CBFA2T3 (core-binding factor, runt domain, alpha subunit 2; translocated to, 3)

2005-10-01   Anthony J Bais 

Department of Haematology, Genetic Pathology, Flinders University, Bedford Park, Adelaide, SA 5042, Australia





CBFA2T3 encodes two alternative transcripts, CBFA2T3A and CBFA2T3B, via the use of alternative start sites at exons 1A and 1B, respectively.
  • CBFA2T3A is 4,265-bp in length, composed of 13 exons (1A and 2 to 12) spanning approximately 130-kb of genomic DNA, and has an ORF of 1,959-bp encoding a protein of 653 amino acids.
  • CBFA2T3B is 4,034-bp in length, composed of 12 exons (1B to 12 splicing out exon 3) spanning approximately 50-kb of genomic DNA, and has an ORF of 1,701-bp encoding a protein of 567 amino acids.
  • Additional CBFA2T3C and CBFA2T3D isoforms have been identified in leukemic and HEL cell lines. CBFA2T3C encodes a protein that lacks exons 2 and 3, and CBFA2T3D is a truncated protein with out-of-frame splicing of exon 1A to exon 5.
  • The CBFA2T3A open-reading-frame (ORF) may include an additional 177 amino acids beyond the originally proposed methionine start codon.
  • The CBFA2T3B isoform contains a high-density 1-kb CpG island within and five prime to the exon 1B start site.
  • A hypothetical protein FLJ26728 located within and proximal to the CpG island transcribes antisense to CBFA2T3. Another hypothetical protein FLJ23429 transcribes antisense starting from within the first alternative intron.
  • Pseudogene

    None identified.



    ETO proteins are composed of four evolutionarily conserved domains termed nervy homology regions (NHR1 to 4) and three proline-serine-threonine (PST) rich regions. The fourth NHR region is also referred to as the zinc-finger MYND (zf myeloid-nervy-DEAF-1) domain.
  • NHR1 shares significant homology to human TATA-binding protein (TBP)-associated factor 130 (hTAF 130), hTAF 105, Drosophila accessory or activation factor TAF 110, and is often referred to as the TAF 110 domain.
  • NHR2 is a small region containing homo and heterodimerization domains and a hydrophobic heptad repeat (HHR) unit.
  • The sequence of NHR3 is unremarkable in homology and often referred to as the nervy domain.
  • The C-terminal NHR4 domain exists in numerous human, murine, Caenorhabditis elegans and Drosophila proteins, and contains a MYND zinc-finger motif. The motif is composed of CXXC and two (C-H)XXXC regions which correspond to cysteine-histidine knuckle structures that are the basic building blocks of many zinc-finger proteins. The zinc-finger is common to the developmental proteins rat programmed cell death (RP-8), the human homolog programmed cell death 2 (PDCD2), deformed epidermal autoregulatory factor-1 (DEAF-1), suppressin (SPN), BLU or zinc-finger MYND domain containing 10 (ZMYND10), adenovirus 5 E1A binding protein (BS69), and CD8 beta opposite (BOP).
  • Expression

    CBFA2T3 is widely expressed in B-cells, blood, brain, breast, cervix, colon, eye, kidney tumor, lymph, marrow, muscle, pancreas, placenta and tonsil. CBFA2T3 exists predominantly as 4.5 and 4.2-kb transcripts along with several other minor RNAs in heart, brain, placenta, lung, liver, skeletal muscle, kidney, pancreas, spleen, thymus, prostate, testis, ovary, small intestine, colon and peripheral blood leukocyte.


    All ETO members contain nuclear localization signals (NLS), some of which may be abrogated through five prime variations to enable extracellular targeting. For instance, CBFA2T1 has been detected in the cytoplasm of Purkinje cells in adult human brain, and both CBFA2T1 and CBFA2T3B have been detected in the Golgi apparatus, where they may function as cAMP-dependent protein kinase anchoring proteins. The majority of ETO proteins presumably remain in the nucleus for transcriptional regulation.


