{"gene":"INO80B","run_date":"2026-06-10T01:55:23","timeline":{"discoveries":[{"year":2011,"finding":"INO80B (hIes2) is a subunit of the human INO80 chromatin-remodeling complex, residing in the core module that also contains the hIno80 Snf2 ATPase domain, Ies6, AAA+ ATPases Tip49a/Tip49b, and Arp5. This core complex catalyzes ATP-dependent nucleosome remodeling; the metazoan-specific module (which does not contain Ies2) is dispensable for this activity.","method":"Biochemical purification of hINO80 subassemblies, ATP-dependent nucleosome remodeling assays, characterization of modular assembly via domain mapping of hIno80","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution of subassemblies with functional nucleosome remodeling assays; module assignment validated by multiple biochemical approaches in a focused mechanistic study","pmids":["21303910"],"is_preprint":false},{"year":2013,"finding":"INO80B (hIes2/Ies2) functions as a potent activator of the intrinsic ATPase catalytic activity of the Ino80 SNF2 ATPase within the human INO80 complex, acting at the level of the enzyme's intrinsic catalytic rate rather than substrate (nucleosome) binding.","method":"Biochemical reconstitution of INO80 subcomplexes with and without Ies2; ATPase activity assays comparing complexes; subunit-specific dissection of regulatory contributions","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with defined subcomplexes and direct ATPase activity measurement; single lab but multiple orthogonal biochemical approaches","pmids":["24297934"],"is_preprint":false},{"year":2016,"finding":"Ies2 (INO80B ortholog in S. cerevisiae) is required for the stable association of the Arp5-Ies6 module with the catalytic components of the INO80 complex; deletion of IES2 results in loss of Arp5-Ies6 chromatin association. Ectopic addition of wild-type Arp5-Ies6 stimulates INO80-mediated ATP hydrolysis and nucleosome sliding in vitro, coupling ATPase activity to productive nucleosome movement.","method":"Genetic deletion of IES2 and INO80 in yeast, co-immunoprecipitation to assess module assembly, chromatin association assays, in vitro ATP hydrolysis and nucleosome sliding assays with reconstituted complexes","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — genetic epistasis combined with in vitro reconstitution and functional assays (ATPase, nucleosome sliding); multiple orthogonal approaches in a single focused study","pmids":["26306040"],"is_preprint":false},{"year":2016,"finding":"Ies2 (INO80B ortholog) functions as a regulatory subunit of the recombinant minimal human INO80 core complex. Removal of Ies2 from the complex reveals that it controls coupling of ATPase activity to nucleosome sliding; this coupling can be bypassed by a specific bypass mutation in Arp5, indicating Ies2 and Arp5/Ies6 act synergistically to link ATP hydrolysis to productive nucleosome movement. Inositol hexaphosphate (IP6) is a non-competitive inhibitor acting by blocking the stimulatory effect of nucleosomes on ATPase activity, with the binding site in the C-terminal region of Ino80.","method":"Recombinant expression and purification of minimal human INO80 core complex in insect cells; preparation of subcomplexes lacking Ies2 and/or Arp5/Ies6; ATPase activity assays; nucleosome sliding assays; IP6 inhibition kinetics; bypass mutagenesis of Arp5","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — fully recombinant system with reconstitution, mutagenesis, and multiple functional assays; single lab with multiple orthogonal approaches","pmids":["27257055"],"is_preprint":false},{"year":2009,"finding":"Deletion of ies2 in fission yeast causes defects in DNA damage repair, response to replication stress, and nucleotide metabolism, placing Ies2 functionally within the INO80 complex for these cellular processes.","method":"Gene deletion in Schizosaccharomyces pombe; phenotypic analysis of DNA damage sensitivity and nucleotide metabolism defects; purification of fission yeast Ino80 complex","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean loss-of-function genetic analysis with specific phenotypic readouts; ortholog (fission yeast) with conserved complex; replicated across multiple deletion strains in a single study","pmids":["19933844"],"is_preprint":false},{"year":2004,"finding":"PAPA-1 (INO80B) is localized to the nucleolus in transfected HeLa cells, and its lysine/histidine cluster is essential for nucleolar localization. Ectopic expression of PAPA-1 induces growth suppression and cell cycle arrest at the G1 phase in a nucleolar-localization-dependent manner; expression of a deletion mutant lacking nucleolar localization abolishes the growth-suppressive effect.","method":"Transfection and confocal microscopy for subcellular localization; tetracycline-inducible expression system in HeLa cells; cell cycle analysis by flow cytometry after synchronization with thymidine, colcemid, or mimosine; deletion mutant analysis","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — direct subcellular localization by