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PRDM16 (PR domain containing 16)

Identity

Other namesMEL1 (MDS1/EVI1-like gene)
PR-domain zinc finger protein 16
HGNC (Hugo) PRDM16
Location 1p36.3
Location_base_pair Starts at 2975604 and ends at 3345045 bp from pter ( according to hg18-Mar_2006)  [Mapping]
Note orientation plus strand

DNA/RNA

Description spans 369 kb; 17exons; 3827 bp coding sequence.
Transcription alternative transcripts MEL1 and MEL1S (MEL1 short)

Protein

Description 17O kDa (MEL1) and 150 Da (MEL1S); like MDS1/EVI1, The MEL1contains a PR domain (homologous to the SET domain present in MLL ) in the N term, two DNA binding domains (made of 7 and 3 zing fingers) separated by a repression domain, and an acidic domain at the C-term.
MEL1S lacks the PR domain, like EVI1 alone.
MEL1 and MEL1S, in a "yin-yang fashion", are hypothezised to display antagonistic properties; the PR domain may act as an inhibitor of tumorigenesis.
Expression wide, contrarily to what was previously found
Localisation nuclear
Homology 63% homology with MDS1/EVI1; both are members of the PR domain family

Implicated in

Entity t(1;3)(p36;q21) myeloid leukemias --> involving RPN1 and MEL1
Disease myelodysplastic syndromes (MDS), acute non lymphoblastic leukemias (ANLL), therapy-related leukemias and myeloprolifrative syndromes; with features similar to those of the 3q21q26 syndrome, including megakaryocytic dysplasia (see also 3q rearrangements in myeloid malignancies).
Prognosis very poor
Hybrid/Mutated Gene juxtaposition of the enhancer of the constitutively expressed housekeeping gene RPN1, normally sitting in 3q21, in 5' of MEL1 on der(1); both genes are orientated telomere to centromere; the same situation occurs between RPN1 in 5' of EVI1 in the t(3;3)(q21;q26) )
Oncogenesis the translocation results in either an ectopic expression of MEL1 driven by RPN1or by disruption of its PR domain; this probable heterogenity may be associated with different clinical features. The short form, MEL1S, is mainly expressed
  

External links

Nomenclature
HGNC (Hugo)PRDM16   14000
Entrez_Gene (NCBI)PRDM16  63976  PR domain containing 16
Cards
AtlasPRDM16MEL1ID408
GeneCards (Weizmann)PRDM16
Ensembl (Hinxton)ENSG00000142611 [Gene_View]  PRDM16 [Vega]
AceView (NCBI)PRDM16
Genatlas (Paris)PRDM16
euGene (Indiana)63976
SOURCE (Stanford)NM_022114 NM_199454
Gene Expression (Array Express) ENSG00000142611
Genomic and cartography
GoldenPath (UCSC)PRDM16  -  1p36.3   chr1:2975604-3345045 +  1p36.23-p33   [Description]    (hg18-Mar_2006)
EnsemblPRDM16 - 1p36.23-p33 [CytoView]
Mapping of homologs : NCBIPRDM16 [Mapview]
OMIM605557   
Gene and transcription
Gene : Genbank (Entrez)AB051462 AB078876 AF294278 AI623202 AK093853
Reference sequence (RefSeq transcript) :SRSNM_022114 NM_199454
Reference transcript : EntrezNM_022114 NM_199454
RefSeq genomic : SRSAC_000044 AC_000133 NC_000001 NT_004350 NW_001838618 NW_922461
RefSeq genomic : EntrezAC_000044 AC_000133 NC_000001 NT_004350 NW_001838618 NW_922461
Consensus coding sequences : CCDS NCBIPRDM16
Cluster EST : UnigeneHs.99500 [ SRS ] Hs.99500 [ NCBI ]
Alternative Splicing : Fast-db (Paris)1649
Protein : pattern, domain, 3D structure
Protein : UniProt/SwissProtQ9HAZ2 (SRS) Q9HAZ2 (Expasy) Q9HAZ2 (Uniprot)
With graphics : InterProQ9HAZ2
Splice isoforms : VarSplice FASTAQ9HAZ2(VarSplice FASTA)
Domaine pattern : Prosite (SRS)SET (PS50280)    ZINC_FINGER_C2H2_1 (PS00028)    ZINC_FINGER_C2H2_2 (PS50157)   
Domain pattern : Prosite (Expaxy)SET (PS50280)    ZINC_FINGER_C2H2_1 (PS00028)    ZINC_FINGER_C2H2_2 (PS50157)   
Domains : Interpro (SRS)SET_dom    Znf_C2H2    Znf_C2H2-like    Znf_C2H2/integrase_DNA-bd   
Domains : Interpro (EBI)SET_dom    Znf_C2H2    Znf_C2H2-like    Znf_C2H2/integrase_DNA-bd   
Related proteins : CluSTrQ9HAZ2
Domain families : Pfam SRSzf-C2H2 (PF00096)   
Domain families : Pfam Sangerzf-C2H2 (PF00096)   
Domain families : Pfam NCBIpfam00096   
Domain families : Smart EMBLSET (SM00317)  ZnF_C2H2 (SM00355)  
Blocks (Seattle)Q9HAZ2
Crystal structure of protein : PDB SRS
Crystal structure of protein : PDBSum
Crystal structure of protein : IMB
Crystal structure of protein : PDB RSDB
HPRD16122
Protein Interaction databases
DIP (DOE-UCLA)Q9HAZ2
IntAct (EBI)Q9HAZ2
Polymorphism : SNP, mutations, diseases
Single Nucleotide Polymorphism (SNP) : dbSNP NCBIPRDM16
SNP : GeneSNP UtahPRDM16
SNP : HGBasePRDM16
Genetic variants : HAPMAPPRDM16
Cancer Gene: CensusPRDM16 
Somatic Mutations in Cancer : COSMICPRDM16 
Mutations and Diseases : HGMDPRDM16
Hereditary diseases : OMIM605557   
Hereditary diseases : GENETests605557   
Diseases : Genetic AssociationPRDM16
General knowledge
Homologs : HomoloGenePRDM16
Homology/Alignments : Family Browser UCSCPRDM16
Phylogenetic Trees/Animal Genes : TreeFamPRDM16
Chemical/Protein Interactions : CTD63976
Keywords Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  transcription coactivator activity  intracellular  nucleus  zinc ion binding  transcription repressor activity  transcriptional repressor complex  neurogenesis  cell differentiation  negative regulation of transforming growth factor beta receptor signaling pathway  negative regulation of transforming growth factor beta receptor signaling pathway  regulation of cellular respiration  sequence-specific DNA binding  regulation of transcription  SMAD binding  metal ion binding  brown fat cell differentiation  
Keywords Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  transcription coactivator activity  intracellular  nucleus  zinc ion binding  transcription repressor activity  transcriptional repressor complex  neurogenesis  cell differentiation  negative regulation of transforming growth factor beta receptor signaling pathway  negative regulation of transforming growth factor beta receptor signaling pathway  regulation of cellular respiration  sequence-specific DNA binding  regulation of transcription  SMAD binding  metal ion binding  brown fat cell differentiation  
Pathways : BIOCARTA
Pathways : KEGG
Other databases
Probes
Probes : ImagenesPRDM16 Related clones (RZPD - Berlin)
Literature
PubMed21 Pubmed reference(s) in Entrez
PubGenePRDM16

