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Information on EC 2.1.1.366 - [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase
for references in articles please use BRENDA:EC2.1.1.366
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EC Tree 2 Transferases
2.1 Transferring one-carbon groups
2.1.1 Methyltransferases
2.1.1.366 [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase
IUBMB Comments
The enzyme methylates only dimethylated lysine9 of histone H3 (H3K9), forming the trimethylated form. This modification influences the binding of chromatin-associated proteins. In general, the methylation of H3K9 leads to transcriptional repression of the affected target genes. The enzyme is highly upregulated in Huntington disease patients. cf. EC 2.1.1.367, [histone H3]-lysine9 N-methyltransferase, and EC 2.1.1.368, [histone H3]-lysine9 N-dimethyltransferase, and EC 2.1.1.355, [histone H3]-lysine9 N-trimethyltransferase.
The enzyme appears in viruses and cellular organisms
Reaction Schemes
showSynonyms
kmt1e, erg-associated protein with set domain, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
histone methyltransferase SETDB1
KIAA0067
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KMT1E
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SET domain bifurcated histone lysine methyltransferase 1
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SETDB1
SETDB1
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine9 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine9
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PATHWAY SOURCE
PATHWAYS
KEGG
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SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:[histone H3]-N6,N6-dimethyl-L-lysine9 N6-methyltransferase
The enzyme methylates only dimethylated lysine9 of histone H3 (H3K9), forming the trimethylated form. This modification influences the binding of chromatin-associated proteins. In general, the methylation of H3K9 leads to transcriptional repression of the affected target genes. The enzyme is highly upregulated in Huntington disease patients. cf. EC 2.1.1.367, [histone H3]-lysine9 N-methyltransferase, and EC 2.1.1.368, [histone H3]-lysine9 N-dimethyltransferase, and EC 2.1.1.355, [histone H3]-lysine9 N-trimethyltransferase.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine9
S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine9
S-adenosyl-L-methionine + [histone H3 peptide 1-15]-L-lysine9
S-adenosyl-L-homocysteine + [histone H3 peptide 1-15]-N6-methyl-L-lysine9
Substrates: -
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S-adenosyl-L-methionine + [histone H3 peptide 1-15]-N6,N6-dimethyl-L-lysine9
S-adenosyl-L-homocysteine + [histone H3 peptide 1-15]-N6,N6,N6-trimethyl-L-lysine9
Substrates: -
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S-adenosyl-L-methionine + [histone H3 peptide 1-15]-N6-methyl-L-lysine9
S-adenosyl-L-homocysteine + [histone H3 peptide 1-15]-N6,N6-dimethyl-L-lysine9
Substrates: -
Products: -
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S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine9
S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine9
Substrates: -
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S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine9
S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine9
Substrates: the presence of H3K14ac is required for SETDB1 recruitment via 3TD binding to H3K9me1/2/3-K14ac regions and establishment of H3K9me3
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S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine9
S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine9
Substrates: -
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additional information
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Substrates: H3K9 methylation by SETDB1 occurs in a distributive manner
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additional information
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Substrates: ESET can specifically methylate histone H3 while inactive toward histone H2A, H2B and H4
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine9
S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine9
S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine9
S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine9
Substrates: -
Products: -
Products: -
