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IUBMB CommentsThis entry describes several enzymes that methylate the L-lysine-9 residue of histone H3 (H3K9) only once, generating a monomethylated form. These modifications influence the binding of chromatin-associated proteins. cf. EC 2.1.1.368, [histone H3]-lysine9 N-dimethyltransferase, EC 2.1.1.355, [histone H3]-lysine9 N-trimethyltransferase, and EC 2.1.1.366, [histone H3]-N6,N6-dimethyl-lysine9 N-methyltransferase.
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physiological function
Prdm3 and Prdm16 are redundant histone H3K9me1-specific methyltransferases that direct cytoplasmic H3K9me1 methylation. The H3K9me1 is converted in the nucleus to H3K9me3 by the Suv39h enzymes to reinforce heterochromatin. Simultaneous depletion of Prdm3 and Prdm16 abrogates H3K9me1 methylation, prevents Suv39h-dependent H3K9me3 trimethylation, and derepresses major satellite transcription. Combined impairment of Prdm3 and Prdm16 results in disintegration of heterochromatic foci and disruption of the nuclear lamina
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
loss of Prdm16 causes craniofacial defects including anterior mandibular hypoplasia, clefting in the secondary palate and severe middle ear defects. Loss of Prdm16 significantly decreases histone 3 lysine 9 methylation in the palatal shelves but does not change histone 3 lysine 4 methylation
physiological function
loss of Prdm3 or Prdm16 in zebrafish causes craniofacial defects including hypoplasia of the craniofacial cartilage elements, undefined posterior ceratobranchials, and decreased mineralization of the parasphenoid. Prdm3 and Prdm16 compensate for each other as well as a Prdm1a. Combinatorial loss of Prdm1a, Prdm3, and Prdm16 alleles results in severe hypoplasia of the anterior cartilage elements, abnormal formation of the jaw joint, complete loss of the posterior ceratobranchials, and clefting of the ethmoid plate. Loss of Prdm3 and Prdm16 reduces methylation of histone 3 lysine 9 (repression) and histone 3 lysine 4 (activation) in zebrafish
physiological function
overexpression of the PR domain of PRDM16 represses the differentiation of porcine preadipocytes. Overexpression of the PR domain significantly increases the level of lipolysis and mitochondrial oxidative capacity during differentiation. The protein coded by the PR domain has H3K9me1 methyltransferase activity
physiological function
PRDM16 is a histone H3 K9 methyltransferase on chromatin. Mutation in the N-terminal PR-domain of PRDM16 completely abolishes the intrinsic enzymatic activity of PRDM16. The methyltransferase activity of PRDM16 is required for specific suppression of mixed lineage leukemia leukemogenesis both in vitro and in vivo. PRDM16 directly activates the SNAG family transcription factor GFI1b, which in turn down regulates the HOXA gene cluster. Knockdown GFI1b represses PRDM16-mediated tumor suppression while GFI1b overexpression mimics PRDM16 overexpression. Silencing PRDM16 by DNA methylation is concomitant with mixed lineage leukemia MLL-AF9 induced leukemic transformation
physiological function
simultaneous depletion of Prdm3 and Prdm16 abrogates H3K9me1 methylation, prevents Suv39h-dependent H3K9me3 trimethylation, and derepresses major satellite transcription. Combined impairment of Prdm3 and Prdm16 results in disintegration of heterochromatic foci and disruption of the nuclear lamina
