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evolution
human JMJD2 (KDM4) H3K9 and H3K36 demethylases can be divided into members that act on both H3K9 and H3K36 and H3K9 alone, structural and phylogenetic analysis, overview. KDM4D and -E only act on H3K9, with no evidence for demethylation of H3K36, while KDM4A/B/C act on both H3K9 and, less efficiently, on H3K36-methylated substrates, substrate selectivity of the human KDM4 histone demethylase subfamily, overview
evolution
KDM4A belongs to the KDM4 family
evolution
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the enzyme belongs to the family of KDM4A-D histone demethylases
evolution
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the enzyme belongs to the JMJD2/KDM4 subfamily (JMJD2A, B, C and D) specifically demethylates H3K9 and H3K36 either di- or trimethylated
evolution
the enzyme belongs to the JMJD2/KDM4 subfamily (JMJD2A, B, C and D) specifically demethylates H3K9 and H3K36 either di- or trimethylated
evolution
the enzyme belongs to the Jmjd2 family of H3K9/H3K36 histone demethylases
evolution
the enzyme belongs to the KDM2-8 family, KDM4 (also known as JMJD2) subfamily, which divided into five isoforms A-E
evolution
the enzyme JMJD2B belongs to the jumonji C (JmjC) domain-containing, iron-dependent dioxygenases (JMJC demethylases)
evolution
enzyme CG15835 shows higher identity to mammalian JMJD2D (40%) than to any of the other mammalian JMJD2 isoforms (22%)
evolution
enzyme CG33182 shows higher identity to mammalian JMJD2D (40%) than to any of the other mammalian JMJD2 isoforms (22%)
evolution
JMJD2A is a JmjC histone demethylase (HDM)
evolution
KDM4C is a member of the KDM4 subgroup of JmjC domain-containing proteins which catalyzes the demethylation of tri- and dimethylated lysine 9 and lysine 36 on histoneH3
evolution
the Drosophila melanogaster HDM gene Dmel\Kdm4A is a homologue of the human JMJD2 family. Dmel\JHMD1, Dmel\JHMD2, and Dmel\Kdm4A are each highly conserved with their human homologue counterparts
evolution
the enzyme belongs to the KDM4/JmjC demethylase histone demethylase family. KDM4F is very similar to KDM4E sharing 94% identity over 369 residues. The selectivity of KDM4 enzymes is determined by multiple interactions within the catalytic domain but outside the active site. Evolutionary analysis of the KDM4 demethylase subfamily
evolution
the enzyme belongs to the KDM4/JmjC demethylase histone demethylase family. The selectivity of KDM4 enzymes is determined by multiple interactions within the catalytic domain but outside the active site. All KDM4 subfamily members have highly conserved residues lining the methylammonium-binding pocket. The exceptions are Ser288A/Ser-289B/Ser290C and Thr289A/Thr290B/Thr291C in KDM4A, B, and C, which are substituted by Ala287D/Ala289E/Ala286F and Ile288D/Ile290E/Ile287F in KDM4D-F, respectively. Evolutionary analysis of the KDM4 demethylase subfamily
evolution
the enzyme belongs to the KDM4/JmjC demethylase histone demethylase family. The selectivity of KDM4 enzymes is determined by multiple interactions within the catalytic domain but outside the active site. Evolutionary analysis of the KDM4 demethylase subfamily
evolution
the enzyme belongs to the KDM4/JmjC demethylase histone demethylase family. The selectivity of KDM4 enzymes is determined by multiple interactions within the catalytic domain but outside the active site. Evolutionary analysis of the KDM4 demethylase subfamily, a KDM4D type activity is important in eutherian biology
evolution
the enzyme encoded by gene AN1060 (designated as kdmA) is a member of the mammalian KDM4 family of proteins (also known as JHDM3/JMJD2 in mammals)
evolution
the human KDM4 family consists of four members, KDM4A-D (also known as JMJD2A-D). These enzymes specifically catalyze the demethylation of H3K9me3/me2, H3K36me2/me3 and H1.4K26me2/me3 in a Fe2+ and 2-oxoglutarate-dependent manner. Besides the catalytic JmjC domain, KDM4 demethylases contain the JmjN domain, which is also required for the demethylase activity. In addition, all KDM4 members, except the shortest KDM4D protein, contain two Plant homeodomain (PHD) and two Tudor domains. Gene KDM4D is Y chromosome-encoded and a truncated enzyme variant compared to KDM4A-C
evolution
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the enzyme encoded by gene AN1060 (designated as kdmA) is a member of the mammalian KDM4 family of proteins (also known as JHDM3/JMJD2 in mammals)
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evolution
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the enzyme encoded by gene AN1060 (designated as kdmA) is a member of the mammalian KDM4 family of proteins (also known as JHDM3/JMJD2 in mammals)
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evolution
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the enzyme encoded by gene AN1060 (designated as kdmA) is a member of the mammalian KDM4 family of proteins (also known as JHDM3/JMJD2 in mammals)
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evolution
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the enzyme belongs to the Jmjd2 family of H3K9/H3K36 histone demethylases
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evolution
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the enzyme encoded by gene AN1060 (designated as kdmA) is a member of the mammalian KDM4 family of proteins (also known as JHDM3/JMJD2 in mammals)
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evolution
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the enzyme encoded by gene AN1060 (designated as kdmA) is a member of the mammalian KDM4 family of proteins (also known as JHDM3/JMJD2 in mammals)
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malfunction
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depletion of JMJD2B impairs the estrogen-induced G1/S transition of the cell cycle in vitro and inhibits breast tumorigenesis in vivo. Cells with loss of function of JMJD2B display a substantial retention of H3K9me3 in the TFF1 and EBAG9 promoters upon estrogen receptor alpha activation, although the total histone H3 levels and H3K9me3 status on other gene promoters are not affected. H3K4 hypermethylation and H3K9 hypomethylation are prevalent histone marks that are associated with transcriptional activation
malfunction
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enzyme depletion suppresses tumor formation
malfunction
siRNA-mediated reduction of expression of JMJD2B in bladder and lung cancer cell lines significantly suppresses the proliferation of cancer cells, and suppressing JMJD2B expression leads to a decreased population of cancer cells in S phase, with a concomitant increase of cells in G1 phase
malfunction
dysregulated expression of KDM4A-D family promotes chromosomal instabilities
malfunction
JMJD2B knockdown using siRNA in 3T3-L1 preadipocytes represses the expression of PPARgamma and C/EBPalpha, resulting in inhibition of adipogenesis. This is accompanied by increased enrichment of H3K9me3/me2 on the promoter of PPARgamma and C/EBPalpha. In contrast, overexpression of JMJD2B increases the expression of PPARgamma and C/EBPalpha, which is accompanied by decreased enrichment of H3K9me3/me2 on the promoter and activated adipogenesis
malfunction