    CBFA2T3 has been considered to function as a transcriptional repressor via interaction with corepressor complexes.
  • The CBFA2T3A isoform oligomerizes and drags MTG8 and MTGR1 to the nucleus, oligomerizes with RUNX1-MTG16 fusion proteins in the nucleoplasm, interacts with nuclear HDACs 1 and 3, and when overexpressed accumulates at the periphery of nucleoli in characteristic rings. Because clustered arrays of inactive methylated ribosomal DNA (rDNA) repeats are also found at the nucleoli periphery, it has been speculated that CBFAT23A could be involved in methylation silencing of rDNA in the nucleolus.
  • The CBFA2T3B isoform has been shown to function in T lymphocytes as a kinase anchorage protein, and interact with cyclic nucleotide phosphodiesterases, suggesting it may function in T cell activation and inflammatory response. CBFA2T3B has been shown to function as a transcriptional repressor when tethered to a GAL4 DNA-binding domain in gene reporter assays, and inhibit the growth of breast tumor cell lines with reduced expression when ectopically expressed using retrovirus.

    CBFA2T3 has been found to interact with a novel zinc finger protein KIA00924 to mediate potent transcriptional repression as determined by CAT reporter gene assays. The presence of a zinc-finger motif common to developmental proteins suggests that CBFA2T3 might function in regulating differentiation and morphogenesis. The RP-8 and human homolog PDCD2 proteins assume a role in programmed cell death, a process essential for epithelial turnover. DEAF-1 is essential for early embryonic dorsal epidermal, eye and wing development in Drosophila. BOP encodes a muscle-restricted protein essential for cardiomyocyte differentiation and morphogenesis. BLU is a candidate tumor suppressor gene from the 3p21.3 LOH region in many human cancers, and SPN from rat functions as a potent tumor suppressor of leukemia, lymphoma and thymoma cells and tumor cells from the brain, breast, pituitary and adrenal glands.
    CBFA2T3 transcripts of CD34(+) progenitor cells have been shown to be rapidly reduced by cytokine-induced differentiation into myeloid or erythroid lineages, supporting suggestion that CBFA2T3 may function in hematopoietic differentiation. The CBFA2T3B CpG island contains several Specificity protein 1 (Sp1), homeotic, epidermal and insulin growth factor recognition sites. High conserved binding sites include GATA-1, CREB, F-1 and PKNOX1.

  • Homology

    The human gene CBFA2T3 is a member of the eight-twenty-one (ETO) family of proteins. The human ETO family consists of the ETO gene, also known as the myeloid translocation gene 8 (MTG8, CBFA2T1), the myeloid translocation gene related protein-1 (EHT, MTGR1, CBFA2T2), and the myeloid translocation gene 16 (MTG16, MTGR2, ZMYND4, HGNC:1537, CBFA2T3).
    Murine homologs of the ETO family include mETO (cbfa2t1h), ET0-2 (cbfa2t3h), and cbfa2t2h, the latter of which is uncharacterised. Chicken cETO and Drosophila nervy homologs have also been identified.
    The ETO protein family members and NHRs are highly homologous and conserved to each other. The CBFA2T3A and B isoforms share significant homology to MTG8 (67 and 75%, respectively) and MTGR1 (54 and 61%, respectively), and approximately 30% homology to nervy. CBFA2T3 shares 86% homology to the murine ETO-2 (cbfa2t3h), which in turn shares 75 and 60% homology to MTG8 and MTGR1, respectively, suggesting that ETO-2 is the murine homolog of CBFA2T3. MTG8 is approximately 99, 65 and 30% homologous to murine ETO, MTGR1 and nervy, respectively.



    None recorded.

