Affinage

ACTR5

Actin-related protein 5 · UniProt Q9H9F9

Round 2 corrected
Length
607 aa
Mass
68.3 kDa
Annotated
2026-04-28
40 papers in source corpus 14 papers cited in narrative 14 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

ACTR5 is a conserved actin-related protein that functions as an essential subunit of the INO80 ATP-dependent chromatin remodeling complex, where it partners with IES6 to form a module that couples ATP hydrolysis to nucleosome sliding and histone H2A-H2B dimer exchange. The ACTR5-IES6 module engages nucleosomes through a grappler domain containing an arginine anchor required for nucleosome mobilization and a hydrophobic/acidic patch required for dimer displacement, and its unique insertion domains are necessary to convert ATPase activity into productive nucleosome movement (PMID:26306040, PMID:39676660). Within the INO80 complex, ACTR5 contributes to homologous recombination-based DNA repair, YY1-dependent transcriptional activation, genome-wide nucleosome positioning at promoters, and regulation of cell cycle gene expression including CDKN2A (PMID:18026119, PMID:17721549, PMID:26755556, PMID:36563143). Independent of INO80, ACTR5 suppresses myocardin-SRF-driven smooth muscle gene transcription by binding the RPEL motif of myocardin and the DNA-binding domain of SRF, and its expression is downregulated during muscle differentiation through alternative splicing coupled to nonsense-mediated mRNA decay (PMID:24567363, PMID:36977368).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 2000 Medium

    Establishing that the ARP5 gene product is a nuclear actin-related protein essential for cell viability answered the basic question of where this uncharacterized ARP functions and whether it is required for growth.

    Evidence GFP-fusion imaging and gene deletion in yeast (W303 strain)

    PMID:10923024

    Open questions at the time
    • Single yeast strain; essentiality not confirmed in other strain backgrounds
    • No interaction partners or complex membership identified
    • Mechanism of nuclear function unknown
  2. 2005 High

    Identification of human ACTR5 as an integral subunit of the INO80 complex, which possesses nucleosome-stimulated ATPase and nucleosome sliding activities, established the functional context of ACTR5 in chromatin remodeling.

    Evidence Affinity purification, mass spectrometry, and in vitro ATPase/nucleosome sliding assays of hINO80

    PMID:16230350

    Open questions at the time
    • Individual contribution of ACTR5 versus other subunits to remodeling activity not dissected
    • No structural information on how ACTR5 contacts the nucleosome
  3. 2007 Medium

    Demonstrating that the hINO80 complex participates in homologous recombination repair and transcriptional coactivation via YY1 recruitment expanded ACTR5's functional context beyond nucleosome sliding to DNA damage repair and gene regulation.

    Evidence RNAi knockdown of INO80 subunits with HR repair assays and DNA damage sensitivity (PMID:18026119); co-IP, ChIP, and reporter assays for YY1-INO80 interaction (PMID:17721549)

    PMID:17721549 PMID:18026119

    Open questions at the time
    • ACTR5 was implicated as part of the INO80 complex rather than individually tested for these roles
    • Direct protein contacts between ACTR5 and HR or transcriptional machinery not defined
  4. 2011 High

    Biochemical fractionation placed ACTR5 into a defined core module of INO80 (with IES6, IES2, Tip49a/b, and the Ino80 ATPase domain), demonstrating that ACTR5 resides in the evolutionarily conserved remodeling engine rather than a peripheral regulatory arm.

    Evidence Subassembly reconstitution with in vitro nucleosome remodeling assays

    PMID:21303910

    Open questions at the time
    • How ACTR5 physically contacts other module components was not resolved
    • Structural basis for module assembly unknown at this point
  5. 2014 High

    Discovery that ACTR5 directly binds myocardin and SRF to suppress smooth muscle gene expression — independent of INO80 chromatin remodeling — revealed a moonlighting function for this actin-related protein in cell differentiation.