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S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine9
S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine9
Substrates: -
Products: -
Products: -
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1-methyl-5H-[1,2,4]triazolo[4,3-a][3,1]benzoxazine
SETDB1-TTD inhibitor, binds to the acetyl lysine (Kac) pocket of the SETDB1-TTD
1-[(3,4-dimethoxyphenyl)methyl]-4-[[2-(trifluoromethyl)-7H-pyrrolo[2,3-b]pyridin-7-yl]methyl]piperidin-4-ol
peptidecompetitive SETDB1 inhibitor, decreases SETDB1/ESET levels without changing the mRNA levels (FRET) and exerts noticeable inhibitory effects on H3K9 trimethylation. Induces neuronal cytotoxicity at 0.1 mM
2-([5-[4-(benzyloxy)phenyl]-1-methylpiperidin-3-yl]amino)-3-(prop-2-en-1-yl)-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
SETDB1-TTD inhibitor, inhibits the interaction of H3 peptide with the SETDB1-TTD
3,3-dimethyl-1-[(3S)-1,2,3,4-tetrahydroisoquinolin-3-yl]butan-1-one
SETDB1-TTD inhibitor, very weak binding in the aromatic cage of the dimethyl lysine (Kme2) pocket of the SETDB1-TTD
5-[(prop-2-en-1-yl)oxy]-2-(pyrrolidin-1-yl)quinoline
SETDB1 SET domain inhibitor, inhibits SETDB1 activity and H3K9me3 expression, and improves motor function and neuropathological symptoms with minimal toxicity in mouse HD models
7-chloro-2-[3-(dimethylamino)propyl]-1-(3-ethoxyphenyl)-1,2,3a,9a-tetrahydro[1]benzopyrano[2,3-c]pyrrole-3,9-dione
peptidecompetitive SETDB1 inhibitor, decreases H3K9me3 levels and shows neuronal effects without cytotoxicity
ATF7IP
SETDB1 partner protein. SETDB1 and the SETDB1:ATF7IP complex efficiently catalyze both monomethylation and dimethylation of H3K9 peptide substrates. The activity of the binary complex is 4fold lower than SETDB1 alone
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N-[(furan-2-yl)methyl]-1-[(3S)-1,2,3,4-tetrahydroisoquinoline-3-carbonyl]piperidine-4-carboxamide
SETDB1-TTD inhibitor, binds in the aromatic cage
N-[2-(diethylamino)ethyl]-2-([5,7-dimethyl-6-[(2-methylphenyl)methyl][1,2,4]triazolo[1,5-a]pyrimidin-2-yl]sulfanyl)acetamide
competitive SETDB1 inhibitor, decreases H3K9me3 levels and shows neuronal effects without cytotoxicity
N-[[1,1'-bi(cyclohexan)]-4-yl]-6-methoxy-7-[3-(piperidin-1-yl)propoxy]-2-[4-(propan-2-yl)-1,4-diazepan-1-yl]quinazolin-4-amine
competitive inhibition, the inhibitor docks in the Tudor domain
N-[[2-(3,5-dimethyl-4H-1,2,4-triazol-4-yl)cyclohexyl]methyl]acetamide
SETDB1-TTD inhibitor, binds in the aromatic cage of the Kac pocket of the SETDB1-TTD. It displayed weak binding by SPR and ITC
N2-(3'-[[4-(4-butylpiperazin-1-yl)pyridine-2-carbonyl]amino][1,1'-biphenyl]-4-carbonyl)-6-pyrrolidin-1-yl-L-norleucinamide
SETDB1-TTD inhibitor, shows competitive inhibition and docked between the Tudor 2 and 3
N2-(3'-[[4-(4-butylpiperazin-1-yl)pyridine-2-carbonyl]amino][1,1'-biphenyl]-4-carbonyl)-N6,N6-dimethyl-L-lysinamide
SETDB1-TTD inhibitor, shows competitive inhibition and docks between the Tudor 2 and 3 domains
N2-(3'-[[4-(4-methylpiperazin-1-yl)pyridine-2-carbonyl]amino][1,1'-biphenyl]-4-carbonyl)-6-pyrrolidin-1-yl-L-norleucinamide
SETDB1-TTD inhibitor, shows competitive inhibition and docks between the Tudor 2 and 3 domains
N2-[3'-[(4-[4-[3-(dimethylamino)propyl]piperazin-1-yl]pyridine-2-carbonyl)amino][1,1'-biphenyl]-4-carbonyl]-6-pyrrolidin-1-yl-L-norleucinamide
SETDB1-TTD inhibitor, shows competitive inhibition and docks between the Tudor 2 and 3 domains
N2-[3'-[(4-[4-[3-(dimethylamino)propyl]piperazin-1-yl]pyridine-2-carbonyl)amino][1,1'-biphenyl]-4-carbonyl]-N6,N6-dimethyl-L-lysinamide
SETDB1-TTD inhibitor, shows competitive inhibition and docks between the Tudor 2 and 3 domains
N4-[6-(dimethylamino)hexyl]-N2-[5-(dimethylamino)pentyl]-6,7-dimethoxyquinazoline-2,4-diamine
SETDB1-TTD inhibitor, shows competitive inhibition and docks between the Tudor 2 and 3 domains
N6,N6-dimethyl-L-lysyl-L-serylthreonyl-N-([4-[2-(acetamidomethyl)cyclohexyl]-4H-1,2,4-triazol-3-yl]methyl)glycinamide
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Lung Neoplasms
H3K9 histone methyltransferase, KMT1E/SETDB1, cooperates with the SMAD2/3 pathway to suppress lung cancer metastasis.
Neoplasm Metastasis
H3K9 histone methyltransferase, KMT1E/SETDB1, cooperates with the SMAD2/3 pathway to suppress lung cancer metastasis.
Neoplasms
H3K9 histone methyltransferase, KMT1E/SETDB1, cooperates with the SMAD2/3 pathway to suppress lung cancer metastasis.