Kdm3b knockout mice show restricted postnatal growth and female infertility. Kdm3b ablation decreases IGFBP-3 expressed in the kidney by 53% and significantly reduces IGFBP-3 in the blood, which causes an accelerated degradation of IGF-1 and a 36% decrease in circulating IGF-1 concentration. Kdm3b is highly expressed in the female reproductive organs including ovary, oviduct and uterus. Knockout of Kdm3b in female mice causes irregular estrous cycles, decreases 45% of the ovulation capability and 47% of the fertilization rate, and reduces 44% of the uterine decidual response, which are accompanied with a more than 50% decrease in the circulating levels of the 17beta-estradiol. These female reproductive phenotypes are associated with significantly increased levels of H3K9me1/2/3 in the ovary and uterus. Kdm3bKO mice exhibit restricted somatic growth, low levels of circulating IGF-1 and IGFBP-3 and fast degradation of IGF-1. Female Kdm3bKO mice exhibit a severely impaired reproductive function. Knockout of Kdm3b in female mice prolonges their estrous cycles and reduces their ovulation capacity and fertilization efficiency. Phenotype, overview
malfunction
the percentage loss of H3K9me3 in KDM4A-induced U2OS cells at 1% O2 is relatively consistent with loss of H3K9me3 found in HeLa cells transiently transfected with KDM4A (50% compared with 40%, respectively), indicating a similar effect of hypoxia on KDM4A activity in different cell lines
malfunction
attenuation of Jmjd2b by si RNA, increases expression of Jmjd3, the H3K27me3 demethylase, and of Ccl2, overview. Jmjd2b attenuation inhibits the gene expression of p65, inducible nitric oxide synthase, B cell lymphoma 2, and transforming growth factor beta in Jmjd2b-knockdown NE-4C cells. In NE-4C cells, Jmjd2b attenuation alters the expression of different genes including Notch1, Notch2, Efna5, Cyr61, Efnb2, Tgf-b2, Nodal, Nrp2, Cntfr, Plxnc1, Hivep2, Lef1, Gabrb2, Sema3e, Meis1, and Itgb8, which all experiencing downregulation of more than 2fold
malfunction
disruption of Dmel\Kdm4A results in a reduction of the male life span and a male-specific wing extension/twitching phenotype that occurs in response to other males and is reminiscent of an inter-male courtship phenotype involving the courtship song, phenotypes overview. Certain genes associated with each of these phenotypes are significantly downregulated in response to Dmel\Kdm4A loss, most notably the longevity associated Hsp22 gene and the male sex-determination fruitless gene
malfunction
dysregulated expression of KDM4A-D family promotes chromosomal instabilities. Dysregulation of KDM4C expression promotes mitotic chromosome missegregation. KDM4B-C members are overexpressed in several types of human cancer and its depletion impairs cancer cell proliferation
malfunction
dysregulated expression of KDM4A-D family promotes chromosomal instabilities. KDM4B-C members are overexpressed in several types of human cancer and its depletion impairs cancer cell proliferation
malfunction
Jmjd2c depletion leads to embryonic stem cell differentiation, which is accompanied by a reduction in the expression of embryonic stem cell-specific genes and an induction of lineage marker genes. The level of H3K36Me3 is not significantly affected by Jmjd2c depletion. Knockdown of Jmjd1a does not appreciably affect Jmjd2c and vice versa
malfunction
Jmjd2c is dispensable for embryonic stem cell maintenance and embryogenesis, while combined deficiency for specifically Jmjd2a and Jmjd2c leads to early embryonic lethality and impaired embryonic stem cell (ESC) self-renewal, with spontaneous differentiation towards primitive endoderm under permissive culture conditions, phenotype, overview. Only specific genomic elements are affected upon loss of Jmjd2 function. Loss of Jmjd2a and Jmjd2c has a drastic effect on ESC proliferation
malfunction
KDM4A/JMJD2A overexpression leads to localized copy gain of 1q12, 1q21, and Xq13.1 without global chromosome instability, KDM4A-amplified tumors have increased copy gains for these same regions. 1q12h copy gain occurs within a single cell cycle, requires S phase, and is not stable but is regenerated each cell division. Sites with increased copy number are rereplicated and have increased KDM4A, MCM, and DNA polymerase occupancy. Suv39h1/KMT1A or HP1g overexpression suppresses the copy gain, whereas H3K9/K36 methylation interference promotes gain. Overexpression of a chromatin modifier results in site-specific copy gains
malfunction
Kdm4d-null mice are viable and fertile and do not show any obvious phenotype. But H3K9me3 accumulates significantly in Kdm4d-null round spermatids, and the distribution of methylated H3K9 in germ cells is dramatically changed. Nevertheless, the progression of spermatogenesis and the number of spermatozoa are normal, likely secondary to the earlier nuclear localization of another H3K9 tridemethylase, KDM4B, in Kdm4d-null elongating spermatids
malfunction
knocking down JMJD2B expression by siRNA in gastric and other cancer cells inhibits cell proliferation and/or induces apoptosis and elevates the expression of p53 and p21CIP1 proteins, mechanism of JMJD2B inhibition, overview. The enhanced p53 expression results from activation of the DNA damage response pathway
malfunction
lack of either Jmjd2a or Jmjd2b is compatible with embryonic stem cell self-renewal and embryonic development. Only specific genomic elements are affected upon loss of Jmjd2 function
malfunction
lack of either Jmjd2a or Jmjd2b is compatible with embryonic stem cell self-renewal and embryonic development. While individual Jmjd2 family members are dispensable for embryonic stem cell maintenance and embryogenesis, combined deficiency for specifically Jmjd2a and Jmjd2c leads to early embryonic lethality and impaired embryonic stem cell (ESC) self-renewal, with spontaneous differentiation towards primitive endoderm under permissive culture conditions, phenotype, overview. Only specific genomic elements are affected upon loss of Jmjd2 function. Loss of Jmjd2a and Jmjd2c has a drastic effect on ESC proliferation
malfunction
loss of JmjD2A function causes dramatic downregulation of neural crest specifier genes analyzed by multiplex NanoString and in situ hybridization. Cells overexpressing JmjD2A completely lack either H3K9me3 or H3K36me3 marks. Overexpression of JmjD2A in chicken fibroblasts specifically depletes H3K9me3 and H3K36me3. JmjD2A loss of function depletes Sox10 expression and expression of neural crest specifier genes Sox9, FoxD3, and Snail2, but not dorsal neural tube markers. JmjD2A knockdown inhibits demethylation of H3K9me3 on the Sox10 promoter
malfunction
mutations of the G12-G13 motif abrogate H3K9me3 demethylation by JMJD2A
malfunction
mutations of the residues comprising the methylammonium-binding pocket abrogate demethylation by JMJD2A, with the exception of an S288A substitution, which augments activity, particularly toward H3K9me2
malfunction
overexpression of CG15835 results in spreading of HP1 into euchromatin and a strong decrease on the levels of H3K9me3 and H3K36me3, while the levels of H3K4me3 and H3K27me3 are not significantly altered. Demethylase activity of dJMJD2(1)/CG15835 depends on the JmjC domain, as it is abolished by mutations that affect its catalytic activity. The single-point mutation H195A, mutating one of the Fe2+ binding residues, abolishes demethylase activity of dJMJD2(1)/CG15835
malfunction
overexpression of the histone lysine demethylase KDM4A is related to the pathology of several human cancers
malfunction
Pim1 knockdown and P21(WAF1/Cip1) overexpression fully abrogates the oncogenic function of JMJD2A. A 39KD JMJD2A transcript, JMJD2ADELTA, is significantly increased in JMJD2A or miR372 overexpressing Hep3B cell line
malfunction
siRNA silencing of DELTAN-JMJD2A results in drastic impairment of MHC expression and myotube formation, the Myog promoter is a specific target of DElTAN-JMJD2A. Genome-wide expression profiling and exon-specific siRNA knockdown indicate that, in contrast to the full-length protein, the N-terminal demethylase domain is necessary for myotube formation and muscle-specific gene expression
