Affinage

PHC1

Polyhomeotic-like protein 1 · UniProt P78364

Length
1004 aa
Mass
105.5 kDa
Annotated
2026-04-28
60 papers in source corpus 15 papers cited in narrative 15 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

PHC1 (RAE28/mph1) is a core subunit of canonical Polycomb Repressive Complex 1 (cPRC1) that functions as an epigenetic repressor of developmental gene expression, maintaining Hox gene expression boundaries, sustaining hematopoietic stem cell self-renewal, and supporting B-cell maturation and cardiac development (PMID:11044623, PMID:11901201, PMID:11164110, PMID:12122109). Its SAM/SPM domain mediates self-association and heterotypic interactions with PcG proteins BMI1, M33/CBX2, and SCMH1 to assemble large multimeric chromatin-associated complexes, and PHC1 functions synergistically with PHC2 in dose-dependent Hox repression (PMID:9499582, PMID:9571155, PMID:16024804). PHC1 is required for histone H2A ubiquitination and proper DNA damage repair, and loss-of-function mutations in human PHC1 cause primary microcephaly with defective H2A ubiquitination and Geminin accumulation (PMID:23418308). Independently of PRC1, PHC1 interacts directly with NANOG to activate Nanog transcription by stabilizing long-range chromatin interactions at the Nanog locus, linking it to pluripotency maintenance (PMID:33990559).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 1998 High

    Establishing that PHC1 assembles into PcG complexes through its SAM domain resolved how mammalian Polycomb proteins oligomerize: the SAM/SPM domain mediates both self-association and heterotypic binding with BMI1 and M33, with specific hydrophobic residues forming the critical interface.

    Evidence In vitro binding assays with mutagenesis of SAM domain constructs; co-immunoprecipitation and gel filtration from embryonic nuclear extracts with domain mapping

    PMID:9499582 PMID:9571155

    Open questions at the time
    • Structural basis of the SAM polymer at atomic resolution not determined
    • Stoichiometry of PHC1 within native PRC1 complexes not defined
    • Whether SAM-mediated polymerization is regulated in vivo remains unknown
  2. 1999 Medium

    Identification of SPM-domain-mediated interaction between RAE28/PHC1 and SCMH1 extended the PcG interaction network, paralleling the Drosophila polyhomeotic–Scm axis in mammals.

    Evidence In vitro SPM domain interaction assay; northern analysis for expression correlation

    PMID:10653359

    Open questions at the time
    • Interaction not validated by reciprocal Co-IP or in-cell assay
    • Functional consequence of PHC1–SCMH1 interaction not tested
  3. 2000 High

    Knockout studies established that PHC1 is not required for initial Hox gene activation but is essential for maintaining expression boundaries, defining it as an epigenetic maintenance factor rather than an establishment factor.

    Evidence Rae28-deficient mouse model with in situ hybridization for Hoxb3 and epistasis analysis of upstream regulators kreisler and Krox20

    PMID:11044623

    Open questions at the time
    • Direct chromatin occupancy of PHC1 at Hox loci not shown in this study
    • Mechanism by which PHC1 maintains but does not establish boundaries not resolved
  4. 2002 High

    Multiple in vivo studies demonstrated that PHC1 is required for hematopoietic stem cell self-renewal, B-cell maturation, and cardiac development, establishing it as a pleiotropic developmental regulator acting through tissue-specific transcriptional programs.

    Evidence Serial transplantation and CRU quantification from rae28-deficient fetal liver; chimeric mice with flow cytometry of B-cell populations; genetic complementation with NKX2.5 and rae28 transgenes for cardiac rescue

    PMID:11164110 PMID:11901201 PMID:12122109

    Open questions at the time
    • Direct transcriptional targets beyond Nkx2.5 in cardiac tissue not identified
    • Whether HSC and B-cell defects reflect the same downstream targets is unknown
    • Cell-autonomous versus non-autonomous effects in cardiac development partially but not fully resolved
  5. 2003 Medium

    Demonstrating that PHC1 dissociates from condensed chromatin during mitotic prophase and meiotic prophase revealed that PRC1 chromatin association is dynamically regulated during cell division, correlating with transcriptional silencing.

