| 2004 |
The yeast INO80 complex is recruited to HO endonuclease-induced DNA double-strand breaks (DSBs) through interaction with phosphorylated histone H2A (γ-H2AX) at S129; recruitment requires the Nhp10 HMG-like subunit. Loss of INO80 (arp8 or H2A S129 mutants) impairs conversion of the DSB into ssDNA, implicating INO80-mediated chromatin remodeling in DSB end-processing. |
Chromatin immunoprecipitation (ChIP) at HO-induced DSB; genetic epistasis with H2A S129 mutants and nhp10 deletions; sensitivity assays to DNA damaging agents |
Cell |
High |
15607974 15607975
|
| 2004 |
The INO80 complex is recruited to DSBs via a specific interaction between the Nhp10 subunit and γ-H2AX; loss of Nhp10 or γ-H2AX reduces INO80 recruitment. INO80 components show synthetic genetic interactions with the RAD52 DSB repair pathway. |
ChIP at HO-induced DSB; Nhp10 deletion and γ-H2AX mutant analysis; genetic interaction screen with RAD52 pathway |
Cell |
High |
15607974
|
| 2005 |
Human INO80 (hINO80) complex was identified and purified, containing orthologs of 8 of 15 yeast INO80 subunits plus at least five metazoan-specific subunits. The complex exhibits DNA- and nucleosome-activated ATPase activity and catalyzes ATP-dependent nucleosome sliding. |
Affinity purification / mass spectrometry; ATPase activity assay; nucleosome sliding assay in vitro |
The Journal of biological chemistry |
High |
16230350
|
| 2006 |
Ino80 is required for cell cycle checkpoint adaptation in response to a persistent DSB. Cells lacking Ino80 fail to maintain high γ-H2AX levels and show increased H2A.Z (Htz1) incorporation near DSBs via Swr1. Inactivation of Swr1 restores H2AX phosphorylation and checkpoint adaptation in ino80 mutants, revealing antagonism between Ino80 and Swr1 at DSB-flanking chromatin. |
ChIP; genetic epistasis (ino80 × swr1 double mutants); checkpoint adaptation assays |
Genes & development |
High |
16951256
|
| 2007 |
Swr1 is recruited to DSBs in a γ-H2AX-dependent manner. INO80 (but not SWR1) mediates removal of H2A.Z, γ-H2AX, and core histones near DSBs. Loss of INO80-specific subunits Arp8 or Nhp10 impairs Mre11, yKu80, and Mec1 binding at DSBs, causing defective end-processing and checkpoint activation. |
ChIP at DSBs; genetic analysis of INO80- vs SWR1-specific subunit mutants; immunofluorescence of repair factors |
The EMBO journal |
High |
17762868
|
| 2007 |
YY1 is tightly associated with the human INO80 complex. YY1 recruits INO80 to YY1-activated gene promoters where INO80 functions as a coactivator. YY1 binding to its DNA target sites requires INO80 activity. |
Co-immunoprecipitation; ChIP at YY1 target genes; RNAi knockdown of INO80 with transcriptional readout |
Nature structural & molecular biology |
High |
17721549
|
| 2007 |
YY1 forms a complex with INO80 subunits in mammalian cells. Both YY1 and INO80 are essential for homologous recombination-based DNA repair (HRR); YY1 preferentially binds recombination-intermediate structures in vitro. RNAi knockdown of either increases cellular sensitivity to DNA-damaging agents. |
Co-immunoprecipitation; RNAi knockdown; HR functional assays; in vitro DNA-binding assays with recombination intermediates |
Nature structural & molecular biology |
High |
18026119
|
| 2007 |
The Ies3 subunit of yeast INO80 interacts with the tetratricopeptide repeat domain of telomerase subunit Est1p. Deletion of IES3 causes telomere elongation, altered telomere position effect, delayed recombinational survivor formation, and stimulated extrachromosomal telomeric circles. Multiple INO80 subunits preferentially localize to telomeres. |
Co-immunoprecipitation; telomere length assays; ChIP at telomeres; genetic analysis of ies3Δ and arp8Δ in telomerase-negative strains |
Molecular and cellular biology |
Medium |
17562861
|
| 2007 |
