SMARCB1

SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 is a protein that in humans is encoded by the SMARCB1 gene.[5][6][7]

SMARCB1
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 5AJ1
Identifiers
Aliases	SMARCB1, BAF47, INI1, MRD15, PPP1R144, RDT, RTPS1, SNF5, SNF5L1, SWNTS1, Sfh1p, Snr1, hSNFS, CSS3, SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1
External IDs	OMIM: 601607 MGI: 1328366 HomoloGene: 2310 GeneCards: SMARCB1
Gene location (Human) Chr. Chromosome 22 (human)[1] Band 22q11.23|22q11 Start 23,786,931 bp[1] End 23,838,008 bp[1]
Gene location (Mouse) Chr. Chromosome 10 (mouse)[2] Band 10|10 C1 Start 75,896,769 bp[2] End 75,921,617 bp[2]
RNA expression pattern More reference expression data
Gene ontology Molecular function • GO:0000980 RNA polymerase II cis-regulatory region sequence-specific DNA binding • DNA binding • GO:0001187 RNA polymerase I core promoter sequence-specific DNA binding • GO:0001105 transcription coactivator activity • p53 binding • Tat protein binding • GO:0001948 protein binding • nucleosomal DNA binding Cellular component • nucleoplasm • nuclear chromosome • nucleolus • nuclear chromatin • cell nucleus • fibrillar center • intracellular membrane-bounded organelle • SWI/SNF complex • npBAF complex • nBAF complex • macromolecular complex • brahma complex Biological process • positive regulation of glucose mediated signaling pathway • chromatin remodeling • regulation of transcription, DNA-templated • DNA integration • positive regulation of histone H3-K9 acetylation • regulation of transcription from RNA polymerase II promoter • positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter • positive regulation of sequence-specific DNA binding transcription factor activity • transcription, DNA-templated • nervous system development • ATP-dependent chromatin remodeling • nucleosome disassembly • positive regulation of histone H4 acetylation • single stranded viral RNA replication via double stranded DNA intermediate • cell cycle • negative regulation of histone H3-K9 trimethylation • regulation of histone H4-K16 acetylation • GO:0022415 viral process • negative regulation of histone H3-K9 dimethylation • DNA repair • positive regulation by host of viral transcription • positive regulation of transcription from RNA polymerase II promoter • covalent chromatin modification • negative regulation of cell proliferation • cell differentiation • RNA polymerase I transcriptional preinitiation complex assembly • chromatin organization Sources:Amigo / QuickGO
Orthologs
Species	Human	Mouse
Entrez	6598	20587
Ensembl	ENSG00000099956 ENSG00000275837	ENSMUSG00000000902
UniProt	Q12824	Q9Z0H3
RefSeq (mRNA)	NM_001007468 NM_003073 NM_001317946 NM_001362877	NM_001161853 NM_011418
RefSeq (protein)	NP_001007469 NP_001304875 NP_003064 NP_001349806	NP_001155325 NP_035548
Location (UCSC)	Chr 22: 23.79 – 23.84 Mb	Chr 10: 75.9 – 75.92 Mb
PubMed search	[3]	[4]
Wikidata
View/Edit Human View/Edit Mouse

Function

The protein encoded by this gene is part of a complex that relieves repressive chromatin structures, allowing the transcriptional machinery to access its targets more effectively. The encoded nuclear protein may also bind to and enhance the DNA joining activity of HIV-1 integrase. This gene has been found to be a tumor suppressor and mutations in it have been associated with malignant rhabdoid tumors. Two transcript variants encoding different isoforms have been found for this gene.[8]

Interactions

SMARCB1 has been shown to interact with:

• ARID1A,[9][10]
• BAZ1B,[11]
• BRCA1,[12]
• CREB-binding protein,[13]
• Cyclin-dependent kinase 8,[13]
• Myc,[6]
• P53,[14]
• POLR2A,[9][13][15]
• PPP1CA,[16]
• PPP1CB,[16]
• PPP1CC,[16]
• PPP1R15A,[16][17]
• SMARCA2,[9][15]
• SMARCA4,[9][15][18][19][20]
• SMARCC1,[9][15]
• SMARCE1,[9][18]
• SS18,[10] and
• XPO1.[21]