imaging tied to functional consequence (growth arrest), with domain deletion mutants confirming causality; single lab, multiple cell-based approaches","pmids":["15556297"],"is_preprint":false},{"year":2008,"finding":"PAPA-1 (INO80B) interacts with IGFBP-2 in the nucleus of prostate cancer cells. PAPA-1 suppresses IGFBP-2-mediated growth promotion: siRNA-mediated knockdown of PAPA-1 enhances IGFBP-2-promoted cell growth, while overexpression of PAPA-1 abolishes IGFBP-2-promoted BrdU incorporation. In IGFBP-2 knockout MEFs, FLAG-mPAPA-1 overexpression decreased cell proliferation, but not in wild-type MEFs.","method":"Yeast two-hybrid screen to identify interaction; co-immunoprecipitation and GST pull-down to confirm binding; confocal microscopy for nuclear co-localization; siRNA knockdown; overexpression in LNCaP cells with BrdU incorporation assay; IGFBP-2 knockout MEFs","journal":"Molecular endocrinology (Baltimore, Md.)","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — reciprocal biochemical confirmation of interaction (Co-IP + pulldown), functional epistasis via KD and OE with specific proliferation readout; single lab with multiple orthogonal methods","pmids":["19095771"],"is_preprint":false},{"year":2008,"finding":"In S. cerevisiae, heterozygous diploids for ies2 mutations show impaired DNA repair, demonstrating that the dosage of Ies2 (INO80B ortholog) is important for DNA repair capacity.","method":"Transposon mutagenesis and targeted gene deletions in haploid and diploid yeast; DNA repair assays in heterozygous diploids","journal":"FEBS letters","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single genetic observation in yeast with a functional readout (DNA repair), but limited mechanistic detail and single method","pmids":["18211810"],"is_preprint":false},{"year":2023,"finding":"INO80B (Ies2) subunit of the human INO80 complex participates in transcriptional control of miR-372; knockdown of Ies2 (along with other INO80 subunits) significantly increases miR-372 expression levels, and miR-372 mimics in turn suppress INO80 and Arp8 expression, establishing a mutual regulatory feedback loop. The interaction between the INO80 complex and the p53/p21 signaling pathway is implicated in this regulation.","method":"RNA-seq analysis; siRNA knockdown of multiple INO80 subunits including Ies2; miR-372 mimic transfection; luciferase reporter assays with 3'-UTR constructs and mutagenized binding sites; cell proliferation assays","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — luciferase reporter with mutagenized binding sites validates target relationship; knockdown of specific subunit (Ies2) with defined transcriptional readout; single lab, multiple methods","pmids":["37445863"],"is_preprint":false},{"year":2026,"finding":"Cryo-EM structures of human INO80 bound to canonical H2A nucleosomes, H2A.Z nucleosomes, and hexasomes reveal that IES2 (INO80B) contacts the nucleosome acidic patch. IES2 acidic patch binding can differentiate between nucleosomal and hexasomal substrates: it is important for nucleosome sliding but not hexasome sliding. INO80 adopts different positions on nucleosomes vs. hexasomes governed by entry DNA unwrapping, and IES2 may sense unwrapped exit DNA. Human INO80 slides hexasomes as efficiently as nucleosomes.","method":"Cryo-EM structure determination of human INO80 bound to canonical nucleosomes, H2A.Z nucleosomes, and hexasomes; in vitro nucleosome and hexasome sliding assays; structural analysis of IES2-acidic patch contacts","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structures with functional validation via in vitro sliding assays; mechanistic assignment of IES2 to acidic patch binding and substrate discrimination in a single rigorous study","pmids":["41775336"],"is_preprint":false}],"current_model":"INO80B (hIes2/Ies2) is an evolutionarily conserved subunit of the INO80 ATP-dependent chromatin-remodeling complex that serves multiple regulatory roles: it directly activates the intrinsic ATPase catalytic activity of the Ino80 SNF2 ATPase, is required for stable assembly of the Arp5-Ies6 module onto the catalytic core (thereby coupling ATP hydrolysis to productive nucleosome sliding), and contacts the nucleosome acidic patch to discriminate between canonical nucleosomes and hexasomes—being essential for nucleosome but not hexasome sliding; when expressed independently of the complex, INO80B localizes to the nucleolus via its lysine/histidine cluster and suppresses cell proliferation by inducing G1 arrest, and it also interacts in the nucleus with IGFBP-2 to antagonize its growth-promoting activity."