    Evidence Reciprocal co-IP, ChIP, RNAi rescue, and reporter assays in smooth muscle cells

    PMID:24567363

    Open questions at the time
    • Whether the SRF/myocardin-suppressive role extends to other cell types is unknown
    • Structural basis of ACTR5-RPEL and ACTR5-SRF interactions not determined
  6. 2015 High

    Two studies established that the Arp5-Ies6 heterodimer is a functionally autonomous subcomplex that stimulates INO80 ATPase and sliding activities, and that Arp5's unique insertion domains are specifically required to couple ATPase activity to productive nucleosome movement — distinguishing motor stimulation from mechanical coupling.

    Evidence In vitro ATPase and sliding assays with wild-type and deletion mutant Arp5-Ies6, ChIP-seq, and transcriptomic analysis in yeast

    PMID:26306040 PMID:26755556

    Open questions at the time
    • Precise nucleosome contact sites of the insertion domains not mapped
    • How Arp5-Ies6 occupancy at promoters is regulated remains unclear
  7. 2018 High

    Cryo-EM of human INO80-nucleosome complex resolved the architecture of ACTR5-IES6 binding on the nucleosome face opposite the motor domain, establishing the spatial framework for ACTR5's role in gripping the nucleosome during remodeling.

    Evidence Cryo-EM structure determination of hINO80-nucleosome with functional validation using H3 tail mutants

    PMID:29643506

    Open questions at the time
    • Resolution limited for detailed ACTR5-nucleosome contact mapping
    • Mechanism by which ACTR5 grappler discriminates substrates unknown
  8. 2022 Medium

    A CRISPRi screen identified ACTR5 as essential for hepatocellular carcinoma cell proliferation and revealed that ACTR5 and IES6 suppress CDKN2A expression with an HCC-specific dependency distinct from other INO80 subunits, suggesting an INO80-independent or module-specific oncogenic function.

    Evidence CRISPRi screen, CRISPR gene tiling, expression analysis, and CDK inhibitor synergy assays in HCC models

    PMID:36563143

    Open questions at the time
    • Whether the HCC-specific function is truly INO80-independent or reflects a specialized INO80 sub-complex is unresolved
    • Direct mechanism of CDKN2A repression by ACTR5/IES6 not defined
  9. 2023 Medium

    Identification of AS-NMD regulation of ACTR5 during muscle differentiation revealed a post-transcriptional switch that reduces ACTR5 protein by redirecting mRNA splicing to an NMD-targeted isoform, explaining how ACTR5 levels are dynamically controlled.

    Evidence RT-PCR isoform analysis, splicing factor RNAi, NMD inhibition, and splice site mutagenesis

    PMID:36977368

    Open questions at the time
    • Which splicing factors directly regulate the exon 7a/7b switch in vivo is not fully mapped
    • Functional consequence of ACTR5 reduction for INO80 activity during differentiation not tested
  10. 2025 High

    Mutagenesis of the Arp5 grappler domain resolved two distinct nucleosome-binding modes — an arginine anchor for sliding and a hydrophobic/acidic patch for H2A-H2B dimer exchange — providing the first mechanistic dissection of how a single remodeler subunit separately controls two core chromatin remodeling activities.

    Evidence In vitro nucleosome binding, mutagenesis, sliding and dimer exchange assays, confirmed by in vivo phenotypic analysis in yeast

    PMID:39676660

    Open questions at the time
    • Structural basis for the two binding modes at atomic resolution not yet available
    • Whether these dual activities are independently regulated in cells is unknown

