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evolution
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Fbxl10 (Jhdm1b/Kdm2b) is a conserved and ubiquitously expressed member of the JHDM (JmjC domain-containing histone demethylase) family
evolution
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KDM5C is a member of the evolutionarily conserved KDM5 family of four proteins, KDM5A/B/C and D. KDM5A/C/D demethylate tri- and di-methylated forms of H3K4, whereas KDM5B is capable of demethylating all three forms (tri-, di-, and mono) of H3K4 methylation
evolution
Jhd2 belongs to an expansive protein family distinguished by the presence of a JmjC domain. The JmjC domain, initially identified in the C-terminal region of the mouse Jumonji protein, mediates the demethylation of histone lysine residues
evolution
Jhd2 is an evolutionarily conserved JARID1 family H3 Lys4 demethylase and a Jumonji C (JmjC) domain-containing histone demethylase (JHDM). Jhd2/Kdm5 is an evolutionarily conserved JARID1 family protein that has demethylase activity toward H3K4me3 in vitro or in vivo
evolution
RBR-2 is the sole homolog of the KDM5 family of H3K4me3/2 demethylases in Caenorhabditis elegans
evolution
the enzyme belongs to the superfamily of flavin adenine dinucleotide (FAD)-dependent amine oxidases
evolution
the enzyme blongs to the KDM5/JARID1 subfamily of histone H3 lysine 4 demethylases of the Fe(II)- and 2-oxoglutarate-dependent demethylases family. The KDM5 family is unique among the Jumonji domain-containing histone demethylases in that there is an atypical insertion of a DNA-binding ARID domain and a histone-binding PHD domain into the Jumonji domain, which separates the catalytic domain into two fragments (JmjN and JmjC)
evolution
the enzyme is a member of the KDM5 protein family
evolution
the enzyme is a member of the KDM5 protein family
evolution
the SE14 enzyme is Jumonji C (JmjC) domain-containing protein, overview
evolution
5 isozymes of enzyme Jarid/KDM5 (Jarid1A-D and Jarid2) in Caenorhabditis elegans, overview
evolution
5 isozymes of enzyme Jarid/KDM5 (Jarid1A-D and Jarid2) in Drosophila melanogaster, overview
evolution
JMJ703 is the homolog of the Arabidopsis thaliana H3K4 demethylase JMJ14, which is involved in flowering time regulation and gene silencing
evolution
the enzyme belongs to the JARID family. JARID proteins contain, in addition to the JmjN and JmjC domains, ARID and C5HC2-zinc finger domains, which mediate DNA binding. JARID proteins are, in turn, divided into two subgroups according to the presence, JARID1, or not, JARID2, of chromatin-binding PHD domains. CG3654 is the structural homologue of mammalian JARID2, as it does not contain any chromatin-binding domains. In this case, however, identity is lower (15%) and, in addition, CG3654 is missing the C5HC2-zinc finger domain present in mammalian JARID2
malfunction
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H3K4me3 is an important epigenetic landmark for active transcription, failure to erase this mark can result in aberrant transcription of rDNA repeats and failure to form a single compact nucleolus
malfunction
loss of the enzyme reduces cell division rate of the stem and the size of plant stature
malfunction
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mutations in the X-linked KDM5C gene, encoding a histone H3 lysine 4 demethylase, lading to significant loss of DNA methylation in blood of males with intellectual disability, especially loss of DNA methylation at the promoters of the three top candidate genes FBXL5, SCMH1, CACYBP. Mutant clinical features most consistently reported in males with mutations include mild to severe intellectual disability, epilepsy, short stature, hyperreflexia, aggressive behavior and microcephaly, phenotypes, overview. Significant loss of DNA methylation at specific genomic loci in blood samples of male patients carrying KDM5C mutations, suggesting these genes are epigenetic targets of KDM5C
malfunction
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reduction of Fbxl10 levels results in increased Xist, Ccl2, Ccl5, Ccl7, and Cxcl10 RNA expression. Other genes differentially expressed in D5 cells are not affected by the knockdown of Fbxl10
malfunction