[histone h3]-n6,n6-dimethyl-lysine9 n-methyltransferase deficiency
KMT1E mediated H3K9 methylation is required for the maintenance of embryonic stem cells by repressing trophectoderm differentiation.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.52
S-adenosyl-L-methionine
substrate [histone H3 peptide 1-15]-N6,N6-dimethyl-L-lysine9, SETDB1:ATF7IP complex, pH 7.6, 23°C
0.66
S-adenosyl-L-methionine
substrate [histone H3 peptide 1-15]-N6,N6-dimethyl-L-lysine9, pH 7.6, 23°C
0.39
[histone H3 peptide 1-15]-N6,N6-dimethyl-L-lysine9
SETDB1:ATF7IP complex, pH 7.6, 23°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.013
S-adenosyl-L-methionine
substrate [histone H3 peptide 1-15]-N6,N6-dimethyl-L-lysine9, SETDB1:ATF7IP complex, pH 7.6, 23°C
0.065
S-adenosyl-L-methionine
substrate [histone H3 peptide 1-15]-N6,N6-dimethyl-L-lysine9, pH 7.6, 23°C
0.005
[histone H3 peptide 1-15]-N6,N6-dimethyl-L-lysine9
SETDB1:ATF7IP complex, pH 7.6, 23°C
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.026
S-adenosyl-L-methionine
substrate [histone H3 peptide 1-15]-N6,N6-dimethyl-L-lysine9, SETDB1:ATF7IP complex, pH 7.6, 23°C
0.098
S-adenosyl-L-methionine
substrate [histone H3 peptide 1-15]-N6,N6-dimethyl-L-lysine9, pH 7.6, 23°C
0.013
[histone H3 peptide 1-15]-N6,N6-dimethyl-L-lysine9
SETDB1:ATF7IP complex, pH 7.6, 23°C
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0023
N-[[1,1'-bi(cyclohexan)]-4-yl]-6-methoxy-7-[3-(piperidin-1-yl)propoxy]-2-[4-(propan-2-yl)-1,4-diazepan-1-yl]quinazolin-4-amine
Homo sapiens
pH and temperature not specified in the publication
0.0032
N2-(3'-[[4-(4-butylpiperazin-1-yl)pyridine-2-carbonyl]amino][1,1'-biphenyl]-4-carbonyl)-6-pyrrolidin-1-yl-L-norleucinamide
Homo sapiens
pH and temperature not specified in the publication
0.0031
N2-(3'-[[4-(4-butylpiperazin-1-yl)pyridine-2-carbonyl]amino][1,1'-biphenyl]-4-carbonyl)-N6,N6-dimethyl-L-lysinamide
Homo sapiens
pH and temperature not specified in the publication
0.0035
N2-(3'-[[4-(4-methylpiperazin-1-yl)pyridine-2-carbonyl]amino][1,1'-biphenyl]-4-carbonyl)-6-pyrrolidin-1-yl-L-norleucinamide
Homo sapiens
pH and temperature not specified in the publication
0.0008
N2-[3'-[(4-[4-[3-(dimethylamino)propyl]piperazin-1-yl]pyridine-2-carbonyl)amino][1,1'-biphenyl]-4-carbonyl]-6-pyrrolidin-1-yl-L-norleucinamide
Homo sapiens
pH and temperature not specified in the publication
0.0012
N2-[3'-[(4-[4-[3-(dimethylamino)propyl]piperazin-1-yl]pyridine-2-carbonyl)amino][1,1'-biphenyl]-4-carbonyl]-N6,N6-dimethyl-L-lysinamide
Homo sapiens
pH and temperature not specified in the publication
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
expression is observed mainly in the cytoplasm of various human cell lines
brenda
combined treatment with the nuclear export inhibitor leptomycin B and the proteasome inhibitor MG132 leads to the accumulation of SETDB1 in the nucleus
brenda
Highest Expressing Human Cell Lines
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug target
downregulating SETDB1 is an attractive therapeutic option in AKT-driven cancer and for enhancing the immunotherapeutic response
malfunction
metabolism
CBX7 inhibition reduces H3K9 methylation levels. CBX7 inhibitors abolish the interaction between CBX7 and H3K9 methyltransferases and block both CBX7-and H3K9 methyltransferase-mediated gene repression
physiological function
additional information
SETDB1 exists in three isoforms, with isoform 1 being considered as the canonical sequence, including all the necessary domains for full enzyme activity. Isoform 2 contains the same domains as isoform 1. Isoform 2 is produced by alternate splicing of an in-frame splice site which is present in the 3' coding region, resulting in C-terminal truncation in the post-SET domain, thus producing a shorter protein form. Isoform 3 lacks all the domains of the C-terminus that are required for enzyme activity
malfunction
aberrant SETDB1 activity is linked to disease onset, including nervous, cardiovascular and gastrointestinal system disorders, as well as numerous inherited genetic syndromes. SETDB1 is most significantly involved in tumorigenesis by repressing tumor suppressor genes after establishing the H3K9me3 mark. SETDB1 activity results in higher aggressiveness and worse cancer prognosis and has therefore been regarded as an oncogene
malfunction
aberrant SETDB1 expression, and its oncogenic role is evident in many cancers. Amplified SETDB1 is associated with enhanced tumorigenesis and poor prognosis in a wide variety of cancers. This increased oncogenic effect is probably due to a SETDB1 methylation-associated suppressive effect on various tumor suppressors, AKT hyperactivation, and increased mutant p53 stability. SETDB1 overexpression shows a significant negative correlation with immunomodulatory outcomes through tumor immune evasion and IFN-I pathway repression
physiological function
ATFa-associated factor mAM stimulates ESET enzymatic activity by increasing the Vmax and decreasing the Km. mAM facilitates the ESET-dependent conversion of dimethyl H3-K9 to the trimethyl state both in vitro and in vivo. mAM enhances ESET-mediated transcriptional repression in a SAM-dependent manner, and this repression correlates with histone H3-K9 trimethylation at the promoter
physiological function
