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CHD4 - Wikipedia

From Wikipedia, the free encyclopedia

CHD4

Available structures

PDB

Ortholog search: PDBe RCSB

List of PDB id codes
1MM2, 1MM3, 2EE1, 2L5U, 2L75, 4O9I, 2N5N

Identifiers

Aliases

CHD4, CHD-4, Mi-2b, Mi2-BETA, chromodomain helicase DNA binding protein 4, SIHIWES

External IDs

OMIM: 603277; MGI: 1344380; HomoloGene: 68175; GeneCards: CHD4; OMA:CHD4 - orthologs

Gene location (Human)

Chr.	Chromosome 12 (human)^[1]

Band	12p13.31	Start	6,570,082 bp^[1]
Band	12p13.31	End	6,614,524 bp^[1]

Gene location (Mouse)

Chr.	Chromosome 6 (mouse)^[2]

Band	6 F2\|6 59.28 cM	Start	125,072,944 bp^[2]
Band	6 F2\|6 59.28 cM	End	125,107,554 bp^[2]

RNA expression pattern

Bgee

Human

Mouse (ortholog)

Top expressed in

ventricular zone

ganglionic eminence

epithelium of colon

right lobe of thyroid gland

anterior pituitary

sural nerve

apex of heart

right adrenal cortex

left lobe of thyroid gland

right coronary artery

Top expressed in

Ileal epithelium

Rostral migratory stream

choroid plexus of fourth ventricle

tail of embryo

genital tubercle

entorhinal cortex

perirhinal cortex

neural layer of retina

ventricular zone

yolk sac

More reference expression data

BioGPS


More reference expression data

Gene ontology
Molecular function	RNA polymerase II cis-regulatory region sequence-specific DNA binding DNA binding nucleotide binding helicase activity DNA helicase activity transcription factor binding metal ion binding protein binding nucleosomal DNA binding hydrolase activity ATP binding histone deacetylase activity histone deacetylase binding zinc ion binding
Cellular component	cytoplasm NuRD complex centrosome membrane nucleoplasm microtubule organizing center protein-DNA complex cytoskeleton nucleus protein-containing complex
Biological process	regulation of transcription, DNA-templated regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II transcription, DNA-templated terminal button organization histone deacetylation DNA duplex unwinding regulation of signal transduction by p53 class mediator chromatin organization
Sources:Amigo / QuickGO

Orthologs

Species

Human

Mouse

Entrez


1108


107932

Ensembl


ENSG00000111642


ENSMUSG00000063870

UniProt


Q14839


Q6PDQ2

RefSeq (mRNA)


NM_001273 NM_001297553 NM_001363606


NM_145979 NM_001346610

RefSeq (protein)


NP_001264 NP_001284482 NP_001350535

NP_001333539 NP_666091 NP_001390521 NP_001390522 NP_001390523
NP_001390524 NP_001390525 NP_001390526 NP_001390527

Location (UCSC)

Chr 12: 6.57 – 6.61 Mb

Chr 6: 125.07 – 125.11 Mb

PubMed search

^[3]

^[4]

Wikidata

View/Edit Human

View/Edit Mouse

Chromodomain-helicase-DNA-binding protein 4 is an enzyme that in humans is encoded by the CHD4 gene.^[5]^[6]^[7] CHD4 is the core nucleosome-remodelling component of the Nucleosome Remodelling and Deacetylase (NuRD) complex.^[8]^[9]^[10]

Function

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.^[7]

Interactions

CHD4 has been shown to interact with HDAC1,^[11]^[12]^[13] Histone deacetylase 2,^[13]^[14]^[15] MTA2,^[11] SATB1^[16] and Ataxia telangiectasia and Rad3 related.^[15]

Clinical

Mutations in this gene have been associated with a condition known as Sifrim-Hitz-Weiss syndrome.^[17] This condition is characterized by

Brain anomalies
Macrocephaly
Deafness
Ophthalmic abnormalities
Dysmorphic features
Congenital heart defects
Hypogonadism in males
Skeletal and limb anomalies
Global developmental delay
Mild to moderate intellectual disability