},"narrative":{"mechanistic_narrative":"INO80B (also called hIes2/Ies2 and PAPA-1) is an evolutionarily conserved regulatory subunit of the INO80 ATP-dependent chromatin-remodeling complex, residing in the catalytic core module alongside the Ino80 SNF2 ATPase, Ies6, Tip49a/Tip49b, and Arp5 [PMID:21303910]. Mechanistically, INO80B is a potent activator of the intrinsic ATPase rate of the Ino80 SNF2 ATPase, acting on the enzyme's catalytic turnover rather than on nucleosome binding [PMID:24297934]. It is also required for stable assembly of the Arp5-Ies6 module onto the catalytic core, and through this it couples ATP hydrolysis to productive nucleosome sliding—a coupling that can be restored by a bypass mutation in Arp5, indicating that INO80B and Arp5/Ies6 act synergistically [PMID:26306040, PMID:27257055]. Cryo-EM structures show INO80B contacts the nucleosome acidic patch and uses this contact to discriminate substrates, being essential for canonical nucleosome sliding but dispensable for hexasome sliding [PMID:41775336]. Consistent with a chromatin-remodeling role, loss of the Ies2 ortholog impairs DNA damage repair and the replication-stress response [PMID:19933844]. Independently of the complex, INO80B localizes to the nucleolus via its lysine/histidine cluster and suppresses proliferation by inducing G1 arrest in a nucleolar-localization-dependent manner [PMID:15556297], and it binds IGFBP-2 in the nucleus to antagonize IGFBP-2-driven growth [PMID:19095771].","teleology":[{"year":2004,"claim":"Before its role in chromatin remodeling was known, the question was whether PAPA-1/INO80B had an autonomous cellular function; this established it as a nucleolar protein that restrains the cell cycle.","evidence":"Confocal imaging and inducible expression with deletion mutants in HeLa cells","pmids":["15556297"],"confidence":"Medium","gaps":["Does not connect nucleolar growth suppression to the INO80 complex","Molecular targets of the G1 arrest not identified"]},{"year":2008,"claim":"To find a functional partner explaining the growth suppression, an interaction screen identified IGFBP-2 as a nuclear binding partner that INO80B antagonizes.","evidence":"Yeast two-hybrid, Co-IP, GST pull-down, siRNA/overexpression proliferation assays in prostate cancer cells and IGFBP-2 KO MEFs","pmids":["19095771"],"confidence":"Medium","gaps":["Mechanism by which binding antagonizes IGFBP-2 signaling unresolved","Relationship to nucleolar localization not established"]},{"year":2008,"claim":"An open question was whether Ies2 dosage matters for genome maintenance; heterozygous yeast diploids showed gene dosage affects DNA repair capacity.","evidence":"Transposon mutagenesis and DNA repair assays in haploid/diploid S. cerevisiae","pmids":["18211810"],"confidence":"Low","gaps":["Single genetic observation with limited mechanistic detail","No molecular link to remodeling activity"]},{"year":2009,"claim":"It was unclear which cellular processes require Ies2 within INO80; deletion in fission yeast placed it in DNA damage repair, replication-stress response, and nucleotide metabolism.","evidence":"ies2 deletion and phenotypic analysis in S. pombe with complex purification","pmids":["19933844"],"confidence":"Medium","gaps":["Does not define the biochemical contribution of Ies2 to the complex","Phenotypes not yet mapped to remodeling mechanism"]},{"year":2011,"claim":"The architectural question of where INO80B sits in the human complex was answered by assigning it to the catalytic core module rather than the dispensable metazoan-specific module.","evidence":"Biochemical purification of hINO80 subassemblies, domain mapping, and ATP-dependent remodeling assays","pmids":["21303910"],"confidence":"High","gaps":["Does not define INO80B's specific biochemical activity within the core"]},{"year":2013,"claim":"Having placed INO80B in the core, the question became what it does there; reconstitution showed it directly activates the intrinsic catalytic rate of the Ino80 ATPase.","evidence":"Reconstitution of INO80 subcomplexes ± Ies2 with direct ATPase measurements","pmids":["24297934"],"confidence":"High","gaps":["How activation translates to nucleosome movement not yet defined","Structural basis of ATPase stimulation unknown"]},{"year":2016,"claim":"Two studies resolved how INO80B couples catalysis to remodeling: it is required for stable Arp5-Ies6 module assembly and links ATP hydrolysis to productive nucleosome sliding, bypassable by an Arp5 mutation.","evidence":"Yeast IES2 deletion with Co-IP and chromatin-association assays; recombinant minimal human INO80 core ± Ies2 with sliding/ATPase assays and Arp5 bypass mutagenesis","pmids":["26306040","27257055"],"confidence":"High","gaps":["Atomic-level basis of the Ies2-Arp5/Ies6 synergy not visualized at this stage"]},{"year":2023,"claim":"The question of INO80B's role in transcriptional output identified its participation in a miR-372 regulatory feedback loop tied to p53/p21 signaling.","evidence":"RNA-seq, siRNA knockdown of INO80 subunits including Ies2, miR-372 mimics, and luciferase reporter assays","pmids":["37445863"],"confidence":"Medium","gaps":["Direct chromatin targets of the loop not mapped","Specific contribution of Ies2 versus other subunits not isolated"]},{"year":2026,"claim":"The structural basis of INO80B's substrate selectivity was resolved: it contacts the nucleosome acidic patch to discriminate nucleosomes from hexasomes, being essential for nucleosome but not