Atlas of Genetics and Cytogenetics in Oncology and Haematology

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ZFHX3 (AT-binding transcription factor 1)

Written2003-10Nadine Van Roy, Frank Speleman
Center for Medical Genetics, Ghent University Hospital, 1K5, De Pintelaan 185, B-9000 Gent, Belgium

(Note : for Links provided by Atlas : click)


Other aliasAT motif-binding factor 1
Alpha-fetoprotein enhancer binding protein
LocusID (NCBI) 463
Atlas_Id 357
Location 16q22.2  [Link to chromosome band 16q22]
Location_base_pair Starts at and ends at bp from pter
  Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
SLK (10q24.33) / ZFHX3 (16q22.2)WWOX (16q23.1) / ZFHX3 (16q22.2)ZFHX3 (16q22.2) / AHNAK (11q12.3)
ZFHX3 (16q22.2) / ARL15 (5q11.2)ZFHX3 (16q22.2) / SFXN1 (5q35.2)


Description 10 exons, DNA size: 261.32 kb.
Transcription two isoforms ATBF1-A and ATBF1-B, due to alternative promotor usage combined with alternative splicing, mRNA-size: 11893 bp.


Description 3703 amino acids; 404 kDa; four homeodomains and 23 zinc fingers including 1 pseudo zinc finger motif, one DEAD and one DEAH box, a RNA and an ATP binding site, two large RS domains and multiple phosphorylation sites.
Expression Embryonic and neonatal brain.
Localisation nuclear
Function Transcription factor that binds to the AT-rich core sequence of the enhancer element of the AFP gene and downregulates AFP gene expression, possibly involved in neuronal differentiation (ATBF1-A).
Homology mouse atbf1, drosophila zfh2 and C. Elegans ZC 123.3


Somatic Amplification, in one early neural crest derived cell line SJNB-12 under the form of extrachromosomally double minutes, non-syntenic co-amplification with MYC.
Absence of ATBF1 expression in alpha-fetoprotein expressing gastric cancer cell lines, lack of ATBF1 expression not due to mutation, deletion or translocation but to strong repression at the transcriptional level.

Implicated in

Disease Early neural crest derived cell line (SJNB-12).
Prognosis unknown
Cytogenetics Several structural and numerical chromosomal aberrations and presence of extrachromosomally double minutes and homogenously staining regions, presence of a reciprocal unbalanced t(8;16)(q24.3;q22.3).
Oncogenesis Amplification in one neural crest derived cell line (SJNB-12), non-syntenic co-amplification with MYC.
Disease Alpha-fetoprotein producing gastric cancer cell lines (GCIY and Ist-I).
Prognosis poor (very malignant and highly metastatic cancer)
Oncogenesis Alpha-fetoprotein producing cancer cell lines show absence of ATBF1 expression, lack of ATBF1 expression not due to deletion mutation or translocation but to strong repression at the transcriptional level.


