Affinage

CBX6

Chromobox protein homolog 6 · UniProt O95503

Round 2 corrected
Length
412 aa
Mass
43.9 kDa
Annotated
2026-04-28
42 papers in source corpus 15 papers cited in narrative 15 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

CBX6 is a Polycomb group protein that functions as a subunit of both canonical and non-canonical PRC1 complexes, where it contributes to transcriptional repression of target genes involved in stemness, invasion, and immune evasion. Its chromodomain binds H3K27me3 and H3K9me3 with low affinity, but chromatin recruitment occurs largely independently of these marks through non-conserved protein sequences (PMID:18927235, PMID:21047797, PMID:29089522). CBX6 directly represses promoters of genes including BST2, SOX2, NANOG, MMP-2, and CA9, and its protein stability is controlled by K48-linked polyubiquitination at K214 mediated by the UBE2T–TRIM25 E2–E3 ligase complex, targeting it for proteasomal degradation (PMID:39716485, PMID:30655550, PMID:33028834, PMID:41883712). CBX6 itself is transcriptionally repressed by EZH2/PRC2, embedding it within a layered Polycomb regulatory circuit that governs cell identity and pluripotency (PMID:30655550, PMID:29089522).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2008 Medium

    Resolving how CBX6 associates with chromatin revealed that, unlike the canonical model requiring H3K27me3 recognition, CBX6 binds nucleosomes through non-conserved sequences outside its chromodomain and chromobox, and does so independently of H3K27me3.

    Evidence Bimolecular fluorescence complementation and metaphase spread analysis in wild-type and EED-null ES cells with domain deletion constructs

    PMID:18927235

    Open questions at the time
    • The non-conserved sequences mediating chromatin association are not mapped to specific residues
    • Whether this H3K27me3-independent recruitment applies in all cell types is untested
  2. 2010 High

    Structural determination of the CBX6 chromodomain established that it binds H3K27me3 and H3K9me3 with low affinity and cannot discriminate between them, differing from HP1 homologs due to a more tolerant aromatic cage—raising the possibility that CBX6 engages non-histone methylated targets.

    Evidence X-ray crystallography, NMR, ITC and fluorescence binding assays, peptide permutation arrays, and mutagenesis

    PMID:21047797

    Open questions at the time
    • Physiological non-histone binding partners of the CBX6 chromodomain have not been identified
    • The functional consequence of low-affinity histone mark binding in vivo is unclear
  3. 2012 High

    Proteomic and biochemical studies defined the PRC1 complex landscape, placing CBX6 within canonical PRC1 as a mutually exclusive alternative to RYBP/YAF2 and establishing that CBX-containing PRC1 compacts chromatin but does not stimulate H2AK119ub1 as efficiently as non-canonical complexes.

    Evidence Tandem affinity purification–mass spectrometry, ChIP-seq, and biochemical reconstitution with H2A ubiquitination assays

    PMID:21282530 PMID:22325352 PMID:27705803

    Open questions at the time
    • Specific genomic targets uniquely occupied by CBX6-PRC1 versus other CBX-PRC1 variants remain poorly defined
    • Whether CBX6-PRC1 has distinct functional outputs beyond chromatin compaction is unresolved
  4. 2015 Medium

    Chemical biology efforts identified a unique hydrophobic pocket adjacent to the CBX6 chromodomain aromatic cage that enables selective peptidomimetic inhibition, providing a tool compound to dissect CBX6-specific functions.

    Evidence Peptidomimetic synthesis with competitive binding assays, SAR, and molecular dynamics simulations

    PMID:26985288 PMID:34174168

    Open questions at the time
    • These inhibitors have not been used in genome-wide functional studies to define CBX6-dependent gene programs
    • In vivo pharmacological validation is lacking
  5. 2017 High

    Demonstrating CBX6's role in pluripotency, depletion of CBX6 in mouse ESCs destabilized the pluripotency network and triggered differentiation, and CBX6 was found in both canonical and non-canonical PRC1 complexes—a unique feature among CBX paralogs.