423 genes are upregulated and 333 genes are downregulated in KDM5B knockdown MDA-MB 231 cells, downregulated genes in KDM5B knockdown cells do not cluster. The expression of the KDM5B-dependent genes is validated by quantitative real-time PCR. The PHD1 finger mutants may act as dominant-negative mutants, altering the dynamics and interactions of endogenous KDM5B. In contrast, the W1502A mutant of PHD3 that is defective in H3K4me3 binding shows an inhibitory effect oncell migration similar to the effect of the wild-type protein
malfunction
both pharmacological inhibition of LSD1 and small interfering RNA (siRNA) knockdown prevents interleukin 1beta-induced H3K9 demethylation at the mPGES-1 promoter as well as concomitant mPGES-1 protein expression. The level of LSD1 expression is elevated in osteoarthritis cartilage
malfunction
changes in RENT component recruitment at NTS regions due to loss of H3 methylases or demethylases. JHD2-deficient cells contain the mostly hypercondensed rDNA mislocalized away from the nuclear periphery
malfunction
internal deletion of the ARID and PHD1 domains has a negligible effect on in vitro enzymatic kinetics of the KDM5 family of enzymes
malfunction
Kdm5a-/- mice are highly susceptible to Listeria monocytogenes infection. During natural killer (NK) cell activation, loss of Kdm5a profoundly impairs phosphorylation and nuclear localization of STAT4, along with increased expression of suppressor of cytokine signaling 1 (SOCS1). Kdm5a-/- NK cells are hyporesponsive to inflammatory stimulus in vitro. Loss of Kdm5a profoundly impairs interleukin-12-induced phosphorylation and nuclear localization of STAT4
malfunction
multiple myeloma MM1S cells treated with inhibitor 2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinamide show increased global H3K4 methylation at transcriptional start sites and impaired proliferation. Inhibitor 2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinamide increases H3K4me3 levels in HeLa cells
malfunction
multiple myeloma MM1S cells treated with inhibitor KDOAM-25 show increased global H3K4 methylation at transcriptional start sites and impaired proliferation. Inhibitor KDOAM-25 increases H3K4me3 levels in HeLa cells
malfunction
multiple myeloma MM1S cells treated with inhibitor KDOAM-25 show increased global H3K4 methylation at transcriptional start sites and impaired proliferation. Inhibitor KDOAM-25 increases H3K4me3 levels in HeLa cells. Increased KDM5B expression is associated with shorter survival in myeloma patients and ex vivo inhibition with KDOAM-25 results in cell-cycle arrest
malfunction
mutant jhd2DELTA causes only limited gene expression defects in fermenting cells. Mutnat jhd2DELTA causes increased accumulation of the ETC components Cox2 and Sdh3, but not of the mitochondrial membrane proteins Por1 and Tim23. SDH3 mRNA is almost 2fold upregulated in jhd2DELTA
malfunction
overexpression of Rbp2, but not its enzymatically inactive mutant Rbp2H483G/E485Q, retards the transcription activities of IFNI, whereas small interfering RNA-mediated or short hairpin RNA-mediated knockdown of Rbp2 enhances IFNI promoter responses
malfunction
overexpression of the gene in gain-of-function mutants reduces the plant height with accumulation of lignin in stems, while the loss-of-function mutation does not produce any visible phenotype. The gain-of-function mutants show enhanced salt tolerance, whereas the loss-of-function mutant is more sensitive to salt compared to the wild-type. Overexpression of JMJ15 downregulates many genes which are preferentially marked by H3K4me3 and H3K4me2. Many of the downregulated genes encode transcription regulators involved in stress responses
malfunction
Se14-deficient mutant line HS112 is an early flowering time mutant. The expressions of RFT1, a floral initiator known as a florigen-like gene, and Ehd1, a flowering time activator, are upregulated in Se14-deficient mutant line HS112, whereas this upregulation is not observed in the original variety of Gimbozu. The trimethylated H3K4 in the promoter region of the RFT1 chromatin is significantly increased in mutant line HS112
malfunction
the dynamic regulation of histone modifications is important for modulating transcriptional programs during development. Aberrant H3K4 methylation is associated with neurological disorders. Loss of rbr-2 results in increased levels of H3K4me3 at the transcriptional start site of wsp-1, with concomitant higher wsp-1 expression responsible for defective axon guidance, overexpression of WSP-1 mimics rbr-2 loss, and its depletion restores normal axon guidance in rbr-2 mutants, phenotypes in rbr-2(tm3141) mutants, overview. Re-expression of WSP-1 in rbr-2/wsp-1 double mutants results in a significant increase of PVQ defects
