Affinage

GMEB2

Glucocorticoid modulatory element-binding protein 2 · UniProt Q9UKD1

Round 2 corrected
Length
530 aa
Mass
56.4 kDa
Annotated
2026-04-28
47 papers in source corpus 12 papers cited in narrative 12 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

GMEB2 is a SAND-domain transcription factor that heterodimerizes with GMEB1 to bind glucocorticoid modulatory element (GME) DNA sequences and modulate steroid receptor transactivation. The GMEB1–GMEB2 heterodimer recognizes a bipartite CpG-containing consensus motif via the conserved KDWK alpha-helical surface of the SAND domain, and binding is abolished by CpG methylation (PMID:11743720, PMID:12702733). GMEB2 interacts directly with the glucocorticoid receptor (GR), progesterone receptor (PR), CBP/p300, and the SUMO E2-conjugating enzyme Ubc9, through large overlapping protein regions, to shift agonist dose-response curves and alter partial agonist efficacy (PMID:10894151, PMID:11812797, PMID:14705952, PMID:18215457). In colorectal cancer cells, GMEB2 directly transactivates the ADRM1 promoter to activate NF-κB signaling, and its own mRNA is stabilized by the m6A reader YTHDF1 (PMID:36551532).

Mechanistic history

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

    Identification of GMEB-2 as a novel KDWK-domain transcription factor that heterodimerizes with GMEB-1 on GME DNA established the existence of a heteromeric GME-binding complex and defined a new protein family.

    Evidence PCR cloning from rat, in vitro translation, EMSA with antibody supershift, co-incubation with native GMEB-1

    PMID:9651376

    Open questions at the time
    • No in vivo evidence for heterodimer formation at this stage
    • Endogenous target genes beyond the TAT promoter GME unknown
    • GMEB-2 homodimer function not characterized
  2. 2000 High

    Demonstration that both GMEBs possess intrinsic transactivation activity and physically contact GR and CBP established a mechanistic framework linking GME DNA binding to steroid receptor co-regulation through cofactor interactions.

    Evidence Mammalian one-hybrid, mammalian two-hybrid, GST pull-down, HAT activity assay, and reporter assays in transfected cells

    PMID:10854715 PMID:10894151

    Open questions at the time
    • No identification of direct chromatin targets of GMEB-2
    • HAT-independent mechanism of coactivation not resolved
    • Whether GMEB-2 modulation of GR occurs at endogenous loci unknown
  3. 2001 High

    SELEX-based identification of the bipartite CpG consensus binding motif and its sensitivity to CpG methylation revealed that GMEB DNA binding is epigenetically regulatable and that potential GMEB sites are widespread across human promoters.

    Evidence Recombinant baculovirus-expressed GMEB heterodimer, degenerate oligonucleotide selection (SELEX), EMSA, methylation sensitivity assay

    PMID:11743720

    Open questions at the time
    • Functional significance of methylation-dependent regulation at endogenous loci not tested
    • Which of the many potential target promoters are physiologically bound in vivo remains unknown
  4. 2002 Medium

    Discovery that Ubc9 physically contacts both GMEB-1/GMEB-2 and GR positioned the SUMO conjugation machinery as a functional intermediary in GMEB-mediated modulation of steroid receptor dose-response and partial agonist activity.

    Evidence Mammalian two-hybrid and pull-down assays, reporter assays

    PMID:11812797

    Open questions at the time
    • Whether GMEB-2 itself is SUMOylated was not determined
    • No reciprocal Co-IP from endogenous proteins
    • Functional consequence of Ubc9 interaction on GR SUMOylation not shown
  5. 2003 High

    The 1.55 Å crystal structure of the GMEB-1 SAND domain (80% identical to GMEB-2) defined the KDWK-containing alpha-helical DNA-recognition surface and a structural zinc-binding motif, providing the atomic basis for GME DNA binding by both proteins.