    Evidence Co-IP, AP-MS, ChIP-seq, shRNA depletion with transcriptomic analysis in wild-type and EED-null ESCs

    PMID:29089522

    Open questions at the time
    • Which specific PRC1 subcomplexes mediate CBX6's pluripotency function is not dissected
    • Whether CBX6 depletion effects are cell-autonomous in vivo during embryogenesis is unknown
  6. 2019 Medium

    CBX6 was placed within a layered Polycomb regulatory circuit: EZH2/PRC2 transcriptionally represses CBX6 via H3K27me3 at its own locus, and CBX6 in turn represses BST2 by direct promoter binding, establishing a PRC2→CBX6→target gene cascade.

    Evidence EZH2 knockdown and inhibitor treatment measuring CBX6 levels; CBX6 overexpression functional assays; ChIP at the BST2 promoter in breast cancer cells

    PMID:30655550

    Open questions at the time
    • The generality of PRC2-mediated CBX6 repression across tissue types is not established
    • Whether CBX6 acts on BST2 through canonical PRC1-mediated compaction or another mechanism is unclear
  7. 2020 Medium

    CBX6 protein stability was shown to be regulated by constitutive ubiquitination and proteasomal degradation in invasive mesothelioma cells, with loss of CBX6 de-repressing MMP-2 and promoting invasion—linking post-translational control of CBX6 to tumor cell behavior.

    Evidence Proteasome inhibitor (MG132) rescue, ubiquitination assays, knockdown with collagen matrix invasion assay and transcriptomics in mesothelioma lines

    PMID:33028834

    Open questions at the time
    • The E3 ligase responsible for CBX6 degradation in mesothelioma was not identified in this study
    • Whether epigenetic changes at MMP-2 are direct consequences of CBX6 promoter occupancy was not tested by ChIP
  8. 2024 High

    The molecular mechanism of CBX6 turnover was resolved: UBE2T (E2) and TRIM25 (E3) catalyze K48-linked polyubiquitination at CBX6 K214, targeting it for proteasomal degradation; this degradation de-represses SOX2 and NANOG, enhancing cancer stemness.

    Evidence K48-linkage-specific ubiquitination assays, K214R mutagenesis, Co-IP of UBE2T–TRIM25–CBX6, overexpression/knockdown with reporter assays, organoid models, and MMTV-PyMT in vivo tumor model

    PMID:39716485

    Open questions at the time
    • Whether additional ubiquitination sites contribute to CBX6 turnover under different stimuli is untested
    • The signal or condition that activates UBE2T–TRIM25 toward CBX6 is unknown
    • Whether K214 ubiquitination also regulates CBX6 in non-malignant contexts is unexplored
  9. 2025 Medium

    CBX6 was linked to immune evasion through an unexpected mechanism: CBX6 upregulates SMARCD1 (a SWI/SNF subunit), which promotes CCL8 secretion and MCT4-mediated lactate efflux, suppressing CD8+ T cell cytotoxicity in esophageal squamous cell carcinoma.

    Evidence CBX6/SMARCD1 knockdown–overexpression epistasis, co-culture with CD8+ T cells, in vivo tumor models, metabolic lactate assays

    PMID:41219497

    Open questions at the time
    • Whether CBX6 directly binds the SMARCD1 locus or acts indirectly is not determined
    • The relationship between PRC1 membership and SMARCD1/SWI-SNF regulation is mechanistically unclear
    • Generalizability beyond ESCC is untested

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key open questions include identifying the full set of direct CBX6-PRC1 genomic targets, the physiological non-histone ligands of its chromodomain, the signals governing UBE2T–TRIM25 activation, and whether CBX6's non-canonical PRC1 membership has distinct functional outputs from its canonical PRC1 role.
  • No genome-wide direct target map (ChIP-seq for CBX6 occupancy) exists in most cancer contexts
  • Non-histone chromodomain ligands remain unidentified
  • In vivo developmental phenotype of CBX6 knockout has not been reported

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140110 transcription regulator activity 4 GO:0042393 histone binding 3 GO:0003677 DNA binding 2
Localization
GO:0005634 nucleus 3 GO:0005694 chromosome 2
Pathway
R-HSA-74160 Gene expression (Transcription) 4 R-HSA-4839726 Chromatin organization 3
Partners
EZH2PCGF2RING1BSMARCD1TRIM25UBE2T
Complex memberships
PRC1 (canonical)PRC1 (non-canonical)

