JARID1B

Protein-coding gene in the species Homo sapiens
KDM5B
Available structures
PDBOrtholog search: PDBe RCSB
List of PDB id codes

2MA5, 2MNY, 2MNZ, 5A1F, 5A3N, 5A3P, 5A3T, 5A3W, 5FPL, 5FPU, 5FV3, 5FZ6, 5FUP, 5FUN, 5FZK, 5FYZ, 5FZ7, 5FZ9, 5FYU, 5FZB, 5FZC, 5FYT, 5FZ0, 5FYY, 5FZ1, 5FZ3, 5FZL, 5FZA, 5FZ4

Identifiers
AliasesKDM5B, CT31, JARID1B, PLU-1, PLU1, PPP1R98, PUT1, RBBP2H1A, RBP2-H1, lysine demethylase 5B, MRT65
External IDsOMIM: 605393 MGI: 1922855 HomoloGene: 48448 GeneCards: KDM5B
Gene location (Human)
Chromosome 1 (human)
Chr.Chromosome 1 (human)[1]
Chromosome 1 (human)
Genomic location for KDM5B
Genomic location for KDM5B
Band1q32.1Start202,724,495 bp[1]
End202,808,487 bp[1]
Gene location (Mouse)
Chromosome 1 (mouse)
Chr.Chromosome 1 (mouse)[2]
Chromosome 1 (mouse)
Genomic location for KDM5B
Genomic location for KDM5B
Band1 E4|1 58.24 cMStart134,487,909 bp[2]
End134,563,023 bp[2]
RNA expression pattern
Bgee
HumanMouse (ortholog)
Top expressed in
  • sperm

  • ganglionic eminence

  • stromal cell of endometrium

  • vulva

  • gums

  • skin of abdomen

  • bone marrow cells

  • tibia

  • cervix

  • vagina
Top expressed in
  • spermatocyte

  • maxillary prominence

  • spermatid

  • molar

  • internal carotid artery

  • ganglionic eminence

  • abdominal wall

  • external carotid artery

  • seminiferous tubule

  • hair follicle
More reference expression data
BioGPS




More reference expression data
Gene ontology
Molecular function
  • DNA binding
  • transcription corepressor activity
  • DNA-binding transcription factor activity
  • dioxygenase activity
  • metal ion binding
  • protein binding
  • oxidoreductase activity
  • histone demethylase activity
  • histone H3-tri/di/monomethyl-lysine-4 demethylase activity
  • sequence-specific double-stranded DNA binding
  • histone H3-methyl-lysine-4 demethylase activity
  • histone binding
  • zinc ion binding
  • DNA-binding transcription factor activity, RNA polymerase II-specific
  • DNA-binding transcription repressor activity, RNA polymerase II-specific
  • chromatin binding
  • methylated histone binding
Cellular component
  • nucleoplasm
  • nucleus
  • cytosol
  • histone methyltransferase complex
Biological process
  • response to fungicide
  • positive regulation of mammary gland epithelial cell proliferation
  • regulation of transcription, DNA-templated
  • branching involved in mammary gland duct morphogenesis
  • uterus morphogenesis
  • rhythmic process
  • regulation of estradiol secretion
  • post-embryonic development
  • cellular response to fibroblast growth factor stimulus
  • transcription, DNA-templated
  • single fertilization
  • mammary duct terminal end bud growth
  • positive regulation of gene expression
  • lens fiber cell differentiation
  • negative regulation of transcription, DNA-templated
  • histone H3-K4 demethylation, trimethyl-H3-K4-specific
  • regulation of transcription by RNA polymerase II
  • histone H3-K4 demethylation
  • cellular response to leukemia inhibitory factor
  • chromatin organization
  • negative regulation of transcription by RNA polymerase II
  • chromatin remodeling
Sources:Amigo / QuickGO
Orthologs
SpeciesHumanMouse
Entrez

10765

75605

Ensembl

ENSG00000117139

ENSMUSG00000042207

UniProt

Q9UGL1

Q80Y84

RefSeq (mRNA)

NM_001314042
NM_006618
NM_001347591
NM_001399817

NM_152895

RefSeq (protein)

NP_001300971
NP_001334520
NP_006609

NP_690855

Location (UCSC)Chr 1: 202.72 – 202.81 MbChr 1: 134.49 – 134.56 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Lysine-specific demethylase 5B also known as histone demethylase JARID1B is a demethylase enzyme that in humans is encoded by the KDM5B gene.[5][6][7] JARID1B belongs to the alpha-ketoglutarate-dependent hydroxylase superfamily.