References

^ ^a ^b ^c GRCh38: Ensembl release 89: ENSG00000111642 – Ensembl, May 2017
^ ^a ^b ^c GRCm38: Ensembl release 89: ENSMUSG00000063870 – Ensembl, May 2017
^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
^ Seelig HP, Moosbrugger I, Ehrfeld H, Fink T, Renz M, Genth E (October 1995). "The major dermatomyositis-specific Mi-2 autoantigen is a presumed helicase involved in transcriptional activation". Arthritis and Rheumatism. 38 (10): 1389–1399. doi:10.1002/art.1780381006. PMID 7575689.
^ Seelig HP, Renz M, Targoff IN, Ge Q, Frank MB (October 1996). "Two forms of the major antigenic protein of the dermatomyositis-specific Mi-2 autoantigen". Arthritis and Rheumatism. 39 (10): 1769–1771. doi:10.1002/art.1780391029. PMID 8843877.
^ ^a ^b "Entrez Gene: CHD4 chromodomain helicase DNA binding protein 4".
^ Tong JK, Hassig CA, Schnitzler GR, Kingston RE, Schreiber SL (October 1998). "Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex". Nature. 395 (6705): 917–921. Bibcode:1998Natur.395..917T. doi:10.1038/27699. PMID 9804427. S2CID 4355885.
^ Xue Y, Wong J, Moreno GT, Young MK, Côté J, Wang W (December 1998). "NURD, a novel complex with both ATP-dependent chromatin-remodeling and histone deacetylase activities". Molecular Cell. 2 (6): 851–861. doi:10.1016/S1097-2765(00)80299-3. PMID 9885572.
^ Zhang Y, LeRoy G, Seelig HP, Lane WS, Reinberg D (October 1998). "The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities". Cell. 95 (2): 279–289. doi:10.1016/S0092-8674(00)81758-4. PMID 9790534.
^ ^a ^b Yao YL, Yang WM (October 2003). "The metastasis-associated proteins 1 and 2 form distinct protein complexes with histone deacetylase activity". The Journal of Biological Chemistry. 278 (43): 42560–42568. doi:10.1074/jbc.M302955200. PMID 12920132.
^ Grozinger CM, Hassig CA, Schreiber SL (April 1999). "Three proteins define a class of human histone deacetylases related to yeast Hda1p". Proceedings of the National Academy of Sciences of the United States of America. 96 (9): 4868–4873. Bibcode:1999PNAS...96.4868G. doi:10.1073/pnas.96.9.4868. PMC 21783. PMID 10220385.
^ ^a ^b Tong JK, Hassig CA, Schnitzler GR, Kingston RE, Schreiber SL (October 1998). "Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex". Nature. 395 (6705): 917–921. Bibcode:1998Natur.395..917T. doi:10.1038/27699. PMID 9804427. S2CID 4355885.
^ Hakimi MA, Dong Y, Lane WS, Speicher DW, Shiekhattar R (February 2003). "A candidate X-linked mental retardation gene is a component of a new family of histone deacetylase-containing complexes". The Journal of Biological Chemistry. 278 (9): 7234–7239. doi:10.1074/jbc.M208992200. PMID 12493763.
^ ^a ^b Schmidt DR, Schreiber SL (November 1999). "Molecular association between ATR and two components of the nucleosome remodeling and deacetylating complex, HDAC2 and CHD4". Biochemistry. 38 (44): 14711–14717. CiteSeerX 10.1.1.559.7745. doi:10.1021/bi991614n. PMID 10545197.
^ Yasui D, Miyano M, Cai S, Varga-Weisz P, Kohwi-Shigematsu T (October 2002). "SATB1 targets chromatin remodelling to regulate genes over long distances". Nature. 419 (6907): 641–645. Bibcode:2002Natur.419..641Y. doi:10.1038/nature01084. PMID 12374985. S2CID 25822700.
^ Weiss K, Lazar HP, Kurolap A, Martinez AF, Paperna T, Cohen L, Smeland MF, Wallen S, Solveig H, Keren B, Terhal P, Irving M, Takaku M, Roberts JD, Petrovich RM, Schrier Vergano SA11,12, Kenney A11, Hove H13, DeChene E, Quinonez SC, Colin E, Ziegler A, Rumple M, Jain M, Monteil D, Roeder ER, Nugent K, van Haeringen A, Gambello M, Santani A, Medne L, Krock B, Skraban CM, Zackai EH, Dubbs HA, Smol T, Ghoumid J, Parker M, Wright M, Turnpenny P, Clayton-Smith J, Metcalfe K, Kurumizaka H, Gelb BD, Baris Feldman H, Campeau PM34, Muenke M5, Wade PA, Lachlan K (2019) The CHD4-related syndrome: a comprehensive investigation of the clinical spectrum, genotype-phenotype correlations, and molecular basis. Genet Med

External links

Human CHD4 genome location and CHD4 gene details page in the UCSC Genome Browser.