Evidence

Reading pass · 15 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2008 CBX6 associates with nucleosomes in distinct subnuclear regions compared to other CBX family members (e.g., CBX2 and CBX6 show reciprocal patterns of chromosome association on metaphase spreads). Importantly, the conserved chromodomain and chromobox regions of CBX6 are dispensable for chromatin association, and this association occurs through non-conserved, nonhomologous protein sequences. The absence of H3K27me3 (in EED-null ES cells) had minimal effects on CBX6 chromatin association. Bimolecular fluorescence complementation (BiFC) analysis in ES cells and fibroblasts; metaphase spread analysis; stable cell lines with inducible expression Proceedings of the National Academy of Sciences of the United States of America Medium 18927235
2010 Human CBX6 chromodomain binds trimethylated H3K27 and H3K9 peptides but with lower affinity than HP1 homologs, and cannot distinguish between these two marks. Structural and mutagenic analyses revealed that the Pc subfamily (including CBX6) has a greater sequence tolerance in its chromodomain binding surface and potentially engages alternative non-histone sequences as binding targets. The structural basis for divergent methyllysine binding selectivity in CBX6 versus HP1 proteins was defined. X-ray crystallography, NMR, ITC/fluorescence binding assays, peptide permutation arrays, site-directed mutagenesis The Journal of biological chemistry High 21047797
2011 Tandem affinity purification coupled with mass spectrometry showed that CBX6 defines a distinct PRC1-like complex (~60 interacting proteins identified), and CBX family members are mutually exclusive within PRC1 complexes. CBX6 and CBX8 interact with the largest number of partners and differ in their protein interaction networks from CBX2, CBX4, and CBX7. Protein kinase CK2 associates with all CBX-PRC1 complexes. Different CBX proteins show distinct subnuclear localization, consistent with their different interaction profiles. Tandem affinity purification (TAP) coupled with tandem mass spectrometry (MS/MS) in mammalian cells Molecular & cellular proteomics : MCP Medium 21282530
2012 Proteomic and genomic analysis established that CBX proteins (including CBX6) are incorporated into six major groups of PRC1 complexes, each containing a distinct PCGF subunit and RING1A/B. CBX-containing complexes (canonical PRC1) are distinct from RYBP/YAF2-containing complexes, as RYBP binding prevents incorporation of CBX, PHC, and SCM subunits. Both complex types compact chromatin, but only RYBP stimulates RING1B-mediated H2AK119ub1. Affinity purification-mass spectrometry, genomic localization (ChIP-seq), biochemical reconstitution, H2A ubiquitination assays Molecular cell High 22325352
2015 CBX6 chromodomain can be selectively inhibited by peptidomimetic compounds. A specific chemical modification of a pan-polycomb ligand switches selectivity toward CBX6 by engaging a small hydrophobic pocket adjacent to the aromatic cage that is unique to CBX6. Molecular dynamics simulations confirmed that occupancy of this pocket is the structural basis for selectivity. Competitive binding assays, molecular dynamics simulations, peptidomimetic synthesis and SAR ACS medicinal chemistry letters Medium 26985288
2016 Systematic affinity purification-mass spectrometry mapping of the human PcG complexome identified CBX6 as a component of canonical PRC1 complexes with a defined set of interacting partners, distinct from other CBX paralogs. The high-density interaction network placed CBX6 within the broader PcG interactome architecture. Affinity purification-mass spectrometry (AP-MS) of PcG proteins in human cells Cell reports Medium 27705803
2017 CBX6 promotes HCC cell growth in vitro and in vivo, and mechanistic investigation revealed that the S100A9/NF-κB/MAPK signaling pathway is essential for mediating CBX6 oncogenic function in HCC. Gain- and loss-of-function experiments (overexpression and knockdown), in vivo xenograft, pathway inhibitor experiments, Western blotting Oncotarget Medium 28122351