    Evidence X-ray crystallography, NMR, site-directed mutagenesis of DNA-binding residues

    PMID:12702733

    Open questions at the time
    • Crystal structure of GMEB-2 SAND domain itself not solved
    • No structure of the GMEB-1/GMEB-2 heterodimer on DNA
    • How the SAND domain interfaces with transactivation and GR-binding regions unknown
  6. 2004 Medium

    Systematic deletion mapping of GMEB-2 revealed that oligomerization, GR binding, CBP binding, DNA binding, and dose-response modulation require large overlapping regions, demonstrating that GMEB-2 functions as an integrated multi-domain platform rather than a modular factor with separable activities.

    Evidence Deletion mutagenesis, mammalian two-hybrid, pull-down assays, reporter assays

    PMID:14705952

    Open questions at the time
    • No tertiary structure available to rationalize overlapping domains
    • Relative contributions of hetero- vs. homo-oligomers to each activity unclear
    • Post-translational modifications that may regulate domain activities not examined
  7. 2007 Medium

    Extension of GMEB-2 modulatory activity to the progesterone receptor showed that GMEB-2 differentially adjusts EC50, partial agonist activity, and Vmax for PR vs. GR, establishing receptor-selective co-regulation.

    Evidence Transient transfection with PR and GR reporter assays, GMEB-2 overexpression

    PMID:18215457

    Open questions at the time
    • Mechanism underlying receptor-selective modulation not identified
    • Whether GMEB-2 directly contacts PR was not tested
    • Single cell line; generalizability unknown
  8. 2022 Medium

    In colorectal cancer, GMEB2 was shown to directly transactivate the ADRM1 promoter and activate NF-κB signaling, while YTHDF1-mediated m6A modification stabilizes GMEB2 mRNA, revealing a non-steroid-receptor oncogenic axis and an epitranscriptomic layer of GMEB2 regulation.

    Evidence shRNA/siRNA knockdown, xenograft, ADRM1 promoter-luciferase, NF-κB nuclear translocation assay, RIP for YTHDF1-GMEB2 mRNA, rescue experiments

    PMID:36551532

    Open questions at the time
    • ChIP confirmation of GMEB2 occupancy at the endogenous ADRM1 promoter not provided
    • Whether GMEB2 activates NF-κB independently of ADRM1 not tested
    • Generalizability to other cancer types unknown

Open questions

Synthesis pass · forward-looking unresolved questions
  • The genome-wide set of direct GMEB2 chromatin targets, the structural basis of the GMEB1–GMEB2 heterodimer on DNA, and the physiological consequences of GMEB2 loss in vivo remain unresolved.
  • No ChIP-seq or CUT&RUN data for GMEB2
  • No knockout or conditional knockout mouse phenotype reported
  • No structure of the full-length heterodimer or heterodimer–DNA complex

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003677 DNA binding 3 GO:0140110 transcription regulator activity 3
Localization
GO:0005634 nucleus 3
Pathway
R-HSA-74160 Gene expression (Transcription) 3 R-HSA-162582 Signal Transduction 2
Partners
ADRM1CREBBPGMEB1NR3C1PGRUBE2IYTHDF1
Complex memberships
GMEB1–GMEB2 heterodimer