The Mec1/Tel1 kinases (ATM/ATR orthologs) phosphorylate the Ies4 subunit of the INO80 complex during DNA damage. Mutation of Ies4 phosphorylation sites does not significantly affect DNA repair but influences DNA damage checkpoint responses, functionally linking INO80 to the Mec1/Tel1 checkpoint signaling pathway via Tof1 and Rad53. |
In vivo phosphorylation assays; site-directed mutagenesis of Ies4 phosphosites; checkpoint assays; genetic interaction analysis with tof1 and rad53 |
Cell |
High |
17693258
|
| 2008 |
The Ino80 chromatin remodeling complex binds replication origins and stalled replication forks. Under hydroxyurea-induced fork arrest, INO80 accumulates at stalled forks and unfired origins. ino80 mutants are defective in replication restart after HU release and accumulate DSBs. |
ChIP across four yeast chromosomes; genome-wide mapping; HU treatment and release assays; DSB detection |
Current biology |
High |
18406137
|
| 2008 |
The Ino80 enzyme is recruited to replication origins as cells enter S phase and is required continuously for efficient fork progression, especially under low replication stress. Inducible degradation of Ino80 causes replisome dissociation from stalled forks, indicating Ino80 stabilizes the stalled replisome to ensure proper restart. |
Inducible protein degradation; ChIP at replication origins; replisome component co-precipitation; replication fork stability assays |
Nature structural & molecular biology |
High |
18376411
|
| 2008 |
In the nucleus, the deubiquitinase Uch37 associates with the human INO80 complex where it is held in an inactive state. Uch37 can be activated by transient interaction of hINO80 with the proteasome, suggesting cooperative regulation of transcription or DNA repair. |
Co-immunoprecipitation; DUB activity assays in vitro; mass spectrometry identification of hINO80-Uch37 interaction |
Molecular cell |
Medium |
18922472
|
| 2010 |
INO80 acts as a nucleosome spacing factor in vitro. It requires a minimum of 33–43 bp of extranucleosomal DNA and moves nucleosomes to the center of DNA with high precision. Unlike ISW2/1a, INO80 does not require H4 tails; instead the H2A histone tail negatively regulates nucleosome movement. INO80 spaces arrays with ~30 bp final linker DNA. |
In vitro nucleosome sliding/spacing assays with defined mono- and dinucleosomal arrays; histone tail deletion analysis |
Molecular and cellular biology |
High |
21135121
|
| 2010 |
Human INO80 promotes 5′→3′ resection of DSB ends in mammalian cells. Ino80 depletion impaired focal recruitment of 53BP1 but did not impede Rad51 focus formation, placing Ino80 at early steps of DSB repair. Ino80 associates with chromatin surrounding DSBs. |
RNAi knockdown; comet assay; HR repair reporter; immunofluorescence of 53BP1 and Rad51 foci; BrdU-ssDNA and RPA staining |
Molecular and cellular biology |
Medium |
21947284
|
| 2010 |
Deletion of INO80 or ARP5 in mammalian cells impairs removal of UV-induced photo lesions via NER without affecting NER factor transcription. INO80 and Arp5 are recruited to UV-damaged DNA before NER incision occurs and are required for assembly of NER factors, indicating INO80 promotes chromatin accessibility for NER. |
Genetic knockout models; UV photolesion removal assays; ChIP for NER factors; chromatin accessibility assays |
Proceedings of the National Academy of Sciences |
High |
20855601
|
| 2010 |
Mammalian INO80 complex is recruited to laser-induced DNA damage sites in an ARP8-dependent manner but independently of γ-H2AX, unlike the yeast complex where Nhp10 or Arp4 mediate recruitment. |
Laser micro-irradiation; immunofluorescence; siRNA knockdown of ARP8; live-cell imaging |
Biochemical and biophysical research communications |
Medium |
20971067
|
| 2011 |
