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PHF8

From Wikipedia, the free encyclopedia
Protein-coding gene in the species Homo sapiens

PHF8
Available structures
PDBOrtholog search:PDBeRCSB
List of PDB id codes

4DO0,3K3O,2WWU,3K3N,3KV4,%%s2WWU,3K3N,3K3O,3KV4,4DO0

Identifiers
AliasesPHF8, JHDM1F, MRXSSD, ZNF422, PHD finger protein 8, KDM7B
External IDsOMIM:300560;MGI:2444341;HomoloGene:49405;GeneCards:PHF8;OMA:PHF8 - orthologs
Gene location (Human)
X chromosome (human)
Chr.X chromosome (human)[1]
X chromosome (human)
Genomic location for PHF8
Genomic location for PHF8
BandXp11.22Start53,936,676bp[1]
End54,048,958bp[1]
Gene location (Mouse)
X chromosome (mouse)
Chr.X chromosome (mouse)[2]
X chromosome (mouse)
Genomic location for PHF8
Genomic location for PHF8
BandX|X F3Start150,303,668bp[2]
End150,416,855bp[2]
RNA expression pattern
Bgee
HumanMouse (ortholog)
Top expressed in
  • right testis

  • sural nerve

  • left testis

  • testicle

  • tendon of biceps brachii

  • Achilles tendon

  • epithelium of colon

  • right lobe of liver

  • gonad

  • right uterine tube
Top expressed in
  • zygote

  • primary oocyte

  • otic vesicle

  • saccule

  • blood

  • secondary oocyte

  • otic placode

  • Gonadal ridge

  • granulocyte

  • medial ganglionic eminence
More reference expression data
BioGPS
n/a
Gene ontology
Molecular function
Cellular component
Biological process
Sources:Amigo /QuickGO
Orthologs
SpeciesHumanMouse
Entrez

23133

320595

Ensembl

ENSG00000172943

ENSMUSG00000041229

UniProt

Q9UPP1

Q80TJ7

RefSeq (mRNA)

NM_001184896
NM_001184897
NM_001184898
NM_015107

NM_001113354
NM_177201

RefSeq (protein)

NP_001171825
NP_001171826
NP_001171827
NP_055922

NP_001106825
NP_796175

Location (UCSC)Chr X: 53.94 – 54.05 MbChr X: 150.3 – 150.42 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

PHD finger protein 8 is aprotein that in humans is encoded by thePHF8gene.[5]

Function

[edit]

PHF8 belongs to the family of ferrous iron andalpha-ketoglutarate-dependent hydroxylases superfamily.,[6] and is active as ahistone lysine demethylase with selectivity for the di-and monomethyl states.[7] PHF8 induces an EMT (epithelial to mesenchymal transition)-like process by upregulating key EMT transcription factors SNAI1 and ZEB1.

Regulation during differentiation

[edit]

PHF8 was found to be expressional increased during endothelial differentiation and significantly decreased during cardial differentiation of murine embryonic stem cells.[8]

Clinical significance

[edit]

Mutations in PHF8 cause Siderius typeX-linked intellectual disability (XLMR) (OMIM:300263).[9][10][11] In addition to moderateintellectual disability, features of the Siderius-Hamel syndrome include facial dysmorphism,cleft lip and/or cleft palate, and in some casesmicrocephaly.[12][13][14] A chromosomalmicrodeletion on Xp11.22 encompassing all of thePHF8 andFAM120C genes and a part of theWNK3 gene was reported in two brothers withautism spectrum disorder in addition to Siderius-type XLMR andcleft lip and palate.[15]

This catalytic activity is disrupted by clinically known mutations toPHF8, which were found to cluster in its catalytic JmjC domain. The F279S mutation of PHF8, found in 2 Finnish brothers with mildintellectual disability, facialdysmorphism andcleft lip/palate,[14] was found to additionally preventnuclear localisation of PHF8 overexpressed in human cells.[7]

The catalytic activity of PHF8 depends on molecularoxygen,[7] a fact considered important with respect to reports on increased incidence ofcleft lip/palate in mice that have been exposed tohypoxia duringpregnancy.[16] In humans,fetal cleft lip and othercongenital abnormalities have also been linked to maternal hypoxia, as caused by e.g.maternal smoking,[17] heavy maternalalcohol use, or maternalhypertension treatment.[18]