hexasome sliding.","evidence":"Cryo-EM of human INO80 on canonical, H2A.Z, and hexasome substrates with in vitro sliding assays","pmids":["41775336"],"confidence":"High","gaps":["How acidic-patch sensing is communicated to the ATPase not fully detailed","In vivo consequence of hexasome-vs-nucleosome discrimination untested"]},{"year":null,"claim":"It remains unresolved how INO80B's complex-bound remodeling role mechanistically connects to its complex-independent nucleolar, IGFBP-2-antagonizing, and growth-suppressive functions.","evidence":"","pmids":[],"confidence":"Low","gaps":["No experiment unifies the chromatin-remodeling and free-protein activities","Whether nucleolar INO80B acts within or outside the complex is unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1,2,3]},{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[1,2,3]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[5]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[0,1,2,3,9]},{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[4]}],"complexes":["INO80 chromatin-remodeling complex"],"partners":["INO80","ARP5","IES6","IGFBP2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9C086","full_name":"INO80 complex subunit B","aliases":["High mobility group AT-hook 1-like 4","IES2 homolog","hIes2","PAP-1-associated protein 1","PAPA-1","Zinc finger HIT domain-containing protein 4"],"length_aa":356,"mass_kda":38.6,"function":"Induces growth and cell cycle arrests at the G1 phase of the cell cycle Proposed core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair","subcellular_location":"Nucleus; Nucleus, nucleolus","url":"https://www.uniprot.org/uniprotkb/Q9C086/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/INO80B","classification":"Common Essential","n_dependent_lines":549,"n_total_lines":1208,"dependency_fraction":0.4544701986754967},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/INO80B","total_profiled":1310},"omim":[{"mim_id":"616456","title":"INO80 COMPLEX, SUBUNIT B; INO80B","url":"https://www.omim.org/entry/616456"},{"mim_id":"607331","title":"RP9 PRE-mRNA SPLICING FACTOR; RP9","url":"https://www.omim.org/entry/607331"},{"mim_id":"606961","title":"WW DOMAIN-BINDING PROTEIN 1; WBP1","url":"https://www.omim.org/entry/606961"},{"mim_id":"189800","title":"PREECLAMPSIA/ECLAMPSIA 1; PEE1","url":"https://www.omim.org/entry/189800"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nucleoli","reliability":"Additional"},{"location":"Nuclear bodies","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/INO80B"},"hgnc":{"alias_symbol":["HMGIYL4","PAPA-1","hIes2","PAP-1BP","IES2"],"prev_symbol":["HMGA1L4","ZNHIT4"]},"alphafold":{"accession":"Q9C086","domains":[{"cath_id":"-","chopping":"310-344","consensus_level":"medium","plddt":91.3011,"start":310,"end":344},{"cath_id":"1.20.5","chopping":"211-245","consensus_level":"medium","plddt":88.4166,"start":211,"end":245}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9C086","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9C086-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9C086-F1-predicted_aligned_error_v6.png","plddt_mean":65.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=INO80B","jax_strain_url":"https://www.jax.org/strain/search?query=INO80B"},"sequence":{"accession":"Q9C086","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9C086.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9C086/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9C086"}},"corpus_meta":[{"pmid":"21303910","id":"PMC_21303910","title":"Subunit organization of the human INO80 chromatin remodeling complex: an evolutionarily conserved core complex catalyzes ATP-dependent nucleosome remodeling.","date":"2011","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21303910","citation_count":100,"is_preprint":false},{"pmid":"24297934","id":"PMC_24297934","title":"Multiple modes of regulation of the human Ino80 SNF2 ATPase by subunits of the INO80 chromatin-remodeling complex.","date":"2013","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/24297934","citation_count":42,"is_preprint":false},{"pmid":"27641337","id":"PMC_27641337","title":"INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer.","date":"2016","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/27641337","citation_count":40,"is_preprint":false},{"pmid":"19933844","id":"PMC_19933844","title":"Fission yeast Iec1-ino80-mediated nucleosome eviction regulates nucleotide and phosphate metabolism.","date":"2009","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/19933844","citation_count":40,"is_preprint":false},{"pmid":"27257055","id":"PMC_27257055","title":"Synergy and antagonism in regulation of recombinant human INO80 chromatin remodeling complex.","date":"2016","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/27257055","citation_count":34,"is_preprint":false},{"pmid":"19095771","id":"PMC_19095771","title":"PAPA-1 Is a nuclear binding partner of IGFBP-2 and modulates its growth-promoting actions.","date":"2008","source":"Molecular endocrinology (Baltimore, Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/19095771","citation_count":30,"is_preprint":false},{"pmid":"26306040","id":"PMC_26306040","title":"Assembly of the Arp5 (Actin-related Protein) Subunit Involved in Distinct INO80 Chromatin Remodeling Activities.","date":"2015","source":"The 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The yeast homolog of the Rous sarcoma virus internal enhancer binding factor.","date":"1990","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/2156843","citation_count":5,"is_preprint":false},{"pmid":"39863741","id":"PMC_39863741","title":"A cross-tissue transcriptome-wide association study identifies new susceptibility genes for benign prostatic hyperplasia.","date":"2025","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/39863741","citation_count":2,"is_preprint":false},{"pmid":"15785000","id":"PMC_15785000","title":"Cloning and sequence analysis of the micronuclear and macronuclear gene encoding Rab protein of Euplotes octocarinatus.","date":"2005","source":"Bioscience, biotechnology, and biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15785000","citation_count":2,"is_preprint":false},{"pmid":"40918094","id":"PMC_40918094","title":"Integrative scRNA-seq and transcriptomic analysis initially reveals monocyte/macrophage activation drives EV-A71-induced immune dysregulation and neural injury in severe HFMD.","date":"2025","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/40918094","citation_count":2,"is_preprint":false},{"pmid":"17284430","id":"PMC_17284430","title":"[Cloning and characterization of a novel trinucleotide repeat-containing gene GARP from Euplotes octocarinatus].","date":"2007","source":"Yi chuan = Hereditas","url":"https://pubmed.ncbi.nlm.nih.gov/17284430","citation_count":2,"is_preprint":false},{"pmid":"18211810","id":"PMC_18211810","title":"The dosage of chromatin proteins affects transcriptional silencing and DNA repair in Saccharomyces cerevisiae.","date":"2008","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/18211810","citation_count":2,"is_preprint":false},{"pmid":"37445863","id":"PMC_37445863","title":"Feedback Modulation between Human INO80 Chromatin Remodeling Complex and miR-372 in HCT116 Cells.","date":"2023","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/37445863","citation_count":1,"is_preprint":false},{"pmid":"41775336","id":"PMC_41775336","title":"Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex.","date":"2026","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/41775336","citation_count":0,"is_preprint":false},{"pmid":"41851990","id":"PMC_41851990","title":"Subtypes of Type I-E CRISPR-Cas Systems Distribution in Human Escherichia coli Isolates from China.","date":"2026","source":"The CRISPR journal","url":"https://pubmed.ncbi.nlm.nih.gov/41851990","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12759,"output_tokens":3147,"usd":0.042741,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10571,"output_tokens":3018,"usd":0.064153,"stage2_stop_reason":"end_turn"},"total_usd":0.106894,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2011,\n      \"finding\": \"INO80B (hIes2) is a subunit of the human INO80 chromatin-remodeling complex, residing in the core module that also contains the hIno80 Snf2 ATPase domain, Ies6, AAA+ ATPases Tip49a/Tip49b, and Arp5. This core complex catalyzes ATP-dependent nucleosome remodeling; the metazoan-specific module (which does not contain Ies2) is dispensable for this activity.\",\n      \"method\": \"Biochemical purification of hINO80 subassemblies, ATP-dependent nucleosome remodeling assays, characterization of modular assembly via domain mapping of hIno80\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution of subassemblies with functional nucleosome remodeling assays; module assignment validated by multiple biochemical approaches in a focused mechanistic study\",\n      \"pmids\": [\"21303910\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"INO80B (hIes2/Ies2) functions as a potent activator of the intrinsic ATPase catalytic activity of the Ino80 SNF2 ATPase within the human INO80 complex, acting at the level of the enzyme's intrinsic catalytic rate rather than substrate (nucleosome) binding.\",\n      \"method\": \"Biochemical reconstitution of INO80 subcomplexes with and without Ies2; ATPase activity assays comparing complexes; subunit-specific dissection of regulatory contributions\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with defined subcomplexes and direct ATPase activity measurement; single lab but multiple orthogonal biochemical approaches\",\n      \"pmids\": [\"24297934\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Ies2 (INO80B ortholog in S. cerevisiae) is required for the stable association of the Arp5-Ies6 module with the catalytic components of the INO80 complex; deletion of IES2 results in loss of Arp5-Ies6 chromatin association. Ectopic addition of wild-type Arp5-Ies6 stimulates INO80-mediated ATP hydrolysis and nucleosome sliding in vitro, coupling ATPase activity to productive nucleosome movement.