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FLASH GENE
Symbol KDM5C contributors: mct - updated : 14-02-2014
HGNC name Jumonji, AT rich interactive domain 1C (RBP2-like)
HGNC id 11114
Corresponding disease
XLMR1 X-linked mental retardation 1
Location Xp11.22      Physical location : 53.220.503 - 53.254.604
Synonym name
  • DNA segment,single copy,probe XE169
  • Smcy homolog, X-linked (mouse)
  • XE169 gene (selected mouse cDNA on X, human homolog of)
  • Synonym symbol(s) DXS1272E, XE169, SMCX, JARID1C, MRXJ, MRXSJ,
    DNA
    TYPE functioning gene
    SPECIAL FEATURE escaping inactivation
    text escaping X inactivation
    STRUCTURE 34.10 kb     26 Exon(s)
    MAPPING cloned Y linked N status confirmed
    Map pter - OATL2 - SSX2 - DXS6672E - DXS1008E - ACTGP10 - JARID1C - DXS1000 - DXS988 - SMC1A - DXS1204 - DXS1199 - DXS1013E - FGD1 FGD1 - DXS674 - ALAS2 - DXS991 - DXS1302 - KLF8 - DXS579 - DXF34S1 - DXS580 - DXS429 - MTHFD1P1 - ZXDB - DXS14 - DXS390 - ZXDA - cen
    Authors Miller (95), Consensus (95)
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    26 - 6863 - 1560 - Kim (2008)
    24 - 6097 - 1379 - -
    EXPRESSION
    Type widely
    constitutive of
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Digestivemouthtongue  highly
     stomach   highly
    Lymphoid/Immunelymph node   highly
    Nervousbrain   moderately
    Reproductivefemale systemuterus  highly
    Visualeye   moderately
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Muscularstriatumskeletal  
    cell lineage
    cell lines
    fluid/secretion
    at STAGE
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • coided coil and helix-loop-helix (HLH) domains
  • several DNA-binding motifs that link it to transcriptional regulation and chromatin remodeling
  • an ARID/BRIGHT domain,
  • a PCNA-interaction protein motif (PIP box), involved in the association of KDM5C with PCNA and its interaction with chromatin
  • a C5HC2 zinc finger domain and PHD zinc finger domains
  • a JmjC-domain involved in the demethylase activity
  • atypical insertion of a DNA-binding ARID domain and a histone-binding PHD domain into the Jumonji domain, which separates the catalytic domain into two fragments (JmjN and JmjC)
  • HOMOLOGY
    interspecies homolog to murine selected cDNA on the X,
    intraspecies homolog to JARID1A, JARID1B, JARID1D
    Homologene
    FAMILY ARID protein family
    CATEGORY regulatory , protooncogene
    SUBCELLULAR LOCALIZATION     intracellular
    intracellular,nucleus
    basic FUNCTION
  • may be playing an important role in human brain function
  • involved in transcriptional regulation and chromatin remodeling
  • possessing H3K4 tri-demethylase activity and functioning as a transcriptional repressor
  • playing a direct role in chromatin dynamics, in REST (RE-1 silencing transcription factor )-mediated repression, and REST-mediated neuronal gene regulation
  • having a enzymatic activity required for its role in brain development and functioning as a transcriptional corepressor
  • being a novel Smad3 corepressor that may antagonize the tumor suppressing activity of the TGF-beta/Smad3 signaling pathway and thereby contributing to tumorigenesis
  • essential for notochord development 33 and 44 and dendrite arborization
  • KMD5C demethylase has been shown to remove methyl AAs from lysine 4 of histone H3 (H3K4), and constitutes an important component of the regulatory element-1-silencing transcription factor (REST) protein complex
  • involved in chromatin remodeling
  • histone demethylase specific to dimethylated and trimethylated histone 3 lysine 4 (H3K4ME2 and H3K4ME3, respectively), which are involved in chromatin remodeling
  • enzymatic activity of the KDM5 family required to be the linked JmjN-JmjC domain coupled with the immediate C-terminal helical zinc-binding domain, providing structural characterization of the linked JmjN-JmjC domain for the KDM5 family
  • CELLULAR PROCESS
    PHYSIOLOGICAL PROCESS
    PATHWAY
    metabolism
    signaling
    a component
  • component of at least two distinct large protein complexes, containing E2F6 and REST respectively
  • INTERACTION
    DNA binding
    RNA
    small molecule
    protein
  • associating with the transcriptional repressor E2F6 and its partners DP1, Max and Mga6, the nuclear receptor co-repressor 1 (NCOR1), the RE-1 silencing transcription factor (REST), which represses neuronal genes in non-neuronal tissues
  • associating with HDAC1 and HDAC2, the euchromatin-associated protein HP1, the E3 ubiquitin ligases RING1 and RING2
  • interacting with SMAD3, a genuine DNA-binding transcription factor( SMAD3 transcriptional activity is repressed by JARID1C, identifying it as a novel corepressor of SMAD3)
  • VHL inactivation decreases H3K4Me3 levels through KDM5C, which alters gene expression and suppresses tumor growth
  • intracellular trafficking of KDM5C is controlled by its association with PCNA
  • directly regulated by ARX through the binding in a conserved noncoding element (ARX transactivates the 5prime KDM5C regulatory element by binding to the two “TAAT/ATTA” boxes (BD1 and BD2)
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) XLMR1
    Other morbid association(s)
    TypeGene ModificationChromosome rearrangementProtein expressionProtein Function
    tumoral     --over  
    in prostate tumors and seminomas
    constitutional     --low  
    inversely correlates with an increase in H3K4me3 signaling, potentially as a result of compromised KDM5C activity
    Susceptibility
    Variant & Polymorphism
    Candidate gene
    Marker
    Therapy target
    ANIMAL & CELL MODELS