malfunction
the kdmA mutant shows a significant increase in H3K36me3 during primary metabolism at the aflR and ipnA locus and some slightly higher levels at the aptA genes, the mutant has reduced levels of sterigmatocystin compared to wild-type. Manipulation of kdmA expression reveals genetic and environmental interactions including lethality under light. Deletion of kdmA causes light lethality and sensitivity to oxidative stress during vegetative growth to chronic oxidative stress
malfunction
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enzyme downregulation inhibits cell proliferation in wild type and even more so in p53-deficient HCT-116 colon cancer cells. Enzyme depletion also induces more strongly apoptosis in p53-deficient compared to wild-type HCT-116 cells
malfunction
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enzyme Gasc1 hypomorphic mutant mice exhibit abnormal behaviors including hyperactivity, persistence and many types of learning and memory deficits and abnormal synaptic functions such as prolonged long-term potentiation. Reduced expression of enzyme Gasc1 induces an increase in the number of glial fibrillary acidic protein-positive astrocytes from postnatal day 30 to months 2-3
malfunction
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enzyme loss leads to globally elevated levels of the heterochromatin marker [histone H3]-N6,N6-dimethyl-L-lysine9/[histone H3]-N6,N6,N6-trimethyl-L-lysine9 and impedes transcriptional activation of ecdysone response genes, resulting in developmental arrest.
malfunction
loss of enzyme function results in obesity and hyperlipidemia in mice. Loss of enzyme function disrupts beta-adrenergic-stimulated glycerol release and oxygen consumption in brown fat, and decreases fat oxidation and glycerol release in skeletal muscles
malfunction
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the kdmA mutant shows a significant increase in H3K36me3 during primary metabolism at the aflR and ipnA locus and some slightly higher levels at the aptA genes, the mutant has reduced levels of sterigmatocystin compared to wild-type. Manipulation of kdmA expression reveals genetic and environmental interactions including lethality under light. Deletion of kdmA causes light lethality and sensitivity to oxidative stress during vegetative growth to chronic oxidative stress
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malfunction
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the kdmA mutant shows a significant increase in H3K36me3 during primary metabolism at the aflR and ipnA locus and some slightly higher levels at the aptA genes, the mutant has reduced levels of sterigmatocystin compared to wild-type. Manipulation of kdmA expression reveals genetic and environmental interactions including lethality under light. Deletion of kdmA causes light lethality and sensitivity to oxidative stress during vegetative growth to chronic oxidative stress
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malfunction
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the kdmA mutant shows a significant increase in H3K36me3 during primary metabolism at the aflR and ipnA locus and some slightly higher levels at the aptA genes, the mutant has reduced levels of sterigmatocystin compared to wild-type. Manipulation of kdmA expression reveals genetic and environmental interactions including lethality under light. Deletion of kdmA causes light lethality and sensitivity to oxidative stress during vegetative growth to chronic oxidative stress
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malfunction
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Kdm3b knockout mice show restricted postnatal growth and female infertility. Kdm3b ablation decreases IGFBP-3 expressed in the kidney by 53% and significantly reduces IGFBP-3 in the blood, which causes an accelerated degradation of IGF-1 and a 36% decrease in circulating IGF-1 concentration. Kdm3b is highly expressed in the female reproductive organs including ovary, oviduct and uterus. Knockout of Kdm3b in female mice causes irregular estrous cycles, decreases 45% of the ovulation capability and 47% of the fertilization rate, and reduces 44% of the uterine decidual response, which are accompanied with a more than 50% decrease in the circulating levels of the 17beta-estradiol. These female reproductive phenotypes are associated with significantly increased levels of H3K9me1/2/3 in the ovary and uterus. Kdm3bKO mice exhibit restricted somatic growth, low levels of circulating IGF-1 and IGFBP-3 and fast degradation of IGF-1. Female Kdm3bKO mice exhibit a severely impaired reproductive function. Knockout of Kdm3b in female mice prolonges their estrous cycles and reduces their ovulation capacity and fertilization efficiency. Phenotype, overview
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malfunction
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lack of either Jmjd2a or Jmjd2b is compatible with embryonic stem cell self-renewal and embryonic development. While individual Jmjd2 family members are dispensable for embryonic stem cell maintenance and embryogenesis, combined deficiency for specifically Jmjd2a and Jmjd2c leads to early embryonic lethality and impaired embryonic stem cell (ESC) self-renewal, with spontaneous differentiation towards primitive endoderm under permissive culture conditions, phenotype, overview. Only specific genomic elements are affected upon loss of Jmjd2 function. Loss of Jmjd2a and Jmjd2c has a drastic effect on ESC proliferation
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malfunction
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Jmjd2c is dispensable for embryonic stem cell maintenance and embryogenesis, while combined deficiency for specifically Jmjd2a and Jmjd2c leads to early embryonic lethality and impaired embryonic stem cell (ESC) self-renewal, with spontaneous differentiation towards primitive endoderm under permissive culture conditions, phenotype, overview. Only specific genomic elements are affected upon loss of Jmjd2 function. Loss of Jmjd2a and Jmjd2c has a drastic effect on ESC proliferation
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malfunction
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lack of either Jmjd2a or Jmjd2b is compatible with embryonic stem cell self-renewal and embryonic development. Only specific genomic elements are affected upon loss of Jmjd2 function
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malfunction
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the kdmA mutant shows a significant increase in H3K36me3 during primary metabolism at the aflR and ipnA locus and some slightly higher levels at the aptA genes, the mutant has reduced levels of sterigmatocystin compared to wild-type. Manipulation of kdmA expression reveals genetic and environmental interactions including lethality under light. Deletion of kdmA causes light lethality and sensitivity to oxidative stress during vegetative growth to chronic oxidative stress
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malfunction
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the kdmA mutant shows a significant increase in H3K36me3 during primary metabolism at the aflR and ipnA locus and some slightly higher levels at the aptA genes, the mutant has reduced levels of sterigmatocystin compared to wild-type. Manipulation of kdmA expression reveals genetic and environmental interactions including lethality under light. Deletion of kdmA causes light lethality and sensitivity to oxidative stress during vegetative growth to chronic oxidative stress