malfunction
the rbr-2(tm1231) mutant exhibits complex defects in vulval development, the rbr-2(tm1231) mutant displays the Muv or vulvaless phenotype, overview
malfunction
analysis of demethylase developmental expression patterns and mutant/knockdown phenotypes, overview
malfunction
analysis of demethylase developmental expression patterns and mutant/knockdown phenotypes, overview. Jarid1/Lid mutation leads to derepression of a large number of genes, consistent with its predicted repressor role. The fly Myc homologue is found to interact with the JmjC domain of KDM5/Lid/Jarid1 and this interaction abrogates the demethylase activity of KDM5/Lid
malfunction
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Ndy1 knockdown by siRNA enhances sensitivity to oxidative stress, downregulation of Ndy1 activates the phosphorylation of AMPK, JNK, and p38MAPK and the cleavage of caspase-3 both before and after treatment with H2O2, Ndy1 overexpression protects cells against oxidative stress, overexpression of Ndy1 inhibits the phosphorylation of AMPK, JNK, and p38MAPK and the cleavage of caspase-3 both before and after treatment with H2O2. Knocking down Ndy1 sensitizes the cells to H2O2-induced oxidative stress. Genes Nqo1 and Prdx4 are direct Ndy1 targets. First, Ndy1 but not its DELTACXXC mutant binds specific regions in the promoters of both genes. Second, whereas Ndy1 upregulates their expression, the DELTACXXC mutant does not, suggesting that binding to the promoter region is necessary for their induction
malfunction
overexpression of JMJ703-YFP-HA reduces the levels of H3K4me3/2/1 in vivo. JMJ703 loss-of-function mutant displays pleiotropic phenotypes. Impaired JMJ703 activity leads to elevated levels of H3K4me3, the misregulation of numerous endogenous genes, and the transpositional reactivation of two families of non-LTR retrotransposons. But loss of JMJ703 does not affect transposable elements (such as Tos17) previously found to be silenced by other epigenetic pathways. Overexpression of JMJ703-YFP-HA reduces the levels of H3K4me3/2/1 in vivo. Karma, a non-LTR LINE-type retrotransposon (LOC_Os11g44750, in a chromosome niche depleted in H3K4me3), shows upregulated gene expression and significantly increased association with H3K4me3 in jmj703. In T-DNA insertion disruption mutants of JMJ703, four of the validated target genes show the decreased CpG methylation at their 5' regions with the increased H3K4me3 in the mutant compared to wild-type
malfunction
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enzyme depletion impairs the estrogen-induced G1/S transition of the cell cycle in vitro and inhibits breast tumorigenesis in vivo
malfunction
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enzyme depletion results in a widespread redistribution and disorganization of nucleosomes in a sequence-dependent manner
malfunction
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overexpression of the gene in gain-of-function mutants reduces the plant height with accumulation of lignin in stems, while the loss-of-function mutation does not produce any visible phenotype. The gain-of-function mutants show enhanced salt tolerance, whereas the loss-of-function mutant is more sensitive to salt compared to the wild-type. Overexpression of JMJ15 downregulates many genes which are preferentially marked by H3K4me3 and H3K4me2. Many of the downregulated genes encode transcription regulators involved in stress responses
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metabolism
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interactions between DNA methylation and H3 lysine 4 methylation
metabolism
different roles of histone H3 methylases in regulating Net1/Sir2 recruitment to rDNA regions and the resultant rDNA silencing. In particular, both H3K4 and H3K79 methylation by Set1 and Dot1 positively regulate rDNA silencing, whereas H3K36 methylation by Set2 has the opposite effect
metabolism
KDM5B associates with the deacetylase NuRD complex, i.e. with two catalytic subunits of the NuRD complex. One subunit is a chromodomain helicase DNA binding protein 4 (CHD4) ATPase, which hydrolyses ATP necessary for DNA sliding and repositioning of nucleosomes. The second catalytic subunit is histone deacetylase 1 (HDAC1), which deacetylates acetylated lysine residues of histones. KDM5B is recruited to about 140000 genomic regions, and 76268 of these regions overlap with the regions occupied by HDAC1. About 50% of the KDM5B-HDAC1 binding sites overlap with tri-, di-, or monomethylated H3K4 (H3K4me3/2/1), which are substrates for the KDM5B enzymatic activity
