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IUBMB CommentsThis entry describes several enzymes, characterized from plants, that successively methylate the L-lysine-9 residue of histone H3 (H3K9) twice, ultimately generating a dimethylated form. These modifications influence the binding of chromatin-associated proteins. In general, the methylation of H3K9 leads to transcriptional repression of the affected target genes. cf. EC 2.1.1.367, [histone H3]-lysine9 N-methyltransferase, EC 2.1.1.366, [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase, and EC 2.1.1.355, [histone H3]-lysine9 N-trimethyltransferase.
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S-adenosyl-L-methionine + a [histone H3]-L-lysine9
S-adenosyl-L-homocysteine + a [histone H3]-N6-methyl-L-lysine9
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S-adenosyl-L-methionine + a [histone H3]-N6-methyl-L-lysine9
S-adenosyl-L-homocysteine + a [histone H3]-N6,N6-dimethyl-L-lysine9
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-
-
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S-adenosyl-L-methionine + [histone H3 peptide 1-15]-L-lysine9
S-adenosyl-L-homocysteine + [histone H3 peptide 1-15]-N6-methyl-L-lysine9
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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
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-
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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
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-
-
?
S-adenosyl-L-methionine + [histone H3]-L-lysine9
S-adenosyl-L-homocysteine + [histone H3]-N6-methyl-L-lysine9
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-
-
?
S-adenosyl-L-methionine + [histone H3]-N6-methyl-L-lysine9
S-adenosyl-L-homocysteine + [histone H3]-N6,N6-dimethyl-L-lysine9
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additional information
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additional information
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H3K9 methylation by SETDB1 occurs in a distributive manner
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additional information
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SET1 methylates both K9 and less efficiently K27 of histone H3 in vitro, reactions of EC 2.1.1.368 and 2.1.1.371, respectively
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0.53 - 0.68
S-adenosyl-L-methionine
0.28 - 0.41
[histone H3 peptide 1-15]-L-lysine9
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0.41 - 0.59
[histone H3 peptide 1-15]-N6-methyl-L-lysine9
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0.53
S-adenosyl-L-methionine
substrate [histoneH3 peptide 1-15]-L-lysine9, SETDB1:ATF7IP complex, pH 7.6, 23°C
0.54
S-adenosyl-L-methionine
substrate [histoneH3 peptide 1-15]-N6-methyl-L-lysine9, SETDB1:ATF7IP complex, pH 7.6, 23°C
0.56
S-adenosyl-L-methionine
substrate [histoneH3 peptide 1-15]-N6-methyl-L-lysine9, pH 7.6, 23°C
0.68
S-adenosyl-L-methionine
substrate [histoneH3 peptide 1-15]-L-lysine9, pH 7.6, 23°C
0.28
[histone H3 peptide 1-15]-L-lysine9
SETDB1:ATF7IP complex, pH 7.6, 23°C
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0.41
[histone H3 peptide 1-15]-L-lysine9
pH 7.6, 23°C
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0.41
[histone H3 peptide 1-15]-N6-methyl-L-lysine9
SETDB1:ATF7IP complex, pH 7.6, 23°C
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0.59
[histone H3 peptide 1-15]-N6-methyl-L-lysine9
pH 7.6, 23°C
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0.072 - 0.352
S-adenosyl-L-methionine
0.027 - 0.192
[histone H3 peptide 1-15]-L-lysine9
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0.045 - 0.293
[histone H3 peptide 1-15]-N6-methyl-L-lysine9
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0.072
S-adenosyl-L-methionine
substrate [histone H3 peptide 1-15]-L-lysine9, SETDB1:ATF7IP complex, pH 7.6, 23°C
0.09
S-adenosyl-L-methionine
substrate [histone H3 peptide 1-15]-N6-methyl-L-lysine9, SETDB1:ATF7IP complex, pH 7.6, 23°C
0.337
S-adenosyl-L-methionine
substrate [histone H3 peptide 1-15]-L-lysine9, pH 7.6, 23°C
0.352
S-adenosyl-L-methionine
substrate [histone H3 peptide 1-15]-N6-methyl-L-lysine9, pH 7.6, 23°C
0.027
[histone H3 peptide 1-15]-L-lysine9
SETDB1:ATF7IP complex, pH 7.6, 23°C
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0.192
[histone H3 peptide 1-15]-L-lysine9
pH 7.6, 23°C
-
0.045
[histone H3 peptide 1-15]-N6-methyl-L-lysine9
SETDB1:ATF7IP complex, pH 7.6, 23°C
-
0.293
[histone H3 peptide 1-15]-N6-methyl-L-lysine9
pH 7.6, 23°C
-
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0.135 - 0.628
S-adenosyl-L-methionine
0.095 - 0.467
[histone H3 peptide 1-15]-L-lysine9
-
0.11 - 0.497
[histone H3 peptide 1-15]-N6-methyl-L-lysine9
-
0.135
S-adenosyl-L-methionine
substrate [histoneH3 peptide 1-15]-L-lysine9, SETDB1:ATF7IP complex, pH 7.6, 23°C
0.167
S-adenosyl-L-methionine
substrate [histoneH3 peptide 1-15]-N6-methyl-L-lysine9, SETDB1:ATF7IP complex, pH 7.6, 23°C
0.495
S-adenosyl-L-methionine
substrate [histoneH3 peptide 1-15]-L-lysine9, pH 7.6, 23°C
0.628
S-adenosyl-L-methionine
