SETDB1

SETDB1
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 3DLM, 4X3S, 5KE2
Identifiers
Aliases	SETDB1 , ESET, H3-K9-HMTase4, KG1T, KMT1E, TDRD21, SET domain bifurcated 1, SET domain bifurcated histone lysine methyltransferase 1
External IDs	OMIM: 604396; MGI: 1934229; HomoloGene: 32157; GeneCards: SETDB1; OMA:SETDB1 - orthologs
Gene location (Human) Chr. Chromosome 1 (human) [1] Band 1q21.3 Start 150,926,263 bp [1] End 150,964,744 bp [1]
Gene location (Mouse) Chr. Chromosome 3 (mouse) [2] Band 3|3 F2.1 Start 95,230,836 bp [2] End 95,264,513 bp [2]
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in sural nerve monocyte granulocyte right lobe of thyroid gland right ovary left ovary left testis right testis right uterine tube left lobe of thyroid gland Top expressed in secondary oocyte zygote primary oocyte Ileal epithelium tail of embryo otic placode genital tubercle superior surface of tongue gallbladder ventricular zone More reference expression data BioGPS More reference expression data
Gene ontology Molecular function methyltransferase activity transferase activity DNA binding promoter-specific chromatin binding zinc ion binding histone-lysine N-methyltransferase activity metal ion binding protein binding chromatin binding histone methyltransferase activity (H3-K9 specific) Cellular component intracellular membrane-bounded organelle plasma membrane nucleoplasm chromosome nucleus cytosol cytoplasm Biological process regulation of transcription, DNA-templated positive regulation of DNA methylation-dependent heterochromatin assembly response to vitamin transcription, DNA-templated methylation histone lysine methylation Ras protein signal transduction response to ethanol chromatin organization negative regulation of single stranded viral RNA replication via double stranded DNA intermediate histone H3-K9 methylation Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 9869 84505 Ensembl ENSG00000143379 ENSMUSG00000015697 UniProt Q15047 O88974 RefSeq (mRNA) NM_001145415 NM_001243491 NM_012432 NM_001366417 NM_001366418 NM_001163641 NM_001163642 NM_018877 RefSeq (protein) NP_001138887 NP_001230420 NP_036564 NP_001353346 NP_001353347 n/a Location (UCSC) Chr 1: 150.93 – 150.96 Mb Chr 3: 95.23 – 95.26 Mb PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Histone-lysine N-methyltransferase SETDB1 is an enzyme that in humans is encoded by the SETDB1 gene. ^{[5] [6]} SETDB1 is also known as KMT1E or H3K9 methyltransferase ESET.

Function

The SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure. It was originally identified as part of a larger conserved region present in the Drosophila Trithorax protein and was subsequently identified in the Drosophila Su(var)3-9 and 'Enhancer of zeste' proteins, from which the acronym SET is derived. Studies have suggested that the SET domain may be a signature of proteins that modulate transcriptionally active or repressed chromatin states through chromatin remodeling activities. ^[6]

During meiosis, synapsis of homologous chromosomes ensures correct homologous chromosome segregation. Asynapsed homologs are transcriptionally inactivated by a process of meiotic silencing. ^[7] Meiotic silencing depends on the DNA damage response network. ^[7] SETDB1 protein has been identified as the bridge linking the DNA damage response to chromosome silencing in male mice. ^[7]

