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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)

Identity

Alias_namesATBF1
AT-binding transcription factor 1
Alias_symbol (synonym)ZNF927
HGNC (Hugo) ZFHX3
LocusID (NCBI) 463
Atlas_Id 357
Location 16q22.2  [Link to chromosome band 16q22]
Location_base_pair Starts at 72816786 and ends at 73092534 bp from pter ( according to hg19-Feb_2009)  [Mapping ZFHX3.png]
 
  Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics
Fusion genes
(updated 2016)
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)

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

Note
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.
  

Bibliography

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
 

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;8(1):1-2.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/ATBF1ID357.html


External links

Nomenclature
HGNC (Hugo)ZFHX3   777
Cards
AtlasATBF1ID357
Entrez_Gene (NCBI)ZFHX3  463  zinc finger homeobox 3
AliasesATBF1; ATBT; ZNF927
GeneCards (Weizmann)ZFHX3
Ensembl hg19 (Hinxton)ENSG00000140836 [Gene_View]  chr16:72816786-73092534 [Contig_View]  ZFHX3 [Vega]
Ensembl hg38 (Hinxton)ENSG00000140836 [Gene_View]  chr16:72816786-73092534 [Contig_View]  ZFHX3 [Vega]
ICGC DataPortalENSG00000140836
TCGA cBioPortalZFHX3
AceView (NCBI)ZFHX3
Genatlas (Paris)ZFHX3
WikiGenes463
SOURCE (Princeton)ZFHX3
Genetics Home Reference (NIH)ZFHX3
Genomic and cartography
GoldenPath hg19 (UCSC)ZFHX3  -     chr16:72816786-73092534 -  16q22.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)ZFHX3  -     16q22.3   [Description]    (hg38-Dec_2013)
EnsemblZFHX3 - 16q22.3 [CytoView hg19]  ZFHX3 - 16q22.3 [CytoView hg38]
Mapping of homologs : NCBIZFHX3 [Mapview hg19]  ZFHX3 [Mapview hg38]
OMIM104155   176807   
Gene and transcription
Genbank (Entrez)BC029653 BC043190 D10250 L32832 L32833
RefSeq transcript (Entrez)NM_001164766 NM_006885
RefSeq genomic (Entrez)NC_000016 NC_018927 NG_013211 NT_010498 NW_004929402
Consensus coding sequences : CCDS (NCBI)ZFHX3
Cluster EST : UnigeneHs.598297 [ NCBI ]
CGAP (NCI)Hs.598297
Alternative Splicing GalleryENSG00000140836
Gene ExpressionZFHX3 [ NCBI-GEO ]   ZFHX3 [ EBI - ARRAY_EXPRESS ]   ZFHX3 [ SEEK ]   ZFHX3 [ MEM ]
Gene Expression Viewer (FireBrowse)ZFHX3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)463
GTEX Portal (Tissue expression)ZFHX3
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ15911   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ15911  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ15911
Splice isoforms : SwissVarQ15911
PhosPhoSitePlusQ15911
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    Homeobox_dom    Homeodomain-like    Znf_C2H2    Znf_C2H2-like    Znf_C2H2/integrase_DNA-bd    Znf_U1   
Domain families : Pfam (Sanger)Homeobox (PF00046)   
Domain families : Pfam (NCBI)pfam00046   
Domain families : Smart (EMBL)HOX (SM00389)  ZnF_C2H2 (SM00355)  ZnF_U1 (SM00451)  
Conserved Domain (NCBI)ZFHX3
DMDM Disease mutations463
Blocks (Seattle)ZFHX3
PDB (SRS)2DA1    2DA2    2DA3   
PDB (PDBSum)2DA1    2DA2    2DA3   
PDB (IMB)2DA1    2DA2    2DA3   
PDB (RSDB)2DA1    2DA2    2DA3   
Structural Biology KnowledgeBase2DA1    2DA2    2DA3   
SCOP (Structural Classification of Proteins)2DA1    2DA2    2DA3   
CATH (Classification of proteins structures)2DA1    2DA2    2DA3   
SuperfamilyQ15911
Human Protein AtlasENSG00000140836
Peptide AtlasQ15911
HPRD00075
IPIIPI00014186   IPI00219003   
Protein Interaction databases
DIP (DOE-UCLA)Q15911
IntAct (EBI)Q15911
FunCoupENSG00000140836
BioGRIDZFHX3
STRING (EMBL)ZFHX3
ZODIACZFHX3
Ontologies - Pathways
QuickGOQ15911
