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FLASH GENE
Symbol CHD4 contributors: mct/shn - updated : 12-04-2015
HGNC name chromodomain helicase DNA binding protein 4
HGNC id 1919
Corresponding disease
SIHIWES Sifrim-Hitz-Weiss syndrome
Location 12p13.31      Physical location : 6.679.248 - 6.716.551
Synonym name
  • Mi-2 autoantigen 218 kDa protein
  • ATP-dependent helicase CHD4
  • Mi-2 autoantigen 218 kDa protein
  • chromodomain-helicase-DNA-binding protein 4
  • Synonym symbol(s) Mi-b, MI-2b, Mi2-BETA, MI2, CHD-4
    EC.number 3.6.4.12
    DNA
    TYPE functioning gene
    STRUCTURE 37.30 kb     39 Exon(s)
    10 Kb 5' upstream gene genomic sequence study
    MAPPING cloned Y linked N status provisional
    Map pter - D12S356 - D12S374 - CHD4 - D12S1623 - D12S1625 - cen
    Physical map
    FLJ10665 12p13.32 hypothetical protein FLJ10665 TNFRSF1A 12p13.2 tumor necrosis factor receptor superfamily, member 1A SCNN1A 12p13.3 sodium channel, nonvoltage-gated 1 alpha LTBR 12p13.31 lymphotoxin beta receptor (TNFR superfamily, member 3) LOC390283 12 hypothetical gene supported by X15940; NM_000993 LOC390284 12 similar to signal recognition particle 14kDa (homologous Alu RNA binding protein); signal recognition particle 14kD (homologous Alu RNA-binding protein); signal recognition particle 14kD (homologous Alu RNA binding protein) TNFRSF7 12p13 tumor necrosis factor receptor superfamily, member 7 TAPBP-R 12p13.31 TAP binding protein related VAMP1 12p13.31-p13.2 vesicle-associated membrane protein 1 (synaptobrevin 1) PKP2P1 12p13 vesicle-associated membrane protein 1 (synaptobrevin 1) MRPL51 12p13.3-p13.1 mitochondrial ribosomal protein L51 CNAP1 12p13.3 chromosome condensation-related SMC-associated protein 1 GAPD 12p13.31 glyceraldehyde-3-phosphate dehydrogenase HOM-TES-103 12p13.3 HOM-TES-103 tumor antigen-like NOL1 12p13.31 nucleolar protein 1, 120kDa CHD4 12p13 chromodomain helicase DNA binding protein 4 GPR92 12p13.32 G protein-coupled receptor 92 ACRBP 12p13.32 acrosin binding protein ING4 12p13.32 inhibitor of growth family, member 4 ZNF384 12p12 zinc finger protein 384 DKFZp547D2210 12p13.31 hypothetical protein DKFZp547D2210 COPS7A 12p13.32 COP9 constitutive photomorphogenic homolog subunit 7A (Arabidopsis) MLF2 12p13 myeloid leukemia factor 2 PTMS 12p13.32 parathymosin LAG3 12p13.32 lymphocyte-activation gene 3 CD4 12p13.31 CD4 antigen (p55)
    RNA
    TRANSCRIPTS type messenger
    identificationnb exonstypebpproduct
    ProteinkDaAAspecific expressionYearPubmed
    39 - 6511 218 1912 - 2007 17626165
    EXPRESSION
    Type ubiquitous
       expressed in (based on citations)
    organ(s)
    SystemOrgan level 1Organ level 2Organ level 3Organ level 4LevelPubmedSpeciesStageRna symbol
    Hearing/Equilibriumear     Mus musculus
    Nervousbrain     Mus musculus
    Urinary      Mus musculus
    Visualeye     Mus musculus
    tissue
    SystemTissueTissue level 1Tissue level 2LevelPubmedSpeciesStageRna symbol
    Nervouscentral  highly Mus musculus
    cell lineage highly expressed in thymocytes
    cell lines
    fluid/secretion
    at STAGE
    PROTEIN
    PHYSICAL PROPERTIES
    STRUCTURE
    motifs/domains
  • N-terminal tandem of PHD fingers (PHD1/2) linked by a stretch of 30 AAs, necessary for transcriptional repressive functions (PHD1 and PHD2) each contribute to the activity of CHD4, but PHD2 plays a more important role than PHD1) with tandem chromodomains in addition to centrally located ATPase/helicase domains
  • a nucleosome remodeling ATPase domain along with the two chromodomains
  • a central helicase: ATPase related SNF2 domain and a region with similarity to the Myb-DNA binding domain
  • SWI2/SNF2 ATPase/helicase domain of CHD4 is large (465 AAs) and complex, and ATPase domain with C terminus of CHD4 are necessary for the transcriptional repressive function of NuRD complexe
