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

Summary

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; cardiovascular system; genitourinary 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, Dec 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

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_000072.7 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: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Mi-2beta promotes immune evasion in melanoma by activating EZH2 methylation.
Title: Mi-2β promotes immune evasion in melanoma by activating EZH2 methylation.
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.
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†.
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.
CHD4 ensures stem cell lineage fidelity during skeletal muscle regeneration.
Title: CHD4 ensures stem cell lineage fidelity during skeletal muscle regeneration.
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.
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.
Chd4 choreographs self-antigen expression for central immune tolerance.
Title: Chd4 choreographs self-antigen expression for central immune tolerance.
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.
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)

Endonuclease-mediated (4) 1 citation
Gene trapped (1)
Targeted (7) 1 citation

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

ha2919 (e-PCR)
- UniSTS:515610

RH124259 (e-PCR)
- UniSTS:161081

D6Ertd380e (e-PCR), detects polymorphism
- UniSTS:167483

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

BB284187 (e-PCR)
- UniSTS:208034

AA963793 (e-PCR)
- UniSTS:243386

RH64827 (e-PCR)
- UniSTS:78038

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

EC 3.6.4.12

NP_001390521.1

EC 3.6.4.12

NP_001390522.1

EC 3.6.4.12

NP_001390523.1

EC 3.6.4.12

NP_001390524.1

EC 3.6.4.12

NP_001390525.1

EC 3.6.4.12

NP_001390526.1

EC 3.6.4.12

NP_001390527.1

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.

mRNA and Protein(s)

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

Status: VALIDATED

Source sequence(s)

AC134529, AC166162

UniProtKB/TrEMBL

E9QAS5, Q5DTP7

Related

ENSMUSP00000108009.2, ENSMUST00000112390.8
NM_001403593.1 → NP_001390522.1 chromodomain-helicase-DNA-binding protein 4 isoform b

Status: VALIDATED

Source sequence(s)

AC134529, AC166162

UniProtKB/TrEMBL

Q5DTP7
NM_001403594.1 → NP_001390523.1 chromodomain-helicase-DNA-binding protein 4 isoform c

Status: VALIDATED

Source sequence(s)

AC134529, AC166162

UniProtKB/TrEMBL

Q5DTP7
NM_001403595.1 → NP_001390524.1 chromodomain-helicase-DNA-binding protein 4 isoform d

Status: VALIDATED

Source sequence(s)

AC134529, AC166162

UniProtKB/TrEMBL

Q5DTP7
NM_001403596.1 → NP_001390525.1 chromodomain-helicase-DNA-binding protein 4 isoform e

Status: VALIDATED

Source sequence(s)

AC134529, AC166162

UniProtKB/TrEMBL

Q5DTP7
NM_001403597.1 → NP_001390526.1 chromodomain-helicase-DNA-binding protein 4 isoform f

Status: VALIDATED

Source sequence(s)

AC134529, AC166162

UniProtKB/TrEMBL

E9QAS4, Q5DTP7

Related

ENSMUSP00000108011.2, ENSMUST00000112392.8
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

UniProtKB/TrEMBL

Q5DTP7