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RARA (Retinoic acid receptor, alpha)

Identity

HGNC (Hugo) RARA
Location 17q12
Location_base_pair Starts at 35718972 and ends at 35767420 bp from pter ( according to hg18-Mar_2006)  [Mapping]
 
  c-RARA (17q21) in normal cells: PAC 833D9 - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics. Laboratories willing to validate the probes are wellcome: contact M Rocchi

DNA/RNA

Description 9 exons; total gene sequence: 7450 bp
Transcription 2.8 and 3.6 kb transcripts

Protein

Description 462 amino acids - 5 functional domains A/B (transcriptional regulation), C (DNA binding domain, contains 2 zinc fingers), D (cellular localization signal), E (ligand-binding domain) and F (function?)
Expression in hematopoietic cells
Localisation nuclear
Function
  • ligand-dependent transcription factor specifically involved in hematopoietic cells differentiation and maturation = receptor for all-trans retinoic acid (ATRA) and 9-cis RA which are intracellular metabolites of vitamine A, active in cellular differentiation and morphogenesis
  • after linking with ATRA, RARA binds with a high affinity as a heterodimer with RXR (retinoid X receptor protein) to the RARE domain (retinoic acid response elements), a DNA sequence common to a number of genes and located in their promoter
  • the gene response to RARA binding is modulated by a series of co-repressors and co-activators
  • Homology with RARB and RARG (retinoic acid receptors ? and ?), 9-cis RA receptors (RXRs) and receptors for thyroid and steroid hormones and for vitamine D3

    Implicated in

    Entity t(15;17)(q22;q12) / acute promyelocytic leukemia (APL) -->PML - RARA
    Disease typical APL (or M3 ANLL, FAB classification), approximately 98% of APL cases; abnormal promyelocytes with Auer rods and bundles (faggots); disruption of the PODs with a microspeckeled pattern; maturation response to all-trans retinoic acid (ATRA) therapy
    Prognosis immediate prognosis impaired by intravascular disseminated coagulopathy; long term prognosis is favorable with treatment combining ATRA plus chemotherapy
    Cytogenetics variant or complex t(15;17) translocation in 5% of cases, no known prognosis implication; secondary chromosomal abnormalities in 30 to 35% of APL at diagnosis; association with +8 in 17 to 28% of cases; other associations are rare but recurrent: del(7q), del(9q), ider(17)t(15;17), +21
    Hybrid/Mutated Gene
  • the crucial fusion transcript is 5'PML-3'RARA, encoded by der(15) chromosome; the counterpart 5'RARA-3'PML encoded by der(17) is inconstant
  • breakpoint in RARA gene is always located in intron between A and B domains
  • three breakpoint clusters in PML gene: bcr1 (70% of patients), bcr2 (10%) and bcr3 (20%), giving rise respectively to the long (L), intermediate (V) and short (S) length hybrid PML-RARAtranscripts; V form would be linked to ATRA decreased sensitivity and S form to association with an excess of secondary chromosome changes.
  • Abnormal Protein 106 Kda fusion protein; role in the leukemogenic process by probable interference with the signalling pathway leading to differentiation and maturation of myeloid precursors (mainly dysregulation of retinoid-inducible genes involved in myeloid differentiation)
      
    Entity t(11;17)(q23;q12) / acute promyelocytic leukemia -->PLZF-RARA
    Disease variant acute promyelocytic leukemia (APL) form with atypical cytologic aspects (intermediate morphology between M2 and M3, no Auer rods) and no response to ATRA therapy; less than 1% of APL cases.
      
    Entity t(5;17)(q35;q12) / acute promyelocytic leukemia --> NPM-RARA
    Disease exceptional; probable response to ATRA
      
    Entity t(11;17)(q13;q12) / acute promyelocytic leukemia --> NuMA-RARA
    Disease exceptional: probable response to ATRA
      
    Entity t(11;17)(q23;q12) / M5 acute non lymphocytic leukemia --> MLL-RARA
    Disease 1 case to date; not to be confused with the t(11;17)(q23;q12) mentioned above; not found in APL; belongs to the MLL/11q23 leukemias
      

    Breakpoints

     

