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    Chd4 chromodomain helicase DNA binding protein 4 [ Mus musculus (house mouse) ]

    Gene ID: 107932, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Chd4provided by MGI
    Official Full Name
    chromodomain helicase DNA binding protein 4provided by MGI
    Primary source
    MGI:MGI:1344380
    See related
    Ensembl:ENSMUSG00000063870 AllianceGenome:MGI:1344380
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Mi-2beta; mKIAA4075; D6Ertd380e; 9530019N15Rik
    Summary
    Enables DNA-binding transcription factor binding activity. Predicted to be involved in several processes, including double-strand break repair via homologous recombination; negative regulation of macromolecule biosynthetic process; and terminal button organization. Located in nucleus. Part of NuRD complex and protein-DNA complex. Is expressed in several structures, including alimentary system; branchial arch; genitourinary system; hemolymphoid system; and nervous system. Used to study left ventricular noncompaction. Human ortholog(s) of this gene implicated in Sifrim-Hitz-Weiss syndrome; colorectal cancer (multiple); lung cancer (multiple); and lymphoma. Orthologous to human CHD4 (chromodomain helicase DNA binding protein 4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 47.4), CNS E14 (RPKM 29.1) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Chd4 in Genome Data Viewer
    Location:
    6 F2; 6 59.28 cM
    Exon count:
    39
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (125073144..125107554)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (125095980..125130591)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene proacrosin binding protein Neighboring gene lysophosphatidic acid receptor 5 Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:125039823-125040010 Neighboring gene STARR-positive B cell enhancer ABC_E4864 Neighboring gene microRNA 7045 Neighboring gene predicted gene, 23751 Neighboring gene STARR-positive B cell enhancer ABC_E9675 Neighboring gene NOP2 nucleolar protein Neighboring gene intermediate filament family orphan 1 Neighboring gene STARR-seq mESC enhancer starr_17330

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. The role of the chromatin remodeler Mi-2beta in hematopoietic stem cell self-renewal and multilineage differentiation. Yoshida T, et al. Genes Dev, 2008 May 1. PMID 18451107, Free PMC Article
    2. The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain. Goodman JV, et al. Nat Commun, 2020 Jul 9. PMID 32647123, Free PMC Article
    3. Rational targeting of a NuRD subcomplex guided by comprehensive in situ mutagenesis. Sher F, et al. Nat Genet, 2019 Jul. PMID 31253978, Free PMC Article
    4. Chromatin restriction by the nucleosome remodeler Mi-2β and functional interplay with lineage-specific transcription regulators control B-cell differentiation. Yoshida T, et al. Genes Dev, 2019 Jul 1. PMID 31123064, Free PMC Article
    5. CHD4 ensures stem cell lineage fidelity during skeletal muscle regeneration. Sreenivasan K, et al. Stem Cell Reports, 2021 Sep 14. PMID 34450038, Free PMC Article

    See all (142) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Mi-2beta promotes immune evasion in melanoma by activating EZH2 methylation.
      Title: Mi-2β promotes immune evasion in melanoma by activating EZH2 methylation.
    2. The Chd4 Helicase Regulates Chromatin Accessibility and Gene Expression Critical for beta-Cell Function In Vivo.
      Title: The Chd4 Helicase Regulates Chromatin Accessibility and Gene Expression Critical for β-Cell Function In Vivo.
    3. CHD4 acts as a critical regulator in the survival of spermatogonial stem cells in micedagger.
      Title: CHD4 acts as a critical regulator in the survival of spermatogonial stem cells in mice†.
    4. Interplay between the Chd4/NuRD Complex and the Transcription Factor Znf219 Controls Cardiac Cell Identity.
      Title: Interplay between the Chd4/NuRD Complex and the Transcription Factor Znf219 Controls Cardiac Cell Identity.
    5. CHD4 ensures stem cell lineage fidelity during skeletal muscle regeneration.
      Title: CHD4 ensures stem cell lineage fidelity during skeletal muscle regeneration.
    6. A regulatory role for CHD4 in maintenance of the spermatogonial stem cell pool.
      Title: A regulatory role for CHD4 in maintenance of the spermatogonial stem cell pool.
    7. The NuRD chromatin-remodeling complex enzyme CHD4 prevents hypoxia-induced endothelial Ripk3 transcription and murine embryonic vascular rupture.
      Title: The NuRD chromatin-remodeling complex enzyme CHD4 prevents hypoxia-induced endothelial Ripk3 transcription and murine embryonic vascular rupture.
    8. Chd4 choreographs self-antigen expression for central immune tolerance.
      Title: Chd4 choreographs self-antigen expression for central immune tolerance.
    9. The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain.
      Title: The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain.
    10. CHD4 is essential for early B cell development. Loss of CHD4 in mature B cells impairs class switch recombination. CHD4 represses p53 expression to promote B cell proliferation.
      Title: Distinct Requirements of CHD4 during B Cell Development and Antibody Response.
    Submit: New GeneRIF Correction See all GeneRIFs (36)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA4075, MGC11769