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metabolism
expression levels of JMJD2B and CDK6 were significantly correlated in various types of cell lines
metabolism
the methylation of lysine residues in histones is a main epigenetic modification in the regulation of eukaryotic gene expression. While methylation of histone H3 at the lysine 4 (H3K4) and 36 (H3K36) residues primarily associates with active transcription, methylation of histone H3 at the lysine 9 (H3K9) and 27 (H3K27) residues and histone H4 at lysine 20 (H4K20) associates with gene repression. Histone methylation by histone methyltransferase is antagonized by histone demethylases, which are divided into two classes: amine oxidases (LSD demethylases), and jumonji C (JmjC) domain-containing, iron-dependent dioxygenases (JMJC demethylases). Histone H3K9 demethylase JMJD2B decreases H3K9me3/me2 on the promoter of PPARgamma and C/EBPalpha, which in turn stimulated the expression of PPARgamma and C/EBPalpha. JMJD2B-mediated reduction of H3K9me3 increases H3K4me3 level on PPARgamma and C/EBPalpha
metabolism
exposure to Co2+ increases gene repression markers (H3K9me3, H3K27me3, H3K36me3, H3K9me2, uH2A and lack of AcH4), as well as gene activation markers (H3K4me3 and uH2B) in both A549 and Beas-2B cells. Cobalt ions increase H3K9me3 and H3K36me3 by inhibiting histone demethylation process in vivo
metabolism
expression of histone H3 Lys 9 demethylases Jmjd1a (EC 1.14.11.65) and Jmjd2c is positively correlated with the pluripotent state of ES and iPS cells. Jmjd1a and Jmjd2c regulate the global levels of H3K9Me2 and H3K9Me3, respectively
metabolism
hyperglycemia/hyperinsulinemia induces changes in expression of chromatin modifying genes and their regulation by histone modifications, overview. Crosstalk between these histone modifications under hyperinsulinemic/hyperglycemic conditions: no change in H3K9me1 levels at the coding regions of histone H3K9 demethylase (Jmjd2b) and H3K4 demethylase (Aof1), and decreased H3K4me1 levels at Myst4 and Jmjd2b, and increased H3K4me1 levels at Set and Aof1. Levels of H3K9me1 are only changed at histone acetylase (Myst4) and deacetylase (Set), highlighting the role of this modification in regulating histone acetylation only. The chromatin remodelling genes Myst4, Jmjd2b, Set, and Aof1 show similar pattern of change for H3Ac and H3K4me1 on Myst4, Jmjd2b, Aof1 and Set gene promoter regions under both low glucose and high glucose condition after insulin stimulation
metabolism
KDM4A possesses the potential to act as an oxygen sensor in the context of epigenetic regulation
metabolism
many JmjC HDMs appear to function in the context of large multimeric complexes that govern their localization, transcriptional functions, and potentially their substrate specificity. In the case of certain JmjC enzymes, these complexes appear to be critical in conferring specificity for nucleosomal substrates
physiological function
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LSD1 is associated with co-repressor complexes and promotes suppression or activation of gene expression, e.g. LSD1 might be associated to cooperative recruitment to the NFkappaB p65 site for activation in hyperglycemia
physiological function
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LSD1 is associated with co-repressor complexes and promotes suppression or activation of gene expression, e.g. LSD1 might be associated to cooperative recruitment to the NFkappaB p65 site for activation in hyperglycemia
physiological function
rice JMJ706 encodes a heterochromatin-associated H3K9 demethylase involved in the regulation of flower development in rice. JMJ706 regulates a subset of flower development regulatory genes
physiological function
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JmjD2A is specific for H3K9me3 and H3K36me3 substrates in fibroblasts. H3K9me3 and H3K36me3 occupancy regulates neural crest specifier expression in vivo. Dynamic changes in both JmjD2A and H3K9me3 occupancy of the Sox10 promoter between stages 8 and 9
physiological function
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JMJD2b histone demethylase antagonizes H3K9me3 in the pericentromeric heterochromatin
physiological function
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JMJD2B regulates multiple biological processes including the cell cycle. The histone demethylase JMJD2B is regulated by both estrogen receptor alpha and HIF-1alpha, drives breast cancer cell proliferation in normoxia and hypoxia, and epigenetically regulates the expression of cell cycle genes such as CCND1, CCNA1, and WEE1. Histone demethylase function of JMJD2B in hypoxia, overview
physiological function
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Derepression of the promoter of the gene encoding the myogenic factor myogenin (Myog) is key for initiation of muscle differentiation, mechanism of H3K9 demethylation at the Myog promoter, overview. Genome-wide expression profiling and exon-specific siRNA knockdown indicate that, in contrast to the full-length protein, N-terminal demethylase domainis necessary for myotube formation and muscle-specific gene expression. promotes MyoD-induced conversion of NIH3T3 cells into muscle cells. ChIP-on-chip analysis indicates that DN-JMJD2A binds to genes mainly involved in transcriptional control and that this binding is linked to gene activation. DN-JMJD2A is recruited to the Myog promoter at the onset of differentiation. This binding is essential to promote the demethylation of H3K9me2 and H3K9me3
physiological function
histone demethylase JMJD2B plays an essential role in human carcinogenesis through positive regulation of cyclin-dependent kinase 6, transactivation of JMJD2B in lung cancer, elevated levels of JMJD2B expression in bladder cancer. The demethylase activity of JMJD2B possesses an oncogenic activity
physiological function
histone demethylase JMJD2B regulates chromatin structure or gene expression by removing methyl residues from trimethylated lysine 9 on histone H3 and is required for tumor cell proliferation and survival in vitro and in vivo, and is overexpressed in gastric cancer
physiological function
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JMJD2B is able to demethylate H3K9me3 at pericentric heterochromatin in mammalian cells. Histone demethylase JMJD2B coordinates H3K4/H3K9 methylation and promotes hormonally responsive breast carcinogenesis. JMJD2B promotes cell proliferation in vitro and tumorigenesis in vivo. The JMJD2B/MLL2 complex colocalizes with estrogen receptor alpha and is required for estrogen receptor alpha-regulated transcription. H3K9 demethylation and H3K4 methylation are coordinated in estrogen receptor alpha-activated transcription such that H3K9 demethylation is a prerequisite for H3K4 methylation. JMJD2B itself is an estrogen receptor alpha target gene, and forms a feed-forward regulatory loop in regulation of the hormone response, analysis of the in vivo interaction between JMJD2B and the MLL2 complex, overview
physiological function
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KDM4A-D histone demethylases selectively demethylates H3K9 and H3K36 and is implicated in key cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis
physiological function
enzyme Kdm3b is a Jumonji C domain-containing protein that demethylates mono- and dimethylated lysine 9 of histone H3 (H3K9me1 and H3K9me2). Kdm3b-mediated H3K9 demethylation plays essential roles in maintenance of the circulating IGF-1, postnatal somatic growth, circulating 17beta-estradiol, and female reproductive function
physiological function
