Affinage

PHC2

Polyhomeotic-like protein 2 · UniProt Q8IXK0

Round 2 corrected
Length
858 aa
Mass
90.7 kDa
Annotated
2026-04-28
42 papers in source corpus 10 papers cited in narrative 10 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

PHC2 is a core subunit of canonical Polycomb Repressive Complex 1 (PRC1) that mediates transcriptional silencing of developmental target genes, including Hox cluster loci and Vcam1, through direct chromatin association and promotion of H2AK119 monoubiquitination and H3K27me3-dependent epigenetic marks (PMID:16024804, PMID:15386022, PMID:31375680). Within the PRC1 family, PHC2 resides specifically in CBX/PHC/SCM-containing canonical complexes that are functionally distinct from RYBP/YAF2-containing variant PRC1, and its interaction with the CBX7C splice isoform modulates PRC1 phase separation into Polycomb bodies and chromatin compaction (PMID:22325352, PMID:38600974). PHC2 protein stability is regulated by SIAH-1-mediated ubiquitination and proteasomal degradation through a PxVxAxP degron motif (PMID:20471960). In vivo, Phc2 loss causes posterior homeotic transformations, premature senescence, defective hematopoietic stem cell mobilization from bone marrow stroma, and systemic immunodeficiency (PMID:16024804, PMID:31375680).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 1997 Medium

    Establishing the composition of human PcG complexes answered whether Drosophila Polyhomeotic-like proteins form conserved repressive assemblies in mammals, revealing that PHC-family proteins co-reside with RING1, BMI1, and Pc homologues in nuclear Polycomb domains.

    Evidence Yeast two-hybrid, co-IP, immunofluorescence, and reporter repression assay in human cells (focused on PHC1/HPH1 as representative family member)

    PMID:9199346

    Open questions at the time
    • Study focused on HPH1; direct biochemical evidence for PHC2 within the same complex was not provided here
    • Repressive mechanism (compaction vs. enzymatic) not resolved
  2. 2002 High

    Biochemical purification of hPRC-H from HeLa cells confirmed that PHC2 (HPH2) is a bona fide subunit of a functionally conserved PRC1 complex that blocks SWI/SNF-mediated nucleosome remodeling, establishing its direct role in chromatin-level repression.

    Evidence Affinity purification of endogenous hPRC-H, functional nucleosome remodeling inhibition assay

    PMID:12167701

    Open questions at the time
    • The enzymatic activity responsible for silencing (ubiquitination) was not yet identified
    • Whether PHC2 contributes structurally or catalytically to the remodeling block was unknown
  3. 2004 High

    Demonstrating that the PRC1 complex containing PHC2 monoubiquitinates H2A at K119 resolved the key catalytic output of canonical PRC1 and linked PHC2 to the histone-modification arm of Polycomb silencing.

    Evidence In vitro ubiquitination of nucleosomal H2A, RNAi of Ring2 in HeLa cells, ChIP in Drosophila

    PMID:15386022

    Open questions at the time
    • Whether PHC2 is required for the ubiquitination activity per se or serves a scaffolding/targeting role was not distinguished
    • In vivo phenotypic consequences of PHC2 loss not yet tested
  4. 2005 High

    Genetic ablation of Phc2 in mice revealed its non-redundant requirement for Hox gene repression and anterior-posterior patterning, establishing the first in vivo loss-of-function phenotype and demonstrating dose-sensitive genetic synergy with Phc1 and Rnf110.

    Evidence Phc2-knockout mice, ChIP at Hox loci with anti-Phc2 antibody, co-IP from embryonic extracts, double/triple mutant epistasis

    PMID:16024804

    Open questions at the time
    • Cell-type-specific contributions of Phc2 versus Phc1 were not resolved
    • Non-Hox target genes were not systematically identified
  5. 2010 Medium

    Identification of SIAH-1 as the E3 ligase that ubiquitinates PHC2 for proteasomal degradation resolved how PHC2 protein levels are post-translationally controlled, introducing a regulatory layer upstream of PRC1 assembly.

