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CHD4 chromodomain helicase DNA binding protein 4 [ Homo sapiens (human) ]

Gene ID: 1108, updated on 3-Nov-2024

Summary

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Official Symbol
CHD4provided by HGNC
Official Full Name
chromodomain helicase DNA binding protein 4provided by HGNC
Primary source
HGNC:HGNC:1919
See related
Ensembl:ENSG00000111642 MIM:603277; AllianceGenome:HGNC:1919
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CHD-4; Mi-2b; SIHIWES; Mi2-BETA
Summary
The product of this gene belongs to the SNF2/RAD54 helicase family. It represents the main component of the nucleosome remodeling and deacetylase complex and plays an important role in epigenetic transcriptional repression. Patients with dermatomyositis develop antibodies against this protein. Somatic mutations in this gene are associated with serous endometrial tumors. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2014]
Expression
Ubiquitous expression in thyroid (RPKM 37.2), endometrium (RPKM 27.5) and 25 other tissues See more
Orthologs
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Genomic context

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See CHD4 in Genome Data Viewer
Location:
12p13.31
Exon count:
40
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (6570082..6607379, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (6580442..6617741, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (6679248..6716545, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5866 Neighboring gene intermediate filament family orphan 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6658582-6659082 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6659083-6659583 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6660263-6660762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6661035-6661552 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6663184-6663684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6663685-6664185 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4169 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4170 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4171 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:6677307-6677928 Neighboring gene NOP2 nucleolar protein Neighboring gene Sharpr-MPRA regulatory region 3501 Neighboring gene small Cajal body-specific RNA 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6705357-6705858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6705859-6706358 Neighboring gene uncharacterized LOC124902867 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5868 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4172 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4173 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5869 Neighboring gene CRISPRi-validated cis-regulatory element chr12.325 Neighboring gene uncharacterized LOC105369631 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6729027-6729548 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:6729549-6730069 Neighboring gene lysophosphatidic acid receptor 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5871 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4176 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:6756019-6756532 Neighboring gene acrosin binding protein

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Predicting Response to Histone Deacetylase Inhibitors Using High-Throughput Genomics. Geeleher P, et al. J Natl Cancer Inst, 2015 Nov. PMID 26296641, Free PMC Article
  2. Is Prenatal Diagnosis Necessary for Fetal Isolated Nasal Bone Absence or Hypoplasia? Zhang F, et al. Int J Gen Med, 2021. PMID 34408481, Free PMC Article
  3. CHD4 variants are associated with childhood idiopathic epilepsy with sinus arrhythmia. Liu XR, et al. CNS Neurosci Ther, 2021 Oct. PMID 34109749, Free PMC Article
  4. [Clinical and genetic analysis of a novel CHD4 gene variant in a Chinese patient with Sifrim-Hitz-Weiss syndrome]. Zhou X, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2021 Jan 10. PMID 33423261
  5. CHD4 Predicts Aggressiveness in PTC Patients and Promotes Cancer Stemness and EMT in PTC Cells. Pratheeshkumar P, et al. Int J Mol Sci, 2021 Jan 6. PMID 33419089, Free PMC Article