Open questions

Synthesis pass · forward-looking unresolved questions
  • Major open questions include whether ACTR5's INO80-independent functions (SRF suppression, HCC-specific CDKN2A regulation) operate through a common mechanism, how the ACTR5-IES6 module is selectively deployed at genomic loci, and what structural rearrangements within the grappler domain switch between nucleosome sliding and dimer exchange modes.
  • No atomic-resolution structure of ACTR5 grappler bound to nucleosome in both functional modes
  • INO80-independent versus INO80-dependent roles not biochemically separated
  • Upstream signals regulating ACTR5-IES6 module engagement at specific genomic loci undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0042393 histone binding 2 GO:0008092 cytoskeletal protein binding 1 GO:0140110 transcription regulator activity 1
Localization
GO:0005634 nucleus 2 GO:0005654 nucleoplasm 1
Pathway
R-HSA-4839726 Chromatin organization 6 R-HSA-74160 Gene expression (Transcription) 3 R-HSA-73894 DNA Repair 2 R-HSA-1640170 Cell Cycle 1
Partners
IES2IES6INO80MYOCDRUVBL1RUVBL2SRFUCHL5
Complex memberships
Arp5-Ies6 moduleINO80 complex

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2000 Yeast ARP5 (YNL059c) is a nuclear protein essential for vegetative growth in W303 strain; GFP-tagging demonstrated nuclear localization of Arp5, establishing it as a nuclear actin-related protein. Gene deletion (KanMX4 replacement), GFP fusion localization, tetrad analysis Yeast (Chichester, England) Medium 10923024
2005 Human ACTR5 (Arp5) is an integral subunit of the mammalian INO80 chromatin remodeling complex (hINO80), which exhibits DNA- and nucleosome-stimulated ATPase activity and catalyzes ATP-dependent nucleosome sliding, establishing ACTR5's role in chromatin remodeling. Affinity purification, mass spectrometry, in vitro ATPase assay, nucleosome sliding assay The Journal of biological chemistry High 16230350
2007 ACTR5, as a component of hINO80, participates in homologous recombination-based DNA repair; knockdown of INO80 subunits (including ACTR5-containing complex) increases cellular sensitivity to DNA-damaging agents and impairs HR repair. RNA interference, HR repair functional assay, sensitivity assays to DNA-damaging agents Nature structural & molecular biology Medium 18026119
2007 ACTR5-containing hINO80 complex is recruited by transcription factor YY1 to YY1-activated gene promoters, where INO80 functions as a coactivator; YY1 binding to DNA at target genes requires INO80, indicating ACTR5 participates in transcriptional activation. Co-immunoprecipitation, ChIP, reporter assays, RNAi knockdown Nature structural & molecular biology Medium 17721549
2008 ACTR5-containing hINO80 complex associates with the deubiquitinating enzyme Uch37 in the nucleus and holds it in an inactive state; transient interaction of hINO80 with the proteasome can activate Uch37, linking ACTR5's complex to ubiquitin-mediated regulation of transcription or DNA repair. Affinity purification, mass spectrometry, DUB activity assays, co-immunoprecipitation Molecular cell Medium 18922472
2009 Arabidopsis ARP5, the plant ortholog of ACTR5, localizes to the nucleoplasm, is required for normal cell size and organ development, and is necessary for DNA repair (null mutants hypersensitive to hydroxyurea, MMS, and bleocin), supporting a conserved role for ARP5 in INO80-mediated DNA repair. Monoclonal antibody localization, promoter-reporter fusions, null mutant phenotypic analysis, DNA damage sensitivity assays, complementation Developmental biology Medium 19679120
2011 Human ACTR5 (Arp5) is assigned to a distinct third module of the hINO80 complex, together with the hIno80 Snf2 ATPase domain, Ies2, Ies6, Tip49a, and Tip49b; this core evolutionarily conserved module is required for ATP-dependent nucleosome remodeling activity. Biochemical fractionation, affinity purification, in vitro nucleosome remodeling assay, subassembly reconstitution The Journal of biological chemistry High 21303910