Yeast INO80 has a histone exchange activity: it can replace nucleosomal H2A.Z/H2B dimers with free H2A/H2B dimers. In the absence of INO80, H2A.Z nucleosomes are mislocalized genome-wide and fail to respond dynamically to transcriptional changes. Genetic interactions between ino80 and htz1 (H2A.Z) support a model where INO80 removes unacetylated H2A.Z to promote genome stability. |
Genome-wide ChIP-seq for H2A.Z; in vitro histone exchange assays; genetic interaction analysis (ino80 × htz1) |
Cell |
High |
21241891
|
| 2011 |
The human INO80 complex is organized in three modules assembling on distinct domains of hIno80 ATPase: (i) an N-terminal module with metazoan-specific subunits dispensable for remodeling, (ii) a module containing Arp4, Arp8, and YY1 on the HSA/PTH domain, and (iii) a catalytic core module with Ies2, Ies6, Arp5, Tip49a, and Tip49b. ATP-dependent nucleosome remodeling requires the evolutionarily conserved core comprising HSA/PTH and Snf2 ATPase domains together with YY1 and conserved subunits. |
Affinity purification of hINO80 subassemblies; mass spectrometry; in vitro nucleosome remodeling assays with subassemblies |
The Journal of biological chemistry |
High |
21303910
|
| 2011 |
Loss of INO80 subunits Ies6 or Ino80 causes rapid polyploidy and chromosome missegregation. Chromatin structure flanking centromeres is altered in these mutants, not in the Cse4-containing centromeric nucleosome itself, but in pericentric chromatin. These effects are mediated through misincorporation of H2A.Z into pericentric regions. |
Flow cytometry (ploidy); live-cell imaging of chromosome segregation; ChIP for H2A.Z and histones at centromeres; genetic analysis |
Genes & development |
High |
23207916
|
| 2012 |
Targeted recruitment of INO80 to a chromosomal locus enhances large-scale chromatin mobility in budding yeast, requiring Ino80's ATPase activity. This enhanced mobility correlates with increased rates of spontaneous gene conversion, indicating that INO80-dependent nucleosome remodeling promotes chromatin flexibility and homologous recombination. |
High-precision live fluorescence microscopy of tagged chromosomal loci; targeted tethering of INO80; ATPase-dead mutant analysis; gene conversion assays |
Genes & development |
High |
22345518
|
| 2012 |
Crystal structure of the Arp8 C-terminal domain shows three insertions within the actin fold. Arp8 forms a dimer that binds the nucleosome core primarily through H3 and H4 histones via one of these insertions, exploiting the twofold symmetry of the nucleosome. |
X-ray crystallography; biochemical binding assays (pull-down, EM); nucleosome co-purification with recombinant Arp8 |
Proceedings of the National Academy of Sciences |
High |
23213201
|
| 2013 |
Nuclear actin in the INO80 complex exists as a monomer with its barbed end inaccessible for polymerization. An actin mutation in subdomain 2 reduces INO80 chromatin remodeling activity in vitro and disrupts in vivo nuclear functions. The pointed end subdomain 2 of actin contributes to INO80-chromatin interactions. |
Biochemical fractionation; actin polymerization assays; actin subdomain mutagenesis; in vitro chromatin remodeling assays; genetic complementation |
Nature structural & molecular biology |
High |
23524535
|
| 2013 |
The Ies2 subunit potently activates the intrinsic catalytic ATPase activity of the human Ino80 SNF2 ATPase, while Ies6 and Arp5 together promote binding of the Ino80 ATPase to nucleosomes. Thus the Ino80 ATPase is regulated at multiple levels within the complex. |
Purified subunit reconstitution; in vitro ATPase assays; nucleosome-binding assays with defined subunit deletions |
Proceedings of the National Academy of Sciences |
High |
24297934
|
| 2014 |
