ARID1B

ARID1B
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 2CXY, 2EH9
Identifiers
Aliases	ARID1B , 6A3-5, BAF250B, BRIGHT, DAN15, ELD/OSA1, MRD12, OSA2, P250R, CSS1, AT-rich interaction domain 1B, SMARCF2
External IDs	OMIM: 614556; MGI: 1926129; HomoloGene: 32344; GeneCards: ARID1B; OMA:ARID1B - orthologs
Gene location (Human) Chr. Chromosome 6 (human) [1] Band 6q25.3 Start 156,776,020 bp [1] End 157,210,779 bp [1]
Gene location (Mouse) Chr. Chromosome 17 (mouse) [2] Band 17|17 A1 Start 5,044,607 bp [2] End 5,397,931 bp [2]
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in bone marrow cells epithelium of colon sural nerve buccal mucosa cell skin of arm Achilles tendon tonsil superior surface of tongue seminal vesicula left ovary Top expressed in Rostral migratory stream hand ciliary body lobe of prostate medullary collecting duct zygote cervix pineal gland epithelium of lens secondary oocyte More reference expression data BioGPS n/a
Gene ontology Molecular function DNA binding transcription coactivator activity protein binding DNA-binding transcription factor activity, RNA polymerase II-specific Cellular component nBAF complex nucleus nucleoplasm cytosol plasma membrane cytoplasm SWI/SNF superfamily-type complex SWI/SNF complex brahma complex Biological process chromatin remodeling regulation of transcription, DNA-templated transcription, DNA-templated nervous system development neuron-neuron synaptic transmission dendritic spine development dendritic cell dendrite assembly response to ischemia cellular response to angiotensin chromatin organization regulation of transcription by RNA polymerase II Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 57492 239985 Ensembl ENSG00000049618 ENSMUSG00000069729 UniProt Q8NFD5 E9Q4N7 RefSeq (mRNA) NM_017519 NM_001363725 NM_001371656 NM_001374820 NM_001374828 NM_001085355 RefSeq (protein) NP_059989 NP_001350654 NP_001358585 NP_001361749 NP_001361757 NP_001078824 Location (UCSC) Chr 6: 156.78 – 157.21 Mb Chr 17: 5.04 – 5.4 Mb PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

AT-rich interactive domain-containing protein 1B is a protein that in humans is encoded by the ARID1B gene. ^[5] ARID1B is a component of the human SWI/SNF chromatin remodeling complex.

Clinical significance

Germline mutations in ARID1B are associated with Coffin–Siris syndrome. ^{[6] [7]} Somatic mutations in ARID1B are associated with several cancer subtypes, suggesting that it is a tumor suppressor gene. ^{[8] [9] [10] [11]}

Interactions

ARID1B has been shown to interact with SMARCA4 ^{[12] [13]} and SMARCA2. ^[13]