Evidence

Reading pass · 12 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1998 GMEB-2 (67 kDa) was cloned from rat; in vitro translated GMEB-2 bound GME DNA in gel-shift assays, and binding increased markedly upon mixing with authentic GMEB-1, reconstituting a heteromeric complex similar to that derived from HTC cell cytosol. GMEB-2 shares the KDWK domain with DEAF-1, Suppressin, and C. elegans ORFs, placing it in a novel family of transcription factors. PCR cloning, in vitro transcription/translation, gel-shift/EMSA, co-incubation with native GMEB-1 The Journal of biological chemistry High 9651376
2000 GMEB-1 and GMEB-2 each possess intrinsic transactivation activity in mammalian one-hybrid assays. Both proteins interact with the glucocorticoid receptor (GR) in mammalian two-hybrid and GST pull-down assays. Both GMEBs also interact with CREB-binding protein (CBP) in two-hybrid assays. Neither protein has intrinsic histone acetyltransferase (HAT) activity. Overexpression of GMEB-1 and/or GMEB-2 produces a reversible right shift in the GR dose-response curve and decreases agonist activity of antisteroids, consistent with squelching of limiting co-factors. Mammalian one-hybrid, mammalian two-hybrid, GST pull-down, HAT activity assay, transient transfection/reporter assay Molecular endocrinology (Baltimore, Md.) High 10894151
2000 Mechanistic analysis of GME activity showed: phasing between the GME and downstream GREs is unimportant; GME activity decreases when placed far 3' of a GRE; a minimal promoter is less effective for GME than GRE activity; CREB overexpression reduces GRE but not GME activity; a CRE cannot substitute for the GME; the GME does not affect GR binding to a single GRE; a GME upstream of a single GRE cannot shift the Dex dose-response curve; and in the absence of GREs the GME elevates basal expression. These results indicate GME and GRE activities use parallel, not common, pathways and require an optimal position within 250 bp upstream of a tandem GRE in a complex promoter. Transient transfection with reporter genes, positional/spacing mutants, overexpression of CREB, gel-shift assays for GR binding Molecular and cellular endocrinology Medium 10854715
2000 Human GMEB-1 (chromosome 1) and rat GMEB-2 (chromosome 20) are encoded by distinct genes that evolved from a single parent gene and show highly conserved genomic structure including intron architecture. Multiple splice isoforms were identified and their splicing patterns determined. Both gene promoters drive high transcription in transiently transfected cells. Tissue distribution of each GMEB differs and is highest in fetal and developing tissues, supporting roles for homo- and hetero-oligomers in development. Genomic sequencing, chromosomal mapping (human-rodent hybrid panels), RT-PCR, promoter-reporter transfection assays Nucleic acids research Medium 10734202
2000 Mouse GMEB-1 was identified by yeast two-hybrid screening using the activation domain 2 of nuclear receptor coactivator TIF2 as bait, demonstrating a physical interaction between mGMEB-1 and TIF2-AD2. In vitro translated mGMEB-1 bound GME oligonucleotides alone or as a heterodimer with rGMEB-2. Transient transfection with TAT promoter reporters suggested a role as a transcriptional regulator. Yeast two-hybrid, in vitro translation/EMSA, transient transfection/reporter assay FEBS letters Medium 10692587
2001 PIF (parvovirus initiation factor), which is identical to the GMEB heterodimer (p96=GMEB-1, p79=GMEB-2), binds as a heterodimer and as homodimers to a consensus DNA motif ACGPy N(1-9) PuCGPy with optimum N=6. Binding of all three complexes is abolished by CpG methylation of the invariant CpG half-site cores, indicating that GMEB binding can be regulated by DNA methylation. Over half of 100 human promoters tested contain at least one such consensus site, and binding of GMEB heterodimer to five representative oligonucleotides was confirmed by EMSA. Recombinant baculovirus expression, degenerate oligonucleotide selection (SELEX), EMSA, methylation sensitivity assay, promoter database analysis Journal of molecular biology High 11743720