    Evidence In vitro pull-down, co-IP, ubiquitination assay with SIAH-1 catalytic mutant, proteasome inhibitor rescue

    PMID:20471960

    Open questions at the time
    • Physiological signals that trigger SIAH-1-mediated PHC2 turnover are unknown
    • Whether SIAH-1 targets other PRC1 subunits was not tested
    • Single-lab finding without independent replication
  6. 2012 High

    Systematic proteomic dissection of six PRC1 sub-complexes placed PHC2 exclusively within canonical CBX/PHC-containing PRC1, distinct from RYBP/YAF2-containing variant PRC1 that has enhanced H2AK119ub1 activity, clarifying that PHC2-containing complexes preferentially mediate chromatin compaction.

    Evidence Affinity purification-mass spectrometry, ChIP-seq, RNAi in ESCs, reconstituted ubiquitination assay

    PMID:22325352

    Open questions at the time
    • The structural basis for mutual exclusivity of PHC and RYBP in PRC1 was not determined
    • Genome-wide target specificity of PHC2-containing versus variant PRC1 was not fully resolved
  7. 2019 High

    Demonstrating that Phc2 represses Vcam1 in bone marrow stromal cells via H3K27me3/H2AK119ub and that its loss causes HSPC mobilization failure and immunodeficiency established a cell-extrinsic niche function for Phc2 beyond developmental Hox regulation.

    Evidence Conditional/global Phc2-knockout mice, flow cytometry, ChIP for H3K27me3 and H2AK119ub at Vcam1, pharmacological VCAM-1 inhibitor rescue

    PMID:31375680

    Open questions at the time
    • Whether other PRC1 target genes in BMSCs contribute to the immunodeficiency phenotype was not exhaustively tested
    • Human relevance of the VCAM-1-dependent niche defect is unconfirmed
  8. 2024 Medium

    Showing that the CBX7C splice isoform preferentially interacts with PHC2 to modulate PRC1 phase separation into Polycomb bodies resolved how isoform-specific interactions tune the biophysical properties and chromatin occupancy of canonical PRC1.

    Evidence Co-IP, FRAP/live-cell imaging, CRISPR knockdown, mESC differentiation assay, chromatin fractionation

    PMID:38600974

    Open questions at the time
    • Whether CBX7C–PHC2 phase separation is relevant outside mESCs is untested
    • Structural determinants of preferential CBX7C–PHC2 interaction are unknown
    • Single-lab observation

Open questions

Synthesis pass · forward-looking unresolved questions
  • The structural basis for PHC2's scaffolding role within canonical PRC1, the full repertoire of PHC2-specific versus PHC1/PHC3-redundant genomic targets, and the signals controlling SIAH-1-mediated PHC2 turnover in physiological contexts remain unresolved.
  • No high-resolution structure of PHC2 in the context of PRC1
  • Genome-wide target specificity of PHC2 versus other PHC paralogues not systematically mapped
  • Upstream signals regulating SIAH-1-dependent PHC2 degradation unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0042393 histone binding 4 GO:0140110 transcription regulator activity 2
Localization
GO:0005634 nucleus 3 GO:0005694 chromosome 3
Pathway
R-HSA-4839726 Chromatin organization 4 R-HSA-1266738 Developmental Biology 2 R-HSA-168256 Immune System 2 R-HSA-74160 Gene expression (Transcription) 2
Partners
BMI1CBX7MEL18PHC1RING1RNF2SIAH1
Complex memberships
PRC1 (canonical CBX/PHC-containing Polycomb Repressive Complex 1)