Positive and negative regulation of myogenic differentiation of C2C12 cells by isoforms of the multiple homeodomain zinc finger transcription factor ATBF1.
Berry FB, Miura Y, Mihara K, Kaspar P, Sakata N, Hashimoto-Tamaoki T, Tamaoki T
The Journal of biological chemistry. 2001 ; 276 (27) : 25057-25065.
PMID 11312261
Regulation and activities of alpha-fetoprotein.
Chen H, Egan JO, Chiu JF
Critical reviews in eukaryotic gene expression. 1997 ; 7 (1-2) : 11-41.
PMID 9034713
ATBF1-A protein, but not ATBF1-B, is preferentially expressed in developing rat brain.
Ishii Y, Kawaguchi M, Takagawa K, Oya T, Nogami S, Tamura A, Miura Y, Ido A, Sakata N, Hashimoto-Tamaoki T, Kimura T, Saito T, Tamaoki T, Sasahara M
The Journal of comparative neurology. 2003 ; 465 (1) : 57-71.
PMID 12926016
Myb-interacting protein, ATBF1, represses transcriptional activity of Myb oncoprotein.
Kaspar P, Dvor´kov´ M, Kr´lov´ J, Pajer P, Kozmik Z, Dvor´k M
The Journal of biological chemistry. 1999 ; 274 (20) : 14422-14428.
PMID 10318867
AT motif binding factor 1-A (ATBF1-A) negatively regulates transcription of the aminopeptidase N gene in the crypt-villus axis of small intestine.
Kataoka H, Joh T, Miura Y, Tamaoki T, Senoo K, Ohara H, Nomura T, Tada T, Asai K, Kato T, Itoh M
Biochemical and biophysical research communications. 2000 ; 267 (1) : 91-95.
PMID 10623580
Alpha-fetoprotein producing gastric cancer lacks transcription factor ATBF1.
Kataoka H, Miura Y, Joh T, Seno K, Tada T, Tamaoki T, Nakabayashi H, Kawaguchi M, Asai K, Kato T, Itoh M
Oncogene. 2001 ; 20 (7) : 869-873.
PMID 11314020
Characterization of trinucleotide- and tandem repeat-containing transcripts obtained from human spinal cord cDNA library by high-density filter hybridization.
Kaushik N, Malaspina A, de Belleroche J
DNA and cell biology. 2000 ; 19 (5) : 265-273.
PMID 10855793
DNA/RNA-dependent ATPase activity is associated with ATBF1, a multiple homeodomain-zinc finger protein.
Kawaguchi M, Miura Y, Ido A, Morinaga T, Sakata N, Oya T, Hashimoto-Tamaoki T, Sasahara M, Koizumi F, Tamaoki T
Biochimica et biophysica acta. 2001 ; 1550 (2) : 164-174.
PMID 11755205
Expression of homeobox genes in cervical cancer.
Li H, Huang CJ, Choo KB
Gynecologic oncology. 2002 ; 84 (2) : 216-221.
PMID 11812077
Cloning and characterization of an ATBF1 isoform that expresses in a neuronal differentiation-dependent manner.
Miura Y, Tam T, Ido A, Morinaga T, Miki T, Hashimoto T, Tamaoki T
The Journal of biological chemistry. 1995 ; 270 (45) : 26840-26848.
PMID 7592926
A human alpha-fetoprotein enhancer-binding protein, ATBF1, contains four homeodomains and seventeen zinc fingers.
Morinaga T, Yasuda H, Hashimoto T, Higashio K, Tamaoki T
Molecular and cellular biology. 1991 ; 11 (12) : 6041-6049.
PMID 1719379
Regulation of the alpha-fetoprotein gene by the isoforms of ATBF1 transcription factor in human hepatoma.
Ninomiya T, Mihara K, Fushimi K, Hayashi Y, Hashimoto-Tamaoki T, Tamaoki T
Hepatology (Baltimore, Md.). 2002 ; 35 (1) : 82-87.
PMID 11786962
Cloning and characterization of a novel RNA-binding protein SRL300 with RS domains.
Sawada Y, Miura Y, Umeki K, Tamaoki T, Fujinaga K, Ohtaki S
Biochimica et biophysica acta. 2000 ; 1492 (1) : 191-195.
PMID 11004489
Automated fluorescent dye-terminator sequencing of G+C-rich tracts with the aid of dimethyl sulfoxide.
Scheidl TM, Miura Y, Yee HA, Tamaoki T
BioTechniques. 1995 ; 19 (5) : 691-694.
PMID 8588896
[ZFH/ATBF1 gene family: transcription factors containing both homeo- and zinc finger-domains]
Tamaoki T, Hashimoto T
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme. 1996 ; 41 (11) : 1550-1559.
PMID 8827889
Combined M-FISH and CGH analysis allows comprehensive description of genetic alterations in neuroblastoma cell lines.
Van Roy N, Van Limbergen H, Vandesompele J, Van Gele M, Poppe B, Salwen H, Laureys G, Manoel N, De Paepe A, Speleman F
Genes, chromosomes & cancer. 2001 ; 32 (2) : 126-135.
PMID 11550280
Developmental changes in expression of the ATBF1 transcription factor gene.
Watanabe M, Miura Y, Ido A, Sakai M, Nishi S, Inoue Y, Hashimoto T, Tamaoki T
Brain research. Molecular brain research. 1996 ; 42 (2) : 344-349.
PMID 9013792
Assignment of the human ATBF1 transcription factor gene to chromosome 16q22.3-q23.1.
Yamada K, Miura Y, Scheidl T, Yoshida MC, Tamaoki T
Genomics. 1995 ; 29 (2) : 552-553.
PMID 8666409
ATBF1, a multiple-homeodomain zinc finger protein, selectively down-regulates AT-rich elements of the human alpha-fetoprotein gene.
Yasuda H, Mizuno A, Tamaoki T, Morinaga T
Molecular and cellular biology. 1994 ; 14 (2) : 1395-1401.
PMID 7507206


This paper should be referenced as such :
Van Roy, N ; Speleman, F
ATBF1 (AT-binding transcription factor 1)
Atlas Genet Cytogenet Oncol Haematol. 2004;8(1):1-2.
Free journal version : [ pdf ]   [ DOI ]
On line version :

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]
  t(5;16)(q11;q22) ZFHX3/ARL15
t(10;16)(q24;q22) SLK/ZFHX3

External links

Genomic and cartography
Gene and transcription
RefSeq transcript (Entrez)
RefSeq genomic (Entrez)
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
BioGPS (Tissue expression)463
Protein : pattern, domain, 3D structure
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Protein Interaction databases
Ontologies - Pathways
Clinical trials, drugs, therapy
canSAR (ICR) (select the gene name)
Other database
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Oct 18 17:28:46 CEST 2018

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