See all (356) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. NEAT1 promotes genome stability via m[6]A methylation-dependent regulation of CHD4.
    Title: NEAT1 promotes genome stability via m(6)A methylation-dependent regulation of CHD4.
  2. CHD4 R975H mutant activates tumorigenic pathways and promotes stemness and M2-like macrophage polarization in endometrial cancer.
    Title: CHD4 R975H mutant activates tumorigenic pathways and promotes stemness and M2-like macrophage polarization in endometrial cancer.
  3. FOXM1 and CHD4 expression is associated with chemoresistance in hepatoblastoma.
    Title: FOXM1 and CHD4 expression is associated with chemoresistance in hepatoblastoma.
  4. CHD4 and SMYD1 repress common transcriptional programs in the developing heart.
    Title: CHD4 and SMYD1 repress common transcriptional programs in the developing heart.
  5. Genomic transcription factor binding site selection is edited by the chromatin remodeling factor CHD4.
    Title: Genomic transcription factor binding site selection is edited by the chromatin remodeling factor CHD4.
  6. Fbxw7 suppresses carcinogenesis and stemness in triple-negative breast cancer through CHD4 degradation and Wnt/beta-catenin pathway inhibition.
    Title: Fbxw7 suppresses carcinogenesis and stemness in triple-negative breast cancer through CHD4 degradation and Wnt/β-catenin pathway inhibition.
  7. The Chromatin Remodeler CHD4 Sustains Ewing Sarcoma Cell Survival by Controlling Global Chromatin Architecture.
    Title: The Chromatin Remodeler CHD4 Sustains Ewing Sarcoma Cell Survival by Controlling Global Chromatin Architecture.
  8. Evidence of a synthetic lethality interaction between SETDB1 histone methyltransferase and CHD4 chromatin remodeling protein in a triple negative breast cancer cell line.
    Title: Evidence of a synthetic lethality interaction between SETDB1 histone methyltransferase and CHD4 chromatin remodeling protein in a triple negative breast cancer cell line.
  9. 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.
  10. Dermatomyositis autoantigen CHD4 forms immune stimulatory complexes with endogenous DNA.
    Title: Dermatomyositis autoantigen CHD4 forms immune stimulatory complexes with endogenous DNA.
Submit: New GeneRIF Correction See all GeneRIFs (69)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Sifrim-Hitz-Weiss syndrome
MedGen: C4310688 OMIM: 617159 GeneReviews: CHD4 Neurodevelopmental Disorder
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Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2022-11-30)

ClinGen Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated 2022-11-30)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
A genome-wide association study provides evidence for association of chromosome 8p23 (MYP10) and 10q21.1 (MYP15) with high myopia in the French Population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

  • DKFZp686E06161

Gene Ontology Provided by GOA

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 IDA
Inferred from Direct Assay
more info
 PubMed 
enables ATP-dependent chromatin remodeler activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ATP-dependent chromatin remodeler activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II-specific DNA-binding transcription factor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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 IPI
Inferred from Physical Interaction
more info
 PubMed 
contributes_to nucleosomal DNA binding HDA PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription coregulator binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transcription corepressor activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion binding TAS
Traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin remodeling HDA PubMed 
involved_in chromatin remodeling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chromatin remodeling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in double-strand break repair via homologous recombination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation of gene expression IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of gene expression IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
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 IEA
Inferred from Electronic Annotation
more info
  
involved_in terminal button organization IEA
Inferred from Electronic Annotation
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 NAS
Non-traceable Author Statement
more info
 PubMed 
part_of RNA polymerase II transcription regulator complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cerebellar granule cell to Purkinje cell synapse IEA
Inferred from Electronic Annotation
more info
  
located_in chromatin HDA PubMed 
located_in chromatin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in chromosome, telomeric region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane HDA PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
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 
part_of protein-containing complex HDA PubMed 
located_in site of DNA damage IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
chromodomain-helicase-DNA-binding protein 4
Names
ATP-dependent helicase CHD4
Mi-2 autoantigen 218 kDa protein
NP_001264.2
NP_001284482.1
NP_001350535.1

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.