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATP hydrolysis activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ATP hydrolysis activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables ATP-dependent H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent chromatin remodeler activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATP-dependent chromatin remodeler activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ATP-dependent chromatin remodeler activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA clamp loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables RNA polymerase II-specific DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables double-stranded DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables forked DNA-dependent helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables four-way junction helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone deacetylase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables single-stranded 3'-5' DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription coregulator binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription corepressor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA duplex unwinding IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin looping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in double-strand break repair via homologous recombination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA-templated transcription NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of cell fate specification NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of stem cell differentiation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of synapse assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in terminal button organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of NuRD complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of NuRD complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of NuRD complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of NuRD complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of RNA polymerase II transcription regulator complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in centrosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in centrosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cerebellar granule cell to Purkinje cell synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in chromosome, telomeric region ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of protein-DNA complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in site of DNA damage ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    chromodomain-helicase-DNA-binding protein 4
    Names
    CHD-4
    Mi-2 beta
    NP_001333539.1
    NP_001390521.1
    NP_001390522.1
    NP_001390523.1
    NP_001390524.1
    NP_001390525.1
    NP_001390526.1
    NP_001390527.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001346610.2 → NP_001333539.1  chromodomain-helicase-DNA-binding protein 4 isoform g

      Status: VALIDATED

      Source sequence(s)
      AC134529, AC166162
      Consensus CDS
      CCDS20543.1
      UniProtKB/Swiss-Prot
      Q6PDQ2
      UniProtKB/TrEMBL
      Q5DTP7
      Related
      ENSMUSP00000060054.9, ENSMUST00000056889.15

    2. NM_001403592.1 → NP_001390521.1  chromodomain-helicase-DNA-binding protein 4 isoform a

      Status: VALIDATED

      Source sequence(s)
      AC134529, AC166162
      UniProtKB/TrEMBL
      E9QAS5
      Related
      ENSMUSP00000108009.2, ENSMUST00000112390.8

    3. NM_001403593.1 → NP_001390522.1  chromodomain-helicase-DNA-binding protein 4 isoform b

      Status: VALIDATED

      Source sequence(s)
      AC134529, AC166162

    4. NM_001403594.1 → NP_001390523.1  chromodomain-helicase-DNA-binding protein 4 isoform c

      Status: VALIDATED

      Source sequence(s)
      AC134529, AC166162

    5. NM_001403595.1 → NP_001390524.1  chromodomain-helicase-DNA-binding protein 4 isoform d

      Status: VALIDATED

      Source sequence(s)
      AC134529, AC166162

    6. NM_001403596.1 → NP_001390525.1  chromodomain-helicase-DNA-binding protein 4 isoform e

      Status: VALIDATED

      Source sequence(s)
      AC134529, AC166162

    7. NM_001403597.1 → NP_001390526.1  chromodomain-helicase-DNA-binding protein 4 isoform f

      Status: VALIDATED

      Source sequence(s)
      AC134529, AC166162
      UniProtKB/TrEMBL
      E9QAS4
      Related
      ENSMUSP00000108011.2, ENSMUST00000112392.8

    8. NM_001403598.1 → NP_001390527.1  chromodomain-helicase-DNA-binding protein 4 isoform g

      Status: VALIDATED

      Source sequence(s)
      AC134529, AC166162
      UniProtKB/Swiss-Prot
      Q6PDQ2

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000072.7 Reference GRCm39 C57BL/6J

      Range
      125073144..125107554
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6PDQ2.1 GenPept UniProtKB/Swiss-Prot:Q6PDQ2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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