SETDB1 is an epigenetic regulator of primordial germ cell fate determination. SETDB1-deficient embryos exhibit drastic reduction of nascent primordial germ cells. Dppa2, Otx2 and Utf1 are derepressed whereas mesoderm development-related genes, including BMP4 signaling-related genes, are downregulated by SETDB1 knockdown during primordial germ cell-like cell induction. Binding of SETDB1 is observed at the flanking regions of Dppa2, Otx2 and Utf1 in cell aggregates containing primordial germ cell-like cell induction, and trimethylation of lysine 9 of histone H3 is reduced by SETDB1 knockdown at those regions
physiological function
deletion of the catalytic domain of either histone methyltransferases EHMT2 or SETDB1 in growing oocytes leads to significant reduction of global H3K9me2 or H3K9me3 levels, respectively, in the maternal pronucleus. The asymmetry of global 5-methylcytosine (5mC) oxidation is significantly reduced in the zygotes that carry maternal mutation of either the Ehmt2 or Setdb1 genes. The levels of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine increase, and 5mC levels decrease in the mutant maternal pronuclei. H3K9me3-rich rings around the nucleolar-like bodies retain 5mC in the maternal mutant zygotes. The maternal pronuclei expand in size in the mutant zygotes and contain a significantly increased number of nucleolar-like bodies compared with normal zygotes
physiological function
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H3K9 methylation reader M-phase phosphoprotein 8 (MPP8) interacts physically and functionally with SETDB1 in embryonic stem cells. MPP8 and SETDB1 coregulate a significant number of common genomic targets, especially the DNA satellite repeats
physiological function
bivalend combinantion, dually marked histones H3K9me3/H3K14ac modification in the liver, is significantly decreased in old hepatocytes. A correlation between H3K9me3/H3K14ac bulk bivalent genomic regions and dually marked single nucleosomes is suggested. Histone H3K9 deacetylase Hdac3, as well as H3K9 methyltransferase Setdb1, found in complex Kap1, occupy both bulk and single nucleosome bivalent regions in both young and old livers, correlating to presence of H3K9me3. Expression of genes associated with bivalent regions in young liver, including those regulating cholesterol secretion and triglyceride synthesis, is upregulated in old liver once the bivalency is lost
physiological function
histone H3K9 methyltransferases G9a/KMT1C, GLP/KMT1D, SETDB1/KMT1E, and Suv39h1/KMT1A, coexist in the same megacomplex. In Suv39h or G9a null cells, the remaining histone H3K9 methyltransferases are destabilized at the protein level, indicating. The four enzymes are recruited to major satellite repeats, a known Suv39h1 genomic target, but also to multiple G9a target genes. The four H3K9 histone H3K9 methyltransferases display a functional cooperation in the regulation of known G9a target genes
physiological function
embryonic stem cells exhibit high expression of the ubiquitin-conjugating enzyme UBE2K. Loss of UBE2K upregulates the trimethyltransferase SETDB1, resulting in H3K9 trimethylation and repression of neurogenic genes during differentiation
physiological function
microRNA, miR-152-3p is involved in the regulation of SETDB1 protein levels and plays a positive regulatory role for SETDB1 expression. Inhibition of miR-152-3p results in a robust reduction in SETDB1 protein levels, though SETDB1 mRNA levels are unaffected. This is accompanied by a blockade of the biochemical pathway proceeding from H3K9me2 to H3K9me3. H3K9me2 accumulates in cells treated with an anti-miR that targets miR-152-3p. The action of a miR-152-3p mimic increases flux of the reaction leading to H3K9me3
physiological function
Setdb1 in macrophages potently suppresses Toll-like receptor TLR4-mediated expression of proinflammatory cytokines including interleukin-6 through its methyltransferase activity. Setdb1-deficiency decreases the basal H3K9 methylation levels and augments TLR4-mediated NF-kappaB recruitment on the proximal promoter region of interleukin-6, thereby accelerating interleukin-6 promoter activity. Macrophage-specific Setdb1-knockout mice exhibit higher serum interleukin-6 concentrations in response to lipopolysaccharide challenge and are more susceptible to endotoxin shock than wild-type mice
physiological function
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deletion of Setdb1 in Meckel's cartilage tissue leads to its enlargement. Chondrocytes from the Meckel's cartilage of Setdb1 conditional KO mice show increased size. At embryonic days 16.5 and 18.5, part of the perichondrium is disrupted and mineralization is observed in the Meckel's cartilage. Inhibition of Setdb1 causes increased proliferation in chondrocytes in the Meckel's cartilage as well as in siRNA-treated ATDC5 cells. Decreased expression of chondrogenic genes, such as Sox9, Mmp13, Collagen II, and Aggrecan, is observed as a result of Setdb1 inhibition in ATDC5 cells. SMAD-dependent BMP signaling is significantly increased by the loss of Setdb1 in both the Meckel's cartilage of Setdb1 conditional KO mice and siRNA-treated ATDC5 cells
physiological function