metabolism
NURF-1, an H3K4me3-binding protein and member of the chromatin-remodeling complex NURF, is required for promoting aberrant wsp-1 transcription in rbr-2 mutants and its ablation restores wild-type expression of wsp-1 and axon guidance
metabolism
yeast possesses solitary H3K4 methyltransferase and demethylase enzymes
metabolism
model of the distinct mechanisms controlling transposable element silencing, overview. A transposable element located in a euchromatic region containing active genes associated with H3K4me3 is silenced by additional repressive marks like H3K9me2. If H3K9me2 methyltransferase is impaired, the repressive marks are removed and the transposable element is activated. A transposable element located in a heterochromatic region is silenced by active H3K4me3 demethylase
metabolism
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Ndy1 epigenetically regulates several redox genes and the regulation of these genes by Ndy1 is responsible for the modulation of H2O2 levels and for the resistance of Ndy1-expressing cells to oxidative stress. Genes Nqo1 and Prdx4 are direct Ndy1 targets
metabolism
the enzyme is involved in patterns of specific lysine methyl modifications achieved by a precise lysine methylation system, consisting of proteins that add, remove and recognize the specific lysine methyl marks. H3K27me3 and H3K4me3 demethylation are likely to be coupled, the demethylases are also likely to be involved in the developmentally programmed silencing of PcG targets
metabolism
the enzyme is involved in patterns of specific lysine methyl modifications achieved by a precise lysine methylation system, consisting of proteins that add, remove and recognize the specific lysine methyl marks. H3K27me3 and H3K4me3 demethylation are likely to be coupled, the demethylases are also likely to be involved in the developmentally programmed silencing of PcG targets
metabolism
the protein-protein interactions between KDM5A and the histone H3 tail extend beyond the amino acids proximal to the substrate mark. Deletion or mutation of residues at positions 14-18 on the H3 tail results in an 8fold increase in the KMapp value, compared to wild-type 18mer peptide. Post-translational modifications on this distal epitope can modulate KDM5A-dependent demethylation
physiological function
dJMJD2(1)/CG15835 is excluded from heterochromatin and localizes to multiple euchromatic sites, where it regulates H3K36 methylation and heterochromatin organization. CG15835 contributes to delimit hetero- and euchromatic territories through the regulation of H3K36 methylation in euchromatin
physiological function
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dKDM2 plays an important role in nucleolar structure organization
physiological function
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function of Lid in gene activation, the biochemical activity of this protein entails the removal of a histone mark that is correlated with active transcription
physiological function
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KDM5b regulates cell cycle control genes in cancer. It KDM5b reduces the terminally differentiated cells and increases proliferating progenitors in cell differentiation, mechanisms, overview. Role for KDM5b in the choice between proliferation and differentiation during development
physiological function
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role of RBP2 in mitochondrial biogenesis, which involves regulation of H3K4me3-modified nucleosomes
physiological function
the enzyme is involved in setting histone H3-K4 methylation patterns in the oocyte and follicle during folliculogenesis, these epigenetic markers serve an essential regulatory role during folliculogenesis
physiological function
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the enzyme is involved in the mechanism for repression of developmental genes by the coordinated regulation of epigenetic marks involved in repression and activation of transcription
physiological function