2014 In smooth muscle cells, ACTR5 (Arp5) directly binds the RPEL motif of myocardin (Myocd) — suppressing Myocd transcriptional activity — and also binds the DNA-binding domain of SRF via its C-terminal sequence, preventing the Myocd-SRF complex from associating with smooth muscle gene promoters. Arp5 knockdown in dedifferentiated smooth muscle cells restored differentiated phenotype via Myocd activation. Expression of a specific Arp5 splicing variant is reduced in well-differentiated smooth muscle cells through partial mRNA decay and translational suppression. Co-immunoprecipitation, ChIP, RNAi knockdown, reporter assays, differentiation phenotype assays The Journal of cell biology High 24567363
2015 The yeast Arp5 and Ies6 subunits of INO80 form a distinct and abundant subcomplex in vivo; this Arp5-Ies6 subcomplex stimulates INO80-mediated ATPase and nucleosome remodeling activities in vitro; relative Arp5-Ies6 occupancy correlates with nucleosome positioning at transcriptional start sites and regulates >1,000 genes involved in metabolic pathways, with arp5Δ mutants showing deregulated glycolysis and elevated mitochondrial respiration. In vitro ATPase assay, nucleosome remodeling assay, ChIP-seq, genome-wide transcriptomic analysis, metabolic measurements Molecular and cellular biology High 26755556
2015 Assembly of the Arp5-Ies6 module with the INO80 complex requires the Ies2 subunit and conserved domains within Arp5, Ies6, and the spacer region of the Ino80 ATPase domain; Arp5-Ies6 interacts with chromatin only when assembled into the full INO80 complex. Ectopic addition of wild-type Arp5-Ies6 stimulates both INO80 ATPase activity and nucleosome sliding, but mutant Arp5 lacking unique insertion domains stimulates ATPase activity without promoting nucleosome sliding, demonstrating that Arp5 insertion domains are required to couple ATP hydrolysis to productive nucleosome movement. Co-immunoprecipitation, in vitro ATPase assay, nucleosome sliding assay, domain deletion mutagenesis, ChIP The Journal of biological chemistry High 26306040
2018 Cryo-EM structure of human INO80 bound to a nucleosome revealed that the ARP5-IES6 module makes contacts on the opposite face of the nucleosome from the motor domains (which bind at the DNA entry point rather than SHL2); the histone H3 tails regulate INO80 motor domain activity, a mechanism distinct from other remodelers where H4 tails regulate the motor. Cryo-EM structure determination, functional validation with H3 tail mutants Nature High 29643506
2022 ACTR5, identified by CRISPR interference screen, is essential for hepatocellular carcinoma (HCC) tumor progression; ACTR5 suppression activates CDKN2A expression and ablates CDK/E2F-driven cell cycle signaling. High-density CRISPR gene tiling revealed that ACTR5 and IES6 have an HCC-specific function distinct from other INO80 complex members, suggesting an INO80-independent mechanism; synergism was found between ACTR5/IES6 targeting and CDK pharmacological inhibition. CRISPRi screen, CRISPR tiling, gene expression analysis, tumor growth assays, pharmacological combination assays Science advances Medium 36563143
2023 ACTR5 expression in muscle tissues is regulated by alternative splicing coupled to nonsense-mediated mRNA decay (AS-NMD): during muscle differentiation, switching from the canonical Arp5(7a) isoform to an NMD-targeted isoform Arp5(7b) (containing premature termination codons in alternative exon 7b) reduces ACTR5 protein levels. Splicing factor knockdown increases Arp5(7b) and decreases Arp5(7a) levels, identifying splicing factors as upstream regulators of ACTR5 expression. RT-PCR isoform quantification, splicing factor RNAi, NMD inhibition assays, mutation of splice acceptor sequence Biochemical and biophysical research communications Medium 36977368
2025 Arp5 contains two distinct regions within its grappler domain that bind near the acidic pocket of nucleosomes: (1) an arginine anchor required for INO80-mediated nucleosome mobilization, and (2) a hydrophobic/acidic patch (Leu/Asp) that binds free histone H2A-H2B dimers and is required for displacing DNA from the H2A-H2B surface and for histone dimer exchange by INO80. These two binding modes have distinct functional roles demonstrated both in vitro and in vivo. In vitro nucleosome binding assays, mutagenesis, nucleosome sliding assay, histone dimer exchange assay, in vivo phenotypic analysis Nucleic acids research High 39676660

