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

Summary

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: mouse all
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Genomic context

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_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
FOXM1 and CHD4 expression is associated with chemoresistance in hepatoblastoma.
Title: FOXM1 and CHD4 expression is associated with chemoresistance in hepatoblastoma.
CHD4 and SMYD1 repress common transcriptional programs in the developing heart.
Title: CHD4 and SMYD1 repress common transcriptional programs in the developing heart.
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.
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.
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.
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.
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.
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	Compare labs

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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-17749 (e-PCR)
- UniSTS:23809

RH48433 (e-PCR)
- UniSTS:34590

RH125 (e-PCR)
- UniSTS:82479

SHGC-78606 (e-PCR)
- UniSTS:101711

G41277 (e-PCR)
- UniSTS:52316

MARC_17871-17872:1025017089:1 (e-PCR)
- UniSTS:268430

D12S925 (e-PCR)
- UniSTS:149925

RH48724 (e-PCR)
- UniSTS:76743

RH64827 (e-PCR)
- UniSTS:78038

D12S1958 (e-PCR)
- UniSTS:47586

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 more info	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 more info	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 more info	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 more info	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 more info	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

EC 3.6.4.12

NP_001284482.1

EC 3.6.4.12

NP_001350535.1

EC 3.6.4.12

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

NG_052823.1 RefSeqGene

Range

5061..42358

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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