    External links

    Nomenclature
    HGNC (Hugo)RARA   9864
    Entrez_Gene (NCBI)RARA  5914  retinoic acid receptor, alpha
    Cards
    AtlasRARAID46
    GeneCards (Weizmann)RARA
    Ensembl (Hinxton)ENSG00000131759 [Gene_View]  RARA [Vega]
    AceView (NCBI)RARA
    Genatlas (Paris)RARA
    euGene (Indiana)5914
    SOURCE (Stanford)NM_000964 NM_001024809 NM_001145301 NM_001145302
    Genomic and cartography
    GoldenPath (UCSC)RARA  -  17q12   chr17:35718972-35767420 +  17q21   [Description]    (hg18-Mar_2006)
    EnsemblRARA - 17q21 [CytoView]
    Mapping of homologs : NCBIRARA [Mapview]
    OMIM180240   612376   
    Gene and transcription
    Gene : Genbank (Entrez)AK098172 AK130192 AK292205 AK303868 AK312564
    Reference sequence (RefSeq transcript) :SRSNM_000964 NM_001024809 NM_001145301 NM_001145302
    Reference transcript : EntrezNM_000964 NM_001024809 NM_001145301 NM_001145302
    RefSeq genomic : SRSAC_000060 AC_000149 NC_000017 NT_010755 NW_001838435 NW_926828
    RefSeq genomic : EntrezAC_000060 AC_000149 NC_000017 NT_010755 NW_001838435 NW_926828
    Consensus coding sequences : CCDS NCBIRARA
    Cluster EST : UnigeneHs.654583 [ SRS ] Hs.654583 [ NCBI ]
    Alternative Splicing : Fast-db (Paris)9825
    Protein : pattern, domain, 3D structure
    Protein : UniProt/SwissProtP10276 (SRS) P10276 (Expasy) P10276 (Uniprot)
    With graphics : InterProP10276
    Splice isoforms : VarSplice FASTAP10276(VarSplice FASTA)
    Domaine pattern : Prosite (SRS)NUCLEAR_REC_DBD_1 (PS00031)    NUCLEAR_REC_DBD_2 (PS51030)   
    Domain pattern : Prosite (Expaxy)NUCLEAR_REC_DBD_1 (PS00031)    NUCLEAR_REC_DBD_2 (PS51030)   
    Domains : Interpro (SRS)Nucl_hormone_rcpt_ligand-bd    Nucl_hrmn_rcpt_lig-bd_core    Retinoic_acid_rcpt    Str_hrmn_rcpt    Znf_hrmn_rcpt   
    Domains : Interpro (EBI)Nucl_hormone_rcpt_ligand-bd    Nucl_hrmn_rcpt_lig-bd_core    Retinoic_acid_rcpt    Str_hrmn_rcpt    Znf_hrmn_rcpt   
    Related proteins : CluSTrP10276
    Domain families : Pfam SRSHormone_recep (PF00104)    zf-C4 (PF00105)   
    Domain families : Pfam SangerHormone_recep (PF00104)    zf-C4 (PF00105)   
    Domain families : Pfam NCBIpfam00104    pfam00105   
    Domain families : Smart EMBLHOLI (SM00430)ZnF_C4 (SM00399)
    Domain structure : Prodom (Prabi Lyon)Znf_C4steroid (PD000035)   
    Blocks (Seattle)P10276
    Crystal structure of protein : PDB SRS1DKF    1DSZ   
    Crystal structure of protein : PDBSum1DKF    1DSZ   
    Crystal structure of protein : IMB1DKF    1DSZ   
    Crystal structure of protein : PDB RSDB1DKF    1DSZ   
    HPRD06769
    Protein Interaction databases
    DIP (DOE-UCLA)P10276
    IntAct (EBI)P10276
    Polymorphism : SNP, mutations, diseases
    Single Nucleotide Polymorphism (SNP) : dbSNP NCBIRARA
    SNP : GeneSNP UtahRARA
    SNP : HGBaseRARA
    Genetic variants : HAPMAPRARA
    Somatic Mutations in Cancer : COSMICRARA 
    Translocation Breakpoints in Cancer : TICdbRARA 
    Mutations and Diseases : HGMDRARA
    Hereditary diseases : OMIM180240    612376   
    Hereditary diseases : GENETests180240    612376   
    Diseases : Genetic AssociationRARA
    General knowledge
    Homologs : HomoloGeneRARA
    Homology/Alignments : Family Browser UCSCRARA
    Phylogenetic Trees/Animal Genes : TreeFamRARA
    Chemical/Protein Interactions : CTD5914
    Keywords Ontology : AmiGOretinoic acid binding  transcription factor activity  steroid hormone receptor activity  retinoic acid receptor activity  transcription coactivator activity  protein binding  nucleus  transcription  regulation of transcription, DNA-dependent  signal transduction  zinc ion binding  cell surface  estrogen receptor signaling pathway  response to estradiol stimulus  response to retinoic acid  negative regulation of interferon-gamma production  negative regulation of tumor necrosis factor production  positive regulation of interleukin-13 production  positive regulation of interleukin-4 production  positive regulation of interleukin-5 production  sequence-specific DNA binding  positive regulation of T-helper 2 cell differentiation  metal ion binding  retinoic acid receptor signaling pathway  
    Keywords Ontology : EGO-EBIretinoic acid binding  transcription factor activity  steroid hormone receptor activity  retinoic acid receptor activity  transcription coactivator activity  protein binding  nucleus  transcription  regulation of transcription, DNA-dependent  signal transduction  zinc ion binding  cell surface  estrogen receptor signaling pathway  response to estradiol stimulus  response to retinoic acid  negative regulation of interferon-gamma production  negative regulation of tumor necrosis factor production  positive regulation of interleukin-13 production  positive regulation of interleukin-4 production  positive regulation of interleukin-5 production  sequence-specific DNA binding  positive regulation of T-helper 2 cell differentiation  metal ion binding  retinoic acid receptor signaling pathway  
    Pathways : BIOCARTATranscription Regulation by Methyltransferase of CARM1 [Genes]    Map Kinase Inactivation of SMRT Corepressor [Genes]    Nuclear Receptors in Lipid Metabolism and Toxicity [Genes]    Regulation of transcriptional activity by PML [Genes]    Degradation of the RAR and RXR by the proteasome [Genes]    Nuclear receptors coordinate the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription in carcinoma cells [Genes]   
    Pathways : KEGG
    Other databases
    Probes
    ProbeRARA (17q21) in normal cells (Bari)
    Probes : ImagenesRARA Related clones (RZPD - Berlin)
    Literature
    PubMed177 Pubmed reference(s) in Entrez
    PubGeneRARA

