exposed H3–H4; TORC1-Rpd3L-mediated deacetylation of Ino80-K929 protects it from autophagic degradation, linking metabolic signaling to chromatin remodeling output.\",\n      \"evidence\": \"Cryo-EM of INO80–hexasome, ATPase/sliding assays; MS-identified acetylation site mutagenesis, rapamycin treatment, autophagy assays\",\n      \"pmids\": [\"37384673\", \"36888706\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the spin-rotation mechanism applies to full nucleosome sliding is unknown\", \"How TORC1 regulation of Ino80 stability interfaces with other degradation pathways (e.g. TRIM3) is not integrated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular basis by which INO80 switches between H2A.Z removal and H2A.Z deposition in different genomic and cellular contexts remains unresolved, as does the structural mechanism of R-loop resolution and the in vivo relevance of hexasome intermediates during processive sliding.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural or reconstitution data for context-dependent H2A.Z deposition vs. removal switch\", \"Mechanism of R-loop resolution (direct RNA displacement vs. nucleosome remodeling) undefined\", \"In vivo evidence for hexasome intermediates during INO80-mediated sliding lacking\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [2, 14, 23, 29, 31, 34, 37, 39, 42]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [13, 34, 51, 52]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [41, 43, 48]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005694\", \"supporting_discovery_ids\": [0, 1, 4, 10, 19, 39, 40, 55]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [5, 11, 15, 25, 44]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [2, 13, 14, 30, 34, 48, 51]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [0, 1, 3, 4, 12, 16, 17, 27, 35]},\n      {\"term_id\": \"R-HSA-69306\", \"supporting_discovery_ids\": [9, 10, 24, 45, 54]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [5, 25, 32, 49]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [7, 19, 55]}\n    ],\n    \"complexes\": [\n      \"INO80 chromatin remodeling complex\",\n      \"Arp5-Ies6 subcomplex\",\n      \"Arp8-Arp4-actin module\"\n    ],\n    \"partners\": [\n      \"ARP5\",\n      \"ARP8\",\n      \"IES6\",\n      \"RUVBL1\",\n      \"RUVBL2\",\n      \"YY1\",\n      \"BAP1\",\n      \"ACTIN\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}