INO80 binds replication forks in human cells and promotes fork progression under normal conditions. Ino80 is recruited to replication forks through interaction with ubiquitinated H2A, aided by BAP1 (a nuclear deubiquitinase that also stabilizes Ino80 protein). BAP1 deficiency in cancer cells downregulates Ino80 by disrupting this stabilization mechanism. |
Co-immunoprecipitation of Ino80 with ubiquitinated H2A; ChIP at replication forks; BAP1 knockdown/knockout; Ino80 protein stability assays; mouse embryo Ino80 deletion |
Nature communications |
High |
25283999
|
| 2014 |
INO80 occupies pluripotency gene promoters with master transcription factors OCT4 and WDR5. Ino80 maintains open chromatin architecture at these promoters and licenses Mediator and RNA Pol II recruitment. Ino80 is required for ESC self-renewal, somatic cell reprogramming, and blastocyst development. |
ChIP-seq; ATAC-seq; RNAi knockdown; genetic knockout in mouse; reprogramming assays |
Cell stem cell |
High |
24792115
|
| 2014 |
INO80-dependent Mps3 (inner nuclear membrane SUN domain protein) binding to DSBs is S/G2-phase specific and requires both INO80 and Rad51. DSB relocation to Nup84 nuclear pore occurs independently of INO80 and cell-cycle phase. Thus INO80 determines choice of perinuclear anchorage site for DSBs. |
Live-cell imaging of DSB subnuclear position; genetic epistasis with ino80, rad51, swr1 mutants; cell-cycle synchronization |
Molecular cell |
Medium |
25066231
|
| 2015 |
Mammalian INO80 rapidly removes H2A.Z from chromatin flanking DNA damage. Depletion of INO80 or histone chaperone ANP32E impairs homologous recombination, and the HR defect can be rescued by co-depletion of H2A.Z, demonstrating that H2A.Z removal is the primary function of INO80 and ANP32E in promoting HR. |
RNAi knockdown; H2A.Z ChIP after DNA damage; HR functional assay; epistasis by co-depletion of H2A.Z |
EMBO reports |
High |
26142279
|
| 2015 |
The yeast Ino80 chromatin remodeling complex is required for RNAPII turnover under transcriptional stress. INO80 forms a ternary complex with RNAPII and Cdc48/p97, and cells lacking INO80 accumulate ubiquitinated Rpb1 tightly bound to chromatin, indicating INO80 nucleosome remodeling activity promotes dissociation of ubiquitinated RNAPII from chromatin for proteasomal degradation. |
Co-immunoprecipitation; in vivo Rpb1 ubiquitination/degradation assays; ChIP for ubiquitinated Rpb1; genetic epistasis with cdc48 and proteasome mutants |
Molecular cell |
High |
26656161
|
| 2015 |
The Arp8/Arp4/actin module in INO80 binds extranucleosomal DNA 37-51 bp from the nucleosome edge and functions as a DNA-length sensor that regulates nucleosome sliding. Disruption of Arp8/Arp4 DNA binding uncouples ATP hydrolysis from nucleosome mobilization by disengaging Arp5 from the H2A-H2B acidic patch. |
In vitro DNA-binding assays (EMSA); site-directed mutagenesis of Arp8/Arp4; ATPase assays; nucleosome sliding assays; photo-crosslinking |
Nature communications |
High |
30120252
|
| 2015 |
EM structural analysis shows INO80-C and SWR-C share similar overall architectures with a compact head containing Rvb1/Rvb2 as single heterohexameric rings. The Arp8/Arp4/Act1 module enhances nucleosome-binding affinity but is largely dispensable for remodeling. The Ies6/Arp5 module is essential for remodeling activity and controls conformational changes coupling nucleosome binding to remodeling. |
Electron microscopy; 2D class averaging; mass spectrometry; nucleosome remodeling assays with module deletions |
Nature communications |
High |
25964121
|
| 2016 |
The Arp5-Ies6 subcomplex forms an abundant distinct subcomplex in vivo and stimulates INO80-mediated ATPase and nucleosome sliding activity in vitro. Ies2 is required for Arp5-Ies6 association with the catalytic INO80 components. Mutant Arp5 lacking unique insertion domains allows ATP hydrolysis without nucleosome sliding, uncoupling the two activities. |