    Bibliography

    The t(15;17) translocation of acute promyelocytic leukaemia fuses the retinoic acid receptor alpha gene to a novel transcribed locus.
    de Thˆ© H, Chomienne C, Lanotte M, Degos L, Dejean A
    Nature. 1990 ; 347 (6293) : 558-561.
    PMID 2170850
     
    Chromosomal translocation t(15;17) in human acute promyelocytic leukemia fuses RAR alpha with a novel putative transcription factor, PML.
    Kakizuka A, Miller WH Jr, Umesono K, Warrell RP Jr, Frankel SR, Murty VV, Dmitrovsky E, Evans RM
    Cell. 1991 ; 66 (4) : 663-674.
    PMID 1652368
     
    Characterization of the PML-RAR alpha chimeric product of the acute promyelocytic leukemia-specific t(15;17) translocation.
    Nervi C, Poindexter EC, Grignani F, Pandolfi PP, Lo Coco F, Avvisati G, Pelicci PG, Jetten AM
    Cancer research. 1992 ; 52 (13) : 3687-3692.
    PMID 1319828
     
    Genetics of APL and the molecular basis of retinoic acid treatment.
    Casini T, Grignani F, Pelicci PG
    International journal of cancer. Journal international du cancer. 1997 ; 70 (4) : 473-474.
    PMID 9033658
     
    The pathogenesis of acute promyelocytic leukaemia: evaluation of the role of molecular diagnosis and monitoring in the management of the disease.
    Grimwade D
    British journal of haematology. 1999 ; 106 (3) : 591-613.
    PMID 10468848
     
    Deconstructing a disease: RARalpha, its fusion partners, and their roles in the pathogenesis of acute promyelocytic leukemia.
    Melnick A, Licht JD
    Blood. 1999 ; 93 (10) : 3167-3215.
    PMID 10233871
     
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    Contributor(s)

    Written10-2000Franck Viguié

    Citation

    This paper should be referenced as such :
    Viguié F . RARA (Retinoic acid receptor, alpha). Atlas Genet Cytogenet Oncol Haematol. October 2000 .
    URL : http://AtlasGeneticsOncology.org/Genes/RARAID46.html

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    indexed on : Sat Jun 27 16:40:45 CEST 2009

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