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JARID1B act as transcriptional repressor, with hPc2 acting as a transcriptional co-repressor, overview
physiological function
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the histone demethylase KDM5A is an integral, conserved component of Notch/RBP-J gene silencing. KDM5A regulates gene expression at Notch target genes. Methylation of histone H3 Lys 4 is dynamically erased and re-established at RBP-J sites upon inhibition and reactivation of Notch signaling. KDM5A interacts physically with the core transcription factor RBP-J, this interaction is crucial for Notch-induced growth and tumorigenesis responses. Interaction analysis by ChIP-sequencing. KDM5A but not KDM5C binds strongly to GST-RBP-J
physiological function
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The lysine-specific histone demethylase 1 is a chromatin modifying enzyme that specifically removes methyl groups from lysine 4 of histone 3 and induces transcriptional repression. Tightly regulated distribution for LSD1 in the brain of rats under ischemic insult, suggesting a critical role in neuron function, overview
physiological function
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Fbxl10 is described as a nucleolar protein to repress rRNA transcription, to be involved in apoptosis, and inhibition of cellular senescence. Fbxl10 is implicated in the demethylation of H3K4me3 or H3K36me2 thereby removing active chromatin marks and inhibiting gene transcription, but Fbxl10 is rather a H3K4me3 than a H3K36me2 histone demethylase. The PHD domain exerts a dual function in binding H3K4me3 and H3K36me2 and exhibiting E3 ubiquitin ligase activity. Fbxl10 regulates genes involved in the cellular metabolome and anatomical structures
physiological function
the JmjC domain-containing protein, JMJ703, is a histone lysine demethylase that specifically reverses all three forms of H3K4me, mono-, di-, or trimethylated state histone 3, in rice. Histone H3 lysine 4 demethylase is required for stem elongation in rice, importance of the protein in plant growth
physiological function
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The KDM5C protein is likely to play a role not only in intellectual disability but also in sex-specific differences in brain function, parallel sex-specific DNA methylation profiles in brain samples from control males and females were observed at FBXL5 and CACYBP
physiological function
changes in histone H3 lysine methylation levels distinctly regulate rDNA silencing by recruiting different silencing proteins to rDNA, thereby contributing to rDNA silencing and nucleolar organization in yeast. Jhd2 regulates rDNA recombination through the Tof2/Csm1/Lrs4 pathway and prevents excessive recruitment of Tof2, Csm1/Lrs4 and condensin subunits to the replication fork barrier site within the NTS1 region. The demethylase activity of Jhd2 regulates telomeric silencing and mitotic rDNA condensation and rDNA repeat stability and rDNA silencing in a Sir2-independent manner by maintaining Csm1/Lrs4 and condensin association with rDNA regions during mitosis. Jhd2 is the only JmjC demethylase that contributes to the regulation of rDNA silencing and acts through a pathway that is independent of Net1 and Sir2, but through a Tof2/Csm1/Lrs4 pathway. Jhd2-mediated alleviation of excessive Csm1/Lrs4 or condensin at the NTS1 region of rDNA is required for the integrity of rDNA repeats and proper rDNA silencing during mitosis. The role of yeast JmjC-demethylases in regulating telomeric silencing is not restricted to Jhd2. The effect of Jhd2 on rDNA silencing is independent on the enzymatic activity of Jhd2
physiological function
histone H3K4 methylation is linked to transcriptional activation. KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex, KDM5A and the NuRD complex cooperatively function to control developmentally regulated genes, and KDM5A and the NuRD complex cooperatively regulate H3K4me2/3 levels. CHD4 modulates H3K4 methylation levels at the promoter and coding regions of target genes
physiological function
histone H3K4 methylation is linked to transcriptional activation. KDM5A, a histone H3K4 demethylase, physically interacts with the nucleosome remodeling and deacetylase (NuRD) complex, KDM5A and the NuRD complex cooperatively function to control developmentally regulated genes. Caenorhabditis elegans homologues of KDM5, RBR-2, and CHD4 functions cooperatively with NuRD in vulval development, functional interaction between KDM5 and the NuRD complex during developmental processes