the SETDB1 repressor complex, which involves multiple KRAB zinc finger proteins, shields neuronal genomes from excess CTCF binding and is critically required for structural maintenance of cPcdh topologically associated domain. Neuronal ablation of Setdb1 leads to locus-specific disintegration of megabase-scale chromosomal conformations. The cPcdh topologically associated domain in neurons from mutant mice shows abnormal accumulation of the transcriptional regulator and three-dimensional genome organizer CTCF at cryptic binding sites, in conjunction with DNA cytosine hypomethylation, histone hyperacetylation and upregulated expression. Genes encoding stochastically expressed protocadherins are transcribed by increased numbers of cortical neurons. SETDB1-dependent loop formations bypass 0.2-1 Mb of linear genome and radiate from the cPcdh topologically associated domain fringes toward cis-regulatory sequences within the cPcdh locus
physiological function
SETDB1 regulates the PTEN/AKT/FOXO1 pathway to inhibit spermatogonial stem cell apoptosis. SETDB1 interacts and coordinates with AKT to regulate FOXO1 activity and expression of the downstream target genes Bim and Puma. Among the SETDB1-bound genes, the H3K9me3 levels on the promoter regions of Bim and Pten decrease in the SETDB1-knock down group. The H3K9me3 status on promoters of Bax and Puma remains unchanged
physiological function
Setdb1 has a constant role in endogenous retrovirus silencing. Distinctive sets of endogenous retroviruses are reactivated in different types of Setdb1-deficient somatic cells, including the VL30-class of endogenous retroviruses in mouse embryonic fibroblasts. A viral defense response is induced in immortalized Setdb1 knock-out embryonic fibroblasts
physiological function
SETDB1 is the bridge linking the DNA damage response to meiotic silencing in male mice. At the onset of silencing, X chromosome H3K9 trimethylation enrichment is downstream of DNA damage response factors. Without SETDB1, the X chromosome accrues DNA damage response proteins but not H3K9me3, so sex chromosome remodeling and silencing fail, causing germ cell apoptosis. Setdb1 deletion causes midpachytene apoptosis. SETDB1 is required for epigenetic remodeling of the XY pair, for condensation of the XY pair and for XY silencing at pachynema
physiological function
SETDB1 methylation regulates H3K9me3 in the OTX2 promoter region and inhibits the expression of OTX2. SETDB1 expression is downregulated in osteoporotic femoral tissues and is involved in osteogenic differentiation. Upregulation of SETDB1 promotes osteogenic differentiation by inhibiting OTX2 and activating the BMP-Smad and Wnt/beta-catenin pathways in osteoporosis
physiological function
SETDB1 has a central role in normal physiology and nervous system development, having been implicated in the regulation of cell cycle progression, inactivation of the X chromosome, immune cells function, expression of retroelements and formation of promyelocytic leukemia nuclear bodies. SETDB1 has been frequently deregulated in carcinogenesis, being implicated in the pathogenesis of gliomas, melanomas, as well as in lung, breast, gastrointestinal and ovarian tumors, where it mainly exerts an oncogenic role
physiological function
the enzyme is involved in heterochromatin formation and silencing of repeat elements
physiological function
histone methyltransferase SETDB1 safeguards mouse fetal hematopoiesis by suppressing activation of cryptic enhancers maintaining the proper balance and differentiation of mouse fetal liver hematopoietic stem and progenitor cells
physiological function
the cytoplasmic fraction of the histone lysine methyltransferase Setdb1 is essential for survival of embryonic stem cells. Setdb1 interacts with many RNA-binding proteins and translation regulators such as Trim71. Setdb1 is required for Trim71 complex integrity cSetdb1 regulates the abundance of specific mRNAs, of which Trim71 and hnRNPc targets
physiological function
SETDB1 regulates the development of cortical Htr3a-positive interneurons and mood behaviors
physiological function
SETDB1 strengthens non-small cell lung cancer cell migratory and invasive abilities by promoting invadopodia formation and extracellular matrix degradation. At the molecular level, SETDB1 suppresses the expression of FOXA2, a crucial tumor and metastasis suppressor via coordinated epigenetic mechanisms. SETDB1 not only catalyzes histone H3K9 methylation on FOXA2 genomic locus, but also recruits DNMT3A to regulate DNA methylation on CpG island. Setdb1 is essential for malignant progression and metastasis of murine lung adenocarcinoma
physiological function
the enzyme is involved in various regulatory processes such as cell proliferation, progression, migration, survival, and apoptosis. The enzyme is an important epigenetic regulator catalyzing histone H3 lysine 9 (H3K9) methylation, specifically di-/tri-methylation. This regulation promotes gene silencing through heterochromatin formation. SETDB1 altered lymphocyte and cytokine expression, disrupts the IFN-I response, promotes TAM recruitment, induces ERV silencing, and facilitates tumor immune escape
physiological function
SETDB1 is a major enzyme for H3K9 histone methylation in heterochromatin
Show AA Sequence and Transmembrane Helices (1419 entries)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
x * 145000, calculated from sequence, x * 180000, SDS-PAGE of recombinant protein
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C1242T
