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

Gene ID: 107932, updated on 11-Apr-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
Predicted to enable RNA polymerase II-specific DNA-binding transcription factor binding activity; histone deacetylase binding activity; and transcription coregulator binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II and terminal button organization. Predicted to act upstream of or within chromatin organization. Located in nucleus. Part of NuRD complex and protein-DNA complex. Is expressed in several structures, including alimentary system; branchial arch; cardiovascular system; genitourinary system; and nervous system. Orthologous to human CHD4 (chromodomain helicase DNA binding protein 4). [provided by Alliance of Genome Resources, Apr 2022]
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. CHD4 acts as a critical regulator in the survival of spermatogonial stem cells in mice†. Li P, et al. Biol Reprod, 2022 Nov 14. PMID 35980806
  2. 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
  3. 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
  4. 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
  5. 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

See all (132) 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-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 DNA binding IBA
Inferred from Biological aspect of Ancestor
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 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 hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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
acts_upstream_of_or_within chromatin organization 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 ISO
Inferred from Sequence Orthology
more info
  
is_active_in cerebellar granule cell to Purkinje cell synapse ISO
Inferred from Sequence Orthology
more info
  
part_of 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 ISO
Inferred from Sequence Orthology
more info
  
located_in cytoskeleton IEA
Inferred from Electronic Annotation
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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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.

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