physiological function
histone lysine demethylase KDM5B regulates gene transcription and cell differentiation and is implicated in carcinogenesis
physiological function
histone lysine methylation is an important epigenetic modification for gene expression in eukaryotic cells. Increased JMJ15 levels may regulate the gene expression program that enhances stress tolerance
physiological function
LSD1 modulates gene expression through demethylation of either H3K4 or H3K9. H3K9 methylation usually suppresses transcription, whereas H3K4 methylation generally activates transcription. H3K4 methylation is a critical epigenetic marker of transcriptional activation. Lysine-specific demethylase 1-mediated demethylation of histone H3 lysine 9, but not lysine 4, contributes to interleukin 1beta-induced microsomal prostaglandin E synthase 1 (mPGES-1) expression in human osteoarthritic chondrocytes. Levels of di- and trimethylated H3K4 are significantly enhanced after 4 h of interleukin-1beta stimulation, reach a maximum at 12 h, persist through 24 h and decrease at 48 h. In contrast, the level of monomethylated H3K4 remain almost unchanged following interleukin-1beta stimulation. The increase in H3K4 di- and trimethylation by interleukin-1beta at the mPGES-1 promoter paralleles the increased transcription of mPGES-1, suggesting that, in addition to H3K9 demethylation, H3K4 methylation also contributes to interleukin-1beta-induced mPGES-1 expression, the induction of mPGES-1 by interleukin-1beta is associated with H3K4 methylation
physiological function
retinoblastoma binding protein 2 (Rbp2) is a H3K4me3 demethylase that interacts with Piasy, a Pias (protein inhibitor of activated signal transducer and activator of transcription) family member, which possesses the ability to suppress IFNI transcriptions in mouse embryonic fibroblasts (MEFs). The H3K4me3 levels, one activation mark of genes, in MEFsthat are stimulated by poly(I:C), are impaired by Piasy in the IFN-beta gene. Piasy binds to the Jmjc domain (residues 451-503) of Rbp2 via its PINIT domain (residues 101-218), which is consistent with the domain required for their attenuation of transcription and H3K4me3 levels of IFNI genes. Piasy may prevent exaggerated transcription of IFNI by Rbp2-mediated demethylation of H3K4me3 of IFNI, avoiding excessive immune responses. Piasy reduces H3K4me3 levels of IFNI genes upon activation in MEFs, the Jmjc domain of Rbp2 and the PINIT domain of Piasy are prerequisites. Demethylase activity of Rbp2, but not DNA contact by K152, is indispensable
physiological function
role for KDM5A (JARID1A/RBP2) as oncogenic driver
physiological function
role for KDM5B (JARID1B/PLU1) as oncogenic driver
physiological function
Saccharomyces cerevisiae Jumonji demethylase Jhd2 opposes the accumulation of H3K4me3 in fermenting cells only when they are nutritionally manipulated to contain an elevated 2-oxoglutarate/succinate ratio. Jhd2 opposes H3K4me3 in respiratory cells that do not exhibit such an elevated 2-oxoglutarate/succinate ratio. JHD2 restrains respiration in nonfermentable growth conditions. Enzyme JHD2 restricts mitochondrial respiratory capacity in cells grown in non-fermentable carbon in an H3K4me-dependent manner. JHD2 limits yeast proliferative capacity under physiologically challenging conditions as measured by both replicative lifespan and colony growth on non-fermentable carbon. JHD2's impact on nutrient response may reflect an ancestral role of its gene family in mediating mitochondrial regulation. The JmjC domain mediates the demethylation of histone lysine residues. Nutritional conditions impact Jhd2 control of H3K4me3 and gene expression. JHD2 controls mitochondrial respiration through H3K4me
physiological function
Se14 is a photoperiod-sensitivity gene that has a suppressive effect on floral transition (flowering time) under long day-length conditions through the modification of chromatin structure by H3K4me3 demethylation in the promoter region of RFT1
physiological function