2002 GMEB-1 and GMEB-2 physically contact Ubc9 (mammalian E2 SUMO-conjugating enzyme), as shown in two-hybrid and pull-down assays. Ubc9 also binds GR directly. These interactions place Ubc9 as a functional intermediary between the GMEB complex and GR in the modulation of EC50 and partial agonist activity. Mammalian two-hybrid, pull-down assays, transient transfection/reporter assay The Journal of biological chemistry Medium 11812797
2003 The 1.55 Å crystal structure of the GMEB-1 SAND domain (sharing 80% sequence identity with the GMEB-2 SAND domain) was solved. NMR and binding studies mapped the DNA recognition surface to an alpha-helical region exposing the conserved KDWK motif. Site-directed mutagenesis identified key residues for GME DNA binding. The SAND domain is necessary and sufficient for GME DNA binding. The GMEB1 SAND domain contains a zinc-binding motif that determines C-terminal conformation but is not required for DNA binding. A subset of other SAND domain proteins share homologous zinc-binding motifs. X-ray crystallography (1.55 Å), NMR, site-directed mutagenesis, DNA binding assays Molecular endocrinology (Baltimore, Md.) High 12702733
2004 Structure/activity analysis of GMEB-2 showed that homo- and heterooligomerization, binding to GR, binding to CBP, DNA binding, and modulation of GR dose-response curve and partial agonist activity each require large, overlapping regions of the protein, precluding assignment to discrete small domains. Only intrinsic transactivation activity could be localized to a small region. Domain organization of GMEB-2 and GMEB-1 is extremely similar, indicating quantitative differences in activity arise from amino acid sequence variation rather than global structural differences. Deletion mutagenesis, mammalian two-hybrid, pull-down assays, transient transfection/reporter assay Biochemistry Medium 14705952
2007 GMEB-2 (and the GME element) can differentially modulate progesterone receptor (PR) vs. glucocorticoid receptor (GR) transactivation properties, altering EC50, partial agonist activity, and Vmax in opposite or differing directions under identical conditions, demonstrating that GMEB-2's modulatory activity is not restricted to GR in a specific cell line. Transient transfection with PR/GR reporter assays, overexpression of GMEB-2 Molecular and cellular endocrinology Medium 18215457
2011 IL-12 induces expression of both GMEB1 and GMEB2 in human T cells. siRNA knockdown of GMEB1 reverses the protective effect of IL-12 against dexamethasone-induced T cell apoptosis, placing GMEB1 (and by induction GMEB2) downstream of IL-12/PI3K/Akt signaling in T cell survival. The protective mechanism involves reduction of glucocorticoid receptor transactivation and induction of apoptotic genes. siRNA knockdown, flow cytometry (apoptosis), IL-12 stimulation, qRT-PCR for GMEB mRNA Immunobiology Medium 21840619
2022 GMEB2 functions as a transcription factor in colorectal cancer cells by directly transactivating the ADRM1 promoter, thereby increasing ADRM1 expression and inducing nuclear translocation of NF-κB to activate NF-κB signaling. Rescue experiments showed ADRM1 downregulation partially reversed GMEB2-driven tumor growth. Additionally, the m6A reader YTHDF1 binds to m6A sites on GMEB2 mRNA and enhances its stability, placing GMEB2 downstream of YTHDF1-mediated post-transcriptional regulation. GMEB2 knockdown (shRNA/siRNA), in vitro proliferation and in vivo xenograft assays, promoter-luciferase reporter assays (ADRM1 promoter), NF-κB nuclear translocation assay, RIP assay and m6A site mutation for YTHDF1-GMEB2 mRNA interaction, rescue experiments Cancers Medium 36551532