References

1. GRCh38: Ensembl release 89: ENSG00000049618 – Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000069729 – 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. "Entrez Gene: ARID1B AT rich interactive domain 1B (SWI1-like)".
6. Tsurusaki Y, Okamoto N, Ohashi H, Kosho T, Imai Y, Hibi-Ko Y, Kaname T, Naritomi K, Kawame H, Wakui K, Fukushima Y, Homma T, Kato M, Hiraki Y, Yamagata T, Yano S, Mizuno S, Sakazume S, Ishii T, Nagai T, Shiina M, Ogata K, Ohta T, Niikawa N, Miyatake S, Okada I, Mizuguchi T, Doi H, Saitsu H, Miyake N, Matsumoto N (April 2012). "Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome". Nat. Genet. 44 (4): 376–8. doi:10.1038/ng.2219. PMID   22426308. S2CID   205345340.
7. Santen GW, Aten E, Sun Y, Almomani R, Gilissen C, Nielsen M, Kant SG, Snoeck IN, Peeters EA, Hilhorst-Hofstee Y, Wessels MW, den Hollander NS, Ruivenkamp CA, van Ommen GJ, Breuning MH, den Dunnen JT, van Haeringen A, Kriek M (April 2012). "Mutations in SWI/SNF chromatin remodeling complex gene ARID1B cause Coffin-Siris syndrome". Nat. Genet. 44 (4): 379–80. doi:10.1038/ng.2217. PMID   22426309. S2CID   205345323.
8. Shain AH, Pollack JR (2013). "The spectrum of SWI/SNF mutations, ubiquitous in human cancers". PLOS ONE. 8 (1): e55119. Bibcode:2013PLoSO...855119S. doi: 10.1371/journal.pone.0055119 . PMC   3552954 . PMID   23355908.
9. Sausen M, Leary RJ, Jones S, Wu J, Reynolds CP, Liu X, Blackford A, Parmigiani G, Diaz LA, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE, Hogarty MD (January 2013). "Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma". Nat. Genet. 45 (1): 12–7. doi:10.1038/ng.2493. PMC   3557959 . PMID   23202128.
10. Shain AH, Giacomini CP, Matsukuma K, Karikari CA, Bashyam MD, Hidalgo M, Maitra A, Pollack JR (January 2012). "Convergent structural alterations define SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeler as a central tumor suppressive complex in pancreatic cancer". Proc. Natl. Acad. Sci. U.S.A. 109 (5): E252–9. Bibcode:2012PNAS..109E.252S. doi: 10.1073/pnas.1114817109 . PMC   3277150 . PMID   22233809.
11. Fujimoto A, Totoki Y, Abe T, Boroevich KA, Hosoda F, Nguyen HH, Aoki M, Hosono N, Kubo M, Miya F, Arai Y, Takahashi H, Shirakihara T, Nagasaki M, Shibuya T, Nakano K, Watanabe-Makino K, Tanaka H, Nakamura H, Kusuda J, Ojima H, Shimada K, Okusaka T, Ueno M, Shigekawa Y, Kawakami Y, Arihiro K, Ohdan H, Gotoh K, Ishikawa O, Ariizumi S, Yamamoto M, Yamada T, Chayama K, Kosuge T, Yamaue H, Kamatani N, Miyano S, Nakagama H, Nakamura Y, Tsunoda T, Shibata T, Nakagawa H (July 2012). "Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators". Nat. Genet. 44 (7): 760–4. doi:10.1038/ng.2291. PMID   22634756. S2CID   54585617.
12. Hurlstone AF, Olave IA, Barker N, van Noort M, Clevers H (May 2002). "Cloning and characterization of hELD/OSA1, a novel BRG1 interacting protein". Biochem. J. 364 (Pt 1): 255–64. doi:10.1042/bj3640255. PMC   1222568 . PMID   11988099.
13. Inoue H, Furukawa T, Giannakopoulos S, Zhou S, King DS, Tanese N (November 2002). "Largest subunits of the human SWI/SNF chromatin-remodeling complex promote transcriptional activation by steroid hormone receptors". J. Biol. Chem. 277 (44): 41674–85. doi: 10.1074/jbc.M205961200 . PMID   12200431.