    Implicated in

    Entity name
    t(16;21)(q24;q22) in therapy related acute myeloid leukemia (t-AML) --> CBFA2T3/ RUNX1
    CBFA2T3 or MTG16 was identified by molecular characterization of a second less common therapy-related AML translocation involving t(16;21). Characterization of the t(16;21) demonstrated that RUNX1-MTG16 fusion transcripts similar to RUNX1-ETO were generated
    Fusion protein
  • The RUNX1-MTG8, and to a lesser extent the RUNX1-MTG16, fusion transcripts of the t(8;21)(q22;q22) and t(16;21) events are most recognized for their ability to function as transcriptional repressors of genes normally activated by RUNX1 through their interaction with corepressor complexes involving N-CoR, mSin3A, SMRT, and HDACs.
  • The MTG8 or CBFA2T1 gene is the most studied member of the ETO family and is additionally recognized for its ability to function independently as a nuclear transcriptional repressor through nuclear corepressor complex interaction. Gene targeting experiments demonstrating that homozygous mutant mice with an inactivating insertion of LacZ in exon 2 of the MTG8 locus resulted in massive gastrointestinal defects, have also shown that MTG8 and perhaps ETO family members are essential for gastrointestinal development .
  • Multiple NHRs of the ETO family of proteins are required and cooperate to mediate transcriptional repression. Most of the proteins that interact with NHRs have been assigned from studies of RUNX1-MTG8 and its interacting proteins. Studies originally demonstrated that MTG8s NHR2 and NHR4 were required for AML-MTG8 to inhibit RUNX1 mediated transcriptional activation and initiated the search for corepressor complexes that bind to these regions. Several yeast two-hybrid systems using portions of MTG8 as bait demonstrated that specific portions of NHR2, NHR3 and NHR4 interact with the human nuclear receptor co-repressor (HuN-CoR)-mSin3A-HDAC1 corepressor complex.
  • The N-CoR protein was originally described to interact with DNA-bound nuclear receptors to repress transcription of target genes through recruitment of HDAC containing complexes and was latter shown to form complexes with mammalian Sin3 to alter chromatin structure and mediate transcriptional repression via nuclear receptors and oncoregulatory proteins.
  • A similar yeast two-hybrid approach also established that the corepressor silencing mediator of retinoic acid and thyroid hormone receptors (SMRT) interacts with MTG8. The zinc-finger NHR4 is necessary but not sufficient for repression and interaction with SMRT and N-CoR in vitro. The direct physical association of MTG8 with corepressors is more complex. A core-repressor domain containing NHR2 and the neighboring amino and carboxy terminal sequences was defined and found to be the strongest region of interaction with mSin3a and transcriptional repression.
  • In the RUNX1-MTG8 translocation product associated with myeloid malignancies, the transactivation domain of the RUNX1 gene, which normally binds the transcriptional coactivators p300-CBP, is replaced by almost the entire MTG8 protein. The resultant fusion protein recruits a corepressor complex containing HDAC activity instead of the coactivators p300-CBP to RUNX1 responsive genes giving rise to leukemia. The repression activity of the MTG8 protein was demonstrated from a GAL4 DNA binding domain (DBD) MTG8 fusion construct which mediated strong repression through multimerized GAL4 binding sites upstream of a minimal promoter driving a reporter gene. Consistent with a mechanism involving MTG8 and HDAC corepressor interactions, the repressive effect of MTG8 was partially overcome with the addition of the HDAC inhibitor trichostatin A (TSA). Mutational studies of RUNX1-MTG8 have shown that NHR4 is responsible for repression of the multidrug resistance 1 promoter.
  • MTG8 has also been shown to interact with the Dentato-rubral and Pallido-luysian atrophy gene product, atrophin-1, in a yeast two-hybrid assay. Both Dentato-rubral and Pallido-luysian atrophies are neurodegenerative disorders caused by expansion of polyglutamine tracts.
  • Several other transcriptional repressors have been shown to interact with MTG8. The promyelocytic leukemia zinc-finger ( PLZF), a transcriptional repressor found in hematopoietic cells and down-regulated during differentiation of myeloid cell lines was shown to exhibit enhanced repressor activity when interacting with MTG8 in 293T cells and assayed using a reporter plasmid containing four copies of a high affinity PLZF binding site linked to firefly luciferase. The ability of MTG8 to enhance repression was abolished upon addition of HDAC inhibitors TSA and sodium butyrate, suggesting that the MTG8 enhanced repression by PLZF is also mediated through the recruitment of HDACs.
  • The Growth factor independence-1 (Gfi-1), a HDAC interacting transcriptional repressor found in hematopoietic cells, was shown in vitro and in vivo to interact with NHR1 and NHR2 of MTG8. These interactions together with gene targeting experiments demonstrating MTG8s involvement in gastrointestinal development, the well established interactions with corepressor complexes, and the presence of a zinc-finger motif common to numerous developmental proteins, suggests that ETO family members including CBFA2T3 may play function in regulating cell cycle transcription during differentiation and proliferation of specific cell type-lineages, for example hematopoietic cells as indicated for MTG8.
  • Entity name
    Loss of heterozygosity (LOH) of 16q22-qter in breast cancer, prostate cancer, and several other cancers
    This region is frequently deleted in several human cancers causing loss of heterozygosity. The 16q24.3 region including CBFA2T3 spans approximately 3-Mb from the marker D16S498 to the telomere and contains at least two smallest regions of overlap (SROs). These SROs are most frequently deleted in early and late stage breast cancer and in prostate cancer. Loss of normal function of CBFA2T3 may be a key event in the early stage of breast cancer. LOH on the whole 16q22-qter region is frequently detected in breast and prostate cancer.
    CBFA2T3B is a potential tumor suppressor gene affected by LOH, aberrant gene expression and promoter methylation in breast cancer. Quantitative gene expression analysis of 78 genes in the 16q24.3 region demonstrated that CBFA2T3 was the only gene with an aberrant expression profile distinctly similar to the known tumor suppressors SYK and CDKN2A. 68 genes displayed normal expression, six displayed mildly aberrant expression (DPEP1, CDH15, Hs.17074, Hs.189419, SLC7A5 and AA994450), one displayed excessively reduced expression (CA5A), and two displayed moderately aberrant expression (CYBA and FBX031). The CBFA2T3B promoter region displays aberrant hypo and hypermethylation in breast tumor cell lines and primary breast tumor samples in correlation with aberrant gene expression.
    16q22-qter LOH is detected in bilateral breast cancer and ductal lavage, in rare inflammatory breast cancer, and in several other cancers, including central nervous system neuroectodermal and primary ependymomas, colorectal liver metastases, gastric tumor, head and neck squamous cell carcinoma, hepatocellular carcinoma, lung tumor, nasopharyngeal tumor, ovarian tumor, rhabdomyosarcoma, and Wilms tumor. 16q22-qter LOH in ovarian, hepatocellular and particularly breast and prostate cancers, exhibit similar SROs, suggesting common molecular pathways are affected.