References

[edit]
  1. ^abcGRCh38: Ensembl release 89: ENSG00000172943Ensembl, May 2017
  2. ^abcGRCm38: Ensembl release 89: ENSMUSG00000041229Ensembl, 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.
  5. ^"Entrez Gene: PHF8 PHD finger protein 8".
  6. ^Loenarz C, Schofield CJ (Mar 2008). "Expanding chemical biology of 2-oxoglutarate oxygenases".Nature Chemical Biology.4 (3):152–6.doi:10.1038/nchembio0308-152.PMID 18277970.
  7. ^abcLoenarz C, Ge W, Coleman ML, Rose NR, Cooper CD, Klose RJ, et al. (Jan 2010)."PHF8, a gene associated with cleft lip/palate and mental retardation, encodes for an Nepsilon-dimethyl lysine demethylase".Human Molecular Genetics.19 (2):217–22.doi:10.1093/hmg/ddp480.PMC 4673897.PMID 19843542.
  8. ^Boeckel JN, Derlet A, Glaser SF, Luczak A, Lucas T, Heumüller AW, et al. (July 2016)."JMJD8 Regulates Angiogenic Sprouting and Cellular Metabolism by Interacting With Pyruvate Kinase M2 in Endothelial Cells".Arteriosclerosis, Thrombosis, and Vascular Biology.36 (7):1425–1433.doi:10.1161/ATVBAHA.116.307695.PMID 27199445.
  9. ^Siderius LE, Hamel BC, van Bokhoven H, de Jager F, van den Helm B, Kremer H, et al. (Jul 1999)."X-linked mental retardation associated with cleft lip/palate maps to Xp11.3-q21.3".American Journal of Medical Genetics.85 (3):216–20.doi:10.1002/(SICI)1096-8628(19990730)85:3<216::AID-AJMG6>3.0.CO;2-X.PMID 10398231.
  10. ^"OMIM: Siderius X-linked mental retardation syndrome". Retrieved2009-10-21.
  11. ^"OMIM: PHD finger protein 8; PHF8". Retrieved2009-10-21.
  12. ^Abidi F, Miano M, Murray J, Schwartz C (Jul 2007)."A novel mutation in the PHF8 gene is associated with X-linked mental retardation with cleft lip/cleft palate".Clinical Genetics.72 (1):19–22.doi:10.1111/j.1399-0004.2007.00817.x.PMC 2570350.PMID 17594395.
  13. ^Laumonnier F, Holbert S, Ronce N, Faravelli F, Lenzner S, Schwartz CE, et al. (Oct 2005)."Mutations in PHF8 are associated with X linked mental retardation and cleft lip/cleft palate".Journal of Medical Genetics.42 (10):780–6.doi:10.1136/jmg.2004.029439.PMC 1735927.PMID 16199551.
  14. ^abKoivisto AM, Ala-Mello S, Lemmelä S, Komu HA, Rautio J, Järvelä I (Aug 2007). "Screening of mutations in the PHF8 gene and identification of a novel mutation in a Finnish family with XLMR and cleft lip/cleft palate".Clinical Genetics.72 (2):145–9.doi:10.1111/j.1399-0004.2007.00836.x.PMID 17661819.S2CID 23326755.
  15. ^Qiao Y, Liu X, Harvard C, Hildebrand MJ, Rajcan-Separovic E, Holden JJ, et al. (Aug 2008). "Autism-associated familial microdeletion of Xp11.22".Clinical Genetics.74 (2):134–44.doi:10.1111/j.1399-0004.2008.01028.x.PMID 18498374.S2CID 22008997.
  16. ^Millicovsky G, Johnston MC (Sep 1981)."Hyperoxia and hypoxia in pregnancy: simple experimental manipulation alters the incidence of cleft lip and palate in CL/Fr mice".Proceedings of the National Academy of Sciences of the United States of America.78 (9):5722–3.Bibcode:1981PNAS...78.5722M.doi:10.1073/pnas.78.9.5722.PMC 348841.PMID 6946511.
  17. ^Shi M, Wehby GL, Murray JC (Mar 2008)."Review on genetic variants and maternal smoking in the etiology of oral clefts and other birth defects".Birth Defects Research. Part C, Embryo Today.84 (1):16–29.doi:10.1002/bdrc.20117.PMC 2570345.PMID 18383123.
  18. ^Hurst JA, Houlston RS, Roberts A, Gould SJ, Tingey WG (Oct 1995). "Transverse limb deficiency, facial clefting and hypoxic renal damage: an association with treatment of maternal hypertension?".Clinical Dysmorphology.4 (4):359–63.doi:10.1097/00019605-199510000-00013.PMID 8574428.S2CID 6330050.

External links

[edit]

This article incorporates text from theUnited States National Library of Medicine, which is in thepublic domain.

(1) Basic domains
(1.1) Basicleucine zipper (bZIP)
(1.2) Basic helix-loop-helix (bHLH)
Group A
Group B
Group C
bHLH-PAS
Group D
Group E
Group F
bHLH-COE
(1.3)bHLH-ZIP
(1.4) NF-1
(1.5) RF-X
(1.6) Basic helix-span-helix (bHSH)
(2)Zinc finger DNA-binding domains
(2.1)Nuclear receptor(Cys4)
subfamily 1
subfamily 2
subfamily 3
subfamily 4
subfamily 5
subfamily 6
subfamily 0
(2.2) Other Cys4
(2.3) Cys2His2
(2.4) Cys6
(2.5) Alternating composition
(2.6) WRKY
(3.1)Homeodomain
Antennapedia
ANTP class
protoHOX
Hox-like
metaHOX
NK-like
other
(3.2) Paired box
(3.3)Fork head /winged helix
(3.4)Heat shock factors
(3.5) Tryptophan clusters
(3.6) TEA domain
  • transcriptional enhancer factor
(4)β-Scaffold factors with minor groove contacts
(4.1)Rel homology region
(4.2)STAT
(4.3) p53-like
(4.4)MADS box
(4.6)TATA-binding proteins
(4.7)High-mobility group
(4.9) Grainyhead
(4.10) Cold-shock domain
(4.11) Runt
(0) Other transcription factors
(0.2) HMGI(Y)
(0.3)Pocket domain
(0.5)AP-2/EREBP-related factors
(0.6) Miscellaneous
1.14.11:2-oxoglutarate
1.14.13:NADH orNADPH
1.14.14: reducedflavin orflavoprotein
1.14.15: reducediron–sulfur protein
1.14.16: reducedpteridine (BH4 dependent)
1.14.17: reducedascorbate
1.14.18-19: other
1.14.99 - miscellaneous
Activity
Regulation
Classification
Kinetics
Types
Portal:
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