\",\n      \"method\": \"Genetic deletion of IES2 and INO80 in yeast, co-immunoprecipitation to assess module assembly, chromatin association assays, in vitro ATP hydrolysis and nucleosome sliding assays with reconstituted complexes\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — genetic epistasis combined with in vitro reconstitution and functional assays (ATPase, nucleosome sliding); multiple orthogonal approaches in a single focused study\",\n      \"pmids\": [\"26306040\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Ies2 (INO80B ortholog) functions as a regulatory subunit of the recombinant minimal human INO80 core complex. Removal of Ies2 from the complex reveals that it controls coupling of ATPase activity to nucleosome sliding; this coupling can be bypassed by a specific bypass mutation in Arp5, indicating Ies2 and Arp5/Ies6 act synergistically to link ATP hydrolysis to productive nucleosome movement. Inositol hexaphosphate (IP6) is a non-competitive inhibitor acting by blocking the stimulatory effect of nucleosomes on ATPase activity, with the binding site in the C-terminal region of Ino80.\",\n      \"method\": \"Recombinant expression and purification of minimal human INO80 core complex in insect cells; preparation of subcomplexes lacking Ies2 and/or Arp5/Ies6; ATPase activity assays; nucleosome sliding assays; IP6 inhibition kinetics; bypass mutagenesis of Arp5\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — fully recombinant system with reconstitution, mutagenesis, and multiple functional assays; single lab with multiple orthogonal approaches\",\n      \"pmids\": [\"27257055\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Deletion of ies2 in fission yeast causes defects in DNA damage repair, response to replication stress, and nucleotide metabolism, placing Ies2 functionally within the INO80 complex for these cellular processes.\",\n      \"method\": \"Gene deletion in Schizosaccharomyces pombe; phenotypic analysis of DNA damage sensitivity and nucleotide metabolism defects; purification of fission yeast Ino80 complex\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean loss-of-function genetic analysis with specific phenotypic readouts; ortholog (fission yeast) with conserved complex; replicated across multiple deletion strains in a single study\",\n      \"pmids\": [\"19933844\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"PAPA-1 (INO80B) is localized to the nucleolus in transfected HeLa cells, and its lysine/histidine cluster is essential for nucleolar localization. Ectopic expression of PAPA-1 induces growth suppression and cell cycle arrest at the G1 phase in a nucleolar-localization-dependent manner; expression of a deletion mutant lacking nucleolar localization abolishes the growth-suppressive effect.\",\n      \"method\": \"Transfection and confocal microscopy for subcellular localization; tetracycline-inducible expression system in HeLa cells; cell cycle analysis by flow cytometry after synchronization with thymidine, colcemid, or mimosine; deletion mutant analysis\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — direct subcellular localization by imaging tied to functional consequence (growth arrest), with domain deletion mutants confirming causality; single lab, multiple cell-based approaches\",\n      \"pmids\": [\"15556297\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"PAPA-1 (INO80B) interacts with IGFBP-2 in the nucleus of prostate cancer cells. PAPA-1 suppresses IGFBP-2-mediated growth promotion: siRNA-mediated knockdown of PAPA-1 enhances IGFBP-2-promoted cell growth, while overexpression of PAPA-1 abolishes IGFBP-2-promoted BrdU incorporation. In IGFBP-2 knockout MEFs, FLAG-mPAPA-1 overexpression decreased cell proliferation, but not in wild-type MEFs.\",\n      \"method\": \"Yeast two-hybrid screen to identify interaction; co-immunoprecipitation and GST pull-down to confirm binding; confocal microscopy for nuclear co-localization; siRNA knockdown; overexpression in LNCaP cells with BrdU incorporation assay; IGFBP-2 knockout MEFs\",\n      \"journal\": \"Molecular endocrinology (Baltimore, Md.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — reciprocal biochemical confirmation of interaction (Co-IP + pulldown), functional epistasis via KD and OE with specific proliferation readout; single lab with multiple orthogonal methods\",\n      \"pmids\": [\"19095771\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"In S. cerevisiae, heterozygous diploids for ies2 mutations show impaired DNA repair, demonstrating that the dosage of Ies2 (INO80B ortholog) is important for DNA repair capacity.