Source papers

Stage 0 corpus · 47 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2012 Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 1718 22658674
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
2009 A census of human transcription factors: function, expression and evolution. Nature reviews. Genetics 1191 19274049
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2017 Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science (New York, N.Y.) 934 28473536
2020 A reference map of the human binary protein interactome. Nature 849 32296183
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2006 A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 610 16713569
2013 Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. Nature genetics 463 23535732
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
2011 Toward an understanding of the protein interaction network of the human liver. Molecular systems biology 207 21988832
2001 The DNA sequence and comparative analysis of human chromosome 20. Nature 168 11780052
2022 Human transcription factor protein interaction networks. Nature communications 123 35140242
2007 Toward a confocal subcellular atlas of the human proteome. Molecular & cellular proteomics : MCP 114 18029348
1999 Prediction of the coding sequences of unidentified human genes. XV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. DNA research : an international journal for rapid publication of reports on genes and genomes 111 10574462
2022 Identification and functional characterization of transcriptional activators in human cells. Molecular cell 98 35016035
2002 Ubc9 is a novel modulator of the induction properties of glucocorticoid receptors. The Journal of biological chemistry 78 11812797
2021 Identification of proximal SUMO-dependent interactors using SUMO-ID. Nature communications 45 34795231
2000 Properties of the glucocorticoid modulatory element binding proteins GMEB-1 and -2: potential new modifiers of glucocorticoid receptor transactivation and members of the family of KDWK proteins. Molecular endocrinology (Baltimore, Md.) 44 10894151
2003 Crystal structure and nuclear magnetic resonance analyses of the SAND domain from glucocorticoid modulatory element binding protein-1 reveals deoxyribonucleic acid and zinc binding regions. Molecular endocrinology (Baltimore, Md.) 39 12702733
1998 Cloning and characterization of a novel binding factor (GMEB-2) of the glucocorticoid modulatory element. The Journal of biological chemistry 34 9651376
1999 Two new members of the emerging KDWK family of combinatorial transcription modulators bind as a heterodimer to flexibly spaced PuCGPy half-sites. Molecular and cellular biology 33 10523663
2018 BAP1 regulation of the key adaptor protein NCoR1 is critical for γ-globin gene repression. Genes & development 32 30463901
2020 Adult diffuse glioma GWAS by molecular subtype identifies variants in D2HGDH and FAM20C. Neuro-oncology 31 32386320
2014 Proteomic Analysis of the EWS-Fli-1 Interactome Reveals the Role of the Lysosome in EWS-Fli-1 Turnover. Journal of proteome research 27 24999758
2014 Both genes and lncRNAs can be used as biomarkers of prostate cancer by using high throughput sequencing data. European review for medical and pharmacological sciences 27 25491628
2000 Ability of the glucocorticoid modulatory element to modify glucocorticoid receptor transactivation indicates parallel pathways for the expression of glucocorticoid modulatory element and glucocorticoid response element activities. Molecular and cellular endocrinology 27 10854715
2019 Glucocorticoid modulatory element-binding protein 1 (GMEB1) interacts with the de-ubiquitinase USP40 to stabilize CFLARL and inhibit apoptosis in human non-small cell lung cancer cells. Journal of experimental & clinical cancer research : CR 26 31046799
2022 A Whole-Genome CRISPR Screen Identifies AHR Loss as a Mechanism of Resistance to a PARP7 Inhibitor. Molecular cancer therapeutics 24 35439318
2001 A consensus DNA recognition motif for two KDWK transcription factors identifies flexible-length, CpG-methylation sensitive cognate binding sites in the majority of human promoters. Journal of molecular biology 22 11743720
1999 Cloning and characterization of hGMEB1, a novel glucocorticoid modulatory element binding protein. FEBS letters 22 10386584
2021 PRISMA and BioID disclose a motifs-based interactome of the intrinsically disordered transcription factor C/EBPα. iScience 19 34189442
2022 Cullin 3 Exon 9 Deletion in Familial Hyperkalemic Hypertension Impairs Cullin3-Ring-E3 Ligase (CRL3) Dynamic Regulation and Cycling. International journal of molecular sciences 18 35563538
2000 Genomic organization of human GMEB-1 and rat GMEB-2: structural conservation of two multifunctional proteins. Nucleic acids research 18 10734202
2011 IL-12 inhibits glucocorticoid-induced T cell apoptosis by inducing GMEB1 and activating PI3K/Akt pathway. Immunobiology 17 21840619
2007 Differential modulation of glucocorticoid and progesterone receptor transactivation. Molecular and cellular endocrinology 15 18215457
2000 Cloning of a mouse glucocorticoid modulatory element binding protein, a new member of the KDWK family. FEBS letters 15 10692587
2020 A functional variant on 20q13.33 related to glioma risk alters enhancer activity and modulates expression of multiple genes. Human mutation 14 33169458
2024 Nuclear Factor I Family Members are Key Transcription Factors Regulating Gene Expression. Molecular & cellular proteomics : MCP 10 39617063
2022 GMEB2 Promotes the Growth of Colorectal Cancer by Activating ADRM1 Transcription and NF-κB Signalling and Is Positively Regulated by the m6A Reader YTHDF1. Cancers 10 36551532
2023 Pulse-SILAC and Interactomics Reveal Distinct DDB1-CUL4-Associated Factors, Cellular Functions, and Protein Substrates. Molecular & cellular proteomics : MCP 8 37689310
2020 ZBTB2 protein is a new partner of the Nucleosome Remodeling and Deacetylase (NuRD) complex. International journal of biological macromolecules 8 33301849
2004 Structure/activity relationships for GMEB-2: the second member of the glucocorticoid modulatory element-binding complex. Biochemistry 7 14705952
2018 From Matrices to Knowledge: Using Semantic Networks to Annotate the Connectome. Frontiers in neuroanatomy 2 30581382
2025 Prediction of vaginal birth after induction of labor with maternal circulating RNA transcripts. American journal of obstetrics and gynecology 0 40523495