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ZFHX3 (AT-binding transcription factor 1)

Identity

Other namesAT motif-binding factor 1
Alpha-fetoprotein enhancer binding protein
HGNC (Hugo) ZFHX3
LocusID (NCBI) 463
Location 16q22.2
Location_base_pair Starts at 72816786 and ends at 73092534 bp from pter ( according to hg19-Feb_2009)  [Mapping]
 
  Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics

DNA/RNA

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.

Protein

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

Mutations

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.
  

External links

Nomenclature
HGNC (Hugo)ZFHX3   777
Cards
AtlasATBF1ID357
Entrez_Gene (NCBI)ZFHX3  463  zinc finger homeobox 3
GeneCards (Weizmann)ZFHX3
Ensembl (Hinxton)ENSG00000140836 [Gene_View]  chr16:72816786-73092534 [Contig_View]  ZFHX3 [Vega]
ICGC DataPortalENSG00000140836
cBioPortalZFHX3
AceView (NCBI)ZFHX3
Genatlas (Paris)ZFHX3
WikiGenes463
SOURCE (Princeton)NM_001164766 NM_006885
Genomic and cartography
GoldenPath (UCSC)ZFHX3  -  16q22.2   chr16:72816786-73092534 -  16q22.3   [Description]    (hg19-Feb_2009)
EnsemblZFHX3 - 16q22.3 [CytoView]
Mapping of homologs : NCBIZFHX3 [Mapview]
OMIM104155   176807   
Gene and transcription
Genbank (Entrez)BC029653 BC043190 D10250 L32832
RefSeq transcript (Entrez)NM_001164766 NM_006885
RefSeq genomic (Entrez)AC_000148 NC_000016 NC_018927 NG_013211 NT_010498 NW_001838325 NW_004929402
Consensus coding sequences : CCDS (NCBI)ZFHX3
Cluster EST : UnigeneHs.598297 [ NCBI ]
CGAP (NCI)Hs.598297
Alternative Splicing : Fast-db (Paris)GSHG0011973
Alternative Splicing GalleryENSG00000140836
Gene ExpressionZFHX3 [ NCBI-GEO ]     ZFHX3 [ SEEK ]   ZFHX3 [ MEM ]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ15911 (Uniprot)
NextProtQ15911  [Medical]
With graphics : InterProQ15911
Splice isoforms : SwissVarQ15911 (Swissvar)
Domaine pattern : Prosite (Expaxy)HOMEOBOX_1 (PS00027)    HOMEOBOX_2 (PS50071)    ZINC_FINGER_C2H2_1 (PS00028)    ZINC_FINGER_C2H2_2 (PS50157)   
Domains : Interpro (EBI)Homeobox_CS [organisation]   Homeobox_dom [organisation]   Homeodomain-like [organisation]   Znf_C2H2 [organisation]   Znf_C2H2-like [organisation]   Znf_C2H2/integrase_DNA-bd [organisation]   Znf_U1 [organisation]  
Related proteins : CluSTrQ15911
Domain families : Pfam (Sanger)Homeobox (PF00046)    zf-C2H2 (PF00096)   
Domain families : Pfam (NCBI)pfam00046    pfam00096   
Domain families : Smart (EMBL)HOX (SM00389)  ZnF_C2H2 (SM00355)  ZnF_U1 (SM00451)  
DMDM Disease mutations463
Blocks (Seattle)Q15911
PDB (SRS)2DA1    2DA2    2DA3   
PDB (PDBSum)2DA1    2DA2    2DA3   
PDB (IMB)2DA1    2DA2    2DA3   
PDB (RSDB)2DA1    2DA2    2DA3   
Human Protein AtlasENSG00000140836 [gene] [tissue] [antibody] [cell] [cancer]
Peptide AtlasQ15911
HPRD00075
IPIIPI00014186   IPI00219003   
Protein Interaction databases
DIP (DOE-UCLA)Q15911
IntAct (EBI)Q15911
FunCoupENSG00000140836
BioGRIDZFHX3
InParanoidQ15911
Interologous Interaction database Q15911
IntegromeDBZFHX3
STRING (EMBL)ZFHX3
Ontologies - Pathways
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  sequence-specific DNA binding transcription factor activity  RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity  nucleus  transcription factor complex  mitochondrion  regulation of transcription, DNA-templated  transcription from RNA polymerase II promoter  cell cycle arrest  brain development  muscle organ development  zinc ion binding  enzyme binding  sequence-specific DNA binding  transcription regulatory region DNA binding  negative regulation of myoblast differentiation  positive regulation of myoblast differentiation  regulation of neuron differentiation  negative regulation of transcription, DNA-templated  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  sequence-specific DNA binding