2017 CBX6 is physically associated with both canonical PRC1 (cPRC1) and non-canonical PRC1 (ncPRC1) complexes in mouse embryonic stem cells, as demonstrated by co-immunoprecipitation and mass spectrometry. Unlike CBX7, CBX6 is recruited to chromatin independently of H3K27me3. Depletion of CBX6 destabilizes the pluripotency network and triggers ESC differentiation, establishing CBX6 as an essential component of ESC identity. Co-immunoprecipitation, affinity purification-mass spectrometry, ChIP-seq, shRNA-mediated depletion, gene expression analysis, H3K27me3-independent chromatin recruitment assay using EED-null cells Nature communications High 29089522
2019 CBX6 expression in breast cancer is negatively regulated by EZH2 in a PRC2-dependent manner. EZH2 represses CBX6 transcription via H3K27 methylation at the CBX6 locus. CBX6 overexpression inhibits breast cancer cell proliferation, colony formation, migration and invasion, and induces cell cycle arrest. CBX6 downregulates BST2 expression by binding to its promoter region. EZH2 knockdown and inhibitor treatment with CBX6 mRNA/protein measurement, CBX6 overexpression functional assays (MTT, colony formation, wound healing, Transwell), chromatin immunoprecipitation (ChIP) at BST2 promoter, microarray gene expression analysis Scientific reports Medium 30655550
2020 In invasive mesothelioma cells, CBX6 undergoes constitutive ubiquitination and proteasomal degradation, leading to loss of CBX6-mediated repression of the MMP-2 gene. CBX6 knockdown in non-invasive mesothelioma cells promotes MMP-2 expression and invasion. CBX6 regulates sets of genes involved in cancer cell migration and metastasis through epigenetic mechanisms involving DNA and histone methylation at target gene transcription start sites. Knockdown experiments, proteasome inhibitor treatment (MG132), ubiquitination assays, collagen matrix invasion assay, transcriptome analysis, immunohistochemistry Scientific reports Medium 33028834
2020 CBX6 promotes HCC cell migration and invasion through upregulation of transcription factors Snail and Zeb1, thereby accelerating the epithelial-mesenchymal transition (EMT) process. CBX6 overexpression and shRNA knockdown in HCC cell lines; Western blot for Snail/Zeb1/EMT markers; wound healing and Transwell invasion assays OncoTargets and therapy Low 33311989
2021 Structure-activity relationship studies on CBX6 chromodomain inhibitors identified the -2 position of the peptidomimetic scaffold as a key determinant of selectivity among polycomb paralogs, yielding potent dual-selective inhibitors of CBX6 and CBX8 that are cell permeable and impact cell proliferation in rhabdoid tumor cells. Competitive binding assays, SAR medicinal chemistry, cell proliferation assays in rhabdoid tumor cell line ChemMedChem Medium 34174168
2024 CBX6 is polyubiquitinated at K214 via K48-linked chains by a UBE2T–TRIM25 E2–E3 ligase complex, leading to proteasomal degradation of CBX6. Loss of CBX6 de-represses SOX2 and NANOG transcription, enhancing breast cancer stem cell (BCSC) stemness. CBX6 thus acts as a transcriptional repressor of pluripotency genes SOX2 and NANOG, and its stability is controlled by the UBE2T–TRIM25 axis. Ubiquitination assays (K48-linkage specific), site-directed mutagenesis (K214R), co-immunoprecipitation of UBE2T–TRIM25–CBX6 complex, CBX6 overexpression/knockdown with SOX2/NANOG reporter assays, organoid models, MMTV-PyMT in vivo mouse model, single-cell RNA-seq Cancer letters High 39716485
2025 CBX6 promotes immune evasion in esophageal squamous cell carcinoma by regulating chromatin remodeling via SMARCD1 (a SWI/SNF complex subunit). CBX6 upregulates SMARCD1 expression, which in turn promotes transcription of CCL8 and SLC16A3 (encoding MCT4). This leads to CCL8 secretion and MCT4-mediated lactate efflux, suppressing CD8+ T cell cytotoxicity and promoting tumor development. CBX6 and SMARCD1 knockdown/overexpression in mEC25 cells, co-culture with CD8+ T cells, in vivo tumor models, chromatin remodeling assays, metabolic assays (lactate transport), tissue microarray analysis Cell biology and toxicology Medium 41219497
2026 CBX6 binds directly to the CA9 (carbonic anhydrase 9) gene promoter in GBM cells, as demonstrated by chromatin immunoprecipitation with multiple primer sets, suggesting CBX6 acts as a transcriptional repressor of CA9. Under hypoxic conditions, CBX6 is downregulated, which is associated with CA9 upregulation, indicating a direct regulatory relationship. Chromatin immunoprecipitation (ChIP) with multiple primers, shRNA-mediated knockdown, qRT-PCR, functional proliferation/migration/invasion assays Molecular therapy. Oncology Medium 41883712