In vivo co-immunoprecipitation; in vitro ATPase and nucleosome sliding assays; domain deletion/mutagenesis of Arp5 |
Molecular and cellular biology |
High |
26306040 27255055
|
| 2016 |
Mec1, INO80, and PAF1 complexes cooperate to remove RNAPII from transcribed genes near early-firing replication origins upon HU treatment. Mec1 triggers efficient removal of PAF1C and RNAPII. Failure to evict RNAPII correlates with defective replication fork restart, implicating INO80 in preventing transcription-replication conflicts. |
ChIP-seq for RNAPII and PAF1C; genetic epistasis (mec1, ino80, paf1 mutants); DNA fiber assays for replication restart; proteomic analysis |
Genes & development |
High |
26798134
|
| 2016 |
INO80 occupies >90% of superenhancers in melanoma cells, dependent on transcription factors MITF and Sox9. Ino80 binding reduces nucleosome occupancy and facilitates Mediator recruitment, promoting oncogenic transcription. Ino80 silencing selectively inhibits melanoma cell proliferation and tumorigenesis. |
ChIP-seq; ATAC-seq; Ino80 siRNA knockdown; mouse xenograft assays; Co-IP with Mediator |
Genes & development |
High |
27340176
|
| 2017 |
INO80 translocates along DNA at the H2A-H2B interface of nucleosomes (unlike other remodelers that translocate at the H3-H4 interface), creating DNA torsional strain near the nucleosome entry site. This mechanism promotes both nucleosome mobilization and selective exchange of H2A.Z-H2B dimers with H2A-H2B without additional histone chaperones. INO80 mobilizes H2A.Z-containing nucleosomes more efficiently than H2A nucleosomes. |
Site-directed photo-crosslinking; ATPase assays; nucleosome sliding assays with H2A vs H2A.Z substrates; histone exchange assays in vitro |
Nature communications |
High |
28604691
|
| 2017 |
The INO80 complex removes H2A.Z to promote presynaptic filament formation during homologous recombination in budding yeast. INO80 has at least two distinct functions in HR: DNA end resection and presynaptic filament formation. H2A.Z deletion rescues presynaptic filament formation and HR in INO80-deficient mutants. |
High-resolution ChIP; HR assays; genetic epistasis with H2A.Z deletion (htz1Δ); direct visualization of presynaptic filament formation |
Cell reports |
High |
28514650
|
| 2017 |
An insertion domain (Ino80INS) in the Ino80 ATPase stimulates Rvb1/Rvb2 ATPase activity 16-fold and promotes their dodecamerization. Rvb1/Rvb2 function as protein assembly chaperones within INO80, cycling between hexamers and dodecamers in an ATP-dependent manner. |
ATPase activity assays; mass spectrometry; cryo-EM and integrative modeling; biochemical reconstitution |
Cell reports |
High |
28591576
|
| 2018 |
Cryo-EM structure of evolutionarily conserved INO80 core from Chaetomium thermophilum bound to nucleosome at 4.3/3.7 Å resolution. The Rvb1/Rvb2 AAA+ heterohexamer acts as a stator scaffold. The Swi2/Snf2 ATPase motor binds at SHL-6, unwraps ~15 bp, disrupts H2A-DNA contacts, and is poised to pump entry DNA into the nucleosome. Arp5 and Ies6 bind at SHL-2/-3 as a counter-grip, with the Arp5 grappler element binding the nucleosome dyad. The structure suggests a ratchet mechanism for both nucleosome sliding and histone editing. |
Cryo-electron microscopy (global 4.3 Å, major parts 3.7 Å); biochemical validation of ATPase and sliding activities |
Nature |
High |
29643509
|
| 2018 |
Cryo-EM structure of human INO80 bound to nucleosome reveals the motor domains are located at the DNA entry point (not at SHL2 as in other remodelers). ARP5-IES6 module makes additional contacts on the opposite side. Histone H3 tails regulate the INO80 motor domain (unlike other remodelers where H4 tails play this role). |
Cryo-electron microscopy (9.6 Å overall, 4.1 Å for portions); biochemical validation |
Nature |
