CHD3

CHD3
Identifiers
Aliases	CHD3 , Mi-2a, Mi2-ALPHA, ZFH, chromodomain helicase DNA binding protein 3, SNIBCPS
External IDs	OMIM: 602120 MGI: 1344395 HomoloGene: 62693 GeneCards: CHD3
Gene location (Human)
Chr.	Chromosome 17 (human)
End	7,912,760 bp
Gene location (Mouse)
Chr.	Chromosome 11 (mouse)
End	69,260,232 bp
RNA expression pattern
	Top expressed in
	ganglionic eminence; ; right uterine tube; ; canal of the cervix; ; sural nerve; ; gastric mucosa; ; left uterine tube; ; anterior pituitary; ; right lobe of thyroid gland; ; left lobe of thyroid gland; ; stromal cell of endometrium;
	Top expressed in
	hand; ; external carotid artery; ; internal carotid artery; ; subiculum; ; superior frontal gyrus; ; hippocampus proper; ; superior colliculus; ; ganglionic eminence; ; piriform cortex; ; molar;
	More reference expression data
	; ;
	More reference expression data
Gene ontology
Molecular function	metal ion binding ; nucleotide binding ; DNA helicase activity ; helicase activity ; hydrolase activity ; ATP binding ; protein binding ; DNA binding ; histone deacetylase activity ; RNA binding ; zinc ion binding ; ATPase activity ; double-stranded DNA helicase activity ;
Cellular component	nucleolus ; nucleoplasm ; cytoplasm ; nucleus ; NuRD complex ; centrosome ; cytoskeleton ; microtubule organizing center ;
Biological process	transcription, DNA-templated ; spindle organization ; regulation of transcription by RNA polymerase II ; regulation of transcription, DNA-templated ; chromatin organization ; histone deacetylation ; DNA duplex unwinding ; regulation of signal transduction by p53 class mediator ; centrosome cycle ;
	Sources:Amigo / QuickGO
Orthologs
	1107
	216848
	ENSG00000170004
	ENSMUSG00000018474
	Q12873
	n/a
	NM_001005271 ; NM_001005273 ; NM_005852 ; NM_001272
	NM_146019
	NP_001005271 ; NP_001005273 ; NP_005843
	n/a
	Wikidata
View/Edit Human	View/Edit Mouse

Last updated October 14, 2022

Chromodomain-helicase-DNA-binding protein 3 is an enzyme that in humans is encoded by the CHD3 gene.^[5]^[6]^[7]

Function

This gene encodes a member of the CHD family of proteins which are characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. This protein is one of the components of a histone deacetylase complex referred to as the Mi-2/NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromatin remodeling is essential for many processes including transcription. Autoantibodies against this protein are found in a subset of patients with dermatomyositis. Three alternatively spliced transcripts encoding different isoforms have been described.^[7]

Mutations in CHD3 cause a neurodevelopmental syndrome (Snijders Blok-Campeau syndrome) with macrocephaly and impaired speech and language.^[8]

Interactions

CHD3 has been shown to interact with:

HDAC1,^[9]^[10]
Histone deacetylase 2 ^[9]^[11]^[12] and
SERBP1.^[13]^[14]

Related Research Articles

<span class="mw-page-title-main">Histone deacetylase</span> Class of enzymes important in regulating DNA transcription

Histone deacetylases (EC 3.5.1.98, HDAC) are a class of enzymes that remove acetyl groups (O=C-CH₃) from an ε-N-acetyl lysine amino acid on a histone, allowing the histones to wrap the DNA more tightly. This is important because DNA is wrapped around histones, and DNA expression is regulated by acetylation and de-acetylation. Its action is opposite to that of histone acetyltransferase. HDAC proteins are now also called lysine deacetylases (KDAC), to describe their function rather than their target, which also includes non-histone proteins.

Histone acetylation and deacetylation are the processes by which the lysine residues within the N-terminal tail protruding from the histone core of the nucleosome are acetylated and deacetylated as part of gene regulation.

