Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumours   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

RARA (Retinoic acid receptor, alpha)

Identity

Hugo RARA
Location 17q12
 
  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
    HugoRARA
    GDBRARA
    Entrez_GeneRARA  5914  retinoic acid receptor, alpha
    Cards
    AtlasRARAID46
    GeneCardsRARA
    EnsemblRARA [Search_View]   ENSG00000131759 [Gene_View]
    GenatlasRARA
    GeneLynxRARA
    eGenomeRARA
    euGene5914
    Genomic and cartography
    GoldenPathRARA  -  17q12   chr17:35751868-35767420 +  17q21   [Description]    (hg18-Mar_2006)
    EnsemblRARA - 17q21 [CytoView]
    NCBIMapview
    OMIMDisease map [OMIM]
    HomoloGeneRARA
    Gene and transcription
    GenbankAF012304 [ ENTREZ ]
    GenbankAK098172 [ ENTREZ ]
    GenbankAK130192 [ ENTREZ ]
    GenbankAL522713 [ ENTREZ ]
    GenbankAL834159 [ ENTREZ ]
    RefSeqNM_000964 [ SRS ]    NM_000964 [ ENTREZ ]
    RefSeqNM_001024809 [ SRS ]    NM_001024809 [ ENTREZ ]
    RefSeqNM_001033603 [ SRS ]    NM_001033603 [ ENTREZ ]
    RefSeqAC_000060 [ SRS ]    AC_000060 [ ENTREZ ]
    RefSeqNC_000017 [ SRS ]    NC_000017 [ ENTREZ ]
    RefSeqNT_010755 [ SRS ]    NT_010755 [ ENTREZ ]
    RefSeqNW_926828 [ SRS ]    NW_926828 [ ENTREZ ]
    AceViewRARA AceView - NCBI
    UnigeneHs.654583 [ SRS ]    Hs.654583 [ NCBI ]     HS654583 [ spliceNest ]
    Fast-db9825 (alternative variants)
    Protein : pattern, domain, 3D structure
    SwissProtP10276 [ SRS]    P10276 [ EXPASY ]     P10276 [ INTERPRO ]
    PrositePS00031 NUCLEAR_REC_DBD_1 [ SRS ]    PS00031 NUCLEAR_REC_DBD_1 [ Expasy ]
    PrositePS51030 NUCLEAR_REC_DBD_2 [ SRS ]    PS51030 NUCLEAR_REC_DBD_2 [ Expasy ]
    InterproIPR008946 Nucl_hormone_rcpt_ligand-bd [ SRS ]    IPR008946 Nucl_hormone_rcpt_ligand-bd [ EBI ]
    InterproIPR000536 Nucl_hrmn_rcpt_lig-bd_core [ SRS ]    IPR000536 Nucl_hrmn_rcpt_lig-bd_core [ EBI ]
    InterproIPR003078 Retinoic_acid_rcpt [ SRS ]    IPR003078 Retinoic_acid_rcpt [ EBI ]
    InterproIPR001723 Str_hrmn_rcpt [ SRS ]    IPR001723 Str_hrmn_rcpt [ EBI ]
    InterproIPR001628 Znf_hrmn_rcpt [ SRS ]    IPR001628 Znf_hrmn_rcpt [ EBI ]
    CluSTrP10276
    PfamPF00104 Hormone_recep [ SRS ]    PF00104 Hormone_recep [ Sanger ]    pfam00104 [ NCBI-CDD ]
    PfamPF00105 zf-C4 [ SRS ]    PF00105 zf-C4 [ Sanger ]    pfam00105 [ NCBI-CDD ]
    SmartSM00430 HOLI [EMBL]
    SmartSM00399 ZnF_C4 [EMBL]
    ProdomPD000035 Znf_C4steroid[INRA-Toulouse]
    ProdomP10276 RARA_HUMAN [ Domain structure ]   P10276 RARA_HUMAN  [ sequences sharing at least 1 domain ]
    BlocksP10276
    PDB1DKF [ SRS ]    1DKF [ PdbSum ],   1DKF [ IMB ]   1DKF [ RSDB ]
    PDB1DSZ [ SRS ]    1DSZ [ PdbSum ],   1DSZ [ IMB ]   1DSZ [ RSDB ]
    HPRD06769
    Protein Interaction databases
    DIPP10276
    IntActP10276
    Polymorphism : SNP, mutations, diseases
    OMIM180240    [ map ]   
    GENECLINICS180240
    SNPRARA [dbSNP-NCBI]  
    SNPNM_000964 [SNP-NCI]  
    SNPNM_001024809 [SNP-NCI]  
    SNPNM_001033603 [SNP-NCI]  
    SNPRARA [GeneSNPs - Utah]  RARA] [HGBASE - SRS]
    HAPMAPRARA [HAPMAP]  
    COSMICRARA [Somatic mutation (COSMIC-CGP-Sanger)]  
    TICdbRARA [Translocation breakpoints In Cancer]  
    HGMDRARA
    General knowledge
    Family BrowserRARA [UCSC Family Browser]
    SOURCENM_000964
    SOURCENM_001024809
    SOURCENM_001033603
    SMDHs.654583
    SAGEHs.654583
    GOtranscription factor activity [Amigo]  transcription factor activity
    GOtranscription factor activity [Amigo]  transcription factor activity
    GOsteroid hormone receptor activity [Amigo]  steroid hormone receptor activity
    GOretinoic acid receptor activity [Amigo]  retinoic acid receptor activity
    GOretinoic acid receptor activity [Amigo]  retinoic acid receptor activity
    GOtranscription coactivator activity [Amigo]  transcription coactivator activity
    GOprotein binding [Amigo]  protein binding
    GOnucleus [Amigo]  nucleus
    GOtranscription [Amigo]  transcription
    GOregulation of transcription, DNA-dependent [Amigo]  regulation of transcription, DNA-dependent
    GOsignal transduction [Amigo]  signal transduction
    GOzinc ion binding [Amigo]  zinc ion binding
    GOsequence-specific DNA binding [Amigo]  sequence-specific DNA binding
    GOmetal ion binding [Amigo]  metal ion binding
    BIOCARTATranscription Regulation by Methyltransferase of CARM1    [Genes]
    BIOCARTAMap Kinase Inactivation of SMRT Corepressor    [Genes]
    BIOCARTANuclear Receptors in Lipid Metabolism and Toxicity    [Genes]
    BIOCARTARegulation of transcriptional activity by PML    [Genes]
    BIOCARTADegradation of the RAR and RXR by the proteasome    [Genes]
    BIOCARTANuclear receptors coordinate the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription in carcinoma cells    [Genes]
    PubGeneRARA
    TreeFamRARA
    CTD5914 [Comparative ToxicoGenomics Database]
    Other databases
    Probes
    ProbeRARA (17q21) in normal cells (Bari)
    ProbeRARA Related clones (RZPD - Berlin)
    PubMed
    PubMed146 Pubmed reference(s) in LocusLink

    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
     
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

    Search in all EBI   NCBI

    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

    © Atlas of Genetics and Cytogenetics in Oncology and Haematology
    indexed on : Wed Jul 2 08:26:34 2008


    Home   Genes   Leukemias   Solid Tumours   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

    For comments and suggestions or contributions, please contact us

    j.l.huret@chu-poitiers.fr.