Further reading

• Martens JA, Winston F (2003). "Recent advances in understanding chromatin remodeling by Swi/Snf complexes". Curr. Opin. Genet. Dev. 13 (2): 136–42. doi:10.1016/S0959-437X(03)00022-4. PMID   12672490.
• Bonaldo MF, Lennon G, Soares MB (1997). "Normalization and subtraction: two approaches to facilitate gene discovery". Genome Res. 6 (9): 791–806. doi: 10.1101/gr.6.9.791 . PMID   8889548.
• Imbert G, Saudou F, Yvert G, et al. (1996). "Cloning of the gene for spinocerebellar ataxia 2 reveals a locus with high sensitivity to expanded CAG/glutamine repeats". Nat. Genet. 14 (3): 285–91. doi:10.1038/ng1196-285. PMID   8896557. S2CID   9304975.
• Mangel L, Ternes T, Schmitz B, Doerfler W (1998). "New 5'-(CGG)n-3' repeats in the human genome". J. Biol. Chem. 273 (46): 30466–71. doi: 10.1074/jbc.273.46.30466 . PMID   9804814.
• Phelan ML, Sif S, Narlikar GJ, Kingston RE (1999). "Reconstitution of a core chromatin remodeling complex from SWI/SNF subunits". Mol. Cell. 3 (2): 247–53. doi: 10.1016/S1097-2765(00)80315-9 . PMID   10078207.
• Nagase T, Ishikawa K, Kikuno R, et al. (2000). "Prediction of the coding sequences of unidentified human genes. XV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Res. 6 (5): 337–45. doi: 10.1093/dnares/6.5.337 . PMID   10574462.
• Xue Y, Canman JC, Lee CS, et al. (2001). "The human SWI/SNF-B chromatin-remodeling complex is related to yeast Rsc and localizes at kinetochores of mitotic chromosomes". Proc. Natl. Acad. Sci. U.S.A. 97 (24): 13015–20. Bibcode:2000PNAS...9713015X. doi: 10.1073/pnas.240208597 . PMC   27170 . PMID   11078522.
• Kato H, Tjernberg A, Zhang W, et al. (2002). "SYT associates with human SNF/SWI complexes and the C-terminal region of its fusion partner SSX1 targets histones". J. Biol. Chem. 277 (7): 5498–505. doi: 10.1074/jbc.M108702200 . hdl: 2066/170683 . PMID   11734557.
• Hurlstone AF, Olave IA, Barker N, et al. (2002). "Cloning and characterization of hELD/OSA1, a novel BRG1 interacting protein". Biochem. J. 364 (Pt 1): 255–64. doi:10.1042/bj3640255. PMC   1222568 . PMID   11988099.
• Inoue H, Furukawa T, Giannakopoulos S, et al. (2003). "Largest subunits of the human SWI/SNF chromatin-remodeling complex promote transcriptional activation by steroid hormone receptors". J. Biol. Chem. 277 (44): 41674–85. doi: 10.1074/jbc.M205961200 . PMID   12200431.
• Strausberg RL, Feingold EA, Grouse LH, et al. (2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16899–903. Bibcode:2002PNAS...9916899M. doi: 10.1073/pnas.242603899 . PMC   139241 . PMID   12477932.
• Nie Z, Yan Z, Chen EH, et al. (2003). "Novel SWI/SNF Chromatin-Remodeling Complexes Contain a Mixed-Lineage Leukemia Chromosomal Translocation Partner". Mol. Cell. Biol. 23 (8): 2942–52. doi:10.1128/MCB.23.8.2942-2952.2003. PMC   152562 . PMID   12665591.
• Mungall AJ, Palmer SA, Sims SK, et al. (2003). "The DNA sequence and analysis of human chromosome 6". Nature. 425 (6960): 805–11. Bibcode:2003Natur.425..805M. doi: 10.1038/nature02055 . PMID   14574404.
• Garin G, Badid C, McGregor B, et al. (2004). "Ischemia Induces Early Expression of a New Transcription Factor (6A3-5) in Kidney Vascular Smooth Muscle Cells : Studies in Rat and Human Renal Pathology". Am. J. Pathol. 163 (6): 2485–94. doi:10.1016/S0002-9440(10)63603-6. PMC   1892391 . PMID   14633620.
• Ota T, Suzuki Y, Nishikawa T, et al. (2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40–5. doi: 10.1038/ng1285 . PMID   14702039.
• Bouwmeester T, Bauch A, Ruffner H, et al. (2004). "A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway". Nat. Cell Biol. 6 (2): 97–105. doi:10.1038/ncb1086. PMID   14743216. S2CID   11683986.
• Wilsker D, Patsialou A, Zumbrun SD, et al. (2004). "The DNA-binding properties of the ARID-containing subunits of yeast and mammalian SWI/SNF complexes". Nucleic Acids Res. 32 (4): 1345–53. doi:10.1093/nar/gkh277. PMC   390273 . PMID   14982958.
• Wang X, Nagl NG, Wilsker D, et al. (2005). "Two related ARID family proteins are alternative subunits of human SWI/SNF complexes". Biochem. J. 383 (Pt 2): 319–25. doi:10.1042/BJ20040524. PMC   1134073 . PMID   15170388.
• Colland F, Jacq X, Trouplin V, et al. (2004). "Functional Proteomics Mapping of a Human Signaling Pathway". Genome Res. 14 (7): 1324–32. doi:10.1101/gr.2334104. PMC   442148 . PMID   15231748.

External links

• ARID1B+protein,+human at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
• Human ARID1B genome location and ARID1B gene details page in the UCSC Genome Browser .

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