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TFEB (transcription factor EB)

Identity

Other namesT-cell Transcription Factor EB, TCFEB
HGNC (Hugo) TFEB
Location 6p21
Location_base_pair Starts at 41759694 and ends at 41810776 bp from pter ( according to hg18-Mar_2006)  [Mapping]
Note Member of the basic-helix-loop-helix leucine-zipper transcription factor MiTF/TFE family (also known as the MiT family), which also contains MiTF, TFEC, and TFE3. The four members form homo- and/or heterodimers to bind the Ebox core sequence CAYGTG.

DNA/RNA

 
  Genomic organization of TFEB gene.
Description TFEB gene contains 8 coding exons and 7 alternative first exons that are differentially expressed.
Transcription Alternative first exon usage points towards the existence of up to seven alternative promoters. Alternative splicing of exon 3 (encoding an acidic activation domain) similar to the closely related TFE3, TFEC, and MiTF genes.

Protein

 
  Functional domains in the TFEB protein.
Description 490 amino acids; 65 kDa; N-terminal Gln-rich stretch (Gln, exon 2), N-term acidic transcriptional activation domain (AAD, exon 3), basic helix-loop-helix region (bHLH, exon 6-8), leucine zipper (LZ, exon 8), proline-rich activation domain ( ProAD, exon 9), Ser-rich stretch (Ser)
Expression Wide in fetal and adult tissues, although the various TFEB transcript variants are expressed in a tissue-restricted manner: TFEB-A is enriched in placenta, TFEB-F in spleen, and TFEB-E and TFEB-G in brain.
Localisation Nucleus
Function Transcription factor; member of the basic-helix-loop-helix leucine-zipper transcription factor MiTF/TFE family (also known as the MiT family), which also contains MiTF, TFEC, and TFE3. The four members form homo- and/or heterodimers to bind the Ebox core sequence CAYGTG; the helix-loop-helix - leucine zipper region is implicated in DNA binding and dimerization (homo and heterodimerizations); mice which lack TFEB die due to defects in placental vascularization.
Homology High homology to the other MiTF/TFE members TFE3, TFEC and MiTF, homologous to myc family of bHLH transcription factors.

Implicated in

Entity Renal cell carcinoma with t(6;11)(p21;q13) -> Alpha/TFEB gene fusion
Disease Clear cell renal cell carcinomas
Prognosis Limited follow-up available, prognosis appears to be good; no reports of developed metastases
Cytogenetics t(6;11)(p21;q13), usually as the sole cytogenetic anomaly.
Hybrid/Mutated Gene Alpha/TFEB, both fusion genes are expressed; 5'-Alpha-TFEB-3' fusion transcript contains the entire open reading frame of TFEB.
Abnormal Protein No fusion protein, the Alpha gene is a non-protein-encoding transcript.
Oncogenesis Highly induced expression of full-length TFEB protein due to promoter substitution in the Alpha-TFEB fusion gene.
  

External links

Nomenclature
HGNC (Hugo)TFEB   11753
Entrez_Gene (NCBI)TFEB  7942  transcription factor EB
Cards
AtlasTFEBID531
GeneCards (Weizmann)TFEB
Ensembl (Hinxton)ENSG00000112561 [Gene_View]  TFEB [Vega]
AceView (NCBI)TFEB
Genatlas (Paris)TFEB
euGene (Indiana)7942
SOURCE (Stanford)NM_001167827 NM_007162
Gene Expression (Array Express) ENSG00000112561
Genomic and cartography
GoldenPath (UCSC)TFEB  -  6p21   chr6:41759694-41810776 -  6p21   [Description]    (hg18-Mar_2006)
EnsemblTFEB - 6p21 [CytoView]
Mapping of homologs : NCBITFEB [Mapview]
OMIM600744   
Gene and transcription
Gene : Genbank (Entrez)AA235980 AJ608786 AJ608787 AJ608788 AJ608789
Reference sequence (RefSeq transcript) :SRSNM_001167827 NM_007162
Reference transcript : EntrezNM_001167827 NM_007162
RefSeq genomic : SRSAC_000049 AC_000138 NC_000006 NT_007592 NW_001838981 NW_923073
RefSeq genomic : EntrezAC_000049 AC_000138 NC_000006 NT_007592 NW_001838981 NW_923073
Consensus coding sequences : CCDS NCBITFEB
Cluster EST : UnigeneHs.715310 [ SRS ] Hs.715310 [ NCBI ]
Alternative Splicing : Fast-db (Paris)10538
Protein : pattern, domain, 3D structure
Protein : UniProt/SwissProtP19484 (SRS) P19484 (Expasy) P19484 (Uniprot)
With graphics : InterProP19484
Splice isoforms : VarSplice FASTAP19484(VarSplice FASTA)
Domaine pattern : Prosite (SRS)HLH (PS50888)   
Domain pattern : Prosite (Expaxy)HLH (PS50888)   
Domains : Interpro (SRS)HLH_DNA-bd_dom    HLH_DNA_bd   
Domains : Interpro (EBI)HLH_DNA-bd_dom    HLH_DNA_bd   
Related proteins : CluSTrP19484
Domain families : Pfam SRSHLH (PF00010)   
Domain families : Pfam SangerHLH (PF00010)   
Domain families : Pfam NCBIpfam00010   
Domain families : Smart EMBLHLH (SM00353)  
Blocks (Seattle)P19484
Crystal structure of protein : PDB SRS
Crystal structure of protein : PDBSum
Crystal structure of protein : IMB
Crystal structure of protein : PDB RSDB
HPRD02847
Protein Interaction databases
DIP (DOE-UCLA)P19484
IntAct (EBI)P19484
Polymorphism : SNP, mutations, diseases
Single Nucleotide Polymorphism (SNP) : dbSNP NCBITFEB
SNP : GeneSNP UtahTFEB
SNP : HGBaseTFEB
Genetic variants : HAPMAPTFEB
Cancer Gene: CensusTFEB 
Somatic Mutations in Cancer : COSMICTFEB 
Translocation Breakpoints in Cancer : TICdbTFEB 
Mutations and Diseases : HGMDTFEB
Hereditary diseases : OMIM600744   
Hereditary diseases : GENETests600744   
Diseases : Genetic AssociationTFEB
General knowledge
Homologs : HomoloGeneTFEB
Homology/Alignments : Family Browser UCSCTFEB
Phylogenetic Trees/Animal Genes : TreeFamTFEB
Chemical/Protein Interactions : CTD7942
Keywords Ontology : AmiGOembryonic placenta development  transcription factor activity  transcription factor activity  nucleus  nucleus  transcription factor complex  cytoplasm  humoral immune response  positive regulation of gene-specific transcription from RNA polymerase II promoter  promoter binding  positive regulation of transcription, DNA-dependent  
Keywords Ontology : EGO-EBIembryonic placenta development  transcription factor activity  transcription factor activity  nucleus  nucleus  transcription factor complex  cytoplasm  humoral immune response  positive regulation of gene-specific transcription from RNA polymerase II promoter  promoter binding  positive regulation of transcription, DNA-dependent  
Pathways : BIOCARTA
Pathways : KEGG
Other databases
Probes
Probes : ImagenesTFEB Related clones (RZPD - Berlin)
Literature
PubMed16 Pubmed reference(s) in Entrez
PubGeneTFEB

