Human Gene CHD4 (ENST00000544040.7) from GENCODE V39
  Description: Homo sapiens chromodomain helicase DNA binding protein 4 (CHD4), transcript variant 1, mRNA. (from RefSeq NM_001273)
RefSeq Summary (NM_001273): 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].
Gencode Transcript: ENST00000544040.7
Gencode Gene: ENSG00000111642.16
Transcript (Including UTRs)
   Position: hg38 chr12:6,570,082-6,607,379 Size: 37,298 Total Exon Count: 40 Strand: -
Coding Region
   Position: hg38 chr12:6,570,676-6,606,373 Size: 35,698 Coding Exon Count: 39 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2022-01-17 08:30:34

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:6,570,082-6,607,379)mRNA (may differ from genome)Protein (1912 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
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HGNCLynxMGIneXtProtOMIMPubMed
ReactomeUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CHD4_HUMAN
DESCRIPTION: RecName: Full=Chromodomain-helicase-DNA-binding protein 4; Short=CHD-4; EC=3.6.4.12; AltName: Full=ATP-dependent helicase CHD4; AltName: Full=Mi-2 autoantigen 218 kDa protein; AltName: Full=Mi2-beta;
FUNCTION: Component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Central component of the nucleosome remodeling and histone deacetylase (NuRD) repressor complex. Interacts directly with IKFZ1 in the NuRD complex. Interacts with TRIM27. Part of a complex containing ATR and HDAC2. Interacts with KLF1; the interaction depends on sumoylation of KLF1, and leads to its transcriptional repression (By similarity). Interacts with ZGPAT; the interaction is direct. Interacts with PCNT.
INTERACTION: P01106:MYC; NbExp=2; IntAct=EBI-372916, EBI-447544;
SUBCELLULAR LOCATION: Nucleus. Cytoplasm, cytoskeleton, centrosome. Note=Associates with centrosomes in interphase.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
MISCELLANEOUS: One of the main antigens reacting with anti-MI-2 positive sera of dermatomyositis.
SIMILARITY: Belongs to the SNF2/RAD54 helicase family.
SIMILARITY: Contains 2 chromo domains.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.
SIMILARITY: Contains 2 PHD-type zinc fingers.

-  MalaCards Disease Associations
  MalaCards Gene Search: CHD4
Diseases sorted by gene-association score: sifrim-hitz-weiss syndrome* (1231), dermatomyositis (30), cellular schwannoma (8)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 56.03 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1572.87 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -94.20158-0.596 Picture PostScript Text
3' UTR -191.10594-0.322 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012957 - CHD_C2
IPR012958 - CHD_N
IPR023780 - Chromo_domain
IPR000953 - Chromo_domain/shadow
IPR016197 - Chromodomain-like
IPR002464 - DNA/RNA_helicase_DEAH_CS
IPR009462 - DUF1086
IPR009463 - DUF1087
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR000330 - SNF2_N
IPR019786 - Zinc_finger_PHD-type_CS
IPR011011 - Znf_FYVE_PHD
IPR001965 - Znf_PHD
IPR019787 - Znf_PHD-finger
IPR001841 - Znf_RING
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF08074 - CHDCT2 (NUC038) domain
PF08073 - CHDNT (NUC034) domain
PF00385 - Chromo (CHRromatin Organisation MOdifier) domain
PF06461 - Domain of Unknown Function (DUF1086)
PF06465 - Domain of Unknown Function (DUF1087)
PF00271 - Helicase conserved C-terminal domain
PF00628 - PHD-finger
PF00176 - SNF2 family N-terminal domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1MM2 - NMR MuPIT 1MM3 - NMR MuPIT 2EE1 - NMR MuPIT 2L5U - NMR MuPIT 2L75 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q14839
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0001103 RNA polymerase II repressing transcription factor binding
GO:0003677 DNA binding
GO:0004003 ATP-dependent DNA helicase activity
GO:0004386 helicase activity
GO:0004407 histone deacetylase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0042826 histone deacetylase binding
GO:0046872 metal ion binding
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding
GO:0031492 nucleosomal DNA binding

Biological Process:
GO:0006325 chromatin organization
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0016575 histone deacetylation
GO:0032508 DNA duplex unwinding
GO:0043044 ATP-dependent chromatin remodeling