High |
29643506
|
| 2018 |
Cryo-EM structures of the active core of human INO80 at 9.6 Å reveal an unusual spoked-wheel structural domain of Ino80 subunit engulfed by a single RUVBL1/RUVBL2 AAA+ heterohexamer. RUVBL1/RUVBL2 form a major interaction site for partner proteins that likely communicate to nucleotide-binding sites. |
Cryo-EM; subunit reconstitution; EM class averaging |
Nature structural & molecular biology |
High |
29323271
|
| 2018 |
Crystal structure of the 180-kDa Arp8 module of yeast INO80 shows Arp8 engages nuclear actin in a manner distinct from other actin-fold proteins, recruiting the Arp4-N-actin heterodimer to a segmented scaffold of the helical HSA domain. The HSA domain spans >120 Å and provides an extended binding platform for extranucleosomal entry DNA required for nucleosome sliding and genome-wide nucleosome positioning. |
X-ray crystallography; biochemical DNA-binding assays; in vitro nucleosome sliding assays; genome-wide nucleosome mapping |
Nature structural & molecular biology |
High |
30177756
|
| 2018 |
INO80 operates as a DNA length-sensitive switch: nucleosome sliding rate increases ~100-fold when flanking DNA increases from 40 to 60 bp. Once initiated, INO80 moves nucleosomes rapidly at least 20 bp without pausing. The Nhp10 module plays an auto-inhibitory role tuning this switch-like response. INO80 can change direction of sliding without dissociation. |
Single-molecule enzymology; ensemble ATPase and sliding assays; Nhp10 module deletion analysis |
Molecular cell |
High |
29452642
|
| 2018 |
INO80 deletion in vascular endothelial cells prevents ventricular compaction in the developing mouse heart, correlating with defective coronary vascularization. In vitro, endothelial cells promote myocardial expansion in an Ino80-dependent manner. Ino80 deletion increases E2F-activated gene expression and endothelial S-phase occupancy. |
Conditional endothelial Ino80 knockout (mouse); histological analysis; in vitro co-culture assays; gene expression profiling |
Nature communications |
Medium |
29371594
|
| 2019 |
TRIM3 E3 ubiquitin ligase mediates degradation of INO80 in the nucleus accumbens; TRIM3 and INO80 interact directly, and reduced TRIM3 on abstinence day 30 leads to increased INO80 protein levels. INO80-mediated transcriptional changes regulate cocaine craving during prolonged abstinence. |
Co-immunoprecipitation; viral gene transfer; ChIP-seq; ubiquitin degradation assays |
Science advances |
Medium |
31633032
|
| 2019 |
BAP1 depletion reduces DNA synthesis and impairs restart of HU-induced stalled replication forks. This defect is rescued by ectopic INO80 expression. BAP1 depletion abrogates INO80 binding to stalled replication forks, indicating BAP1 promotes replication stress recovery by recruiting INO80 to stalled forks. |
DNA fiber assays; ChIP at replication forks; siRNA knockdown; ectopic INO80 expression rescue |
The Biochemical journal |
Medium |
31657441
|
| 2020 |
INO80 complex promotes resolution of R-loops to prevent replication-associated DNA damage in cancer cells. R-loops promote INO80 recruitment to chromatin. Overexpression of RNase H1 rescues DNA synthesis defects and suppresses DNA damage caused by INO80 depletion. Artificial tethering of INO80 to a LacO locus enables R-loop turnover in cis. |
RNAi depletion of INO80; R-loop immunofluorescence (S9.6 antibody); DNA fiber assays; RNase H1 rescue; LacO artificial tethering |
Nature communications |
High |
32913330
|
| 2020 |
Ino80 conditional deletion from cortical neural progenitor cells impairs DNA DSB repair selectively via homologous recombination, causing p53-dependent apoptosis and microcephaly. Ino80 function in HR is mechanistically distinct from its role in YY1-associated transcription. Sensitivity is dependent on NPC division mode: symmetric NPC-NPC divisions but not asymmetric neurogenic divisions require Ino80-mediated HR. |