References

1. ENSG00000275837 GRCh38: Ensembl release 89: ENSG00000099956, ENSG00000275837 - Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000000902 - 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. Kalpana GV, Marmon S, Wang W, Crabtree GR, Goff SP (January 1995). "Binding and stimulation of HIV-1 integrase by a human homolog of yeast transcription factor SNF5". Science. 266 (5193): 2002–6. doi:10.1126/science.7801128. PMID 7801128.
6. Cheng SW, Davies KP, Yung E, Beltran RJ, Yu J, Kalpana GV (May 1999). "c-MYC interacts with INI1/hSNF5 and requires the SWI/SNF complex for transactivation function". Nat Genet. 22 (1): 102–5. doi:10.1038/8811. PMID 10319872.
7. Lee D, Sohn H, Kalpana GV, Choe J (June 1999). "Interaction of E1 and hSNF5 proteins stimulates replication of human papillomavirus DNA". Nature. 399 (6735): 487–91. doi:10.1038/20966. PMID 10365963.
8. "Entrez Gene: SMARCB1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1".
9. Wang W, Côté J, Xue Y, Zhou S, Khavari PA, Biggar SR, Muchardt C, Kalpana GV, Goff SP, Yaniv M, Workman JL, Crabtree GR (October 1996). "Purification and biochemical heterogeneity of the mammalian SWI-SNF complex". EMBO J. 15 (19): 5370–82. doi:10.1002/j.1460-2075.1996.tb00921.x. PMC 452280. PMID 8895581.
10. Kato H, Tjernberg A, Zhang W, Krutchinsky AN, An W, Takeuchi T, Ohtsuki Y, Sugano S, de Bruijn DR, Chait BT, Roeder RG (February 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. PMID 11734557.
11. Kitagawa H, Fujiki R, Yoshimura K, Mezaki Y, Uematsu Y, Matsui D, Ogawa S, Unno K, Okubo M, Tokita A, Nakagawa T, Ito T, Ishimi Y, Nagasawa H, Matsumoto T, Yanagisawa J, Kato S (June 2003). "The chromatin-remodeling complex WINAC targets a nuclear receptor to promoters and is impaired in Williams syndrome". Cell. 113 (7): 905–17. doi:10.1016/s0092-8674(03)00436-7. PMID 12837248.
12. Bochar DA, Wang L, Beniya H, Kinev A, Xue Y, Lane WS, Wang W, Kashanchi F, Shiekhattar R (July 2000). "BRCA1 is associated with a human SWI/SNF-related complex: linking chromatin remodeling to breast cancer". Cell. 102 (2): 257–65. doi:10.1016/s0092-8674(00)00030-1. PMID 10943845.
13. Cho H, Orphanides G, Sun X, Yang XJ, Ogryzko V, Lees E, Nakatani Y, Reinberg D (September 1998). "A human RNA polymerase II complex containing factors that modify chromatin structure". Mol. Cell. Biol. 18 (9): 5355–63. doi:10.1128/MCB.18.9.5355. PMC 109120. PMID 9710619.
14. Lee D, Kim JW, Seo T, Hwang SG, Choi EJ, Choe J (June 2002). "SWI/SNF complex interacts with tumor suppressor p53 and is necessary for the activation of p53-mediated transcription". J. Biol. Chem. 277 (25): 22330–7. doi:10.1074/jbc.M111987200. PMID 11950834.
15. Sif S, Saurin AJ, Imbalzano AN, Kingston RE (March 2001). "Purification and characterization of mSin3A-containing Brg1 and hBrm chromatin remodeling complexes". Genes Dev. 15 (5): 603–18. doi:10.1101/gad.872801. PMC 312641. PMID 11238380.
16. Wu DY, Tkachuck DC, Roberson RS, Schubach WH (August 2002). "The human SNF5/INI1 protein facilitates the function of the growth arrest and DNA damage-inducible protein (GADD34) and modulates GADD34-bound protein phosphatase-1 activity". J. Biol. Chem. 277 (31): 27706–15. doi:10.1074/jbc.M200955200. PMID 12016208.
17. Adler HT, Chinery R, Wu DY, Kussick SJ, Payne JM, Fornace AJ, Tkachuk DC (October 1999). "Leukemic HRX fusion proteins inhibit GADD34-induced apoptosis and associate with the GADD34 and hSNF5/INI1 proteins". Mol. Cell. Biol. 19 (10): 7050–60. doi:10.1128/mcb.19.10.7050. PMC 84700. PMID 10490642.
18. Zhao K, Wang W, Rando OJ, Xue Y, Swiderek K, Kuo A, Crabtree GR (November 1998). "Rapid and phosphoinositol-dependent binding of the SWI/SNF-like BAF complex to chromatin after T lymphocyte receptor signaling". Cell. 95 (5): 625–36. doi:10.1016/s0092-8674(00)81633-5. PMID 9845365.
19. Sullivan EK, Weirich CS, Guyon JR, Sif S, Kingston RE (September 2001). "Transcriptional activation domains of human heat shock factor 1 recruit human SWI/SNF". Mol. Cell. Biol. 21 (17): 5826–37. doi:10.1128/mcb.21.17.5826-5837.2001. PMC 87302. PMID 11486022.
20. Otsuki T, Furukawa Y, Ikeda K, Endo H, Yamashita T, Shinohara A, Iwamatsu A, Ozawa K, Liu JM (November 2001). "Fanconi anemia protein, FANCA, associates with BRG1, a component of the human SWI/SNF complex". Hum. Mol. Genet. 10 (23): 2651–60. doi:10.1093/hmg/10.23.2651. PMID 11726552.
21. Craig E, Zhang ZK, Davies KP, Kalpana GV (January 2002). "A masked NES in INI1/hSNF5 mediates hCRM1-dependent nuclear export: implications for tumorigenesis". EMBO J. 21 (1–2): 31–42. doi:10.1093/emboj/21.1.31. PMC 125819. PMID 11782423.