Interactions

SETDB1 has been shown to interact with TRIM28. ^[8] >

See also

• SETD1A, a protein that is highly homologous to SETDB1

References

1. GRCh38: Ensembl release 89: ENSG00000143379 – Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000015697 – 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. Harte PJ, Wu W, Carrasquillo MM, Matera AG (June 1999). "Assignment of a novel bifurcated SET domain gene, SETDB1, to human chromosome band 1q21 by in situ hybridization and radiation hybrids". Cytogenet. Cell Genet. 84 (1–2): 83–6. doi:10.1159/000015220. PMID   10343109. S2CID   10805552.
6. "Entrez Gene: SETDB1 SET domain, bifurcated 1".
7. Hirota T, Blakeley P, Sangrithi MN, Mahadevaiah SK, Encheva V, Snijders AP, ElInati E, Ojarikre OA, de Rooij DG, Niakan KK, Turner JM (December 2018). "SETDB1 Links the Meiotic DNA Damage Response to Sex Chromosome Silencing in Mice". Dev Cell. 47 (5): 645–659.e6. doi:10.1016/j.devcel.2018.10.004. PMC   6286383 . PMID   30393076.
8. Schultz DC, Ayyanathan K, Negorev D, Maul GG, Rauscher FJ (April 2002). "SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins". Genes Dev. 16 (8): 919–32. doi:10.1101/gad.973302. PMC   152359 . PMID   11959841.