Chromatin remodeling is the dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression. Such remodeling is principally carried out by 1) covalent histone modifications by specific enzymes, e.g., histone acetyltransferases (HATs), deacetylases, methyltransferases, and kinases, and 2) ATP-dependent chromatin remodeling complexes which either move, eject or restructure nucleosomes. Besides actively regulating gene expression, dynamic remodeling of chromatin imparts an epigenetic regulatory role in several key biological processes, egg cells DNA replication and repair; apoptosis; chromosome segregation as well as development and pluripotency. Aberrations in chromatin remodeling proteins are found to be associated with human diseases, including cancer. Targeting chromatin remodeling pathways is currently evolving as a major therapeutic strategy in the treatment of several cancers.

Histone deacetylase 2 (HDAC2) is an enzyme that in humans is encoded by the HDAC2 gene. It belongs to the histone deacetylase class of enzymes responsible for the removal of acetyl groups from lysine residues at the N-terminal region of the core histones. As such, it plays an important role in gene expression by facilitating the formation of transcription repressor complexes and for this reason is often considered an important target for cancer therapy.

Paired amphipathic helix protein Sin3a is a protein that in humans is encoded by the SIN3A gene.

Histone-binding protein RBBP4 is a protein that in humans is encoded by the RBBP4 gene.

Methyl-CpG-binding domain protein 2 is a protein that in humans is encoded by the MBD2 gene.

Histone-binding protein RBBP7 is a protein that in humans is encoded by the RBBP7 gene.

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 is a protein that in humans is encoded by the SMARCA5 gene.

Methyl-CpG-binding domain protein 3 is a protein that in humans is encoded by the MBD3 gene.

Sin3A-associated protein, 30kDa, also known as SAP30, is a protein which in humans is encoded by the SAP30 gene.

Chromodomain-helicase-DNA-binding protein 4 is an enzyme that in humans is encoded by the CHD4 gene.

Metastasis-associated protein MTA2 is a protein that in humans is encoded by the MTA2 gene.

The Chromodomain-Helicase DNA-binding 1 is a protein that, in humans, is encoded by the CHD1 gene. CHD1 is a chromatin remodeling protein that is widely conserved across many eukaryotic organisms, from yeast to humans. CHD1 is named for three of its protein domains: two tandem chromodomains, its ATPase catalytic domain, and its DNA-binding domain.

Chromodomain-helicase-DNA-binding protein 8 is an enzyme that in humans is encoded by the CHD8 gene.

In the field of molecular biology, the Mi-2/NuRDcomplex, is a group of associated proteins with both ATP-dependent chromatin remodeling and histone deacetylase activities. As of 2007, Mi-2/NuRD was the only known protein complex that couples chromatin remodeling ATPase and chromatin deacetylation enzymatic functions.

H4K8ac, representing an epigenetic modification to the DNA packaging protein histone H4, is a mark indicating the acetylation at the 8th lysine residue of the histone H4 protein. It has been implicated in the prevalence of malaria.

H3K23ac is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the acetylation at the 23rd lysine residue of the histone H3 protein.

H3K56ac is an epigenetic modification to the DNA packaging protein Histone H3. It is a mark that indicates the acetylation at the 56th lysine residue of the histone H3 protein.

Chromodomain helicase DNA-binding (CHD) proteins is a subfamily of ATP-dependent chromatin remodeling complexes (remodelers). All remodelers fall under the umbrella of RNA/DNA helicase superfamily 2. In yeast, CHD complexes are primarily responsible for nucleosome assembly and organization. These complexes play an additional role in multicellular eukaryotes, assisting in chromatin access and nucleosome editing.

