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)

Identity

Alias_namesATBF1
C16orf47
AT-binding transcription factor 1
chromosome 16 open reading frame 47
Alias_symbol (synonym)ZNF927
FLJ26184
Other aliasAT motif-binding factor 1
Alpha-fetoprotein enhancer binding protein
HGNC (Hugo) ZFHX3
LocusID (NCBI) 463
Atlas_Id 357
Location 16q22.2  [Link to chromosome band 16q22]
Location_base_pair Starts at 72782887 and ends at 73048375 bp from pter ( according to hg19-Feb_2009)  [Mapping ZFHX3.png]
 
  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)

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


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

Nomenclature
HGNC (Hugo)ZFHX3   777
Cards
AtlasATBF1ID357
Entrez_Gene (NCBI)ZFHX3  463  zinc finger homeobox 3
AliasesATBF1; ATBT; C16orf47; ZFH-3; 
ZNF927
GeneCards (Weizmann)ZFHX3
Ensembl hg19 (Hinxton)ENSG00000140836 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000140836 [Gene_View]  ENSG00000140836 [Sequence]  chr16:72782887-73048375 [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 hg38 (UCSC)ZFHX3  -     chr16:72782887-73048375 -  16q22.2-q22.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)ZFHX3  -     16q22.2-q22.3   [Description]    (hg19-Feb_2009)
GoldenPathZFHX3 - 16q22.2-q22.3 [CytoView hg19]  ZFHX3 - 16q22.2-q22.3 [CytoView hg38]
ImmunoBaseENSG00000140836
Mapping of homologs : NCBIZFHX3 [Mapview hg19]  ZFHX3 [Mapview hg38]
OMIM104155   176807   
Gene and transcription
Genbank (Entrez)AK129695 BC029653 BC043190 D10250 L32832
RefSeq transcript (Entrez)NM_001164766 NM_006885 NM_207385
RefSeq genomic (Entrez)
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]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)463
GTEX Portal (Tissue expression)ZFHX3
Human Protein AtlasENSG00000140836-ZFHX3 [pathology]   [cell]   [tissue]
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-like_sf    Homeobox_CS    Homeobox_dom    Matrin/U1-like-C_Znf_C2H2    Znf_C2H2_sf    Znf_C2H2_type   
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 (RSDB)2DA1    2DA2    2DA3   
PDB Europe2DA1    2DA2    2DA3   
PDB (PDBSum)2DA1    2DA2    2DA3   
PDB (IMB)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 Atlas [tissue]ENSG00000140836-ZFHX3 [tissue]
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 by RNA polymerase II  negative regulation of transcription by RNA polymerase II  negative regulation of transcription by RNA polymerase II  RNA polymerase II proximal promoter sequence-specific DNA binding  RNA polymerase II proximal promoter sequence-specific DNA binding  RNA polymerase II proximal promoter sequence-specific DNA binding  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription repressor activity, RNA polymerase II-specific  DNA-binding transcription factor activity  protein binding  nucleus  nucleus  nucleus  nucleoplasm  transcription factor complex  cytoplasm  regulation of transcription, DNA-templated  transcription by RNA polymerase II  cell cycle arrest  brain development  muscle organ development  zinc ion binding  nuclear body  enzyme binding  circadian regulation of gene expression  transcription regulatory region DNA binding  regulation of neuron differentiation  positive regulation of cell adhesion  positive regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  response to transforming growth factor beta  regulation of locomotor rhythm  
Ontology : EGO-EBInegative regulation of transcription by RNA polymerase II  negative regulation of transcription by RNA polymerase II  negative regulation of transcription by RNA polymerase II  RNA polymerase II proximal promoter sequence-specific DNA binding  RNA polymerase II proximal promoter sequence-specific DNA binding  RNA polymerase II proximal promoter sequence-specific DNA binding  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription repressor activity, RNA polymerase II-specific  DNA-binding transcription factor activity  protein binding  nucleus  nucleus  nucleus  nucleoplasm  transcription factor complex  cytoplasm  regulation of transcription, DNA-templated  transcription by RNA polymerase II  cell cycle arrest  brain development  muscle organ development  zinc ion binding  nuclear body  enzyme binding  circadian regulation of gene expression  transcription regulatory region DNA binding  regulation of neuron differentiation  positive regulation of cell adhesion  positive regulation of transcription, DNA-templated  positive regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  response to transforming growth factor beta  regulation of locomotor rhythm  
REACTOMEQ15911 [protein]
REACTOME PathwaysR-HSA-8941855 [pathway]   
NDEx NetworkZFHX3
Atlas of Cancer Signalling NetworkZFHX3
Wikipedia pathwaysZFHX3
Orthology - Evolution
OrthoDB463
GeneTree (enSembl)ENSG00000140836
Phylogenetic Trees/Animal Genes : TreeFamZFHX3
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 PortalSLK 10q24.33 ZFHX3 16q22.2 LUAD
Fusion PortalZFHX3 16q22.2 ARL15 5q11.2 PRAD
Fusion : FusionGDB30326    34698    42117    42788    42789    42790    42791    42792    42793    42794    42795    42796    42797    42798    42799   
Fusion : Fusion_HubFAM49B--ZFHX3    LMF1--ZFHX3    NFIC--ZFHX3    PHF17--ZFHX3    PRPF18--ZFHX3    RPL29--ZFHX3    SLK--ZFHX3    STX7--ZFHX3    WWOX--ZFHX3    ZFHX3--AHNAK    ZFHX3--ALS2CR11    ZFHX3--AP1G1    ZFHX3--ARL15    ZFHX3--C16ORF47    ZFHX3--CMTM4   
ZFHX3--DIP2A    ZFHX3--ENY2    ZFHX3--GLG1    ZFHX3--GTF3C5    ZFHX3--GYS1    ZFHX3--IL34    ZFHX3--LMF1    ZFHX3--LRRC36    ZFHX3--LYRM1    ZFHX3--MGP    ZFHX3--NAT8L    ZFHX3--OXCT1    ZFHX3--PNRC1    ZFHX3--PSMB1    ZFHX3--SFXN1   
ZFHX3--SKP1    ZFHX3--ST6GALNAC3    ZFHX3--TMCO3    ZFHX3--USP47    ZFHX3--WWP2    ZFHX3--ZMAT4    ZFHX3--ZMYND11    ZFHX3--ZNF423    ZFHX3--ZNF821   
Fusion : QuiverZFHX3
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)ENSG00000140836
GNOMAD BrowserENSG00000140836
Varsome BrowserZFHX3
Genetic variants : HAPMAP463
Genomic Variants (DGV)ZFHX3 [DGVbeta]
DECIPHERZFHX3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisZFHX3 
Mutations
ICGC Data PortalZFHX3 
TCGA Data PortalZFHX3 
Broad Tumor PortalZFHX3
OASIS PortalZFHX3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICZFHX3  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DZFHX3
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] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM104155    176807   
Orphanet
DisGeNETZFHX3
MedgenZFHX3
Genetic Testing Registry ZFHX3
NextProtQ15911 [Medical]
TSGene463
GENETestsZFHX3
Target ValidationZFHX3
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)
DataMed IndexZFHX3
Other databasehttp://cancergenome.broadinstitute.org/index.php?tgene=ZFHX3
Probes
Litterature
PubMed89 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 : Wed Nov 13 21:02:12 CET 2019

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