  • a pericentrin-binding domain
  • two domains of unknown function (DUFs)
  • C-terminal domain (CTD)
  • HOMOLOGY
    interspecies homolog to C.elegans f26f12.7
    ortholog to Chd4, Mus musculus
    ortholog to Chd4, Rattus norvegicus
    ortholog to CHD4, Pan troglodytes
    intraspecies paralog to CHD2, CHD7, CHD8
    Homologene
    FAMILY SNF2/RAD54 helicase family
    CATEGORY regulatory , DNA associated , transcription factor
    SUBCELLULAR LOCALIZATION     intracellular
    intracellular,cytoplasm,cytoskeleton,microtubule,centrosome
    intracellular,nucleus,chromatin/chromosome
    text
  • is a core component of the nucleosome remodeling and deacetylase (NuRD) complex, which possesses both chromatin remodeling and histone deacetylation activities
  • basic FUNCTION
  • involved in transcriptional repression in the nucleus, co-localize with MCRS1 in the nucleolus and appear to activate the rRNA transcription
  • required at several steps during T cell development: for differentiation of beta selected immature thymocytes, for developmental expression of CD4, and for cell divisions in mature T cells
  • novel functions for CHD4 in the DNA-damage response (DDR) and cell-cycle control
  • acts as an important regulator of the G1/S cell-cycle transition by controlling TP53 deacetylation
  • an important role of CHD4 in controlling homologous recombination repair to maintain genome stability
  • SMARCA4 and CHD4 antagonistically modulate Wnt signaling in developing yolk sac vessels to mediate normal vascular remodeling
  • ATP-dependent chromatin remodeler involved in epigenetic regulation of gene transcription, DNA repair, and cell cycle progression
  • is not only a chromatin remodeler but also a critical subunit of a multiprotein histone deacetylase complex, suggesting that alteration in chromatin modeling and histone acetylation may be the culprit
  • CELLULAR PROCESS nucleotide, chromatin organization, remodeling
    nucleotide, repair
    nucleotide, transcription, regulation
    PHYSIOLOGICAL PROCESS
    PATHWAY
    metabolism
    signaling
    a component
  • core component of the NURD complex
  • ATP dependent chromatin remodeler and a major subunit of the repressive NURD complex
  • INTERACTION
    DNA binding
    RNA
    small molecule
    protein
  • HDAC1/2
  • Ataxia telangiectasia mutated (ATM)- and Rad3-related protein, ATR
  • Ikaros
  • BRG1 and RET finger protein
  • RORgamma
  • microspherule protein1, MCRS1
  • c-MYC
  • Pericentrin
  • DJ-1
  • TWIST protein complex
  • ATM kinase
  • could bind to two H3 N-terminal tails on the same nucleosome or on two separate nucleosomes simultaneously, presenting exciting implications for the mechanism by which CHD4 and the NuRD complex could direct chromatin remodeling
  • BRD4
  • CBX1 and CBX3
  • BRIT1
  • histone binding by the CHD4 PHD1/2 fingers is required for transcriptional repressive activity of the CHD4/NURD complex, supporting the mechanism of multivalent engagement
  • CHD4/NuRD maintains demethylation state of rDNA promoters through inhibiting the expression of the rDNA methyltransferase recruiter BAZ2A
  • genes commonly regulated by both KDM5A and CHD4 were categorized as developmentally regulated genes
  • cell & other
    REGULATION
    ASSOCIATED DISORDERS
    corresponding disease(s) SIHIWES
    Susceptibility dermatomyositis
    Variant & Polymorphism
    Candidate gene
    Marker
    Therapy target
    ANIMAL & CELL MODELS
  • CHD4 deficiency impairs the recruitment of DNA repair proteins BRIT1, BRCA1, and replication protein A at early steps of homologous recombination repair
  • null Chd4 mouse embryos cannot complete the first lineage step at the blastocyst stage