References

1 2 3 GRCh38: Ensembl release 89: ENSG00000170004 - Ensembl, May 2017
1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000018474 - 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.
↑ Woodage T, Basrai MA, Baxevanis AD, Hieter P, Collins FS (Oct 1997). "Characterization of the CHD family of proteins". Proceedings of the National Academy of Sciences of the United States of America. 94 (21): 11472–7. Bibcode:1997PNAS...9411472W. doi: 10.1073/pnas.94.21.11472 . PMC 23509 . PMID 9326634.
↑ Ge Q, Nilasena DS, O'Brien CA, Frank MB, Targoff IN (Oct 1995). "Molecular analysis of a major antigenic region of the 240-kD protein of Mi-2 autoantigen". The Journal of Clinical Investigation. 96 (4): 1730–7. doi:10.1172/JCI118218. PMC 185809 . PMID 7560064.
1 2 "Entrez Gene: CHD3 chromodomain helicase DNA binding protein 3".
↑ Snijders Blok L, Rousseau J, Twist J, Ehresmann S, Takaku M, Venselaar H, et al. (November 2018). "CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language". Nature Communications. 9 (1): 4619. Bibcode:2018NatCo...9.4619S. doi:10.1038/s41467-018-06014-6. PMC 6218476 . PMID 30397230.
1 2 Tong JK, Hassig CA, Schnitzler GR, Kingston RE, Schreiber SL (Oct 1998). "Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex". Nature. 395 (6705): 917–21. Bibcode:1998Natur.395..917T. doi:10.1038/27699. PMID 9804427. S2CID 4355885.
↑ Kuzmichev A, Zhang Y, Erdjument-Bromage H, Tempst P, Reinberg D (Feb 2002). "Role of the Sin3-histone deacetylase complex in growth regulation by the candidate tumor suppressor p33(ING1)". Molecular and Cellular Biology. 22 (3): 835–48. doi:10.1128/mcb.22.3.835-848.2002. PMC 133546 . PMID 11784859.
↑ Hakimi MA, Dong Y, Lane WS, Speicher DW, Shiekhattar R (Feb 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): 7234–9. doi: 10.1074/jbc.M208992200 . PMID 12493763.
↑ Hakimi MA, Bochar DA, Schmiesing JA, Dong Y, Barak OG, Speicher DW, Yokomori K, Shiekhattar R (Aug 2002). "A chromatin remodelling complex that loads cohesin onto human chromosomes". Nature. 418 (6901): 994–8. Bibcode:2002Natur.418..994H. doi:10.1038/nature01024. PMID 12198550. S2CID 4344470.
↑ Lemos TA, Passos DO, Nery FC, Kobarg J (Jan 2003). "Characterization of a new family of proteins that interact with the C-terminal region of the chromatin-remodeling factor CHD-3". FEBS Letters. 533 (1–3): 14–20. doi: 10.1016/s0014-5793(02)03737-7 . PMID 12505151. S2CID 41197943.
↑ Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, Toksöz E, Droege A, Krobitsch S, Korn B, Birchmeier W, Lehrach H, Wanker EE (Sep 2005). "A human protein-protein interaction network: a resource for annotating the proteome". Cell. 122 (6): 957–68. doi:10.1016/j.cell.2005.08.029. hdl: 11858/00-001M-0000-0010-8592-0 . PMID 16169070. S2CID 8235923.

External links

Human CHD3 genome location and CHD3 gene details page in the UCSC Genome Browser .