Denslow SA, Wade PA (August 2007). "The human Mi-2/NuRD complex and gene regulation". Oncogene. 26 (37): 5433–5438. doi:10.1038/sj.onc.1210611. PMID 17694084. S2CID 26445975.
Ge Q, Nilasena DS, O'Brien CA, Frank MB, Targoff IN (October 1995). "Molecular analysis of a major antigenic region of the 240-kD protein of Mi-2 autoantigen". The Journal of Clinical Investigation. 96 (4): 1730–1737. doi:10.1172/JCI118218. PMC 185809. PMID 7560064.
Woodage T, Basrai MA, Baxevanis AD, Hieter P, Collins FS (October 1997). "Characterization of the CHD family of proteins". Proceedings of the National Academy of Sciences of the United States of America. 94 (21): 11472–11477. Bibcode:1997PNAS...9411472W. doi:10.1073/pnas.94.21.11472. PMC 23509. PMID 9326634.
Zhang Y, LeRoy G, Seelig HP, Lane WS, Reinberg D (October 1998). "The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities". Cell. 95 (2): 279–289. doi:10.1016/S0092-8674(00)81758-4. PMID 9790534. S2CID 18786866.
Tong JK, Hassig CA, Schnitzler GR, Kingston RE, Schreiber SL (October 1998). "Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex". Nature. 395 (6705): 917–921. Bibcode:1998Natur.395..917T. doi:10.1038/27699. PMID 9804427. S2CID 4355885.
Zhang Y, Ng HH, Erdjument-Bromage H, Tempst P, Bird A, Reinberg D (August 1999). "Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation". Genes & Development. 13 (15): 1924–1935. doi:10.1101/gad.13.15.1924. PMC 316920. PMID 10444591.
Schmidt DR, Schreiber SL (November 1999). "Molecular association between ATR and two components of the nucleosome remodeling and deacetylating complex, HDAC2 and CHD4". Biochemistry. 38 (44): 14711–14717. CiteSeerX 10.1.1.559.7745. doi:10.1021/bi991614n. PMID 10545197.
Humphrey GW, Wang Y, Russanova VR, Hirai T, Qin J, Nakatani Y, Howard BH (March 2001). "Stable histone deacetylase complexes distinguished by the presence of SANT domain proteins CoREST/kiaa0071 and Mta-L1". The Journal of Biological Chemistry. 276 (9): 6817–6824. doi:10.1074/jbc.M007372200. PMID 11102443.
Andersen JS, Lyon CE, Fox AH, Leung AK, Lam YW, Steen H, et al. (January 2002). "Directed proteomic analysis of the human nucleolus". Current Biology. 12 (1): 1–11. Bibcode:2002CBio...12....1A. doi:10.1016/S0960-9822(01)00650-9. PMID 11790298. S2CID 14132033.
Koipally J, Georgopoulos K (August 2002). "A molecular dissection of the repression circuitry of Ikaros". The Journal of Biological Chemistry. 277 (31): 27697–27705. doi:10.1074/jbc.M201694200. PMID 12015313.
Saito M, Ishikawa F (September 2002). "The mCpG-binding domain of human MBD3 does not bind to mCpG but interacts with NuRD/Mi2 components HDAC1 and MTA2". The Journal of Biological Chemistry. 277 (38): 35434–35439. doi:10.1074/jbc.M203455200. PMID 12124384.
Hakimi MA, Dong Y, Lane WS, Speicher DW, Shiekhattar R (February 2003). "A candidate X-linked mental retardation gene is a component of a new family of histone deacetylase-containing complexes". The Journal of Biological Chemistry. 278 (9): 7234–7239. doi:10.1074/jbc.M208992200. PMID 12493763.
Kwan AH, Gell DA, Verger A, Crossley M, Matthews JM, Mackay JP (July 2003). "Engineering a protein scaffold from a PHD finger". Structure. 11 (7): 803–813. doi:10.1016/S0969-2126(03)00122-9. PMID 12842043.
Shimono Y, Murakami H, Kawai K, Wade PA, Shimokata K, Takahashi M (December 2003). "Mi-2 beta associates with BRG1 and RET finger protein at the distinct regions with transcriptional activating and repressing abilities". The Journal of Biological Chemistry. 278 (51): 51638–51645. doi:10.1074/jbc.M309198200. PMID 14530259.
Williams CJ, Naito T, Arco PG, Seavitt JR, Cashman SM, De Souza B, et al. (June 2004). "The chromatin remodeler Mi-2beta is required for CD4 expression and T cell development". Immunity. 20 (6): 719–733. doi:10.1016/j.immuni.2004.05.005. PMID 15189737.
Lehner B, Sanderson CM (July 2004). "A protein interaction framework for human mRNA degradation". Genome Research. 14 (7): 1315–1323. doi:10.1101/gr.2122004. PMC 442147. PMID 15231747.

v t e PDB gallery
1mm2: Solution structure of the 2nd PHD domain from Mi2b

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