Conditional knockout mouse; in vivo DSB repair pathway assay; apoptosis markers; phenotype comparison with Brca2 conditional knockout |
Nature communications |
High |
32737294
|
| 2020 |
In fission yeast, INO80 subunit Iec5 promotes histone turnover at heterochromatin, enabling INO80 to counter epigenetic inheritance of heterochromatin. Mutations in INO80 components allow pericentric heterochromatin inheritance in RNAi mutants. This function is distinct from nucleosome positioning at heterochromatin. |
Genetic screen; heterochromatin inheritance assays; histone turnover measurements; ChIP |
Cell reports |
Medium |
33378674
|
| 2021 |
INO80 processes DNA shape/mechanical properties encoded in the genome through allosteric interplay between its core and Arp8 modules to position nucleosomes genome-wide. At promoters, INO80 integrates DNA mechanics readout with general regulatory factor binding to position the +1 nucleosome. This establishes a molecular mechanism for robust, adjustable +1 nucleosome positioning. |
Genome-wide chromatin reconstitution on physiological yeast templates; nucleosome positioning assays; module deletion analysis; biophysical DNA shape analysis |
Nature communications |
High |
34050142
|
| 2021 |
In the primed pluripotent state (but not naïve), INO80 promotes H2A.Z occupancy at bivalent gene promoters, facilitating H3K27me3 installation and maintenance. INO80 pre-marks gene promoters in naïve ESCs that adopt bivalent modifications upon transition to the primed state. This reveals a context-dependent role for INO80 in H2A.Z deposition (in addition to its known removal activity). |
Conditional Ino80 deletion in naïve vs primed ESCs; ChIP-seq for H2A.Z, H3K4me3, H3K27me3; gene expression analysis |
Nucleic acids research |
Medium |
34139016
|
| 2022 |
INO80 prefers hexasomes (nucleosomes lacking one H2A-H2B dimer) as substrates over canonical nucleosomes, with up to ~60-fold preference at short flanking DNA overhangs (~18 bp linkers found in gene bodies. INO80 deletion significantly affects positions of hexasome-sized particles within yeast genes in vivo. |
In vitro nucleosome sliding assays comparing hexasome vs nucleosome substrates; yeast genetics; MNase-seq in ino80Δ |
Molecular cell |
High |
35597239
|
| 2022 |
Cryo-EM structures of the INO80 regulatory A-module bound to DNA reveal the mechanism of linker DNA binding. The A-module connects to the motor via an HSA/post-HSA lever element that chemomechanically couples motor and linker DNA sensing. Two sites of curved DNA recognition by the four actin/actin-related proteins and the motor regulate sliding. YY1/Ies4 subunit recruitment and deep architectural similarities to SWI/SNF regulatory modules are revealed. |
Cryo-electron microscopy; functional DNA-binding and remodeling assays |
Science advances |
High |
36490333
|
| 2023 |
Cryo-EM structure of INO80 in complex with a hexasome reveals a large structural rearrangement of the INO80 catalytic core into a 'spin-rotated' remodeling mode upon hexasome recognition. The nuclear actin module remains tethered to unwrapped linker DNA. An exposed H3-H4 interface in the hexasome activates INO80 independently of the H2A-H2B acidic patch. |
Cryo-electron microscopy; in vitro hexasome remodeling assays; mutagenesis |
Science |
High |
37384673
|
| 2023 |
TORC1 activates the Rpd3L histone deacetylase complex to deacetylate Ino80 at K929, protecting Ino80 from autophagic degradation. Stabilized Ino80 promotes H2A.Z eviction from autophagy-related gene promoters, repressing their transcription. Rpd3L also deacetylates H2A.Z to further block its chromatin deposition. This pathway links nutrient signaling (TORC1) to chromatin remodeling and autophagy regulation. |