histone H3K9 demethylase JMJD2B activates adipogenesis by regulating H3K9 methylation on PPARgamma and C/EBPalpha during adipogenesis in 3T3-L1 preadipocytes, overview. JMJD2B decreases H3K9me3/me2 on the promoter of PPARgamma and C/EBPalpha, which in turn stimulated the expression of PPARgamma and C/EBPalpha
physiological function
the JmjC histone lysine demethylases (KDMs) are epigenetic regulators involved in the removal of methyl groups from post-translationally modified lysyl residues within histone tails, modulating gene transcription. The activity of some KDMs, including the pseudogene-encoded KDM4E, may be sensitive to changing oxygen concentrations, U2OS cells conditionally overexpressing KDM4A show that the cellular activity of KDM4A against its primary substrate, H3K9me3, displays a graded response to depleting oxygen concentrations in line with the data obtained using isolated protein. KDM4A possesses the potential to act as an oxygen sensor in the context of chromatin modifications, with possible implications for epigenetic regulation in hypoxic disease states
physiological function
a distinct short isoform, DELTAN-JMJD2A, of the histone demethylase JMJD2A/KDM4A is required for skeletal muscle differentiation, induction of the DELTAN-JMJD2A isoform at the onset of differentiation. In proliferating myoblasts, muscle specific genes are silenced by epigenetic modifications at their promoters, including histone H3K9 methylation. Derepression of the promoter of the gene encoding the myogenic factor myogenin (Myog) through demethylation of H3K9 residues is a key for initiation of muscle differentiation. By directing the removal of repressive chromatin marks at the Myog promoter, enzyme DELTAN-JMJD2A promotes transcriptional activation of the Myog gene and thus contributes to initiation of muscle-specific gene expression. DELTAN-JMJD2A is essential for differentiation and acts as an activator
physiological function
H3K9me3 demethylase KDM4A/JMJD2A is able to increase accessibility and alter the replication timing at specific heterochromatic regions. KDM4A overexpression promotes copy gain of 1q12, 1q21, and Xq13.1 in cancer cells and results in site-specific copy gain of regions amplified in human tumors. These copy gains are not stably inherited but are generated transiently in each subsequent S phase and cleared by late G2. KDM4A is the only KDM4 family member that generated the gains in a catalytically dependent manner, copy gains are antagonized by coexpression of Suv39h1/KMT1A or HP1gamma, and promoted by H3K9 or H3K36 methylation interference. KDM4A associates with replication machinery and promotes rereplication of 1q12. KDM4A overexpression promotes chromatin state changes and recruitment of replication machinery. KDM4A-dependent 1q12h copy gain requires catalytic activity and Tudor domains, the KDM4A catalytic domain alone is insufficient to generate 1q12h gain
physiological function
histone demethylase Dmel\Kdm4A controls genes required for life span and male-specific sex determination in Drosophila melanogaster. Essential role for Dmel\Kdm4A in the transcriptional activation of genes involved in the aging process and male-specific neuronal formation and courtship behavior
physiological function
histone demethylases such as members of the Jumonji family revert histone trimethylation. Unlike other demethylases, JmjD2/KDM4 proteins have been shown to remove both lysine 9 and 36 trimethyl marks. Dynamic histone modifications are critical for proper temporal control of neural crest gene expression in vivo. The histone demethylase, JumonjiD2A (JmjD2A/KDM4A), is expressed in the forming neural folds. Direct stage-specific interactions of JmjD2A with regulatory regions of neural crest genes, associated temporal modifications in methylation states of lysine residues are directly affected by JmjD2A activity. Chromatin modifications directly control neural crest genes in vertebrate embryos via modulating histone methylation. JmjD2A plays an important role in neural crest development. H3K9me3 and H3K36me3 occupancy regulates neural crest specifier expression in vivo
physiological function
HP1 is known to recognize H3K9me3/me2, a modification that is specifically enriched at heterochromatin
physiological function
JMJD2A accelerates malignant progression of liver cancer cells in vitro and in vivo. Mechanistically, JMJD2A promotes the expression and mature of pre-miR372 epigenetically. Notably, miR372 blocks the editing of 13th exon-introns-14th exon and forms a novel transcript (JMJD2ADELTA) of JMJD2A. Enzyme JMJD2A is overexpressed in cancer and inhibits repair of DNA damage by reducing homologous recombination repair. Histone H3K36 trimethylation (H3K36me3) is associated with carcinogenesis. Histone H3 demethylase JMJD2A promotes growth of liver cancer cells, via Pim1-ppRB1-CDK2-CycinE-C-myc pathway, through upregulating miR372, JMJD2A enhances miR372 expression epigenetically, mechanism, overview. In particular, JMJD2A inhibits P21 (WAF1/Cip1) expression by decreasing H3K9me3 dependent on JMJD2ADELTA. JMJD2A enhances Pim1 transcription by suppressing P21(WAF1/Cip1) involving altered histone H3 lysine 9 methylation. Furthermore, through increasing the expression of Pim1, JMJD2A facilitates the interaction among pRB, CDK2 and CyclinE which prompts the transcription and translation of oncogenic C-myc. JMJD2A may trigger the demethylation of Pim1
physiological function
Jmjd2a and Jmjd2c both localize to H3K4me3-positive promoters, where they have widespread and redundant roles in preventing accumulation of H3K9me3 and H3K36me3. Jmjd2 catalytic activity is required for embryonic stem cell (ESC) maintenance. Jmjd2a and Jmjd2c are essential for early embryonic development. Recruitment of the Jmjd2 H3K9/H3K36 demethylases to H3K4me3-marked nucleosomes. Jmjd2a and Jmjd2c redundantly regulate histone methylation levels
physiological function
JMJD2A is implicated in transcriptional silencing and is associated with the retinoblastoma protein, class I HDACs, and the nuclear corepressor N-CoR. JMJD2A and its paralogue JMJD2D associate with the androgen receptor (AR) to upregulate the expression of AR-dependent genes. The transcriptional functions of JMJD2 enzymes appear to be context-dependent
physiological function
Jmjd2b, histone-3 lysine-9 di-/tri-methyl (H3K9me2/3) demethylase, is functional following lipopolysaccharide (LPS) treatment and is crucial in multiple signaling pathways and biological processes. Jmjd2b specifically targets the trimethylated lysine 9 of histone H3 (H3K9) for demethylation at pericentric heterochromatin and euchromatin. Jmjd2b plays a role in LPS-mediated inflammation, whith an epigenetic regulation in NE-4C cells. Effect of LPS on cell viability and NO production in NE-4C cells, overview
physiological function
Jmjd2c acts as a positive regulator for Nanog, which encodes for a key transcription factor for self-renewal in ES cells. Jmjd2c is required to reverse the H3K9Me3 marks at the Nanog promoter region and consequently prevents transcriptional repressors HP1 and KAP1 from binding. Jmjd2c regulates expression of Nanog through demethylation of H3K9Me3, overview. The ES cell transcription circuitry is connected to chromatin modulation through H3K9 demethylation in pluripotent cells
physiological function