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005815 microtubule organizing center
GO:0005856 cytoskeleton
GO:0016020 membrane
GO:0016581 NuRD complex
GO:0032991 macromolecular complex


-  Descriptions from all associated GenBank mRNAs
  BC038596 - Homo sapiens chromodomain helicase DNA binding protein 4, mRNA (cDNA clone MGC:46187 IMAGE:5528023), complete cds.
AK128741 - Homo sapiens cDNA FLJ16830 fis, clone UTERU3022536, highly similar to Chromodomain helicase-DNA-binding protein 4 (EC 3.6.1.-).
CR936680 - Homo sapiens mRNA; cDNA DKFZp686E06161 (from clone DKFZp686E06161).
X86691 - H.sapiens mRNA for 218kD Mi-2 protein.
JD437607 - Sequence 418631 from Patent EP1572962.
JD219395 - Sequence 200419 from Patent EP1572962.
DL491697 - Novel nucleic acids.
DL490279 - Novel nucleic acids.
JD499009 - Sequence 480033 from Patent EP1572962.
JD541765 - Sequence 522789 from Patent EP1572962.
JD444568 - Sequence 425592 from Patent EP1572962.
JD461413 - Sequence 442437 from Patent EP1572962.
JD255015 - Sequence 236039 from Patent EP1572962.
JD481985 - Sequence 463009 from Patent EP1572962.
JD534960 - Sequence 515984 from Patent EP1572962.
JD528766 - Sequence 509790 from Patent EP1572962.
JD295915 - Sequence 276939 from Patent EP1572962.
JD495495 - Sequence 476519 from Patent EP1572962.
JD103467 - Sequence 84491 from Patent EP1572962.
EU446505 - Synthetic construct Homo sapiens clone IMAGE:100070329; IMAGE:100011714; FLH262823.01L chromodomain helicase DNA binding protein 4 (CHD4) gene, encodes complete protein.
JD025246 - Sequence 6270 from Patent EP1572962.
JD035267 - Sequence 16291 from Patent EP1572962.
BC014964 - Homo sapiens chromodomain helicase DNA binding protein 4, mRNA (cDNA clone IMAGE:4907274), partial cds.
BC025962 - Homo sapiens chromodomain helicase DNA binding protein 4, mRNA (cDNA clone IMAGE:5018055), partial cds.
DQ584145 - Homo sapiens piRNA piR-51257, complete sequence.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q14839 (Reactome details) participates in the following event(s):

R-HSA-427404 Recruitment of ERCC6 (CSB), EHMT2 (G9a), and NuRD to the promoter of rRNA gene
R-HSA-8943780 SALL4 recruits NuRD to PTEN gene
R-HSA-6805650 MTA2-NuRD complex deacetylates TP53
R-HSA-427336 TTF1:rRNA promoter:ERCC6:EHMT2 complex dimethylates histone H3 at lysine-9.
R-HSA-3769447 HDAC1/2 containing-complexes deacetylate histones
R-HSA-427389 ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression
R-HSA-8943724 Regulation of PTEN gene transcription
R-HSA-5250913 Positive epigenetic regulation of rRNA expression
R-HSA-6807070 PTEN Regulation
R-HSA-6804758 Regulation of TP53 Activity through Acetylation
R-HSA-3214815 HDACs deacetylate histones
R-HSA-212165 Epigenetic regulation of gene expression
R-HSA-1257604 PIP3 activates AKT signaling
R-HSA-5633007 Regulation of TP53 Activity
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-74160 Gene expression (Transcription)
R-HSA-9006925 Intracellular signaling by second messengers
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-4839726 Chromatin organization
R-HSA-162582 Signal Transduction
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription

-  Other Names for This Gene
  Alternate Gene Symbols: CHD4_HUMAN, ENST00000544040.1, ENST00000544040.2, ENST00000544040.3, ENST00000544040.4, ENST00000544040.5, ENST00000544040.6, NM_001273, Q14839, Q8IXZ5, uc001qpo.1, uc001qpo.2, uc001qpo.3, uc001qpo.4, uc001qpo.5, uc001qpo.6
UCSC ID: ENST00000544040.7
RefSeq Accession: NM_001273
Protein: Q14839 (aka CHD4_HUMAN)
CCDS: CCDS8552.1, CCDS76510.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CHD4:
chd4-ndd (CHD4 Neurodevelopmental Disorder)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.