the H3K4me3 demethylase Kdm5a is required for natural killer (NK) cell activation by associating with p50 to suppress suppressor of cytokine signaling 1 (SOCS1), repressor of the JAK-STAT pathway. Kdm5a is recruited to the SOCS1 promoter by p50 to maintain a repressive chromatin configuration. Kdm5a-mediated suppression of SOCS1 is required for NK cell activation and initiation of innate immune responses to infection. Kdm5a promotes NK cell activation by regulating interferon-gamma production. Kdm5a inhibits SOCS1 expression and promotes STAT4 activation. Kdm5a is required for clearance of Listeria monocytogenes. Kdm5a associates with p50 and binds to the Socs1 promoter region in resting NK cells, leading to a substantial decrease in H3K4me3 modification and repressive chromatin configuration at the Socs1 promoter. Kdm5a enhances JAK2-STAT4 signaling by suppressing SOCS1 expression
physiological function
the H3K4me3/2 histone demethylase RBR-2 is required during embryogenesis in the nervous system to ensure correct axon guidance. RBR-2 controls axon guidance by repressing the actin-remodeling gene wsp-1. RBR-2 is essential for establishing correct axon guidance of the PVQ neurons during embryonic development, but it does not play any role in its maintenance. Role of rbr-2 in neuronal development, role of H3K4me3 readers in axon patterning, and epigenetic regulation of transcription. RBR-2 is required specifically in the nervous system (F25B3.3 promoter), but its presence in hypodermal cells (dpy-7 promoter) and in muscles(myo-3 promoter) is not essential
physiological function
histone demethylases play important roles in epigenetic regulation of gene expression, regulatory mechanisms that modulate demethylase recruitment and activity, overview. Modulation of demethylase activity involves regulation at multiple levels, including gene expression, recruitment, coordination with other epigenetic marks, and post translational modifications. Demethylase activity can be modulated by DNA-binding transcription factors, and the local chromatin environment regulates demethylase accessibility. Fly KDM5/Lid/JARID1 is an H3K4me3 demethylase. Non-coding RNAs might also play roles in recruiting H3K4 demethylase complexes to establish locus specific epigenetic patterns
physiological function
histone demethylases play important roles in epigenetic regulation of gene expression, regulatory mechanisms that modulate demethylase recruitment and activity, overview. Modulation of demethylase activity involves regulation at multiple levels, including gene expression, recruitment, coordination with other epigenetic marks, and post translational modifications. Demethylase activity can be modulated by DNA-binding transcription factors, and the local chromatin environment regulates demethylase accessibility. Non-coding RNAs might also play roles in recruiting H3K4 demethylase complexes to establish locus specific epigenetic patterns
physiological function
JMJ703 is an active H3K4-specific demethylase required for transposable elements silencing, overview. The removal of active histone modifications is involved in transposable elements silencing and different subsets of transposable elements may be regulated by distinct epigenetic pathways. Histone demethylation is a unique mechanism to control retrotransposon activity. Effects of JMJ703 on H3K4me3 and gene expression, detailed overview
physiological function
methylation of H3K4 prevents spreading of heterochromatin. Both H3K36 and H3K4 methylation associate to actively transcribed genes, suggesting that gene activity is a main determinant to delimit hetero- and euchromatic territories. H3K4me3 is an epigenetic mark that correlates with transcriptionally active genes
physiological function
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the JmjC domain histone demethylase Ndy1 regulates redox homeostasis and protects cells from oxidative stress. Ndy1 promotes the expression of genes encoding the antioxidant enzymes aminoadipic semialdehyde synthase (Aass), NAD(P)H quinone oxidoreductase-1 (Nqo1), peroxiredoxin-4 (Prdx4), and serine peptidase inhibitor b1b (Serpinb1b) and represses the expression of interleukin-19. At least two of these genes (Nqo1 and Prdx4) are regulated directly by Ndy1, which binds to specific sites within their promoters and demethylates promoter-associated histone H3 dimethylated at K36 and histone H3 trimethylated at K4. Simultaneous knockdown of Aass, Nqo1, Prdx4, and Serpinb1b in Ndy1-expressing cells to levels equivalent to those detected in control cells is sufficient to suppress the Ndy1 redox phenotype. Endogenous Ndy1 is a physiological redox regulator of the cellular response to oxidative stress. The enzyme protects cells against