Source papers

Stage 0 corpus · 40 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2014 Biological insights from 108 schizophrenia-associated genetic loci. Nature 5878 25056061
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2015 The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 1118 26186194
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2020 A reference map of the human binary protein interactome. Nature 849 32296183
2003 Complete sequencing and characterization of 21,243 full-length human cDNAs. Nature genetics 754 14702039
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2012 A census of human soluble protein complexes. Cell 689 22939629
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
2007 Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. Molecular cell 367 17643375
2016 The cell proliferation antigen Ki-67 organises heterochromatin. eLife 265 26949251
2011 A directed protein interaction network for investigating intracellular signal transduction. Science signaling 258 21900206
2016 A High-Density Map for Navigating the Human Polycomb Complexome. Cell reports 216 27705803
2005 A mammalian chromatin remodeling complex with similarities to the yeast INO80 complex. The Journal of biological chemistry 195 16230350
2007 A YY1-INO80 complex regulates genomic stability through homologous recombination-based repair. Nature structural & molecular biology 169 18026119
2001 The DNA sequence and comparative analysis of human chromosome 20. Nature 168 11780052
2019 H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids. Nature cell biology 162 30804502
2007 YY1 functions with INO80 to activate transcription. Nature structural & molecular biology 161 17721549
2018 Structure and regulation of the human INO80-nucleosome complex. Nature 151 29643506
2018 Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains. Molecular cell 136 30554943
2008 Distinct modes of regulation of the Uch37 deubiquitinating enzyme in the proteasome and in the Ino80 chromatin-remodeling complex. Molecular cell 127 18922472
2022 Human transcription factor protein interaction networks. Nature communications 123 35140242
2019 Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity. Genes & development 110 31753913
2011 Subunit organization of the human INO80 chromatin remodeling complex: an evolutionarily conserved core complex catalyzes ATP-dependent nucleosome remodeling. The Journal of biological chemistry 98 21303910
2017 R2TP/Prefoldin-like component RUVBL1/RUVBL2 directly interacts with ZNHIT2 to regulate assembly of U5 small nuclear ribonucleoprotein. Nature communications 94 28561026
2009 Micro-RNA-128 (miRNA-128) down-regulation in glioblastoma targets ARP5 (ANGPTL6), Bmi-1 and E2F-3a, key regulators of brain cell proliferation. Journal of neuro-oncology 88 19941032
2003 Immunomic analysis of human sarcoma. Proceedings of the National Academy of Sciences of the United States of America 85 12601173
2016 The INO80 Complex Requires the Arp5-Ies6 Subcomplex for Chromatin Remodeling and Metabolic Regulation. Molecular and cellular biology 44 26755556
2009 Arabidopsis actin-related protein ARP5 in multicellular development and DNA repair. Developmental biology 33 19679120
2015 Assembly of the Arp5 (Actin-related Protein) Subunit Involved in Distinct INO80 Chromatin Remodeling Activities. The Journal of biological chemistry 29 26306040
2000 Functional analysis of six genes from chromosomes XIV and XV of Saccharomyces cerevisiae reveals YOR145c as an essential gene and YNL059c/ARP5 as a strain-dependent essential gene encoding nuclear proteins. Yeast (Chichester, England) 19 10923024
2014 Arp5 is a key regulator of myocardin in smooth muscle cells. The Journal of cell biology 18 24567363
2022 ACTR5 controls CDKN2A and tumor progression in an INO80-independent manner. Science advances 14 36563143
2025 Conformational switching of Arp5 subunit regulates INO80 chromatin remodeling. Nucleic acids research 2 39676660
2023 Regulation of Arp5 expression by alternative splicing coupled to nonsense-mediated RNA decay. Biochemical and biophysical research communications 1 36977368
2024 Conformational switching of Arp5 subunit differentially regulates INO80 chromatin remodeling. bioRxiv : the preprint server for biology 0 38766108