Further reading

• Miller MD, Bushman FD (1995). "HIV integration. Ini1 for integration?". Curr. Biol. 5 (4): 368–70. doi:10.1016/S0960-9822(95)00074-1. PMID 7627549.
• Van Maele B, Debyser Z (2005). "HIV-1 integration: an interplay between HIV-1 integrase, cellular and viral proteins". AIDS reviews. 7 (1): 26–43. PMID 15875659.
• Van Maele B, Busschots K, Vandekerckhove L, Christ F, Debyser Z (2006). "Cellular co-factors of HIV-1 integration". Trends Biochem. Sci. 31 (2): 98–105. doi:10.1016/j.tibs.2005.12.002. PMID 16403635.
• Judkins AR (2007). "Immunohistochemistry of INI1 expression: a new tool for old challenges in CNS and soft tissue pathology". Advances in Anatomic Pathology. 14 (5): 335–9. doi:10.1097/PAP.0b013e3180ca8b08. PMID 17717433.
• Muchardt C, Sardet C, Bourachot B, Onufryk C, Yaniv M (1995). "A human protein with homology to Saccharomyces cerevisiae SNF5 interacts with the potential helicase hbrm". Nucleic Acids Res. 23 (7): 1127–32. doi:10.1093/nar/23.7.1127. PMC 306820. PMID 7739891.
• Wu DY, Kalpana GV, Goff SP, Schubach WH (1996). "Epstein-Barr virus nuclear protein 2 (EBNA2) binds to a component of the human SNF-SWI complex, hSNF5/Ini1". J. Virol. 70 (9): 6020–8. PMC 190622. PMID 8709224.
• Wang W, Côté J, Xue Y, Zhou S, Khavari PA, Biggar SR, Muchardt C, Kalpana GV, Goff SP, Yaniv M, Workman JL, Crabtree GR (1996). "Purification and biochemical heterogeneity of the mammalian SWI-SNF complex". EMBO J. 15 (19): 5370–82. doi:10.1002/j.1460-2075.1996.tb00921.x. PMC 452280. PMID 8895581.
• Morozov A, Yung E, Kalpana GV (1998). "Structure-function analysis of integrase interactor 1/hSNF5L1 reveals differential properties of two repeat motifs present in the highly conserved region". Proc. Natl. Acad. Sci. U.S.A. 95 (3): 1120–5. doi:10.1073/pnas.95.3.1120. PMC 18693. PMID 9448295.
• Versteege I, Sévenet N, Lange J, Rousseau-Merck MF, Ambros P, Handgretinger R, Aurias A, Delattre O (1998). "Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer". Nature. 394 (6689): 203–6. doi:10.1038/28212. PMID 9671307.
• Cho H, Orphanides G, Sun X, Yang XJ, Ogryzko V, Lees E, Nakatani Y, Reinberg D (1998). "A human RNA polymerase II complex containing factors that modify chromatin structure". Mol. Cell. Biol. 18 (9): 5355–63. doi:10.1128/MCB.18.9.5355. PMC 109120. PMID 9710619.
• Biegel JA, Zhou JY, Rorke LB, Stenstrom C, Wainwright LM, Fogelgren B (1999). "Germ-line and acquired mutations of INI1 in atypical teratoid and rhabdoid tumors". Cancer Res. 59 (1): 74–9. PMID 9892189.
• 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.
• Bruder CE, Dumanski JP, Kedra D (1999). "The mouse ortholog of the human SMARCB1 gene encodes two splice forms". Biochem. Biophys. Res. Commun. 257 (3): 886–90. doi:10.1006/bbrc.1999.0563. PMID 10208879.
• Adler HT, Chinery R, Wu DY, Kussick SJ, Payne JM, Fornace AJ, Tkachuk DC (2000). "Leukemic HRX fusion proteins inhibit GADD34-induced apoptosis and associate with the GADD34 and hSNF5/INI1 proteins". Mol. Cell. Biol. 19 (10): 7050–60. doi:10.1128/mcb.19.10.7050. PMC 84700. PMID 10490642.
• Sévenet N, Sheridan E, Amram D, Schneider P, Handgretinger R, Delattre O (1999). "Constitutional mutations of the hSNF5/INI1 gene predispose to a variety of cancers". Am. J. Hum. Genet. 65 (5): 1342–8. doi:10.1086/302639. PMC 1288286. PMID 10521299.
• Kowenz-Leutz E, Leutz A (2000). "A C/EBP beta isoform recruits the SWI/SNF complex to activate myeloid genes". Mol. Cell. 4 (5): 735–43. doi:10.1016/S1097-2765(00)80384-6. PMID 10619021.

External links

• FactorBook Ini1