In vivo protein stability assays; ChIP for H2A.Z; genetic deletion of Rpd3L, TORC1 inhibition; site-directed mutagenesis of Ino80 K929; autophagy assays |
Science advances |
Medium |
36888706
|
| 2017 |
INO80 nucleosome remodeling requires cooperativity between two INO80 complexes that simultaneously monitor DNA length on either side of a nucleosome. The C-terminal domain of human Ino80 (Ino80CTD) binds DNA cooperatively and dimerizes to provide crosstalk. A single active ATPase motor within the dimer is sufficient for nucleosome sliding, and ATPase activity gradually uncouples as the endpoint is approached, controlled by Ino80CTD. |
Nucleosome sliding assays with mutant complexes; ATPase assays; dimerization biochemistry; sedimentation assays |
eLife |
High |
28585918
|
| 2016 |
Inositol hexaphosphate (IP6) is a non-competitive inhibitor of human INO80 that blocks nucleosomal stimulation of ATPase activity. The IP6 binding site is located within the C-terminal region of the Ino80 subunit. Ies2 and Arp5/Ies6 synergistically couple ATP hydrolysis to nucleosome sliding, and a bypass mutation in Arp5 is active in the absence of Ies2. |
In vitro ATPase assays; nucleosome sliding assays; recombinant complex purification from insect cells; domain mapping of IP6 binding |
Nucleic acids research |
High |
27257055
|
| 2010 |
Yeast Ino80 interacts with the early NER damage recognition complex Rad4-Rad23 and is recruited to chromatin in a UV damage-dependent manner by Rad4. Ino80 acts in the same genetic pathway as NER. While chromatin disruption during UV lesion repair is normal in ino80 mutants, restoration of nucleosome structure after repair is defective. |
Co-immunoprecipitation (Ino80-Rad4-Rad23); ChIP at UV-damaged chromatin; modified ChIP to assess nucleosome reassembly; genetic epistasis |
The Journal of cell biology |
High |
21135142
|
| 2020 |
Hap2 (auxiliary subunit of fission yeast Ino80 complex) promotes de novo CENP-A chromatin assembly on naïve centromere DNA by facilitating transcription from centromere DNA, driving H3 nucleosome turnover and replacement by CENP-A nucleosomes. Chromatin association of Hap2 is Ies4-dependent. |
Affinity purification of CENP-A chromatin; genetic analysis of hap2 and ies4 deletions; de novo CENP-A assembly assays; H3 turnover measurements; ChIP |
Genes & development |
Medium |
31919190
|
| 2007 |
INO80 subunit Arp8 deficiency causes defects in sister chromatid cohesion. Ino80 directly associates with centromeres and cohesin-associated regions. In early S phase, Ino80 is recruited to replication forks along with Ctf18 and PCNA; arp8 mutation disrupts Ctf18 and PCNA association with replication forks. |
ChIP at centromeres and cohesin-associated regions; sister chromatid cohesion assay; Co-IP of Ino80 with replication fork components |
Cell cycle |
Medium |
17471029
|
| 2022 |
INO80 interacts with PRC2 core member SUZ12 and promotes its recruitment to bivalent promoters in spermatocytes. INO80 mediates H2A.Z incorporation at poised promoters, and its loss leads to reduced H3K27me3 and de-repression of poised genes, implicating INO80 in establishing poised chromatin through SUZ12/PRC2 binding. |
Co-immunoprecipitation (INO80-SUZ12); ChIP-seq for H3K27me3, H2A.Z; conditional Ino80 knockout; RNA-seq |
Development |
Medium |
35006254
|
| 2017 |
The INO80 complex acts downstream of the Mec1 checkpoint kinase to increase global chromatin mobility. Mec1 activation by targeted Ddc1/Ddc2 enhances chromatin mobility even in the absence of DNA damage, placing INO80 as an effector of checkpoint-mediated chromatin mobility. |
Live-cell fluorescence tracking of chromosomal loci; genetic epistasis (mec1, rad9, rad53, ino80 mutants); targeted Ddc1/Ddc2 activation |
Genes & development |
Medium |
24029917
|