transcription factor activity  RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity  nucleus  transcription factor complex  mitochondrion  regulation of transcription, DNA-templated  transcription from RNA polymerase II promoter  cell cycle arrest  brain development  muscle organ development  zinc ion binding  enzyme binding  sequence-specific DNA binding  transcription regulatory region DNA binding  negative regulation of myoblast differentiation  positive regulation of myoblast differentiation  regulation of neuron differentiation  negative regulation of transcription, DNA-templated  
Protein Interaction DatabaseZFHX3
Wikipedia pathwaysZFHX3
Gene fusion - rearrangments
Polymorphisms : SNP, mutations, diseases
SNP Single Nucleotide Polymorphism (NCBI)ZFHX3
snp3D : Map Gene to Disease463
SNP (GeneSNP Utah)ZFHX3
SNP : HGBaseZFHX3
Genetic variants : HAPMAPZFHX3
Exome VariantZFHX3
1000_GenomesZFHX3 
ICGC programENSG00000140836 
Somatic Mutations in Cancer : COSMICZFHX3 
CONAN: Copy Number AnalysisZFHX3 
Mutations and Diseases : HGMDZFHX3
Mutations and Diseases : intOGenZFHX3
Genomic VariantsZFHX3  ZFHX3 [DGVbeta]
dbVarZFHX3
ClinVarZFHX3
Pred. of missensesPolyPhen-2  SIFT(SG)  SIFT(JCVI)  Align-GVGD  MutAssessor  Mutanalyser  
Pred. splicesGeneSplicer  Human Splicing Finder  MaxEntScan  
Diseases
OMIM104155    176807   
MedgenZFHX3
GENETestsZFHX3
Disease Genetic AssociationZFHX3
Huge Navigator ZFHX3 [HugePedia]  ZFHX3 [HugeCancerGEM]
General knowledge
Homologs : HomoloGeneZFHX3
Homology/Alignments : Family Browser (UCSC)ZFHX3
Phylogenetic Trees/Animal Genes : TreeFamZFHX3
Chemical/Protein Interactions : CTD463
Chemical/Pharm GKB GenePA162409676
Clinical trialZFHX3
Cancer Resource (Charite)ENSG00000140836
Other databases
Other databasehttp://cancergenome.broadinstitute.org/index.php?tgene=ZFHX3
Probes
Litterature
PubMed49 Pubmed reference(s) in Entrez
CoreMineZFHX3
iHOPZFHX3
OncoSearchZFHX3

Bibliography

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
 
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
 
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
 
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
 
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
 
[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
 
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
 
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
 
Myb-interacting protein, ATBF1, represses transcriptional activity of Myb oncoprotein.
Kaspar P, Dvorˆ°kovˆ° M, Krˆ°lovˆ° J, Pajer P, Kozmik Z, Dvorˆ°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
 
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
 
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
 
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
 
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
 
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
 
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
 
Expression of homeobox genes in cervical cancer.
Li H, Huang CJ, Choo KB
Gynecologic oncology. 2002 ; 84 (2) : 216-221.
PMID 11812077
 
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
 
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
 
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Contributor(s)

Written10-2003Nadine Van Roy, Frank Speleman
Center for Medical Genetics, Ghent University Hospital, 1K5, De Pintelaan 185, B-9000 Gent, Belgium

Citation

This paper should be referenced as such :
Van Roy, N ; Speleman, F
ATBF1 (AT-binding transcription factor 1)
Atlas Genet Cytogenet Oncol Haematol. 2004;7(1):1-2.
Free online version   Free pdf version   [Bibliographic record ]
URL : http://AtlasGeneticsOncology.org/Genes/ATBF1ID357.html

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indexed on : Sat Oct 4 12:57:29 CEST 2014

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