    Pubmed IDLast YearTitleAuthors
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    Other Information

    Locus ID:

    NCBI: 863
    MIM: 603870
    HGNC: 1537
    Ensembl: ENSG00000129993


    dbSNP: 863
    ClinVar: 863
    TCGA: ENSG00000129993


    Gene IDTranscript IDUniprot

    Expression (GTEx)


    Protein levels (Protein atlas)

    Not detected


    Pubmed IDYearTitleCitations
    231535402012An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia.69
    121834142002CBFA2T3 (MTG16) is a putative breast tumor suppressor gene from the breast cancer loss of heterozygosity region at 16q24.3.26
    220101042011Distinct Ldb1/NLI complexes orchestrate γ-globin repression and reactivation through ETO2 in human adult erythroid cells.22
    243494732013Whole exome sequencing identifies novel recurrently mutated genes in patients with splenic marginal zone lymphoma.20
    265939742015Control of developmentally primed erythroid genes by combinatorial co-repressor actions.19
    269685322016RNA-sequencing analysis of core binding factor AML identifies recurrent ZBTB7A mutations and defines RUNX1-CBFA2T3 fusion signature.19
    169664342006ZNF652, a novel zinc finger protein, interacts with the putative breast tumor suppressor CBFA2T3 to repress transcription.14
    282924422017ETO2-GLIS2 Hijacks Transcriptional Complexes to Drive Cellular Identity and Self-Renewal in Pediatric Acute Megakaryoblastic Leukemia.12
    241275502013DHH-RHEBL1 fusion transcript: a novel recurrent feature in the new landscape of pediatric CBFA2T3-GLIS2-positive acute myeloid leukemia.11
    224200282012The CBFA2T3/ACSF3 locus is recurrently involved in IGH chromosomal translocation t(14;16)(q32;q24) in pediatric B-cell lymphoma with germinal center phenotype.9


    Anthony J Bais

    CBFA2T3 (core-binding factor, runt domain, alpha subunit 2; translocated to, 3)

    Atlas Genet Cytogenet Oncol Haematol. 2005-10-01

    Online version: http://atlasgeneticsoncology.org/gene/428/cbfa2t3-(core-binding-factor-runt-domain-alpha-subunit-2;-translocated-to-3)