    Evidence Immunofluorescence in mitotic U2-OS cells and meiotic mouse oocytes with temporal correlation to transcriptional arrest

    PMID:12883906

    Open questions at the time
    • Mechanism driving PHC1 dissociation (e.g., phosphorylation) not identified
    • Whether dissociation is causal for or merely correlative with transcriptional arrest not established
  6. 2005 High

    Genetic and biochemical demonstration that PHC1 and PHC2 function synergistically within PRC1 to repress Hox genes, co-occupying target loci, resolved the question of functional redundancy versus cooperativity among PHC paralogs.

    Evidence Phc2 knockout and double/triple mutant epistasis with Phc1 and Rnf110; co-IP from embryonic extracts; ChIP at Hox loci

    PMID:16024804

    Open questions at the time
    • Whether PHC1 and PHC2 occupy identical or distinct genomic sites genome-wide not determined
    • Contribution of PHC3 to these complexes not addressed
  7. 2013 High

    Patient studies and rescue experiments established that PHC1 is required for H2A ubiquitination and DNA damage repair, and that loss-of-function PHC1 mutations cause primary microcephaly through Geminin accumulation and cell cycle defects.

    Evidence Patient cell functional assays with PHC1 knockdown in controls and overexpression rescue; H2A ubiquitination assay; Geminin quantification; DNA damage repair assays

    PMID:23418308

    Open questions at the time
    • Whether PHC1 directly stimulates the RING1B E3 ligase or acts indirectly through complex assembly is unclear
    • How Geminin accumulation mechanistically links to microcephaly not fully resolved
    • Number of families with PHC1 mutations limited
  8. 2021 High

    Discovery that PHC1 interacts with NANOG and activates Nanog transcription by organizing long-range chromatin interactions—independently of PRC1—revealed a non-canonical, PRC1-independent transcriptional activation function for PHC1 in pluripotency.

    Evidence Co-IP of PHC1 with NANOG; Hi-C at Nanog locus upon Phc1 ablation; KO/knockdown with Nanog overexpression rescue; RNA-seq

    PMID:33990559

    Open questions at the time
    • Structural basis of PHC1–NANOG interaction not determined
    • Whether this PRC1-independent function extends to other pluripotency loci beyond Nanog is unknown
    • Mechanism by which PHC1 organizes chromatin loops without PRC1 not clarified

Open questions

Synthesis pass · forward-looking unresolved questions
  • It remains unknown how PHC1's dual roles as a PRC1-dependent repressor and PRC1-independent activator are partitioned across genomic loci and developmental contexts, and what post-translational modifications regulate PHC1 chromatin association dynamics during the cell cycle.
  • No genome-wide separation-of-function analysis for PRC1-dependent versus PRC1-independent targets
  • Post-translational regulation of PHC1 chromatin binding largely unexplored
  • No high-resolution structure of PHC1 in complex with PRC1 or NANOG

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140110 transcription regulator activity 4 GO:0005198 structural molecule activity 3 GO:0042393 histone binding 1
Localization
GO:0005634 nucleus 3 GO:0005694 chromosome 2
Pathway
R-HSA-1266738 Developmental Biology 4 R-HSA-4839726 Chromatin organization 4 R-HSA-74160 Gene expression (Transcription) 3 R-HSA-73894 DNA Repair 1
Partners
BMI1CBX2NANOGPHC2RING1BSCMH1
Complex memberships
PRC1 (canonical Polycomb Repressive Complex 1)