Further reading

• Nomura N, Nagase T, Miyajima N, Sazuka T, Tanaka A, Sato S, Seki N, Kawarabayasi Y, Ishikawa K, Tabata S (1994). "Prediction of the coding sequences of unidentified human genes. II. The coding sequences of 40 new genes (KIAA0041-KIAA0080) deduced by analysis of cDNA clones from human cell line KG-1". DNA Res. 1 (5): 223–9. doi: 10.1093/dnares/1.5.223 . PMID   7584044.
• Yang L, Xia L, Wu DY, Wang H, Chansky HA, Schubach WH, Hickstein DD, Zhang Y (2002). "Molecular cloning of ESET, a novel histone H3-specific methyltransferase that interacts with ERG transcription factor". Oncogene. 21 (1): 148–52. doi:10.1038/sj.onc.1204998. PMID   11791185. S2CID   10912876.
• Schultz DC, Ayyanathan K, Negorev D, Maul GG, Rauscher FJ (2002). "SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins". Genes Dev. 16 (8): 919–32. doi:10.1101/gad.973302. PMC   152359 . PMID   11959841.
• Yang L, Mei Q, Zielinska-Kwiatkowska A, Matsui Y, Blackburn ML, Benedetti D, Krumm AA, Taborsky GJ, Chansky HA (2003). "An ERG (ets-related gene)-associated histone methyltransferase interacts with histone deacetylases 1/2 and transcription co-repressors mSin3A/B". Biochem. J. 369 (Pt 3): 651–7. doi:10.1042/BJ20020854. PMC   1223118 . PMID   12398767.
• Nakayama M, Kikuno R, Ohara O (2002). "Protein-protein interactions between large proteins: two-hybrid screening using a functionally classified library composed of long cDNAs". Genome Res. 12 (11): 1773–84. doi:10.1101/gr.406902. PMC   187542 . PMID   12421765.
• Ayyanathan K, Lechner MS, Bell P, Maul GG, Schultz DC, Yamada Y, Tanaka K, Torigoe K, Rauscher FJ (2003). "Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation". Genes Dev. 17 (15): 1855–69. doi:10.1101/gad.1102803. PMC   196232 . PMID   12869583.
• Wang H, An W, Cao R, Xia L, Erdjument-Bromage H, Chatton B, Tempst P, Roeder RG, Zhang Y (2003). "mAM facilitates conversion by ESET of dimethyl to trimethyl lysine 9 of histone H3 to cause transcriptional repression". Mol. Cell. 12 (2): 475–87. doi: 10.1016/j.molcel.2003.08.007 . PMID   14536086.
• Paces-Fessy M, Boucher D, Petit E, Paute-Briand S, Blanchet-Tournier MF (2004). "The negative regulator of Gli, Suppressor of fused (Sufu), interacts with SAP18, Galectin3 and other nuclear proteins". Biochem. J. 378 (Pt 2): 353–62. doi:10.1042/BJ20030786. PMC   1223961 . PMID   14611647.
• Colland F, Jacq X, Trouplin V, Mougin C, Groizeleau C, Hamburger A, Meil A, Wojcik J, Legrain P, Gauthier JM (2004). "Functional proteomics mapping of a human signaling pathway". Genome Res. 14 (7): 1324–32. doi:10.1101/gr.2334104. PMC   442148 . PMID   15231748.
• Goehler H, Lalowski M, Stelzl U, Waelter S, Stroedicke M, Worm U, Droege A, Lindenberg KS, Knoblich M, Haenig C, Herbst M, Suopanki J, Scherzinger E, Abraham C, Bauer B, Hasenbank R, Fritzsche A, Ludewig AH, Büssow K, Buessow K, Coleman SH, Gutekunst CA, Landwehrmeyer BG, Lehrach H, Wanker EE (2004). "A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease". Mol. Cell. 15 (6): 853–65. doi: 10.1016/j.molcel.2004.09.016 . PMID   15383276.
• Ichimura T, Watanabe S, Sakamoto Y, Aoto T, Fujita N, Nakao M (2005). "Transcriptional repression and heterochromatin formation by MBD1 and MCAF/AM family proteins". J. Biol. Chem. 280 (14): 13928–35. doi: 10.1074/jbc.M413654200 . PMID   15691849.
• Verschure PJ, van der Kraan I, de Leeuw W, van der Vlag J, Carpenter AE, Belmont AS, van Driel R (2005). "In vivo HP1 targeting causes large-scale chromatin condensation and enhanced histone lysine methylation". Mol. Cell. Biol. 25 (11): 4552–64. doi:10.1128/MCB.25.11.4552-4564.2005. PMC   1140641 . PMID   15899859.
• Gevaert K, Staes A, Van Damme J, De Groot S, Hugelier K, Demol H, Martens L, Goethals M, Vandekerckhove J (2005). "Global phosphoproteome analysis on human HepG2 hepatocytes using reversed-phase diagonal LC". Proteomics. 5 (14): 3589–99. doi:10.1002/pmic.200401217. PMID   16097034. S2CID   895879.
• 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 (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.
• Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M (2005). "Towards a proteome-scale map of the human protein-protein interaction network". Nature. 437 (7062): 1173–8. Bibcode:2005Natur.437.1173R. doi:10.1038/nature04209. PMID   16189514. S2CID   4427026.
• Orouji E, Federico A, Larribere L, Novak D, Lipka DB, Assenov Y, Sachindra S, Hueser L, Granados K, Gebhardt C, Plass C, Umansky V, Utikal J (2019). "Histone methyltransferase SETDB1 contributes to melanoma tumorigenesis and serves as a new potential therapeutic target". Int J Cancer. 145 (12): 3462–3477. doi: 10.1002/ijc.32432 . PMID   31131878.
• Strepkos D, Markouli M, Klonou A, Papavassiliou AG, Piperi C (2021). "Histone methyltransferase SETDB1: A common denominator of tumorigenesis with therapeutic potential". Cancer Research. 81 (3): 525–534. doi: 10.1158/0008-5472.CAN-20-2906 . PMID   33115801. S2CID   226046421.
• Cao N, Yu Y, Zhu H, Chen M, Chen P, Zhuo M, Ye M (2020). "SETDB1 promotes the progression of colorectal cancer via epigenetically silencing p21 expression". Cell Death & Disease. 11 (5) 351. doi:10.1038/s41419-020-2561-6. PMC   7214465 . PMID   32393761.
• Lee S, Lee C, Hwang CY, Kim D, Han Y, Hong SN, Cho KH (2020). "Network inference analysis identifies SETDB1 as a key regulator for reverting colorectal cancer cells into differentiated normal-like cells". Molecular Cancer Research. 18 (1): 118–129. doi: 10.1158/1541-7786.MCR-19-0450 . PMID   31896605.
• Fukuda K, Shinkai Y (2020). "SETDB1-Mediated silencing of retroelements". Viruses. 12 (6): 596. doi: 10.3390/v12060596 . PMC   7354471 . PMID   32486217.

External links

• FactorBook SETDB1
• Overview of all the structural information available in the PDB for UniProt : Q15047 (Histone-lysine N-methyltransferase SETDB1) at the PDBe-KB .

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