KDM4C acts as an oncogene that is amplifiedin esophageal cancer cell line, KYSE-150. Role of the KDM4C in the maintenance of tumor-initiating cells (TICs) in esophageal squamous cell carcinoma (ESCC). The cytoplasmic and nuclear KDM4C staining increased with adverse pathologic phenotypes and poor patient survival. KDM4C blockade selectively decreases the ESCC ALDHbri+ TICs population in vitro and specifically targets the TICs in ALDHbri+-derived xenograft, retarding engraftment. Subsequent studies of the KDM4C functional network identified a subset of pluripotency-associated genes (PAGs) and aldehyde dehydrogenase family members to be preferentially downregulated in KDM4C-inhibited ALDHbri+ TICs. KDM4C maintains permissive histone modifications with a low level of H3K9 methylation at the promoters of several PAGs
physiological function
KdmA, a histone H3 demethylase with bipartite function, differentially regulates primary and secondary metabolism in Aspergillus nidulans. KdmA displays locus-specific histone H3 lysine demethylation activity
physiological function
lysine methylation can be erased by the activity of the Jumonji C (JmjC)-domain-containing proteins that demethylate lysine through an amine oxidative reaction in the presence of iron and 2-oxoglutarate. KDM4D specifically catalyzes the demethylation of H3K9me2/me3. RNA interaction with KDM4D N-terminus is essential for KDM4D association with chromatin
physiological function
specific recognition of H3K9me3/me2 is known to regulate binding of HP1 to chromatin. dJMJD2(1)/CG15835 influences heterochromatin organization, but is excluded from heterochromatin. Overexpression of dJMJD2(1)/CG15835 does not affect the pattern of H3K9me3/me2 at heterochromatin. dJMJD2(1)/CG15835 localizes to multiple euchromatic sites, where it mostly regulates H3K36me3, as its overexpression results in a strong decrease in the levels of H3K36me3. dJMJD2(1)/CG15835 regulates spreading of HP1
physiological function
the histone lysine demethylase KDM4A regulates H3K9 and H3K36 methylation states
physiological function
the JmjC histone lysine demethylases (KDMs) are epigenetic regulators involved in the removal of methyl groups from post-translationally modified lysyl residues within histone tails, modulating gene transcription
physiological function
the testis-enriched histone demethylase, KDM4D, regulates methylation of histone H3 lysine 9 during spermatogenesis in mouse but is dispensable for fertility. Among various methylations of histone H3, methylation of histone H3 lysine 9 (H3K9) by testis-enriched tridemethylase of H3K9 and its regulation are essential for spermatogenesis. Demethylation of H3K9me3 in round spermatids is dispensable for spermatogenesis, possible defects in Kdm4d-null elongating spermatids can be rescued by functional redundancy of the KDM4B demethylase. KDM4D can demethylate H3K9me2 and H3K9me3 into H3K9me1 without significant effects on most of the other histone H3 methylation patterns
physiological function
various types of human cancers exhibit amplification or deletion of KDM4A-D members, which selectively demethylate H3K9 and H3K36, thus implicating their activity in promoting carcinogenesis
physiological function
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enzyme expression in mice results in hepatic steatosis when fed a high-fat diet, which is accompanied with increased expression of hepatic peroxisome proliferator-activated receptor gamma2 and its steatosis target genes
physiological function
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enzyme over-production may induce alterations in epigenetic histone methylation and affects the expression of key genes that are implicated in carcinogenesis and stem cell properties in human cancer
physiological function
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enzyme overexpression contributes to the maintenance of a pluripotent state and induces numerous oncogenic effects. KDM4 proteins are a component of the cellular response to postreplicative and exogenous DNA damage
physiological function
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enzyme overexpression in HepG2 cells stimulates the expression of peroxisome proliferator-activated receptor gamma2 (PPARgamma2) and its steatosis target genes associated with fatty acid uptake and lipid droplet formation, resulting in increased intracellular triglyceride accumulation. Enzyme-dependent upregulation of PPARgamma2 is associated with the removal of di- and trimethylation of histone H3 lysine 9 on the promoter of PPARgamma2
physiological function
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isoforms Kdm4A and Kdm4B are together essential for mediating ecdysteroid hormone signaling during larval development
physiological function
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the enzyme is responsible for histone 3 lysine 9 demethylation at the cyclin E1 promoter, cyclin E1 induction and B cell proliferation
physiological function
the enzyme plays an essential role in regulating metabolic gene expression and normal weight control in mice. The enzyme directly regulates peroxisome proliferator-activated receptor alpha and Ucp1 expression
physiological function
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the enzyme protects HCT-116 cells from apoptosis
physiological function
catalyzes the demethylation of di- and trimethylated Lys9 (reactions of EC 1.14.11.65 and 1.14.11.66) and Lys36 in histone H3 (reactions of EC 1.14.11.27 and 1.14.11.69). Jmjd2a responds to 5-hydroxytryptamine and promotes the expression of the brain-derived neurotrophic factor (Bdnf), a protein critically involved in neuropathic pain. JMJD2A binds to the promoter of Bdnf and demethylates H3K9me3 and H3K36me3 at the Bdnf promoter to promote the expression of Bdnf. JMJD2A promotes the expression of Bdnf during neuropathic pain and neuron-specific knockout of Jmjd2a blocks the hypersensitivity of mice undergoing chronic neuropathic pain
physiological function
depletion of KDM4A in prostate cancer cells inhibits their proliferation and survival in vivo and vitro. Deubiquitinase USP1 regulates KDM4A K48-linked deubiquitination and stability. c-Myc is a key downstream effector of the USP1-KDM4A/androgen receptor axis in driving prostate cancer cell proliferation. Upregulation of KDM4A expression with high USP1 expression is observed in most prostate tumors and inhibition of USP1 promotes prostate cancer cells response to therapeutic agent enzalutamide
physiological function
histone H3 lysine 9 demethylase enzymes, KDM3A, EC 1.14.11.66, and KDM4B cooperate to regulate ER activity via an autoregulatory loop that facilitates the recruitment of each coactivating enzyme to chromatin. KDM3A primes chromatin for deposition of the ER pioneer factor FOXA1 and recruitment of the ER-transcriptional complex, all prior to ER recruitment. A KDM3A/KDM4B/FOXA1 coregulated gene signature is enriched for proproliferative and ER-target gene sets. Depletion of both KDM3A and KDM4B has a greater inhibitory effect on ER activity and cell growth than knockdown of each individual enzyme
physiological function
histone H3.3 G34R substitution mutation, found in paediatric gliomas, causes widespread changes in H3K9me3 and H3K36me3 level by interfering with the KDM4 family of K9/K36 demethylases. Expression of a targeted single-copy of H3.3 G34R at endogenous levels induces chromatin alterations that are comparable to a KDM4 isoforms A/B/C triple-knockout. H3.3 G34R preferentially binds KDM4 while simultaneously inhibiting its enzymatic activity
physiological function
in cancer cells, H3K9me3 is largely enriched in long interspersed nuclear element-1 (LINE-1). A significant proportion of KDM4B-dependent H3K9me3 is located in evolutionarily young LINE-1 elements, which likely retain retrotransposition activity. Ectopic expression of KDM4B promotes LINE-1 expression, while depletion of KDM4B reduces it. KDM4B overexpression enhances LINE-1 retrotransposition efficacy, copy number, and associated DNA damage. Breast cancer cell lines expressing high levels of KDM4B also exhibit increased LINE-1 expression and copy number compared with other cell lines. Pharmacologic inhibition of KDM4B significantly reduces LINE-1 expression and DNA damage in breast cancer cells with excessive KDM4B