Evidence

Reading pass · 15 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1998 The SAM (SPM) domain of RAE28/PHC1 mediates self-association (homotypic binding) and heterologous interactions with the SAM domains of Drosophila Scm and polyhomeotic (ph). Conserved residues L33, L41, and I62 in the ph SAM domain are critical determinants of the binding interface, while W1 and G50 are required for domain structure. In vitro binding assays with SAM domain constructs; mutagenesis of conserved residues to assess self-binding and heterologous association Developmental genetics High 9499582
1998 RAE28/PHC1 (mouse PHC1 ortholog), BMI1, and M33 co-immunoprecipitate from embryonic nuclear extracts and co-purify in large multimeric complexes by gel filtration. RAE28 and M33 interact homotypically and both interact with BMI1 but not with each other. Domain mapping localized the interaction regions within these PcG proteins. Co-immunoprecipitation from embryonic nuclear extracts; gel filtration; domain mapping Biochemical and biophysical research communications High 9571155
1999 RAE28/PHC1 interacts with the mammalian Scm homolog SCMH1 in vitro via their SPM domains, paralleling the Drosophila polyhomeotic–Scm interaction. Interaction was confirmed by northern analysis showing correlated expression patterns. In vitro interaction assay via SPM domains; northern analysis for expression correlation Differentiation; research in biological diversity Medium 10653359
1998 RAE28/PHC1 protein exhibits sequence-specific DNA binding activity, with consensus sequences 5'-ACCA-3', 5'-ACCCA-3', 5'-CTATCA-3', and 5'-TGCC-3' identified by SELEX using GST-RAE28 fusion protein. SELEX (selected and amplified binding site) assay using GST-RAE28 fusion protein Biochemistry and molecular biology international Low 9861444
2000 Rae28/PHC1 is required for maintenance (but not establishment) of Hoxb3 expression boundaries in pharyngeal arch and hindbrain; rae28-deficient mice show ectopic anterior expansion of Hoxb3 expression from E9.5 onward without affecting upstream regulators kreisler or Krox20. Genetic knockout mouse model; in situ hybridization for Hoxb3 expression; neural crest marker (p75) analysis Mechanisms of development High 11044623
2001 Rae28/PHC1 is required for B-cell development; rae28-deficient mice show severe maturation arrest between pro- and pre-B lymphocyte stages, and IL-7-dependent colony-forming ability is impaired in a gene dosage-dependent manner. Chimeric mice reconstituted with GFP-labeled mutant fetal liver cells; in vitro IL-7-dependent culture; flow cytometry of B-cell populations Experimental hematology High 11164110
2002 Rae28/PHC1 sustains Nkx2.5/Csx expression in cardiomyocytes during the maintenance phase of cardiac development; rae28-deficient embryos show cardiac anomalies that can be rescued by overexpression of human NKX2.5/CSX1 or by ubiquitous (but not cardiomyocyte-specific) rae28 re-expression, indicating rae28 acts through a non-cardiomyocyte pathway to maintain Nkx2.5. Knockout mouse; genetic complementation with NKX2.5 transgene and ubiquitous/tissue-specific rae28 transgenes; in situ hybridization for Nkx2.5 The Journal of clinical investigation High 12122109
2002 Rae28/PHC1 is required for sustaining hematopoietic stem cell (HSC) activity; rae28-deficient fetal liver shows a 20-fold reduction in competitive repopulating units (CRUs) and a 15-fold decrease in self-renewal activity, demonstrated by serial transplantation. Competitive repopulation assay; serial transplantation in lethally irradiated mice; long-term culture-initiating cell (LTC-IC) assay The Journal of experimental medicine High 11901201