Function

Jarid1B (also known as KDM5B or PLU1) is in the family of JHDM genes. These are responsible for demethylation of tri- and di-methylated lysines in the 4 position of histone 3 (H3K4me3 and H3K4me2). Jarid1B is a multidomain enzyme that is part of the subfamily KDM5. The whole Jarid1 family is a protein family that possesses H3K4 histone demethylase activity.[8]

Jarid1B has been implicated in the development of prostate, breast, and skin cancer and also has been associated with melanoma maintenance. Knockout mice (Jarid1b−/−) produced are viable in neonatal life. These mice do exhibit the phenotype of premature mortality, decreased fertility in female mice, reduction in body weight and impairment in mammary gland development. It also acted to decrease serum estrogen levels and caused reduced mammary epithelial cell proliferation in the early stages of puberty. These Jarid1b−/− mice seem to be greatly affected in many regulators of the development of mammy development such as FOXA1 and estrogen receptor α.[9] However, others have shown that a Jarid1B knockout embryos usually have neonatal lethality due to the failure of their respiratory system. Knockout embryos have also been seen to have several different neural defects including: disorganized cranial nerves, increased incidences of exencephaly, and defects in eye development.[10]

Interactions

JARID1B has been shown to interact with FOXG1[11] and PAX9.[11]

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000117139 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000042207 – 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.
  5. ^ Lahoud MH, Ristevski S, Venter DJ, Jermiin LS, Bertoncello I, Zavarsek S, Hasthorpe S, Drago J, de Kretser D, Hertzog PJ, Kola I (August 2001). "Gene targeting of Desrt, a novel ARID class DNA-binding protein, causes growth retardation and abnormal development of reproductive organs". Genome Research. 11 (8): 1327–34. doi:10.1101/gr.168801. hdl:10536/DRO/DU:30121320. PMID 11483573.
  6. ^ Zhu L, Hu J, Lin D, Whitson R, Itakura K, Chen Y (August 2001). "Dynamics of the Mrf-2 DNA-binding domain free and in complex with DNA". Biochemistry. 40 (31): 9142–50. doi:10.1021/bi010476a. PMID 11478881.
  7. ^ "Entrez Gene: JARID1B jumonji, AT rich interactive domain 1B".
  8. ^ Kristensen LH, Nielsen AL, Helgstrand C, Lees M, Cloos P, Kastrup JS, Helin K, Olsen L, Gajhede M (June 2012). "Studies of H3K4me3 demethylation by KDM5B/Jarid1B/PLU1 reveals strong substrate recognition in vitro and identifies 2,4-pyridine-dicarboxylic acid as an in vitro and in cell inhibitor". The FEBS Journal. 279 (11): 1905–14. doi:10.1111/j.1742-4658.2012.08567.x. PMID 22420752.
  9. ^ Zou MR, Cao J, Liu Z, Huh SJ, Polyak K, Yan Q (June 2014). "Histone demethylase jumonji AT-rich interactive domain 1B (JARID1B) controls mammary gland development by regulating key developmental and lineage specification genes". The Journal of Biological Chemistry. 289 (25): 17620–33. doi:10.1074/jbc.M114.570853. PMC 4067197. PMID 24802759.
  10. ^ Albert M, Schmitz SU, Kooistra SM, Malatesta M, Morales Torres C, Rekling JC, Johansen JV, Abarrategui I, Helin K (April 2013). "The histone demethylase Jarid1b ensures faithful mouse development by protecting developmental genes from aberrant H3K4me3". PLOS Genetics. 9 (4): e1003461. doi:10.1371/journal.pgen.1003461. PMC 3630093. PMID 23637629.
  11. ^ a b Tan K, Shaw AL, Madsen B, Jensen K, Taylor-Papadimitriou J, Freemont PS (June 2003). "Human PLU-1 Has transcriptional repression properties and interacts with the developmental transcription factors BF-1 and PAX9". The Journal of Biological Chemistry. 278 (23): 20507–13. doi:10.1074/jbc.M301994200. PMID 12657635.