physiological function
JMJD2A displays higher expression in glioma tissues than that in normal brain tissues and lower levels of H3K9me3/H3K36me3are found in glioma tissues. Knockdown of JMJD2A expression attenuates the growth and colony formation in glioma cell lines U251, T98G, and U87MG, whereas JMJD2A overexpression results in opposing effects. JMJD2A knockdown reduces the growth of glioma T98G cells in vivo. JMJD2A activates the Akt-mTOR pathway and promotes protein synthesis in glioma cells via promoting phosphoinositide-dependent kinase-1 expression
physiological function
KDM4 activity is required for hematopoietic stem cell (HSC) maintenance in vivo. The combined knockout of Kdm4a, Kdm4b, and Kdm4c leads to reduction of myeloid and lymphoid cells. In conditional KDM4A/B/C triple-knockout mice, the knockout leads to accumulation of H3K9me3 on transcription start sites and the corresponding downregulation of expression of several genes in HSCs. Genes Taf1b and Nom1, are essential for the maintenance of hematopoietic cells
physiological function
KDM4A is a epigenetic regulator of osteoblast and adipocyte differentiation. KDM4A expression is upregulated during osteogenesis and adipogenesis of primary marrow stromal cells and stromal ST2 line. Overexpression of wild-type KDM4A promotes adipogenic differentiation and blocks osteogenic differentiation of the progenitor cells. Depletion or inactivation of KDM4A in undifferentiated progenitor cells inhibits the formation of adipocytes and promotes the differentiation of osteoblasts. Overexpression of KDM4A upregulates the expression of secreted frizzled-related protein Sfrp4 and CCAAT/enhancer-binding protein C/ebpalpha. KDM4A directly binds the promoters of Sfrp4 and C/ebpalpha, removes the histone methylation mark H3K9me3, and reduces DNA methylation levels of CpG in promoter regions of C/ebpalpha and Sfrp4. Overexpression of KDM4A inactivates canonical Wnt signaling
physiological function
KDM4D is a key regulator of adipogenesis in C3H10T1/2 mesenchymal stem cells. The depletion of KDM4D results in impaired differentiation, which can be rescued by exogenous KDM4D, PPARgamma, and C/EBPalpha, but not by C/EBPbeta. KDM4D interacts physically and functionally with both NFIB and MLL1 complex to regulate C/EBPalpha and PPARgamma expression upon adipogenic hormonal induction. KDM4D is dispensable for the binding of both NFIB and MLL1 complex to the target promoters, but the demethylation of trimethylated H3K9 by KDM4D is required for NFIB and MLL1 complex to deposit trimethylated H3K4 and activate PPARgamma and C/EBPalpha expression
physiological function
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KdmA, a histone H3 demethylase with bipartite function, differentially regulates primary and secondary metabolism in Aspergillus nidulans. KdmA displays locus-specific histone H3 lysine demethylation activity
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physiological function
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KdmA, a histone H3 demethylase with bipartite function, differentially regulates primary and secondary metabolism in Aspergillus nidulans. KdmA displays locus-specific histone H3 lysine demethylation activity
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physiological function
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KdmA, a histone H3 demethylase with bipartite function, differentially regulates primary and secondary metabolism in Aspergillus nidulans. KdmA displays locus-specific histone H3 lysine demethylation activity
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physiological function
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enzyme Kdm3b is a Jumonji C domain-containing protein that demethylates mono- and dimethylated lysine 9 of histone H3 (H3K9me1 and H3K9me2). Kdm3b-mediated H3K9 demethylation plays essential roles in maintenance of the circulating IGF-1, postnatal somatic growth, circulating 17beta-estradiol, and female reproductive function
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physiological function
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Jmjd2a and Jmjd2c both localize to H3K4me3-positive promoters, where they have widespread and redundant roles in preventing accumulation of H3K9me3 and H3K36me3. Jmjd2 catalytic activity is required for embryonic stem cell (ESC) maintenance. Jmjd2a and Jmjd2c are essential for early embryonic development. Recruitment of the Jmjd2 H3K9/H3K36 demethylases to H3K4me3-marked nucleosomes. Jmjd2a and Jmjd2c redundantly regulate histone methylation levels
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physiological function
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KdmA, a histone H3 demethylase with bipartite function, differentially regulates primary and secondary metabolism in Aspergillus nidulans. KdmA displays locus-specific histone H3 lysine demethylation activity
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physiological function
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KdmA, a histone H3 demethylase with bipartite function, differentially regulates primary and secondary metabolism in Aspergillus nidulans. KdmA displays locus-specific histone H3 lysine demethylation activity
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additional information
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in cells with a deficiency in the histone methyltransferase SUV39h, the level of full-length JMJD2b at chromocenters is reduced, corresponding to a global decrease in JMJD2b and H3K9me3. The PHD Zn-fingers and Tudor domains, which are removed in truncated JMJD2b, are responsible for the aberrant JMJD2b function. Nuclear patterns of full-length JMJD2b in comparison with truncated and mutated forms of JMJD2b, overview
additional information
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JMJD2B is important for breast cancer cell proliferation. JMJD2B and the hypoxia marker CA9 together stratify a subclass of breast cancer patients and predict a worse outcome of these breast cancers
additional information
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loss of JmjD2A leads to depletion of neural crest specifier genes, but causes no significant changes in the expression of several neural tube, ectodermal, neural plate, and border genes, or in markers of proliferation and apoptosis, overview
additional information
substrate selectivity is determined by multiple interactions within the catalytic domain but outside the active site, structural basis of sequence celectivity between KDM4 members, overview. Ile71A, Asn86A, Ile87A, Gln88A, and Arg309A may not be required for binding of H3K9 substrate
additional information
substrate selectivity is determined by multiple interactions within the catalytic domain but outside the active site, structural basis of sequence celectivity between KDM4 members, overview. Ile71A, Asn86A, Ile87A, Gln88A, and Arg309A may not be required for binding of H3K9 substrate
additional information
substrate selectivity is determined by multiple interactions within the catalytic domain but outside the active site, structural basis of sequence celectivity between KDM4 members, overview. Ile71A, Asn86A, Ile87A, Gln88A, and Arg309A may not be required for binding of H3K9 substrate
additional information