Source papers

Stage 0 corpus · 42 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
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
2018 VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. Cell discovery 829 29507755
1999 The DNA sequence of human chromosome 22. Nature 808 10591208
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 PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Molecular cell 698 22325352
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2010 An atlas of combinatorial transcriptional regulation in mouse and man. Cell 573 20211142
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2010 A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci. Nature genetics 369 20972438
2010 Recognition and specificity determinants of the human cbx chromodomains. The Journal of biological chemistry 233 21047797
2016 A High-Density Map for Navigating the Human Polycomb Complexome. Cell reports 216 27705803
2010 Ubiquitin-specific proteases 7 and 11 modulate Polycomb regulation of the INK4a tumour suppressor. The EMBO journal 143 20601937
2009 Ubiquitin-mediated proteolysis of HuR by heat shock. The EMBO journal 142 19322201
2018 Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains. Molecular cell 136 30554943
2014 The central role of EED in the orchestration of polycomb group complexes. Nature communications 131 24457600
2013 Genome-wide association study identifies multiple loci associated with bladder cancer risk. Human molecular genetics 129 24163127
2011 Interaction proteomics analysis of polycomb proteins defines distinct PRC1 complexes in mammalian cells. Molecular & cellular proteomics : MCP 115 21282530
2008 Different polycomb group CBX family proteins associate with distinct regions of chromatin using nonhomologous protein sequences. Proceedings of the National Academy of Sciences of the United States of America 102 18927235
2018 Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. Molecular & cellular proteomics : MCP 101 30021884
2014 Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation. Cell reports 80 24981860
2020 Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. Cell reports 79 32814053
2010 Role for the MOV10 RNA helicase in polycomb-mediated repression of the INK4a tumor suppressor. Nature structural & molecular biology 54 20543829
2020 RIG-I regulates myeloid differentiation by promoting TRIM25-mediated ISGylation. Proceedings of the National Academy of Sciences of the United States of America 47 32513696
2017 CBX6 overexpression contributes to tumor progression and is predictive of a poor prognosis in hepatocellular carcinoma. Oncotarget 47 28122351
2022 NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia. Nature immunology 46 36138187
2013 Protein interaction discovery using parallel analysis of translated ORFs (PLATO). Nature biotechnology 43 23503679
2003 Identification and analysis of chromodomain-containing proteins encoded in the mouse transcriptome. Genome research 43 12819141
2015 Selective Inhibition of CBX6: A Methyllysine Reader Protein in the Polycomb Family. ACS medicinal chemistry letters 42 26985288
2019 CBX6 is negatively regulated by EZH2 and plays a potential tumor suppressor role in breast cancer. Scientific reports 40 30655550
2020 CBX6 Promotes HCC Metastasis Via Transcription Factors Snail/Zeb1-Mediated EMT Mechanism. OncoTargets and therapy 33 33311989
2017 The Polycomb group protein CBX6 is an essential regulator of embryonic stem cell identity. Nature communications 32 29089522
2024 Targeting UBE2T suppresses breast cancer stemness through CBX6-mediated transcriptional repression of SOX2 and NANOG. Cancer letters 10 39716485
2021 Polycomb Paralog Chromodomain Inhibitors Active against Both CBX6 and CBX8*. ChemMedChem 10 34174168
2020 Proteasomal degradation of polycomb-group protein CBX6 confers MMP-2 expression essential for mesothelioma invasion. Scientific reports 9 33028834
2023 KMT2A-rearranged sarcoma with unusual fusion gene CBX6::KMT2A::PYGO1. Virchows Archiv : an international journal of pathology 5 37713130
2024 Identification of Cbx6 as a potential biomarker in renal ischemia/reperfusion injury. Transplant immunology 2 38452983
2024 Identification of CCR7 and CBX6 as key biomarkers in abdominal aortic aneurysm: Insights from multi-omics data and machine learning analysis. IET systems biology 2 39602349
2026 CBX6 and CA9 as predictive indicators and therapeutic targets in GBM. Molecular therapy. Oncology 0 41883712
2025 CBX6 induces CD8+ T cell exhaustion and tumor development in esophageal squamous cell carcinoma through SMARCD1-mediated CCL8 secretion and lactate efflux. Cell biology and toxicology 0 41219497