ATBF1 (AT-binding transcription factor 1)

Identity

Other names	AT motif-binding factor 1
	Alpha-fetoprotein enhancer binding protein
HGNC	ZFHX3
Location	16q22.3-q23.1
Location_base_pair	Starts at 71374287 and ends at 71639775 bp from pter ( according to hg18-Mar_2006).

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	ZFHX3   777
Entrez_Gene	ZFHX3  463  zinc finger homeobox 3
	Cards
Atlas	ATBF1ID357
GeneCards	ZFHX3
Ensembl	ZFHX3 [Search_View]   ENSG00000140836 [Gene_View]
Genatlas	ZFHX3
GeneLynx	ZFHX3
eGenome	ZFHX3
euGene	463
	Genomic and cartography
GoldenPath	ZFHX3  -     chr16:71374287-71639775 -  16q22.3   [Description]    (hg18-Mar_2006)
Ensembl	ZFHX3 - 16q22.3 [CytoView]
NCBI	Mapview
OMIM	Disease map [OMIM]
HomoloGene	ZFHX3
	Gene and transcription
Genbank	BC029653 [ ENTREZ ]
Genbank	BC043190 [ ENTREZ ]
Genbank	D10250 [ ENTREZ ]
Genbank	L32832 [ ENTREZ ]
RefSeq	NM_006885 [ SRS ]    NM_006885 [ ENTREZ ]
RefSeq	AC_000059 [ SRS ]    AC_000059 [ ENTREZ ]
RefSeq	AC_000148 [ SRS ]    AC_000148 [ ENTREZ ]
RefSeq	NC_000016 [ SRS ]    NC_000016 [ ENTREZ ]
RefSeq	NT_010498 [ SRS ]    NT_010498 [ ENTREZ ]
RefSeq	NW_001838325 [ SRS ]    NW_001838325 [ ENTREZ ]
RefSeq	NW_926517 [ SRS ]    NW_926517 [ ENTREZ ]
AceView	ZFHX3 AceView - NCBI
Unigene	Hs.652666 [ SRS ]    Hs.652666 [ NCBI ]     HS652666 [ spliceNest ]
Fast-db	11380 (alternative variants)
	Protein : pattern, domain, 3D structure
SwissProt	Q15911 [ SRS]    Q15911 [ EXPASY ]     Q15911 [ INTERPRO ]     Q15911 [ UNIPROT ]
Prosite	PS00027 HOMEOBOX_1 [ SRS ]    PS00027 HOMEOBOX_1 [ Expasy ]
Prosite	PS50071 HOMEOBOX_2 [ SRS ]    PS50071 HOMEOBOX_2 [ Expasy ]
Prosite	PS00028 ZINC_FINGER_C2H2_1 [ SRS ]    PS00028 ZINC_FINGER_C2H2_1 [ Expasy ]
Prosite	PS50157 ZINC_FINGER_C2H2_2 [ SRS ]    PS50157 ZINC_FINGER_C2H2_2 [ Expasy ]
Interpro	IPR001356 Homeobox [ SRS ]    IPR001356 Homeobox [ EBI ]
Interpro	IPR012287 Homeodomain-rel [ SRS ]    IPR012287 Homeodomain-rel [ EBI ]
Interpro	IPR007087 Znf_C2H2 [ SRS ]    IPR007087 Znf_C2H2 [ EBI ]
Interpro	IPR015880 Znf_C2H2-like [ SRS ]    IPR015880 Znf_C2H2-like [ EBI ]
Interpro	IPR013087 Znf_C2H2/integrase_DNA-bd [ SRS ]    IPR013087 Znf_C2H2/integrase_DNA-bd [ EBI ]
Interpro	IPR003604 Znf_U1 [ SRS ]    IPR003604 Znf_U1 [ EBI ]
CluSTr	Q15911
Pfam	PF00046 Homeobox [ SRS ]    PF00046 Homeobox [ Sanger ]    pfam00046 [ NCBI-CDD ]
Pfam	PF00096 zf-C2H2 [ SRS ]    PF00096 zf-C2H2 [ Sanger ]    pfam00096 [ NCBI-CDD ]
Smart	SM00389 HOX [EMBL]
Smart	SM00355 ZnF_C2H2 [EMBL]
Smart	SM00451 ZnF_U1 [EMBL]
Prodom	PD000010 Homeobox[INRA-Toulouse]
Prodom	Q15911 ZFHX3_HUMAN [ Domain structure ]   Q15911 ZFHX3_HUMAN  [ sequences sharing at least 1 domain ]
Blocks	Q15911
PDB	2DA2 [ SRS ]    2DA2 [ PdbSum ],   2DA2 [ IMB ]   2DA2 [ RSDB ]
PDB	2DA3 [ SRS ]    2DA3 [ PdbSum ],   2DA3 [ IMB ]   2DA3 [ RSDB ]
HPRD	00075
	Protein Interaction databases
DIP	Q15911
IntAct	Q15911
	Polymorphism : SNP, mutations, diseases
OMIM	104155;176807    [ map ]
GENECLINICS	104155;176807
SNP	ZFHX3 [dbSNP-NCBI]
SNP	NM_006885 [SNP-NCI]
SNP	ZFHX3 [GeneSNPs - Utah]  ZFHX3] [HGBASE - SRS]
HAPMAP	ZFHX3 [HAPMAP]
HGMD	ZFHX3
	General knowledge
Family Browser	ZFHX3 [UCSC Family Browser]
SOURCE	NM_006885
SMD	Hs.652666
SAGE	Hs.652666
GO	negative regulation of transcription from RNA polymerase II promoter [Amigo]  negative regulation of transcription from RNA polymerase II promoter
GO	RNA polymerase II transcription factor activity, enhancer binding [Amigo]  RNA polymerase II transcription factor activity, enhancer binding
GO	intracellular [Amigo]  intracellular
GO	nucleus [Amigo]  nucleus
GO	transcription factor complex [Amigo]  transcription factor complex
GO	mitochondrion [Amigo]  mitochondrion
GO	regulation of transcription, DNA-dependent [Amigo]  regulation of transcription, DNA-dependent
GO	zinc ion binding [Amigo]  zinc ion binding
GO	transcription repressor activity [Amigo]  transcription repressor activity
GO	sequence-specific DNA binding [Amigo]  sequence-specific DNA binding
GO	metal ion binding [Amigo]  metal ion binding
PubGene	ZFHX3
TreeFam	ZFHX3
CTD	463 [Comparative ToxicoGenomics Database]
	Other databases
	Probes
Probe	ZFHX3 Related clones (RZPD - Berlin)
	PubMed
PubMed	21 Pubmed reference(s) in Entrez

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

REVIEW articles	automatic search in PubMed
Last year publications	automatic search in PubMed

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Contributor(s)

Written	10-2003	Nadine 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. October 2003 . URL : http://AtlasGeneticsOncology.org/Genes/ATBF1ID357.html

© Atlas of Genetics and Cytogenetics in Oncology and Haematology

indexed on : Tue Oct 14 21:15:57 2008