Evidence

Reading pass · 10 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2005 Phc2 (mouse polyhomeotic homologue 2) is a constituent of class II PcG complexes and represses Hox cluster genes through direct binding to the Hox locus. Phc2-deficient mice display posterior axial skeleton transformations and premature senescence of MEFs with derepression of Hox and Cdkn2a genes. Coimmunoprecipitation from embryonic extracts confirmed interaction of Phc2 with Phc1 and Rnf110 products within class II PcG complexes, and ChIP with anti-Phc2 antibodies demonstrated direct chromatin association at Hox loci. Genetic synergy between Phc2, Phc1, and Rnf110 mutations reveals functional overlap and strict dose-dependent requirements for A-P specification. Knockout mouse phenotyping, coimmunoprecipitation from embryonic extracts, chromatin immunoprecipitation (ChIP), genetic epistasis (double/triple mutant analysis) Molecular and cellular biology High 16024804
2002 The mouse Edr2/Phc2 gene produces two transcript isoforms encoding 90-kDa and 36-kDa polypeptides; the 36-kDa form (lacking the N-terminal region) localizes to nuclei and colocalizes with the PcG protein Mel18, indicating it can participate in multimeric PcG complexes despite being a truncated isoform. cDNA/genomic analysis, immunostaining of HA-tagged protein in mammalian cells Gene Medium 12034499
2002 Human PRC1-like complex (hPRC-H) purified from HeLa cells contains HPH2 (PHC2 human orthologue) along with other core PcG proteins (Ring1, BMI1, HPH1) and retains the Polycomb repressive function of blocking nucleosomal array remodeling, establishing HPH2 as a component of functionally conserved PRC1. Biochemical purification of hPRC-H from HeLa cells, functional nucleosome remodeling assay Molecular and cellular biology High 12167701
2004 HPH2 (PHC2) is a subunit of the hPRC1L E3 ubiquitin ligase complex that monoubiquitinates nucleosomal histone H2A at lysine 119, linking PHC2 to the H2AK119ub Polycomb silencing mechanism. Biochemical purification, in vitro ubiquitination assay with nucleosomal substrate, RNAi knockdown of Ring2 in HeLa cells, ChIP in Drosophila Nature High 15386022
1997 HPH1 (a human PHC paralogue) coimmunoprecipitates with RING1, the human Pc homologue, and BMI1 and colocalizes with them in nuclear PcG domains; RING1 functions as a transcriptional repressor when tethered to a reporter gene, establishing the composition and repressive activity of the human PcG protein complex containing PHC-family proteins. Yeast two-hybrid screen, coimmunoprecipitation, immunofluorescence colocalization, reporter gene repression assay Molecular and cellular biology Medium 9199346
2010 SIAH-1 (an E3 ubiquitin ligase) directly associates with HPH2 (PHC2) both in vitro and in vivo; the cysteine-rich RING domain of SIAH-1 and the PxVxAxP motif of HPH2 are essential for this interaction. SIAH-1 facilitates ubiquitination and proteasomal degradation of HPH2, identifying SIAH-1 as a direct E3 ligase that controls PHC2 protein stability. In vitro pull-down, coimmunoprecipitation, colocalization in nuclei, ubiquitination assay, proteasome inhibitor treatment, SIAH-1 E3-dead mutant analysis Biochemical and biophysical research communications Medium 20471960
2012 PHC proteins (including PHC2) are canonical subunits of CBX/PHC/SCM-containing PRC1 complexes. Six distinct PRC1 sub-complexes were defined; RYBP/YAF2-containing PRC1 complexes exclude PHC subunits and show enhanced RING1B H2AK119ub1 activity relative to CBX/PHC-containing complexes, placing PHC2 in complexes with distinct chromatin compaction versus ubiquitination activities. Comprehensive proteomic affinity purification, ChIP-seq, RNAi knockdown in ESCs, biochemical reconstitution of ubiquitination activity Molecular cell High 22325352
2013 Phc2 is expressed in helper T (Th) cells and is down-regulated upon antigen-specific activation. Ectopic expression of Phc2 inhibits Th cell proliferation and IL-2 secretion upon stimulation, establishing Phc2 as a negative regulator of Th cell activation. RT-PCR expression analysis, ectopic overexpression in Th cells, proliferation and cytokine secretion assays upon antigen-specific stimulation In vitro cellular & developmental biology. Animal Low 23605804
2019 Genetic ablation of Phc2 in mice causes severe defects in HSPC mobilization from bone marrow due to derepression of Vcam1 in bone marrow stromal cells (BMSCs), leading to systemic immunodeficiency. Phc2-dependent Vcam1 repression is mediated by epigenetic regulation of H3K27me3 and H2AK119ub at the Vcam1 locus. Pharmacological inhibition of VCAM-1 reverses the mobilization defect in Phc2-deficient mice, demonstrating a cell-extrinsic (niche) role for Phc2. Conditional/global knockout mice, flow cytometry for HSPC trafficking, ChIP for H3K27me3 and H2AK119ub at Vcam1, pharmacological rescue with VCAM-1 inhibitor Nature communications High 31375680
2024 CBX7C, a splicing isoform of CBX7 expressed in mESCs, preferentially interacts with PHC2 to facilitate PRC1 assembly on chromatin. At low levels, the CBX7C·PHC2 interaction promotes formation of dynamic, high-mobility Polycomb bodies; at high doses, the two factors together form large, low-mobility, chromatin-free aggregates. Knockdown of CBX7C abolishes mESC differentiation to embryoid bodies, and the interaction modulates PRC1 phase separation properties. Co-IP, CRISPR knockdown, fluorescence live-cell imaging (FRAP/mobility analysis), mESC differentiation assay, chromatin fractionation iScience Medium 38600974