Bibliography

A helix-loop-helix protein related to the immunoglobulin E box-binding proteins.
Carr CS, Sharp PA
Molecular and cellular biology. 1990 ; 10 (8) : 4384-4388.
PMID 2115126
 
TFEB has DNA-binding and oligomerization properties of a unique helix-loop-helix/leucine-zipper family.
Fisher DE, Carr CS, Parent LA, Sharp PA
Genes & development. 1991 ; 5 (12A) : 2342-2352.
PMID 1748288
 
microphthalmia, a critical factor in melanocyte development, defines a discrete transcription factor family.
Hemesath TJ, Steingrˆ‚msson E, McGill G, Hansen MJ, Vaught J, Hodgkinson CA, Arnheiter H, Copeland NG, Jenkins NA, Fisher DE
Genes & development. 1994 ; 8 (22) : 2770-2780.
PMID 7958932
 
The bHLH-Zip transcription factor Tfeb is essential for placental vascularization.
Steingrˆ‚msson E, Tessarollo L, Reid SW, Jenkins NA, Copeland NG
Development (Cambridge, England). 1998 ; 125 (23) : 4607-4616.
PMID 9806910
 
A distinctive pediatric renal neoplasm characterized by epithelioid morphology, basement membrane production, focal HMB45 immunoreactivity, and t(6;11)(p21.1;q12) chromosome translocation.
Argani P, Hawkins A, Griffin CA, Goldstein JD, Haas M, Beckwith JB, Mankinen CB, Perlman EJ
The American journal of pathology. 2001 ; 158 (6) : 2089-2096.
PMID 11395386
 
Recent advances in pediatric renal neoplasia.
Argani P, Ladanyi M
Advances in anatomic pathology. 2003 ; 10 (5) : 243-260.
PMID 12973047
 
Distinctive neoplasms characterised by specific chromosomal translocations comprise a significant proportion of paediatric renal cell carcinomas.
Argani P, Ladanyi M
Pathology. 2003 ; 35 (6) : 492-498.
PMID 14660099
 
Cloning of an Alpha-TFEB fusion in renal tumors harboring the t(6;11)(p21;q13) chromosome translocation.
Davis IJ, Hsi BL, Arroyo JD, Vargas SO, Yeh YA, Motyckova G, Valencia P, Perez-Atayde AR, Argani P, Ladanyi M, Fletcher JA, Fisher DE
Proceedings of the National Academy of Sciences of the United States of America. 2003 ; 100 (10) : 6051-6056.
PMID 12719541
 
Upregulation of the transcription factor TFEB in t(6;11)(p21;q13)-positive renal cell carcinomas due to promoter substitution.
Kuiper RP, Schepens M, Thijssen J, van Asseldonk M, van den Berg E, Bridge J, Schuuring E, Schoenmakers EF, van Kessel AG
Human molecular genetics. 2003 ; 12 (14) : 1661-1669.
PMID 12837690
 
REVIEW articlesautomatic search in PubMed
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Contributor(s)

Written05-2004Roland P Kuiper

Citation

This paper should be referenced as such :
Kuiper RP . TFEB (transcription factor EB). Atlas Genet Cytogenet Oncol Haematol. May 2004 .
URL : http://AtlasGeneticsOncology.org/Genes/TFEBID531.html

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indexed on : Sat Feb 27 10:50:55 CET 2010

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