2002 Cardiomyocyte-specific overexpression of rae28/PHC1 causes dilated cardiomyopathy with cardiomyocyte apoptosis and abnormal myofibrils, likely by disrupting stoichiometry of PcG complexes in cardiomyocyte nuclei. Transgenic mice with cardiomyocyte-specific rae28 overexpression; histological and molecular analysis of cardiac phenotype Laboratory investigation Medium 11950896
2003 Rae28/PHC1 (along with Ring1B) dissociates from chromatin upon chromatin condensation during mitotic prophase in U2-OS cells and during germinal vesicle-stage meiotic prophase in mouse oocytes; dissociation temporally correlates with transcriptional arrest in both mitosis and meiosis. Immunofluorescence with monoclonal antibodies against Rae28/Ph1 and Ring1B; live imaging in mitotic somatic cells and meiotic oocytes; correlation with transcriptional status Histochemistry and cell biology Medium 12883906
2004 Rae28/PHC1 is indispensable for long-term repopulating ability of HSCs; after transplantation into irradiated mice, rae28-deficient HSCs fail to expand efficiently, cannot support serial transplantation, and show progressive reduction in mean stem cell activity over 12 months. Serial bone marrow transplantation; flow cytometric analysis of Lin-c-kit+Sca-1high HSC population; CRU quantification European journal of haematology High 15245505
2005 PHC1 and PHC2 act synergistically in Polycomb repressive complex 1 (PRC1/class II PcG complex) to repress Hox cluster genes; Phc1 and Phc2 proteins co-immunoprecipitate from embryonic extracts and co-occupy Hox loci as shown by chromatin immunoprecipitation. Genetic interactions reveal strict dose-dependent and functionally overlapping roles during anterior-posterior specification. Phc2-knockout mice; double and triple mutant genetic epistasis with Phc1 and Rnf110; co-immunoprecipitation from embryonic extracts; ChIP with anti-Phc2 antibodies Molecular and cellular biology High 16024804
2013 A loss-of-function mutation in human PHC1 significantly decreases PHC1 protein expression, increases Geminin protein levels, and markedly abolishes histone H2A ubiquitination in patient cells; PHC1 depletion in control cells recapitulates these defects. PHC1 overexpression rescues the ubiquitination defect, Geminin accumulation, cell cycle defect, and aberrant DNA damage repair in patient cells, establishing PHC1 as required for H2A ubiquitination and DNA damage repair in primary microcephaly. Patient cell functional assays; PHC1 knockdown in control cells; PHC1 overexpression rescue; H2A ubiquitination assay; Geminin protein quantification; DNA damage repair assays Human molecular genetics High 23418308
2021 PHC1 interacts with NANOG protein and activates Nanog transcription in a PRC1-independent manner by stabilizing genome-wide chromatin interactions at the Nanog locus; Phc1 depletion reduces Nanog expression and impairs pluripotency, which is partially rescued by Nanog overexpression. Co-immunoprecipitation of PHC1 with NANOG; Hi-C/chromatin conformation capture to assess Nanog locus interactions upon Phc1 ablation; Phc1 knockout/knockdown; Nanog overexpression rescue; RNA-seq Nature communications High 33990559
1999 The rae28/PHC1 gene contains two inverted differentiation response sequences (DRSs) in its 5' flanking region that bind novel transcription factors in F9 cell nuclear extracts and are required for retinoic acid-induced transcriptional activation of rae28/PHC1. Transient transfection reporter assays; EMSA; DNase I footprinting; nucleotide substitution mutagenesis Biochemical and biophysical research communications Medium 10462505