physiological function
SUVH3 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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CLR4_CRYNH
Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)
1820
0
194979
Swiss-Prot
other Location (Reliability: 1)
CLR4_SCHPO
Schizosaccharomyces pombe (strain 972 / ATCC 24843)
490
0
55918
Swiss-Prot
other Location (Reliability: 1)
SUVH3_ARATH
669
0
73439
Swiss-Prot
other Location (Reliability: 3)
SUVH3_CHLRE
957
0
98344
Swiss-Prot
other Location (Reliability: 3)
SUVH4_ARATH
624
0
70056
Swiss-Prot
other Location (Reliability: 5)
SUVH5_ARATH
794
0
88153
Swiss-Prot
other Location (Reliability: 4)
SUVH6_ARATH
790
0
87477
Swiss-Prot
other Location (Reliability: 2)
SUVH7_ARATH
693
0
77632
Swiss-Prot
other Location (Reliability: 3)
SUVH8_ARATH
755
0
84528
Swiss-Prot
other Location (Reliability: 3)
MECOM_HUMAN
1230
0
138136
Swiss-Prot
other Location (Reliability: 3)
MECOM_MOUSE
1232
0
138100
Swiss-Prot
other Location (Reliability: 4)
SETD5_HUMAN
1442
0
157515
Swiss-Prot
other Location (Reliability: 2)
SETD5_MOUSE
1441
0
157426
Swiss-Prot
other Location (Reliability: 2)
MET2_CAEEL
1304
0
148155
Swiss-Prot
other Location (Reliability: 1)
ASH1L_HUMAN
2969
0
332790
Swiss-Prot
other Location (Reliability: 2)
ASH1L_MOUSE
2958
0
331333
Swiss-Prot
other Location (Reliability: 2)
PRD16_HUMAN
1276
0
140251
Swiss-Prot
other Location (Reliability: 4)
PRD16_MOUSE
1275
0
140858
Swiss-Prot
other Location (Reliability: 3)
EHMT1_HUMAN
1298
0
141466
Swiss-Prot
other Location (Reliability: 1)
EHMT1_MOUSE
1296
0
141999
Swiss-Prot
other Location (Reliability: 1)
EHMT2_HUMAN
1210
0
132370
Swiss-Prot
other Location (Reliability: 2)
EHMT2_MOUSE
1263
0
138039
Swiss-Prot
other Location (Reliability: 5)
A5XCD6_DANRE
153
0
17888
TrEMBL
-
I3L9C5_PIG
1278
0
139609
TrEMBL
-
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Pinheiro, I.; Margueron, R.; Shukeir, N.; Eisold, M.; Fritzsch, C.; Richter, F.M.; Mittler, G.; Genoud, C.; Goyama, S.; Kurokawa, M.; Son, J.; Reinberg, D.; Lachner, M.; Jenuwein, T.
Prdm3 and Prdm16 are H3K9me1 methyltransferases required for mammalian heterochromatin integrity
Cell
150
948-960
2012
Mus musculus (A2A935), Mus musculus (P14404), Mus musculus
brenda
Gu, T.; Xu, G.; Jiang, C.; Hou, L.; Wu, Z.; Wang, C.
PRDM16 represses the pig white lipogenesis through promoting lipolysis activity
BioMed Res. Int.
2019
1969413
2019
Sus scrofa (I3L9C5), Sus scrofa
brenda
Shull, L.C.; Sen, R.; Menzel, J.; Goyama, S.; Kurokawa, M.; Artinger, K.B.
The conserved and divergent roles of Prdm3 and Prdm16 in zebrafish and mouse craniofacial development
Dev. Biol.
461
132-144
2020
Mus musculus (A2A935), Mus musculus, Danio rerio (A5XCD6), Danio rerio
brenda
Casas-Mollano, J.A.; Lao, N.T.; Kavanagh, T.A.
Intron-regulated expression of SUVH3, an Arabidopsis Su(var)3-9 homologue
J. Exp. Bot.
57
3301-3311
2006
Arabidopsis thaliana (Q9C5P4), Arabidopsis thaliana
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
Zhou, B.; Wang, J.; Lee, S.Y.; Xiong, J.; Bhanu, N.; Guo, Q.; Ma, P.; Sun, Y.; Rao, R.C.; Garcia, B.A.; Hess, J.L.; Dou, Y.
PRDM16 suppresses MLL1r leukemia via intrinsic histone methyltransferase activity
Mol. Cell
62
222-236
2016
Homo sapiens (Q9HAZ2)
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 (Q9C5P4), Arabidopsis thaliana
brenda
2.1.1.367 [histone H3]-lysine9 N-methyltransferase
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