highly conserved cysteine residues, mutant has lost histone methyltransferase activity
C798L
highly conserved cysteine residues, mutant has lost histone methyltransferase activity
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
overexpression using Bac-to-Bac baculovirus expression system, expression in Escherichia coli
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
miR-152 expression has a positive effect on SETDB1 protein expression and enzyme activity
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
medicine
overexpression of SETDB1 contributes to melanoma tumorigenesis. SETDB1 is highly amplified in melanoma cells and in the patient tumors. Increased expression of SETDB1 correlates with SETDB1 amplification and is associated with a more aggressive phenotype in in vitro and in vivo studies. SETDB1 implements its effects via regulation of thrombospondin 1, and the SET-domain of SETDB1 is essential for the maintenance of its tumorigenic activity. Inhibition of SETDB1 reduces cell growth in melanomas resistant to targeted treatments
medicine
overexpression of SETDB1 contributes to melanoma tumorigenesis. SETDB1 is highly amplified in melanoma cells. Increased expression of SETDB1 correlates with SETDB1 amplification and is associated with a more aggressive phenotype in in vitro and in vivo studies. SETDB1 implements its effects via regulation of thrombospondin 1, and the SET-domain of SETDB1 is essential for the maintenance of its tumorigenic activity. Inhibition of SETDB1 reduces cell growth in melanomas resistant to targeted treatments
medicine
SETDB1 depletion effectively converts stem-like colorectal cancer cells into postmitotic cells and restores normal morphology in patient-derived colorectal cancer organoids. SETDB1 depletion recapitulates global gene expression profiles of normal differentiated cells by restoring the transcriptional activity of core transcription factors such as CDX2, ELF3, HNF4G, PPARG, and VDR, on their target genes
medicine
loss of SETDB1 from pancreas accelerates formation of premalignant lesions in mice with pancreata that express activated KRAS. Expression of genes in the apoptotic pathway is upregulated and genes are regulated by p53 in SETDB1-deficient pancreata. Deletion of Setdb1 from pancreas prevents formation of pancreatic ductal adenocarcinoma, concomitant with increased apoptosis and upregulated expression of Trp53 in mice heterozygous for disruption of Trp53. Pancreata of mice with homozygous disruption of Trp53 have no increased apoptosis, and pancreatic ductal adenocarcinomas develop. SETDB1 binds to the Trp53 promoter to regulate its expression
medicine
expression of an inactivated form of SETDB1 in human pancreatic ductal adenocarcinoma cells with wild-type TP53 results in TP53-induced apoptosis
medicine
SETDB1 expression is highly amplified in colorectal cancer. SETDB1 downregulation in SW480 and HCT116 cells reduces cell proliferation, migration, invasion, and increased colorectal cancer cells apoptosis. SETDB1 overexpression promotes colorectal cancer cells proliferation, migration, and invasion. High expression of SETDB1 is associated with a more aggressive phenotype in vitro. Cell cycle is arrested in G1 phase after SETDB1 silencing. Depletion of SETDB1 in vivo suppresses colorectal cancer cells proliferation. p21 is the target of SETDB1. After transfection with siSETDB1, expression of p21 s distinctly increased. Expression of p21 is significantly decreased after overexpression of SETDB1. SETDB1 can bind to the promoter of p21 and regulate its H3K9me3 enrichment level. Silencing of SETDB1 inhibits colorectal cancer tumorigenesis in vivo
medicine
Setdb1 has a constant role in endogenous retrovirus silencing. Distinctive sets of endogenous retroviruses are reactivated in different types of Setdb1-deficient somatic cells, including the VL30-class of endogenous retroviruses in mouse embryonic fibroblasts. A viral defense response is induced in immortalized Setdb1 knock-out embryonic fibroblasts
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Hachiya, R.; Shiihashi, T.; Shirakawa, I.; Iwasaki, Y.; Matsumura, Y.; Oishi, Y.; Nakayama, Y.; Miyamoto, Y.; Manabe, I.; Ochi, K.; Tanaka, M.; Goda, N.; Sakai, J.; Suganami, T.; Ogawa, Y.
The H3K9 methyltransferase Setdb1 regulates TLR4-mediated inflammatory responses in macrophages
Sci. Rep.
6
28845
2016
Mus musculus (O88974)
brenda
Wang, H.; An, W.; Cao, R.; Xia, L.; Erdjument-Bromage, H.; Chatton, B.; Tempst, P.; Roeder, R.G.; Zhang, L.
mAM facilitates conversion by ESET of dimethyl to trimethyl lysine 9 of histone H3 to cause transcriptional repression
Mol. Cell
12
475-487
2003
Homo sapiens (Q15047)
brenda
Yang, L.; Xia, L.; Wu, D.Y.; Wang, H.; Chansky, H.A.; Schubach, W.H.; Hickstein, D.D.; Zhang, Y.
Molecular cloning of ESET, a novel histone H3-specific methyltransferase that interacts with ERG transcription factor
Oncogene
21
148-152
2002
Mus musculus (O88974)
brenda
Price, A.J.; Manjegowda, M.C.; Kain, J.; Anandh, S.; Bochkis, I.M.
Hdac3, Setdb1, and Kap1 mark H3K9me3/H3K14ac bivalent regions in young and aged liver
Aging Cell
19
e13092
2020
Mus musculus (O88974)
brenda
Tachibana, K.; Gotoh, E.; Kawamata, N.; Ishimoto, K.; Uchihara, Y.; Iwanari, H.; Sugiyama, A.; Kawamura, T.; Mochizuki, Y.; Tanaka, T.; Sakai, J.; Hamakubo, T.; Kodama, T.; Doi, T.