Bowen NJ, Fujita N, Kajita M, Wade PA (Mar 2004). "Mi-2/NuRD: multiple complexes for many purposes". Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 1677 (1–3): 52–7. doi:10.1016/j.bbaexp.2003.10.010. PMID 15020045.
Gieser L, Swaroop A (Jul 1992). "Expressed sequence tags and chromosomal localization of cDNA clones from a subtracted retinal pigment epithelium library" (PDF). Genomics. 13 (3): 873–6. doi:10.1016/0888-7543(92)90173-P. hdl: 2027.42/29973 . PMID 1639417.
Seelig HP, Moosbrugger I, Ehrfeld H, Fink T, Renz M, Genth E (Oct 1995). "The major dermatomyositis-specific Mi-2 autoantigen is a presumed helicase involved in transcriptional activation". Arthritis and Rheumatism. 38 (10): 1389–99. doi:10.1002/art.1780381006. PMID 7575689.
Seelig HP, Renz M, Targoff IN, Ge Q, Frank MB (Oct 1996). "Two forms of the major antigenic protein of the dermatomyositis-specific Mi-2 autoantigen". Arthritis and Rheumatism. 39 (10): 1769–71. doi: 10.1002/art.1780391029 . PMID 8843877.
Bonaldo MF, Lennon G, Soares MB (Sep 1996). "Normalization and subtraction: two approaches to facilitate gene discovery". Genome Research. 6 (9): 791–806. doi: 10.1101/gr.6.9.791 . PMID 8889548.
Aubry F, Mattéi MG, Galibert F (Jun 1998). "Identification of a human 17p-located cDNA encoding a protein of the Snf2-like helicase family". European Journal of Biochemistry. 254 (3): 558–64. doi: 10.1046/j.1432-1327.1998.2540558.x . PMID 9688266.
Tong JK, Hassig CA, Schnitzler GR, Kingston RE, Schreiber SL (Oct 1998). "Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex". Nature. 395 (6705): 917–21. Bibcode:1998Natur.395..917T. doi:10.1038/27699. PMID 9804427. S2CID 4355885.
Kleiderlein JJ, Nisson PE, Jessee J, Li WB, Becker KG, Derby ML, Ross CA, Margolis RL (Dec 1998). "CCG repeats in cDNAs from human brain". Human Genetics. 103 (6): 666–73. doi:10.1007/s004390050889. PMID 9921901. S2CID 23696667.
Kim J, Sif S, Jones B, Jackson A, Koipally J, Heller E, Winandy S, Viel A, Sawyer A, Ikeda T, Kingston R, Georgopoulos K (Mar 1999). "Ikaros DNA-binding proteins direct formation of chromatin remodeling complexes in lymphocytes". Immunity. 10 (3): 345–55. doi: 10.1016/S1074-7613(00)80034-5 . PMID 10204490.
Wade PA, Gegonne A, Jones PL, Ballestar E, Aubry F, Wolffe AP (Sep 1999). "Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation". Nature Genetics. 23 (1): 62–6. doi:10.1038/12664. PMID 10471500. S2CID 52868103.
Cousin P, Billotte J, Chaubert P, Shaw P (Jan 2000). "Physical map of 17p13 and the genes adjacent to p53". Genomics. 63 (1): 60–8. doi:10.1006/geno.1999.6062. PMID 10662545.
Minty A, Dumont X, Kaghad M, Caput D (Nov 2000). "Covalent modification of p73alpha by SUMO-1. Two-hybrid screening with p73 identifies novel SUMO-1-interacting proteins and a SUMO-1 interaction motif". The Journal of Biological Chemistry. 275 (46): 36316–23. doi: 10.1074/jbc.M004293200 . PMID 10961991.
Schultz DC, Friedman JR, Rauscher FJ (Feb 2001). "Targeting histone deacetylase complexes via KRAB-zinc finger proteins: the PHD and bromodomains of KAP-1 form a cooperative unit that recruits a novel isoform of the Mi-2alpha subunit of NuRD". Genes & Development. 15 (4): 428–43. doi:10.1101/gad.869501. PMC 312636 . PMID 11230151.
Yasui D, Miyano M, Cai S, Varga-Weisz P, Kohwi-Shigematsu T (Oct 2002). "SATB1 targets chromatin remodelling to regulate genes over long distances". Nature. 419 (6907): 641–5. Bibcode:2002Natur.419..641Y. doi:10.1038/nature01084. PMID 12374985. S2CID 25822700.
Lemos TA, Passos DO, Nery FC, Kobarg J (Jan 2003). "Characterization of a new family of proteins that interact with the C-terminal region of the chromatin-remodeling factor CHD-3". FEBS Letters. 533 (1–3): 14–20. doi: 10.1016/S0014-5793(02)03737-7 . PMID 12505151. S2CID 41197943.
Fujita N, Jaye DL, Kajita M, Geigerman C, Moreno CS, Wade PA (Apr 2003). "MTA3, a Mi-2/NuRD complex subunit, regulates an invasive growth pathway in breast cancer". Cell. 113 (2): 207–19. doi: 10.1016/S0092-8674(03)00234-4 . PMID 12705869. S2CID 5773916.
Lee BH, Yoshimatsu K, Maeda A, Ochiai K, Morimatsu M, Araki K, Ogino M, Morikawa S, Arikawa J (Dec 2003). "Association of the nucleocapsid protein of the Seoul and Hantaan hantaviruses with small ubiquitin-like modifier-1-related molecules". Virus Research. 98 (1): 83–91. doi:10.1016/j.virusres.2003.09.001. PMID 14609633.