Source papers

Stage 0 corpus · 60 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2002 Polycomb group gene rae28 is required for sustaining activity of hematopoietic stem cells. The Journal of experimental medicine 138 11901201
2014 EDR1 physically interacts with MKK4/MKK5 and negatively regulates a MAP kinase cascade to modulate plant innate immunity. PLoS genetics 129 24830651
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 disease resistance, stress responses, cell death, and ethylene signaling in Arabidopsis by the EDR1 protein kinase. Plant physiology 106 15894742
1988 hph-1: a mouse mutant with hereditary hyperphenylalaninemia induced by ethylnitrosourea mutagenesis. Genetics 80 3360305
2013 Mutation in PHC1 implicates chromatin remodeling in primary microcephaly pathogenesis. Human molecular genetics 79 23418308
1998 The SAM domain of polyhomeotic, RAE28, and scm mediates specific interactions through conserved residues. Developmental genetics 65 9499582
1998 RAE28, BMI1, and M33 are members of heterogeneous multimeric mammalian Polycomb group complexes. Biochemical and biophysical research communications 65 9571155
1988 Biochemical defect of the hph-1 mouse mutant is a deficiency in GTP-cyclohydrolase activity. Journal of neurochemistry 59 3335865
2015 ENHANCED DISEASE RESISTANCE4 associates with CLATHRIN HEAVY CHAIN2 and modulates plant immunity by regulating relocation of EDR1 in Arabidopsis. The Plant cell 58 25747881
2002 Overexpression of a kinase-deficient form of the EDR1 gene enhances powdery mildew resistance and ethylene-induced senescence in Arabidopsis. The Plant journal : for cell and molecular biology 58 12492839
2014 The Arabidopsis EDR1 protein kinase negatively regulates the ATL1 E3 ubiquitin ligase to suppress cell death. The Plant cell 54 25398498
2012 Uncoupling of eNOS causes superoxide anion production and impairs NO signaling in the cerebral microvessels of hph-1 mice. Journal of neurochemistry 54 22784235
2001 Lack of the Polycomb-group gene rae28 causes maturation arrest at the early B-cell developmental stage. Experimental hematology 50 11164110
2008 Structure basis and unconventional lipid membrane binding properties of the PH-C1 tandem of rho kinases. The Journal of biological chemistry 44 18640982
1996 Tetrahydrobiopterin and biogenic amine metabolism in the hph-1 mouse. Journal of neurochemistry 44 8764604
1988 Hyperphenylalaninemia in the hph-1 mouse mutant. Pediatric research 44 3340448
2003 The hph-1 mouse: a model for dominantly inherited GTP-cyclohydrolase deficiency. Annals of neurology 40 12891653
2002 The Polycomb-group gene Rae28 sustains Nkx2.5/Csx expression and is essential for cardiac morphogenesis. The Journal of clinical investigation 39 12122109
1999 A novel member of murine Polycomb-group proteins, Sex comb on midleg homolog protein, is highly conserved, and interacts with RAE28/mph1 in vitro. Differentiation; research in biological diversity 38 10653359
2004 Defective long-term repopulating ability in hematopoietic stem cells lacking the Polycomb-group gene rae28. European journal of haematology 35 15245505
2003 Dissociation of mammalian Polycomb-group proteins, Ring1B and Rae28/Ph1, from the chromatin correlates with configuration changes of the chromatin in mitotic and meiotic prophase. Histochemistry and cell biology 31 12883906
2011 Negative regulation of defence signalling pathways by the EDR1 protein kinase. Molecular plant pathology 30 21726375
2020 Arabidopsis EDR1 Protein Kinase Regulates the Association of EDS1 and PAD4 to Inhibit Cell Death. Molecular plant-microbe interactions : MPMI 25 31876224
2004 Congenic mapping and genotyping of the tetrahydrobiopterin-deficient hph-1 mouse. Molecular genetics and metabolism 24 15234340
2017 Intestinal microbiota as a tetrahydrobiopterin exogenous source in hph-1 mice. Scientific reports 22 28079055
2010 Synergistic activation of defense responses in Arabidopsis by simultaneous loss of the GSL5 callose synthase and the EDR1 protein kinase. Molecular plant-microbe interactions : MPMI 22 20367466
1994 Molecular characterization of HPH-1: a mouse mutant deficient in GTP cyclohydrolase I activity. Biochemical and biophysical research communications 22 7524491
1991 Isolation and characterization of GTP cyclohydrolase I from mouse liver. Comparison of normal and the hph-1 mutant. The Journal of biological chemistry 22 1905717
2013 Impaired behavioural pain responses in hph-1 mice with inherited deficiency in GTP cyclohydrolase 1 in models of inflammatory pain. Molecular pain 21 23421753
2000 Regulation of Hoxb3 expression in the hindbrain and pharyngeal arches by rae28, a member of the mammalian Polycomb group of genes. Mechanisms of development 20 11044623