Further reading

  • Lu PJ, Sundquist K, Baeckstrom D, Poulsom R, Hanby A, Meier-Ewert S, Jones T, Mitchell M, Pitha-Rowe P, Freemont P, Taylor-Papadimitriou J (May 1999). "A novel gene (PLU-1) containing highly conserved putative DNA/chromatin binding motifs is specifically up-regulated in breast cancer". The Journal of Biological Chemistry. 274 (22): 15633–45. doi:10.1074/jbc.274.22.15633. PMID 10336460.
  • Kashuba V, Protopopov A, Podowski R, Gizatullin R, Li J, Klein G, Wahlestedt C, Zabarovsky E (June 2000). "Isolation and chromosomal localization of a new human retinoblastoma binding protein 2 homologue 1a (RBBP2H1A)". European Journal of Human Genetics. 8 (6): 407–13. doi:10.1038/sj.ejhg.5200474. PMID 10878660.
  • Barrett A, Madsen B, Copier J, Lu PJ, Cooper L, Scibetta AG, Burchell J, Taylor-Papadimitriou J (October 2002). "PLU-1 nuclear protein, which is upregulated in breast cancer, shows restricted expression in normal human adult tissues: a new cancer/testis antigen?". International Journal of Cancer. 101 (6): 581–8. doi:10.1002/ijc.10644. PMID 12237901.
  • Tan K, Shaw AL, Madsen B, Jensen K, Taylor-Papadimitriou J, Freemont PS (June 2003). "Human PLU-1 Has transcriptional repression properties and interacts with the developmental transcription factors BF-1 and PAX9". The Journal of Biological Chemistry. 278 (23): 20507–13. doi:10.1074/jbc.M301994200. PMID 12657635.
  • Patsialou A, Wilsker D, Moran E (2005). "DNA-binding properties of ARID family proteins". Nucleic Acids Research. 33 (1): 66–80. doi:10.1093/nar/gki145. PMC 546134. PMID 15640446.
  • Tzschach A, Lenzner S, Moser B, Reinhardt R, Chelly J, Fryns JP, Kleefstra T, Raynaud M, Turner G, Ropers HH, Kuss A, Jensen LR (April 2006). "Novel JARID1C/SMCX mutations in patients with X-linked mental retardation". Human Mutation. 27 (4): 389. doi:10.1002/humu.9420. PMID 16541399.
  • Yamane K, Tateishi K, Klose RJ, Fang J, Fabrizio LA, Erdjument-Bromage H, Taylor-Papadimitriou J, Tempst P, Zhang Y (March 2007). "PLU-1 is an H3K4 demethylase involved in transcriptional repression and breast cancer cell proliferation". Molecular Cell. 25 (6): 801–12. doi:10.1016/j.molcel.2007.03.001. PMID 17363312.
  • Barrett A, Santangelo S, Tan K, Catchpole S, Roberts K, Spencer-Dene B, Hall D, Scibetta A, Burchell J, Verdin E, Freemont P, Taylor-Papadimitriou J (July 2007). "Breast cancer associated transcriptional repressor PLU-1/JARID1B interacts directly with histone deacetylases". International Journal of Cancer. 121 (2): 265–75. doi:10.1002/ijc.22673. PMID 17373667. S2CID 24855452.

External links

This article incorporates text from the United States National Library of Medicine, which is in the public domain.

  • v
  • t
  • e
(1) Basic domains
(1.1) Basic leucine 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) Helix-turn-helix domains
(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
see also transcription factor/coregulator deficiencies
  • v
  • t
  • e
1.14.11: 2-oxoglutarate
1.14.13: NADH or NADPH
1.14.14: reduced flavin or flavoprotein
1.14.15: reduced iron–sulfur protein
1.14.16: reduced pteridine (BH4 dependent)
1.14.17: reduced ascorbate
1.14.18-19: other
1.14.99 - miscellaneous
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