Analysis of the subcellular localization of the human histone methyltransferase SETDB1
Biochem. Biophys. Res. Commun.
465
725-731
2015
Homo sapiens (Q15047)
brenda
Yahiro, K.; Higashihori, N.; Moriyama, K.
Histone methyltransferase Setdb1 is indispensable for Meckels cartilage development
Biochem. Biophys. Res. Commun.
482
883-888
2017
Mus musculus
brenda
Basavapathruni, A.; Gureasko, J.; Porter Scott, M.; Hermans, W.; Godbole, A.; Leland, P.A.; Boriack-Sjodin, P.A.; Wigle, T.J.; Copeland, R.A.; Riera, T.V.
Characterization of the enzymatic activity of SETDB1 and its 1 1 complex with ATF7IP
Biochemistry
55
1645-1651
2016
Homo sapiens (Q15047)
brenda
Liu, T.; Chen, X.; Li, T.; Li, X.; Lyu, Y.; Fan, X.; Zhang, P.; Zeng, W.
Histone methyltransferase SETDB1 maintains survival of mouse spermatogonial stem/progenitor cells via PTEN/AKT/FOXO1 pathway
Biochim. Biophys. Acta
1860
1094-1102
2017
Mus musculus (O88974)
brenda
Cao, N.; Yu, Y.; Zhu, H.; Chen, M.; Chen, P.; Zhuo, M.; Mao, Y.; Li, L.; Zhao, Q.; Wu, M.; Ye, M.
SETDB1 promotes the progression of colorectal cancer via epigenetically silencing p21 expression
Cell Death Dis.
11
351
2020
Homo sapiens (Q15047)
brenda
Fatima, A.; Irmak, D.; Noormohammadi, A.; Rinschen, M.M.; Das, A.; Leidecker, O.; Schindler, C.; Sanchez-Gaya, V.; Wagle, P.; Pokrzywa, W.; Hoppe, T.; Rada-Iglesias, A.; Vilchez, D.
The ubiquitin-conjugating enzyme UBE2K determines neurogenic potential through histone H3 in human embryonic stem cells
Commun. Biol.
3
262
2020
Homo sapiens (Q15047)
brenda
Hirota, T.; Blakeley, P.; Sangrithi, M.N.; Mahadevaiah, S.K.; Encheva, V.; Snijders, A.P.; ElInati, E.; Ojarikre, O.A.; de Rooij, D.G.; Niakan, K.K.; Turner, J.M.A.
SETDB1 links the meiotic DNA damage response to sex chromosome silencing in mice
Dev. Cell
47
645-659.e6
2018
Mus musculus (O88974)
brenda
Mochizuki, K.; Tando, Y.; Sekinaka, T.; Otsuka, K.; Hayashi, Y.; Kobayashi, H.; Kamio, A.; Ito-Matsuoka, Y.; Takehara, A.; Kono, T.; Osumi, N.; Matsui, Y.
SETDB1 is essential for mouse primordial germ cell fate determination by ensuring BMP signaling
Development
145
dev164160
2018
Mus musculus (O88974)
brenda
Singh, S.K.; Bahal, R.; Rasmussen, T.P.
Evidence that miR-152-3p is a positive regulator of SETDB1-mediated H3K9 histone methylation and serves as a toggle between histone and DNA methylation
Exp. Cell Res.
395
112216
2020
Homo sapiens (Q15047)
brenda
Ogawa, S.; Fukuda, A.; Matsumoto, Y.; Hanyu, Y.; Sono, M.; Fukunaga, Y.; Masuda, T.; Araki, O.; Nagao, M.; Yoshikawa, T.; Goto, N.; Hiramatsu, Y.; Tsuda, M.; Maruno, T.; Nakanishi, Y.; Hussein, M.S.; Tsuruyama, T.; Takaori, K.; Uemoto, S.; Seno, H.
SETDB1 inhibits p53-mediated apoptosis and is required for formation of pancreatic ductal adenocarcinomas in mice
Gastroenterology
159
682-696.e13
2020
Homo sapiens (Q15047), Mus musculus (O88974)
brenda
Cruz-Tapias, P.; Robin, P.; Pontis, J.; Del Maestro, L.; Ait-Si-Ali, S.
The H3K9 methylation writer SETDB1 and its reader MPP8 cooperate to silence satellite DNA repeats in mouse embryonic stem cells
Genes (Basel)
10
750
2019
Mus musculus
brenda
Orouji, E.; Federico, A.; Larribere, L.; Novak, D.; Lipka, D.B.; Assenov, Y.; Sachindra, S.; Hueser, L.; Granados, K.; Gebhardt, C.; Plass, C.; Umansky, V.; Utikal, J.
Histone methyltransferase SETDB1 contributes to melanoma tumorigenesis and serves as a new potential therapeutic target
Int. J. Cancer
145
3462-3477
2019
Homo sapiens (Q15047), Mus musculus (O88974)
brenda
Lee, S.; Lee, C.; Hwang, C.Y.; Kim, D.; Han, Y.; Hong, S.N.; Kim, S.H.; Cho, K.H.