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[refGRCh38Ensembl-1] 1 2 3 GRCh38: Ensembl release 89: ENSG00000170004 - Ensembl, May 2017

[refGRCm38Ensembl-2] 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000018474 - Ensembl, May 2017

[3] "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.

[4] "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.

[pmid9326634-5] Woodage T, Basrai MA, Baxevanis AD, Hieter P, Collins FS (Oct 1997). "Characterization of the CHD family of proteins". Proceedings of the National Academy of Sciences of the United States of America. 94 (21): 11472–7. Bibcode:1997PNAS...9411472W. doi: 10.1073/pnas.94.21.11472 . PMC 23509 . PMID 9326634.

[pmid7560064-6] Ge Q, Nilasena DS, O'Brien CA, Frank MB, Targoff IN (Oct 1995). "Molecular analysis of a major antigenic region of the 240-kD protein of Mi-2 autoantigen". The Journal of Clinical Investigation. 96 (4): 1730–7. doi:10.1172/JCI118218. PMC 185809 . PMID 7560064.

[entrez-7] 1 2 "Entrez Gene: CHD3 chromodomain helicase DNA binding protein 3".

[8] Snijders Blok L, Rousseau J, Twist J, Ehresmann S, Takaku M, Venselaar H, et al. (November 2018). "CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language". Nature Communications. 9 (1): 4619. Bibcode:2018NatCo...9.4619S. doi:10.1038/s41467-018-06014-6. PMC 6218476 . PMID 30397230.

[pmid9804427-9] 1 2 Tong JK, Hassig CA, Schnitzler GR, Kingston RE, Schreiber SL (Oct 1998). "Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex". Nature. 395 (6705): 917–21. Bibcode:1998Natur.395..917T. doi:10.1038/27699. PMID 9804427. S2CID 4355885.

[pmid11784859-10] Kuzmichev A, Zhang Y, Erdjument-Bromage H, Tempst P, Reinberg D (Feb 2002). "Role of the Sin3-histone deacetylase complex in growth regulation by the candidate tumor suppressor p33(ING1)". Molecular and Cellular Biology. 22 (3): 835–48. doi:10.1128/mcb.22.3.835-848.2002. PMC 133546 . PMID 11784859.

[pmid12493763-11] Hakimi MA, Dong Y, Lane WS, Speicher DW, Shiekhattar R (Feb 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): 7234–9. doi: 10.1074/jbc.M208992200 . PMID 12493763.

[pmid12198550-12] Hakimi MA, Bochar DA, Schmiesing JA, Dong Y, Barak OG, Speicher DW, Yokomori K, Shiekhattar R (Aug 2002). "A chromatin remodelling complex that loads cohesin onto human chromosomes". Nature. 418 (6901): 994–8. Bibcode:2002Natur.418..994H. doi:10.1038/nature01024. PMID 12198550. S2CID 4344470.

[pmid12505151-13] Lemos TA, Passos DO, Nery FC, Kobarg J (Jan 2003). "Characterization of a new family of proteins that interact with the C-terminal region of the chromatin-remodeling factor CHD-3". FEBS Letters. 533 (1–3): 14–20. doi: 10.1016/s0014-5793(02)03737-7 . PMID 12505151. S2CID 41197943.

[pmid16169070-14] Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, Goehler H, Stroedicke M, Zenkner M, Schoenherr A, Koeppen S, Timm J, Mintzlaff S, Abraham C, Bock N, Kietzmann S, Goedde A, Toksöz E, Droege A, Krobitsch S, Korn B, Birchmeier W, Lehrach H, Wanker EE (Sep 2005). "A human protein-protein interaction network: a resource for annotating the proteome". Cell. 122 (6): 957–68. doi:10.1016/j.cell.2005.08.029. hdl: 11858/00-001M-0000-0010-8592-0 . PMID 16169070. S2CID 8235923.

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