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  core promoter sequence-specific DNA binding  transcription factor activity, sequence-specific DNA binding  transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding  protein binding  nucleus  nucleus  nucleoplasm  transcription factor complex  nucleolus  cytoplasm  regulation of transcription, DNA-templated  transcription from RNA polymerase II promoter  cell cycle arrest  brain development  muscle organ development  zinc ion binding  nuclear body  enzyme binding  circadian regulation of gene expression  intracellular membrane-bounded organelle  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  positive regulation of transcription, DNA-templated  response to transforming growth factor beta  regulation of locomotor rhythm  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  core promoter sequence-specific DNA binding  transcription factor activity, sequence-specific DNA binding  transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding  protein binding  nucleus  nucleus  nucleoplasm  transcription factor complex  nucleolus  cytoplasm  regulation of transcription, DNA-templated  transcription from RNA polymerase II promoter  cell cycle arrest  brain development  muscle organ development  zinc ion binding  nuclear body  enzyme binding  circadian regulation of gene expression  intracellular membrane-bounded organelle  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  positive regulation of transcription, DNA-templated  response to transforming growth factor beta  regulation of locomotor rhythm  
NDEx NetworkZFHX3
Atlas of Cancer Signalling NetworkZFHX3
Wikipedia pathwaysZFHX3
Orthology - Evolution
OrthoDB463
GeneTree (enSembl)ENSG00000140836
Phylogenetic Trees/Animal Genes : TreeFamZFHX3
HOVERGENQ15911
HOGENOMQ15911
Homologs : HomoloGeneZFHX3
Homology/Alignments : Family Browser (UCSC)ZFHX3
Gene fusions - Rearrangements
Fusion : MitelmanSLK/ZFHX3 [10q24.33/16q22.2]  [t(10;16)(q24;q22)]  
Fusion : MitelmanZFHX3/ARL15 [16q22.2/5q11.2]  [t(5;16)(q11;q22)]  
Fusion: TCGASLK 10q24.33 ZFHX3 16q22.2 LUAD
Fusion: TCGAZFHX3 16q22.2 ARL15 5q11.2 PRAD
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerZFHX3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)ZFHX3
dbVarZFHX3
ClinVarZFHX3
1000_GenomesZFHX3 
Exome Variant ServerZFHX3
ExAC (Exome Aggregation Consortium)ZFHX3 (select the gene name)
Genetic variants : HAPMAP463
Genomic Variants (DGV)ZFHX3 [DGVbeta]
DECIPHER (Syndromes)16:72816786-73092534  ENSG00000140836
CONAN: Copy Number AnalysisZFHX3 
Mutations
ICGC Data PortalZFHX3 
TCGA Data PortalZFHX3 
Broad Tumor PortalZFHX3
OASIS PortalZFHX3 [ Somatic mutations - Copy number]
Cancer Gene: CensusZFHX3 
Somatic Mutations in Cancer : COSMICZFHX3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDZFHX3
intOGen PortalZFHX3
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch ZFHX3
DgiDB (Drug Gene Interaction Database)ZFHX3
DoCM (Curated mutations)ZFHX3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)ZFHX3 (select a term)
intoGenZFHX3
NCG5 (London)ZFHX3
Cancer3DZFHX3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM104155    176807   
Orphanet
MedgenZFHX3
Genetic Testing Registry ZFHX3
NextProtQ15911 [Medical]
TSGene463
GENETestsZFHX3
Huge Navigator ZFHX3 [HugePedia]
snp3D : Map Gene to Disease463
BioCentury BCIQZFHX3
ClinGenZFHX3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD463
Chemical/Pharm GKB GenePA162409676
Clinical trialZFHX3
Miscellaneous
canSAR (ICR)ZFHX3 (select the gene name)
Other databasehttp://cancergenome.broadinstitute.org/index.php?tgene=ZFHX3
Probes
Litterature
PubMed59 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineZFHX3
EVEXZFHX3
GoPubMedZFHX3
iHOPZFHX3
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Nov 18 20:05:50 CET 2016

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