Network inference analysis identifies SETDB1 as a key regulator for reverting colorectal cancer cells into differentiated normal-like cells
Mol. Cancer Res.
18
118-129
2020
Homo sapiens (Q15047)
brenda
Fritsch, L.; Robin, P.; Mathieu, J.R.; Souidi, M.; Hinaux, H.; Rougeulle, C.; Harel-Bellan, A.; Ameyar-Zazoua, M.; Ait-Si-Ali, S.
A subset of the histone H3 lysine 9 methyltransferases Suv39h1, G9a, GLP, and SETDB1 participate in a multimeric complex
Mol. Cell
37
46-56
2010
Homo sapiens (Q15047)
brenda
Kato, M.; Takemoto, K.; Shinkai, Y.
A somatic role for the histone methyltransferase Setdb1 in endogenous retrovirus silencing
Nat. Commun.
9
1683
2018
Mus musculus (O88974)
brenda
Jiang, Y.; Loh, Y.E.; Rajarajan, P.; Hirayama, T.; Liao, W.; Kassim, B.S.; Javidfar, B.; Hartley, B.J.; Kleofas, L.; Park, R.B.; Labonte, B.; Ho, S.M.; Chandrasekaran, S.; Do, C.; Ramirez, B.R.; Peter, C.J.; C W, J.T.; Safaie, B.M.; Morishita, H.; Roussos, P.; Nestler, E.J.; Schaefer, A.; Tycko, B.; Brennand, K.
The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain
Nat. Genet.
49
1239-1250
2017
Mus musculus (O88974)
brenda
Zeng, T.; Han, L.; Pierce, N.; Pfeifer, G.; Szabo, P.
EHMT2 and SETDB1 protect the maternal pronucleus from 5mC oxidation
Proc. Natl. Acad. Sci. USA
166
10834-10841
2019
Mus musculus (O88974)
brenda
Koryakov, D.E.
Diversity and functional specialization of H3K9-specific histone methyltransferases
Bioessays
46
e2300163
2024
Caenorhabditis elegans (G5EEU2)
brenda
Li, J.; Zheng, S.; Dong, Y.; Xu, H.; Zhu, Y.; Weng, J.; Sun, D.; Wang, S.; Xiao, L.; Jiang, Y.
Histone methyltransferase SETDB1 regulates the development of cortical Htr3a-positive interneurons and mood behaviors
Biol. Psychiatry
93
279-290
2023
Mus musculus (O88974)
brenda
Prashanth, S.; Radha Maniswami, R.; Rajajeyabalachandran, G.; Jegatheesan, S.K.
SETDB1, an H3K9-specific methyltransferase An attractive epigenetic target to combat cancer
Drug Discov. Today
29
103982
2024
Homo sapiens (Q15047)
brenda
de Groot, A.P.; Nguyen, H.; Pouw, J.S.; Weersing, E.; Dethmers-Ausema, A.; de Haan, G.
CBX7 inhibitors affect H3K9 methyltransferase-regulated gene repression in leukemic cells
Exp. Hematol.
142
104691
2024
Homo sapiens (Q15047)
brenda
Hu, L.; Cheng, Z.; Wu, L.; Luo, L.; Pan, P.; Li, S.; Jia, Q.; Yang, N.; Xu, B.
Histone methyltransferase SETDB1 promotes osteogenic differentiation in osteoporosis by activating OTX2-mediated BMP-Smad and Wnt/beta-catenin pathways
Hum. Cell
36
1373-1388
2023
Mus musculus (O88974)
brenda
Rapone, R.; Del Maestro, L.; Bouyioukos, C.; Albini, S.; Cruz-Tapias, P.; Joliot, V.; Cosson, B.; Ait-Si-Ali, S.
The cytoplasmic fraction of the histone lysine methyltransferase Setdb1 is essential for embryonic stem cells
iScience
26
107386
2023
Mus musculus (O88974)
brenda
Markouli, M.; Strepkos, D.; Piperi, C.
Structure, activity and function of the SETDB1 protein methyltransferase
Life
11
817
2021
Homo sapiens (Q15047)
brenda
Chandrasekaran, T.T.; Choudalakis, M.; Brhm, A.; Weirich, S.; Kouroukli, A.G.; Ammerpohl, O.; Rathert, P.; Bashtrykov, P.; Jeltsch, A.
SETDB1 activity is globally directed by H3K14 acetylation via its triple tudor domain
Nucleic Acids Res.
52
13690-13705
2024
Homo sapiens (Q15047)
brenda
Ueshima, S.; Fang, J.
Histone H3K9 methyltransferase SETDB1 augments invadopodia formation to promote tumor metastasis
Oncogene
41
3370-3380
2022
Mus musculus (O88974)
brenda
Kazerani, M.; Cernilogar, F.; Pasquarella, A.; Hinterberger, M.; Nuber, A; Klein, L.; Schotta, G.
Histone methyltransferase SETDB1 safeguards mouse fetal hematopoiesis by suppressing activation of cryptic enhancers
Proc. Natl. Acad. Sci. USA
121
e2409656121
2024
Mus musculus (O88974)
brenda
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