substrate selectivity is determined by multiple interactions within the catalytic domain but outside the active site, structural basis of sequence celectivity between KDM4 members, overview. Ile71A, Asn86A, Ile87A, Gln88A, and Arg309A may not be required for binding of H3K9 substrate
additional information
substrate selectivity is determined by multiple interactions within the catalytic domain but outside the active site, structural basis of sequence celectivity between KDM4 members, overview. Ile71A, Asn86A, Ile87A, Gln88A, and Arg309A may not be required for binding of H3K9 substrate
additional information
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substrate selectivity is determined by multiple interactions within the catalytic domain but outside the active site, structural basis of sequence celectivity between KDM4 members, overview. Ile71A, Asn86A, Ile87A, Gln88A, and Arg309A may not be required for binding of H3K9 substrate
additional information
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the H3K9 trimethyl demethylase JMJD2B is an integral component of the H3K4-specific methyltransferase, the mixed-lineage leukemia (MLL) 2 complex
additional information
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the molecular chaperon Hsp90 interacts with and stabilizes KDM4B protein, pharmacological inhibition of Hsp90 promotes ubiquitin-dependent proteasomal degradation of KDM4B, but not of KDM4C, suggesting that the turnover of these demethylases is regulated by distinct mechanisms, degradation is accompanied by increased methylation of H3K9. Hsp90 inhibition promotes KDM4B degradation and alters the methylation of H3K9
additional information
the enzyme contains a Jumonji C (JmjC) domain
additional information
cellular demethylase activity of KDM4A demonstrates a graded response to oxygen concentration in U2OS cells. Analysis of the H3K27me3 (cf. EC 1.14.11.68) mark shows loss of this mark upon overexpression of KDM4A in normoxia, with a graded response to oxygen similar to that seen for H3K9me3, although less-pronounced. H3K27me3 is not a canonical substrate for KDM4A, hence, loss of this mark cannot be directly attributed to catalytic KDM4A activity. Effect of oxygen availability on the activity of the KDM4 subfamily member KDM4A, overview. A high level of O2 sensitivity both with isolated protein and in cells is observed
additional information
enzyme structure-function relationships and substrate selectivity, comparisons of KDM4 enzymes, overview
additional information
enzyme structure-function relationships and substrate selectivity, comparisons of KDM4 enzymes, overview
additional information
enzyme structure-function relationships and substrate selectivity, comparisons of KDM4 enzymes, overview
additional information
enzyme structure-function relationships and substrate selectivity, comparisons of KDM4 enzymes, overview
additional information
enzyme structure-function relationships and substrate selectivity, comparisons of KDM4 enzymes, overview
additional information
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enzyme structure-function relationships and substrate selectivity, comparisons of KDM4 enzymes, overview
additional information
in H3K9me3- and H3K36me3-enzyme complexes, the peptides bind in the same directionality within the substrate binding cleft of JMJD2A, depositing the trimethyllysines into the active site. The majority of the interactions between the enzyme and H3 peptides involve hydrogen bond and van der Waals interactions with the backbone atoms in the substrates. The residues N-terminal to the trimethyllysines adopt a similar beta-strand-like conformation, while the C-terminal residues in the peptides adopt distinct binding modes. Mono-, di-, and trimethyllysines bind within a methylammonium binding pocket adjacent to the Fe(II) and 2-oxoglutarate binding sites in JMJD2A. This pocket is lined with an array of oxygen atoms that participate in direct contacts with zeta-methyl groups of the trimethylated substrate. Structure-activity analysis, overview
additional information
interaction between JMJD2A and substrate peptides largely involves the main chains of the enzyme and the peptide. The peptide-binding specificity is primarily determined by the primary structure of the peptide, which explains the specificity of JMJD2A for methylated H3K9 and H3K36 instead of other methylated residues such as H3K27. The specificity for a particular methyl group is affected by multiple factors, such as space and the electrostatic environment in the catalytic center of the enzyme. Mechanisms and specificity of histone demethylation, overview. Residues Q86, N88, D135, and Y175 are involved in the interaction with the peptide, whereas residues Y177, N290, S288, and T289 are involved in methyl group binding. K241 is proposed to recruit the O2 molecule into the catalytic center. Glycine residues at +3 or +4 in the substrate are essential for substrate specificity
additional information
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KDM4D is recruited to chromatin and recognizes its histone substrates. KDM4D binds RNA (isolated from HEK-293T cells) independently of its demethylase activity, and contains two non-canonical RNA binding domains: the first is within the N-terminal spanning amino acids 115 to 236, and the second is within the C-terminal spanning amino acids 348 to 523 of KDM4D. Three surface residues on KDM4D close to the JmjC domain, His115, Arg123 and Lys127, are aligned to specific residues on the cleavage factor known to bind RNA, interaction analysis, overview. RNA interactions with KDM4D N-terminal region are critical for its association with chromatin and subsequently for demethylating H3K9me3 in cells
additional information
KDM4D is recruited to chromatin and recognizes its histone substrates. KDM4D binds RNA (isolated from HEK-293T cells) independently of its demethylase activity, and contains two non-canonical RNA binding domains: the first is within the N-terminal spanning amino acids 115 to 236, and the second is within the C-terminal spanning amino acids 348 to 523 of KDM4D. Three surface residues on KDM4D close to the JmjC domain, His115, Arg123 and Lys127, are aligned to specific residues on the cleavage factor known to bind RNA, interaction analysis, overview. RNA interactions with KDM4D N-terminal region are critical for its association with chromatin and subsequently for demethylating H3K9me3 in cells
additional information
residue S288 modulates the methylation-state specificities of JMJD2 enzymes and other trimethyllysine-specific JmjC HDMs. The mechanisms by which JMJD2A discriminates against the demethylation of H3K4me and H4K20me. An alignment of the H3K4, H3K9, H3K36 and H4K20 methylation sites reveals substantial sequence diversity among the methylation motifs. The methylammonium-binding pocket is composed of the carbonyl oxygen of Gly170, the hydroxyl groups of Tyr177 and Ser288, and the carboxylate side chain of Glu190. Active site structure with bound substrate, overview
additional information
the mechanism for achieving methylation state selectivity involves the orientation of the substrate methyl groups towards a ferryl intermediate. Active site structure and mechanism of JMJD2A, overview
additional information
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the mechanism for achieving methylation state selectivity involves the orientation of the substrate methyl groups towards a ferryl intermediate. Active site structure and mechanism of JMJD2A, overview
additional information
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the enzyme contains a Jumonji C (JmjC) domain
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