substrate [histoneH3 peptide 1-15]-N6-methyl-L-lysine9, pH 7.6, 23°C
0.095
[histone H3 peptide 1-15]-L-lysine9
SETDB1:ATF7IP complex, pH 7.6, 23°C
-
0.467
[histone H3 peptide 1-15]-L-lysine9
pH 7.6, 23°C
-
0.11
[histone H3 peptide 1-15]-N6-methyl-L-lysine9
SETDB1:ATF7IP complex, pH 7.6, 23°C
-
0.497
[histone H3 peptide 1-15]-N6-methyl-L-lysine9
pH 7.6, 23°C
-
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physiological function
ectopic expression of SET1 causes an increase in methylated histone H3 lysine 9 and abnormal chromosome segregation in tobacco suspension cells, and inhibits tobacco plant growth. The inhibition of plant growth is caused by reduced cell expansion as well as by abnormal cell division and differentiation. Deletion of the C-terminally located catalytic domain of the protein abolishes the ectopic effects of SET1 on plant growth
physiological function
in SUVH2 null plants, mono- and dimethyl H3K9, mono- and dimethyl H3K27, and monomethyl H4K20 are significantly reduced. Loss of function suppresses, whereas overexpression enhances, gene silencing, causes ectopic heterochromatization and significant growth defects. Modification of transgene silencing by SUVH2 is partially transmitted to the offspring plants. This epigenetic stability correlates with heritable changes in DNA methylation. Mutational dissection of SUVH2 indicates an implication of its N-terminus and YDG domain in directing DNA methylation to target sequences. Gene silencing by SUVH2 depends on MET1 and DDM1, but not CMT3
physiological function
SET1 methylates both K9 and K27 of histone H3 in vitro. Ectopic expression of SET1 increases the amount of dimethylated H3K9 and induces chromosome-segregation defects in tobacco BY2 cells. The histone methyltransferase activity, the association with specific chromatin regions and with condensed chromosomes, and the cellular effects largely depend on the C-terminal region including the SET domain of the protein. The N-terminal part of SET1 is capable of targeting the green fluorescent protein to interphase chromatin. SET1 binds LHP1, the Arabidopsis homolog of animal heterochromatin protein 1, and LHP1 colocalizes with heterochromatin containing high amounts of dimethylated H3K9
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
ectopic expression of SET1 increases the amount of dimethylated H3K9 and induces chromosome-segregation defects in tobacco BY2 cells. The histone methyltransferase activity, the association with specific chromatin regions and with condensed chromosomes, and the cellular effects largely depend on the C-terminal region including the SET domain of the protein. The N-terminal part of SET1 is capable of targeting the green fluorescent protein to interphase chromatin. SET1 binds LHP1, the Arabidopsis homolog of animal heterochromatin protein 1, and LHP1 colocalizes with heterochromatin containing high amounts of dimethylated H3K9
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
SUVH1 acts as an anti-silencing factor and promotes the expression of several endogenous genes with promoter DNA methylation. SUVH1 mutation does not alter DNA methylation levels, thus, SUVH1 functions downstream of DNA methylation. Histone H3 lysine 4 trimethylation is reduced in a SUVH1 mutant, in contrast, H3K9 methylation levels remain unchanged
physiological function
SUVH1 binds methylated DNA in vitro, is associated with euchromatic methylation in vivo, and forms a complex with two DNAJ domain-containing homologs, DNAJ1 and DNAJ2. Ectopic recruitment of DNAJ1 enhances gene transcription
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Naumann, K.; Fischer, A.; Hofmann, I.; Krauss, V.; Phalke, S.; Irmler, K.; Hause, G.; Aurich, A.C.; Dorn, R.; Jenuwein, T.; Reuter, G.
Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis
EMBO J.
24
1418-1429
2005
Arabidopsis thaliana (O22781)
brenda
Shen, W.H.; Meyer, D.
Ectopic expression of the NtSET1 histone methyltransferase inhibits cell expansion, and affects cell division and differentiation in tobacco plants
Plant Cell Physiol.
45
1715-1719
2004
Nicotiana tabacum (Q93YF5)
brenda
Yu, Y.; Dong, A.; Shen, W.H
Molecular characterization of the tobacco SET domain protein NtSET1 unravels its role in histone methylation, chromatin binding, and segregation
Plant J.
40
699-711
2004
Nicotiana tabacum (Q93YF5)
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
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 (Q96KQ7), Homo sapiens (Q9H9B1)
brenda
Li, S.; Liu, L.; Li, S.; Gao, L.; Zhao, Y.; Kim, Y.J.; Chen, X.
SUVH1, a Su(var)3-9 family member, promotes the expression of genes targeted by DNA methylation
Nucleic Acids Res.
44
608-620
2016
Arabidopsis thaliana (Q9FF80)
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 (Q9Z148)
brenda
Harris, C.J.; Scheibe, M.; Wongpalee, S.P.; Liu, W.; Cornett, E.M.; Vaughan, R.M.; Li, X.; Chen, W.; Xue, Y.; Zhong, Z.; Yen, L.; Barshop, W.D.; Rayatpisheh, S.; Gallego-Bartolome, J.; Groth, M.; Wang, Z.; Wohlschlegel, J.A.; Du, J.; Rothbart, S.B.; Butter, F.; Jacobsen, S.E.
A DNA methylation reader complex that enhances gene transcription
Science
362
1182-1186
2018
Arabidopsis thaliana (Q9FF80), Arabidopsis thaliana
brenda