Source papers

Stage 0 corpus · 42 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2005 Towards a proteome-scale map of the human protein-protein interaction network. Nature 2090 16189514
2005 A human protein-protein interaction network: a resource for annotating the proteome. Cell 1704 16169070
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
2004 Role of histone H2A ubiquitination in Polycomb silencing. Nature 1377 15386022
2004 Large-scale characterization of HeLa cell nuclear phosphoproteins. Proceedings of the National Academy of Sciences of the United States of America 1159 15302935
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
2014 A proteome-scale map of the human interactome network. Cell 977 25416956
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 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 Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers. Cell 639 20850016
2006 A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 610 16713569
2015 Widespread macromolecular interaction perturbations in human genetic disorders. Cell 454 25910212
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
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
2002 The core of the polycomb repressive complex is compositionally and functionally conserved in flies and humans. Molecular and cellular biology 319 12167701
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
2014 Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes. Journal of proteomics 215 25281560
2011 Toward an understanding of the protein interaction network of the human liver. Molecular systems biology 207 21988832
2011 Next-generation sequencing to generate interactome datasets. Nature methods 200 21516116
2011 Protein interactome reveals converging molecular pathways among autism disorders. Science translational medicine 180 21653829
1997 RING1 is associated with the polycomb group protein complex and acts as a transcriptional repressor. Molecular and cellular biology 165 9199346
2019 H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids. Nature cell biology 162 30804502
2007 Bypass of senescence by the polycomb group protein CBX8 through direct binding to the INK4A-ARF locus. The EMBO journal 160 17332741
2005 Mammalian polyhomeotic homologues Phc2 and Phc1 act in synergy to mediate polycomb repression of Hox genes. Molecular and cellular biology 115 16024804
2005 Regulation of plant defense responses in Arabidopsis by EDR2, a PH and START domain-containing protein. The Plant journal : for cell and molecular biology 76 16212604
2007 EDR2 negatively regulates salicylic acid-based defenses and cell death during powdery mildew infections of Arabidopsis thaliana. BMC plant biology 71 17612410
2011 Suppression of edr2-mediated powdery mildew resistance, cell death and ethylene-induced senescence by mutations in ALD1 in Arabidopsis. Journal of genetics and genomics = Yi chuan xue bao 25 21530897
2019 Phc2 controls hematopoietic stem and progenitor cell mobilization from bone marrow by repressing Vcam1 expression. Nature communications 16 31375680
2010 Hph1 and Hph2 are novel components of the Sec63/Sec62 posttranslational translocation complex that aid in vacuolar proton ATPase biogenesis. Eukaryotic cell 15 21097665
2002 The mouse Edr2 (Mph2) gene has two forms of mRNA encoding 90- and 36-kDa polypeptides. Gene 9 12034499
2010 SIAH-1 interacts with mammalian polyhomeotic homologues HPH2 and affects its stability via the ubiquitin-proteasome pathway. Biochemical and biophysical research communications 8 20471960
2013 Expression pattern and functional role of Phc2 during activation of helper T cells after antigenic stimulation. In vitro cellular & developmental biology. Animal 7 23605804
1997 Genetic mapping of hph2, a mutation affecting amino acid transport in the mouse. Mammalian genome : official journal of the International Mammalian Genome Society 6 9060407
2024 CBX7C⋅PHC2 interaction facilitates PRC1 assembly and modulates its phase separation properties. iScience 2 38600974
1994 Regulation of polyunsaturated fat induced postprandial hypercholesterolemia by a novel gene Phc-2. Molecular and cellular biochemistry 1 8190122