2011 Differential effects of eNOS uncoupling on conduit and small arteries in GTP-cyclohydrolase I-deficient hph-1 mice. American journal of physiology. Heart and circulatory physiology 19 21963838
1998 Increased inducible nitric oxide synthase protein but limited nitric oxide formation occurs in astrocytes of the hph-1 (tetrahydrobiopterin deficient) mouse. Brain research 19 9729234
2021 PHC1 maintains pluripotency by organizing genome-wide chromatin interactions of the Nanog locus. Nature communications 18 33990559
2012 PPARδ agonist GW501516 prevents uncoupling of endothelial nitric oxide synthase in cerebral microvessels of hph-1 mice. Brain research 18 22982594
2023 MITOGEN-ACTIVATED PROTEIN KINASE3 enhances disease resistance of edr1 mutants by phosphorylating MAPKKK5. Plant physiology 17 37638889
1999 Stimulation of the brain NO/cyclic GMP pathway by peripheral administration of tetrahydrobiopterin in the hph-1 mouse. Journal of neurochemistry 16 10582619
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
2007 Tetrahydrobiopterin availability, nitric oxide metabolism and glutathione status in the hph-1 mouse; implications for the pathogenesis and treatment of tetrahydrobiopterin deficiency states. Journal of inherited metabolic disease 15 17242981
2002 Overexpression of Polycomb-group gene rae28 in cardiomyocytes does not complement abnormal cardiac morphogenesis in mice lacking rae28 but causes dilated cardiomyopathy. Laboratory investigation; a journal of technical methods and pathology 12 11950896
1996 Impairment of the nitric oxide/cyclic GMP pathway in cerebellar slices prepared from the hph-1 mouse. Brain research 12 8905183
2015 Mutations in the EDR1 Gene Alter the Response of Arabidopsis thaliana to Phytophthora infestans and the Bacterial PAMPs flg22 and elf18. Molecular plant-microbe interactions : MPMI 10 25353364
2014 Infantile hypertrophic pyloric stenosis (IHPS): a study of its pathophysiology utilizing the newborn hph-1 mouse model of the disease. American journal of physiology. Gastrointestinal and liver physiology 10 25359537
2014 Natural loss-of-function mutation of EDR1 conferring resistance to tomato powdery mildew in Arabidopsis thaliana accession C24. Molecular plant pathology 9 24925473
2011 Roles of EDR1 in non-host resistance of Arabidopsis. Plant signaling & behavior 7 22057322
2000 Structure and chromosomal localization of the RAE28/HPH1 gene, a human homologue of the polyhomeotic gene. DNA sequence : the journal of DNA sequencing and mapping 7 10902910
1996 Structural organization of the rae28 gene, a putative murine homologue of the Drosophila polyhomeotic gene. Journal of biochemistry 7 8947844
2020 Plant defensin expression triggered by fungal pathogen invasion depends on EDR1 protein kinase and ORA59 transcription factor in Arabidopsis thaliana. Plant signaling & behavior 6 32985920
2014 Erythropoietin prevents endothelial dysfunction in GTP-cyclohydrolase I-deficient hph1 mice. Journal of cardiovascular pharmacology 6 25490417
2023 EDR1 associates with its homologs to synergistically regulate plant immunity in Arabidopsis. Plant science : an international journal of experimental plant biology 5 36737004
2004 A histological study of the hph-1 mouse mutant: an animal model of phenylketonuria and infantile hypertrophic pyloric stenosis. Anatomia, histologia, embryologia 5 15144277
1999 Linkage analysis of the hph-1 mutation and the GTP cyclohydrolase I structural gene. Molecular genetics and metabolism 5 10479487
2000 Studies on the genotype-phenotype relation in the hph-1 mouse mutant deficient in guanosine triphosphate (GTP) cyclohydrolase I activity. Brain & development 4 10984661
2009 In vivo regulation of phenylalanine hydroxylase in the genetic mutant hph-1 mouse model. Molecular genetics and metabolism 3 19560382
2018 Identification and expression analysis of EDR1-like genes in tobacco (Nicotiana tabacum) in response to Golovinomyces orontii. PeerJ 2 30018863
2005 Cloning, characterization and expression of wheat EDR1 (enhanced disease resistance) gene. Zhi wu sheng li yu fen zi sheng wu xue xue bao = Journal of plant physiology and molecular biology 2 16222089
1999 Characterization of cis-elements required for the transcriptional activation of the rae28/mph1 gene in F9 cells. Biochemical and biophysical research communications 2 10462505
2014 Cloning, overexpression, purification and preliminary X-ray analysis of the protein kinase domain of enhanced disease resistance 1 (EDR1) from Arabidopsis thaliana. Acta crystallographica. Section F, Structural biology communications 1 25005098
1998 Sequence-specific DNA binding activity in the RAE28 protein, a mouse homologue of the Drosophila polyhomeotic protein. Biochemistry and molecular biology international 1 9861444
2026 The EDR1-PP2A phospho-regulatory module fine-tunes MYC2-mediated plant disease resistance. The Plant cell 0 41411321