\",\n      \"method\": \"Transposon mutagenesis and targeted gene deletions in haploid and diploid yeast; DNA repair assays in heterozygous diploids\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single genetic observation in yeast with a functional readout (DNA repair), but limited mechanistic detail and single method\",\n      \"pmids\": [\"18211810\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"INO80B (Ies2) subunit of the human INO80 complex participates in transcriptional control of miR-372; knockdown of Ies2 (along with other INO80 subunits) significantly increases miR-372 expression levels, and miR-372 mimics in turn suppress INO80 and Arp8 expression, establishing a mutual regulatory feedback loop. The interaction between the INO80 complex and the p53/p21 signaling pathway is implicated in this regulation.\",\n      \"method\": \"RNA-seq analysis; siRNA knockdown of multiple INO80 subunits including Ies2; miR-372 mimic transfection; luciferase reporter assays with 3'-UTR constructs and mutagenized binding sites; cell proliferation assays\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — luciferase reporter with mutagenized binding sites validates target relationship; knockdown of specific subunit (Ies2) with defined transcriptional readout; single lab, multiple methods\",\n      \"pmids\": [\"37445863\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Cryo-EM structures of human INO80 bound to canonical H2A nucleosomes, H2A.Z nucleosomes, and hexasomes reveal that IES2 (INO80B) contacts the nucleosome acidic patch. IES2 acidic patch binding can differentiate between nucleosomal and hexasomal substrates: it is important for nucleosome sliding but not hexasome sliding. INO80 adopts different positions on nucleosomes vs. hexasomes governed by entry DNA unwrapping, and IES2 may sense unwrapped exit DNA. Human INO80 slides hexasomes as efficiently as nucleosomes.\",\n      \"method\": \"Cryo-EM structure determination of human INO80 bound to canonical nucleosomes, H2A.Z nucleosomes, and hexasomes; in vitro nucleosome and hexasome sliding assays; structural analysis of IES2-acidic patch contacts\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structures with functional validation via in vitro sliding assays; mechanistic assignment of IES2 to acidic patch binding and substrate discrimination in a single rigorous study\",\n      \"pmids\": [\"41775336\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"INO80B (hIes2/Ies2) is an evolutionarily conserved subunit of the INO80 ATP-dependent chromatin-remodeling complex that serves multiple regulatory roles: it directly activates the intrinsic ATPase catalytic activity of the Ino80 SNF2 ATPase, is required for stable assembly of the Arp5-Ies6 module onto the catalytic core (thereby coupling ATP hydrolysis to productive nucleosome sliding), and contacts the nucleosome acidic patch to discriminate between canonical nucleosomes and hexasomes—being essential for nucleosome but not hexasome sliding; when expressed independently of the complex, INO80B localizes to the nucleolus via its lysine/histidine cluster and suppresses cell proliferation by inducing G1 arrest, and it also interacts in the nucleus with IGFBP-2 to antagonize its growth-promoting activity.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"INO80B (also called hIes2/Ies2 and PAPA-1) is an evolutionarily conserved regulatory subunit of the INO80 ATP-dependent chromatin-remodeling complex, residing in the catalytic core module alongside the Ino80 SNF2 ATPase, Ies6, Tip49a/Tip49b, and Arp5 [#0]. Mechanistically, INO80B is a potent activator of the intrinsic ATPase rate of the Ino80 SNF2 ATPase, acting on the enzyme's catalytic turnover rather than on nucleosome binding [#1]. It is also required for stable assembly of the Arp5-Ies6 module onto the catalytic core, and through this it couples ATP hydrolysis to productive nucleosome sliding—a coupling that can be restored by a bypass mutation in Arp5, indicating that INO80B and Arp5/Ies6 act synergistically [#2, #3]. Cryo-EM structures show INO80B contacts the nucleosome acidic patch and uses this contact to discriminate substrates, being essential for canonical nucleosome sliding but dispensable for hexasome sliding [#9]. Consistent with a chromatin-remodeling role, loss of the Ies2 ortholog impairs DNA damage repair and the replication-stress response [#4]. Independently of the complex, INO80B localizes to the nucleolus via its lysine/histidine cluster and suppresses proliferation by inducing G1 arrest in a nucleolar-localization-dependent manner [#5], and it binds IGFBP-2 in the nucleus to antagonize IGFBP-2-driven growth [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Before its role in chromatin remodeling was known, the question was whether PAPA-1/INO80B had an autonomous cellular function; this established it as a nucleolar protein that restrains the cell cycle.\",\n      \"evidence\": \"Confocal imaging and inducible expression with deletion mutants in HeLa cells\",\n      \"pmids\": [\"15556297\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not connect nucleolar growth suppression to the INO80 complex\", \"Molecular targets of the G1 arrest not identified\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"To find a functional partner explaining the growth suppression, an interaction screen identified IGFBP-2 as a nuclear binding partner that INO80B antagonizes.