Bibliography

Fusion of the transcription factor TFE3 gene to a novel gene, PRCC, in t(X;1)(p11;q21)-positive papillary renal cell carcinomas.
Weterman MA, Wilbrink M, Geurts van Kessel A
Proceedings of the National Academy of Sciences of the United States of America. 1996 ; 93 (26) : 15294-15298.
PMID 8986805
 
A novel gene, MEL1, mapped to 1p36.3 is highly homologous to the MDS1/EVI1 gene and is transcriptionally activated in t(1;3)(p36;q21)-positive leukemia cells.
Mochizuki N, Shimizu S, Nagasawa T, Tanaka H, Taniwaki M, Yokota J, Morishita K
Blood. 2000 ; 96 (9) : 3209-3214.
PMID 11050005
 
A novel EVI1 gene family, MEL1, lacking a PR domain (MEL1S) is expressed mainly in t(1;3)(p36;q21)-positive AML and blocks G-CSF-induced myeloid differentiation.
Nishikata I, Sasaki H, Iga M, Tateno Y, Imayoshi S, Asou N, Nakamura T, Morishita K
Blood. 2003 ; 102 (9) : 3323-3332.
PMID 12816872
 
Breakpoints at 1p36.3 in three MDS/AML(M4) patients with t(1;3)(p36;q21) occur in the first intron and in the 5' region of MEL1.
Xinh PT, Tri NK, Nagao H, Nakazato H, Taketazu F, Fujisawa S, Yagasaki F, Chen YZ, Hayashi Y, Toyoda A, Hattori M, Sakaki Y, Tokunaga K, Sato Y
Genes, chromosomes & cancer. 2003 ; 36 (3) : 313-316.
PMID 12557231
 
Molecular characterization of a t(1;3)(p36;q21) in a patient with MDS. MEL1 is widely expressed in normal tissues, including bone marrow, and it is not overexpressed in the t(1;3) cells.
Lahortiga I, Agirre X, Belloni E, Vˆ°zquez I, Larrayoz MJ, Gasparini P, Lo Coco F, Pelicci PG, Calasanz MJ, Odero MD
Oncogene. 2004 ; 23 (1) : 311-316.
PMID 14712237
 
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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Contributor(s)

Written04-2004Jean-Loup Huret, Sylvie Senon

Citation

This paper should be referenced as such :
Huret JL, Senon S . PRDM16 (PR domain containing 16). Atlas Genet Cytogenet Oncol Haematol. April 2004 .
URL : http://AtlasGeneticsOncology.org/Genes/PRDM16MEL1ID408.html

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indexed on : Sat Feb 27 10:52:08 CET 2010

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