Genomic

  1. NG_052823.1 RefSeqGene

    Range
    5061..42358
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001273.5 → NP_001264.2  chromodomain-helicase-DNA-binding protein 4 isoform 1

    See identical proteins and their annotated locations for NP_001264.2

    Status: REVIEWED

    Source sequence(s)
    AC006064, BC038596, BP234473, X86691
    Consensus CDS
    CCDS8552.1
    UniProtKB/Swiss-Prot
    Q14839, Q8IXZ5
    UniProtKB/TrEMBL
    A0A2R8Y212
    Related
    ENSP00000440542.2, ENST00000544040.7
    Conserved Domains (12) summary
    smart00298
    Location:622 → 676
    CHROMO; Chromatin organization modifier domain
    cd00024
    Location:540 → 577
    CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
    cd00046
    Location:746 → 904
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd15531
    Location:372 → 414
    PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    cd15532
    Location:451 → 493
    PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    pfam00176
    Location:729 → 1025
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:1068 → 1164
    Helicase_C; Helicase conserved C-terminal domain
    pfam06461
    Location:1385 → 1521
    DUF1086; Domain of Unknown Function (DUF1086)
    pfam06465
    Location:1302 → 1352
    DUF1087; Domain of Unknown Function (DUF1087)
    pfam06614
    Location:1517 → 1649
    Neuromodulin; Neuromodulin
    pfam08073
    Location:164 → 216
    CHDNT; CHDNT (NUC034) domain
    pfam08074
    Location:1726 → 1896
    CHDCT2; CHDCT2 (NUC038) domain

  2. NM_001297553.2 → NP_001284482.1  chromodomain-helicase-DNA-binding protein 4 isoform 2

    See identical proteins and their annotated locations for NP_001284482.1

    Status: REVIEWED

    Source sequence(s)
    AC006064, BC038596, CR936680, X86691
    Consensus CDS
    CCDS76510.1
    UniProtKB/TrEMBL
    A0A2R8YFD8, F5GWX5
    Related
    ENSP00000496163.1, ENST00000645022.1
    Conserved Domains (12) summary
    smart00298
    Location:615 → 669
    CHROMO; Chromatin organization modifier domain
    cd00024
    Location:533 → 570
    CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
    cd00046
    Location:739 → 897
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd15531
    Location:365 → 407
    PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    cd15532
    Location:444 → 486
    PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    pfam00176
    Location:722 → 1018
    SNF2_N; SNF2 family N-terminal domain
    pfam00271
    Location:1061 → 1157
    Helicase_C; Helicase conserved C-terminal domain
    pfam06461
    Location:1378 → 1514
    DUF1086; Domain of Unknown Function (DUF1086)
    pfam06465
    Location:1295 → 1345
    DUF1087; Domain of Unknown Function (DUF1087)
    pfam06614
    Location:1510 → 1642
    Neuromodulin; Neuromodulin
    pfam08073
    Location:157 → 209
    CHDNT; CHDNT (NUC034) domain
    pfam08074
    Location:1719 → 1889
    CHDCT2; CHDCT2 (NUC038) domain

  3. NM_001363606.2 → NP_001350535.1  chromodomain-helicase-DNA-binding protein 4 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC006064
    Consensus CDS
    CCDS86267.1
    UniProtKB/TrEMBL
    A0A2R8YFK9, A0A2U3TZM0
    Related
    ENSP00000349508.3, ENST00000357008.7
    Conserved Domains (10) summary
    smart00298
    Location:609 → 663
    CHROMO; Chromatin organization modifier domain
    cd00024
    Location:527 → 564
    CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...
    cd15531
    Location:359 → 401
    PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    cd15532
    Location:438 → 480
    PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
    pfam06461
    Location:1372 → 1508
    DUF1086; Domain of Unknown Function (DUF1086)
    pfam06465
    Location:1289 → 1339
    DUF1087; Domain of Unknown Function (DUF1087)
    pfam08073
    Location:164 → 217
    CHDNT; CHDNT (NUC034) domain
    pfam08074
    Location:1715 → 1886
    CHDCT2; CHDCT2 (NUC038) domain
    cl25758
    Location:1498 → 1633
    DUF4775; Domain of unknown function (DUF4775)
    cl26465
    Location:711 → 1268
    SNF2_N; SNF2 family N-terminal domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    6570082..6607379 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    6580442..6617741 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q14839.2 GenPept UniProtKB/Swiss-Prot:Q14839

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