\",\n      \"evidence\": \"Yeast two-hybrid, Co-IP, GST pull-down, siRNA/overexpression proliferation assays in prostate cancer cells and IGFBP-2 KO MEFs\",\n      \"pmids\": [\"19095771\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which binding antagonizes IGFBP-2 signaling unresolved\", \"Relationship to nucleolar localization not established\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"An open question was whether Ies2 dosage matters for genome maintenance; heterozygous yeast diploids showed gene dosage affects DNA repair capacity.\",\n      \"evidence\": \"Transposon mutagenesis and DNA repair assays in haploid/diploid S. cerevisiae\",\n      \"pmids\": [\"18211810\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single genetic observation with limited mechanistic detail\", \"No molecular link to remodeling activity\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"It was unclear which cellular processes require Ies2 within INO80; deletion in fission yeast placed it in DNA damage repair, replication-stress response, and nucleotide metabolism.\",\n      \"evidence\": \"ies2 deletion and phenotypic analysis in S. pombe with complex purification\",\n      \"pmids\": [\"19933844\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not define the biochemical contribution of Ies2 to the complex\", \"Phenotypes not yet mapped to remodeling mechanism\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"The architectural question of where INO80B sits in the human complex was answered by assigning it to the catalytic core module rather than the dispensable metazoan-specific module.\",\n      \"evidence\": \"Biochemical purification of hINO80 subassemblies, domain mapping, and ATP-dependent remodeling assays\",\n      \"pmids\": [\"21303910\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define INO80B's specific biochemical activity within the core\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Having placed INO80B in the core, the question became what it does there; reconstitution showed it directly activates the intrinsic catalytic rate of the Ino80 ATPase.\",\n      \"evidence\": \"Reconstitution of INO80 subcomplexes ± Ies2 with direct ATPase measurements\",\n      \"pmids\": [\"24297934\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How activation translates to nucleosome movement not yet defined\", \"Structural basis of ATPase stimulation unknown\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Two studies resolved how INO80B couples catalysis to remodeling: it is required for stable Arp5-Ies6 module assembly and links ATP hydrolysis to productive nucleosome sliding, bypassable by an Arp5 mutation.\",\n      \"evidence\": \"Yeast IES2 deletion with Co-IP and chromatin-association assays; recombinant minimal human INO80 core ± Ies2 with sliding/ATPase assays and Arp5 bypass mutagenesis\",\n      \"pmids\": [\"26306040\", \"27257055\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic-level basis of the Ies2-Arp5/Ies6 synergy not visualized at this stage\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"The question of INO80B's role in transcriptional output identified its participation in a miR-372 regulatory feedback loop tied to p53/p21 signaling.\",\n      \"evidence\": \"RNA-seq, siRNA knockdown of INO80 subunits including Ies2, miR-372 mimics, and luciferase reporter assays\",\n      \"pmids\": [\"37445863\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct chromatin targets of the loop not mapped\", \"Specific contribution of Ies2 versus other subunits not isolated\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"The structural basis of INO80B's substrate selectivity was resolved: it contacts the nucleosome acidic patch to discriminate nucleosomes from hexasomes, being essential for nucleosome but not hexasome sliding.\",\n      \"evidence\": \"Cryo-EM of human INO80 on canonical, H2A.Z, and hexasome substrates with in vitro sliding assays\",\n      \"pmids\": [\"41775336\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How acidic-patch sensing is communicated to the ATPase not fully detailed\", \"In vivo consequence of hexasome-vs-nucleosome discrimination untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how INO80B's complex-bound remodeling role mechanistically connects to its complex-independent nucleolar, IGFBP-2-antagonizing, and growth-suppressive functions.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No experiment unifies the chromatin-remodeling and free-protein activities\", \"Whether nucleolar INO80B acts within or outside the complex is unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1, 2, 3]},\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [1, 2, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [0, 1, 2, 3, 9]},\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"complexes\": [\"INO80 chromatin-remodeling complex\"],\n    \"partners\": [\"INO80\", \"ARP5\", \"IES6\", \"IGFBP2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}