oxidative stress by inhibiting reactive oxygen species-dependent signaling, overview. Ndy1 inhibits the oxidation of deoxyguanosine and DNA damage, and the accumulation of H2O2 in both H2O2-treated and untreated cells. Ndy1 enhances the antioxidant activity of cells. The gene Serpinb1b, upregulated by Ndy1, and gene IL-19, which is downregulated by Ndy1, play indirect roles in redox homeostasis, overview. Endogenous Ndy1 is a physiological redox regulator of the cellular response to oxidative stress. Ndy1 functions as an activator of transcription are in agreement with published data showing that Ndy1 promotes the transcriptional activation of the Hoxd1 gene. Ndy1 can also function as a repressor. Genes Nqo1 and Prdx4 are direct Ndy1 targets. First, Ndy1 but not its DELTACXXC mutant binds specific regions in the promoters of both genes. Second, whereas Ndy1 upregulates their expression, the DELTACXXC mutant does not, suggesting that binding to the promoter region is necessary for their induction
physiological function
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demethylation of histone H3 lysine 4 by the enzyme is critical for establishing the DNA methylation imprints during oogenesis
physiological function
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enzyme overexpression promotes the epithelial-mesenchymal transition process of cancer cells. The enzyme increases the expression of transcription factors, ZEB1 and ZEB2, followed by downregulation of E-cadherin and upregulation of mesenchymal marker genes. The enzyme represses the expression of the miR-200 family by changing histone H3 methylation status of their regulatory regions
physiological function
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the enzyme is a corepressor of transforming growth factor-beta inducible early gene-1/Krueppel-like transcription factor 10 (TIEG1/KLF10)
physiological function
the enzyme is involved in the control of flowering time by demethylating [histone H3]-N6,N6,N6-trimethyl-L-lysine4 at flowering locus C chromatin
physiological function
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the enzyme plays a role in neuronal survival and dendritic development
physiological function
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the enzyme plays a role in regulating nucleosome positioning in embryonic stem cells
physiological function
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the enzyme plays an essential role in hypoxia signaling. The enzyme regulates the expression of hypoxia-induced neuroendocrine differentiation genes. The enzyme is essential for maintaining [histone H3]-N6,N6,N6-trimethyl-L-lysine4 levels on hypoxia-inducible genes. In the context of prostate cancer, the enzyme appears to execute its regulatory function during hypoxia signaling in androgen receptor-positive prostate cancer cells
physiological function
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the enzyme promotes cell proliferation of breast cancer in vitro and tumorigenesis in vivo. The enzyme functions as a demethylase in estrogen signaling. The enzyme is transcriptionally regulated by estrogen receptor alpha. Through the up-regulation of the enzyme, estrogen receptor alpha and the enzyme form a feedforward regulatory loop to enhance and amplify the hormone response under physiological as well as pathological conditions
physiological function
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the enzyme represses flowering locus T and twin sister of flowering locus T expression to inhibit the floral transition
physiological function
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the transcription factor TFAP2C-oncoprotein Myc-enzyme complex promotes cell cycle progression via direct cell cycle inhibitor p21cip repression, thereby contributing to tumorigenesis and therapy failure
physiological function
attenuation of isoforms KDM5B and KDM5C mRNA hampers embryo development to the blastocyst stage in fertilized, parthenogenetically activated and nuclear transfer embryos. Isoform KDM5B attenuation increases H3K4me2-3 levels on D3 embryos and H3K4 mono-, di- and trimethylation on D5 embryos. KDM5C attenuation increases H3K9me1 on D3 embryos, and H3K9me1 and H3K4me1 on D5 embryos. KDM5B and KDM5C attenuation affects DNA damage response and increases DNA double-strand breaks, and decreases development of UV-irradiated embryos
physiological function
attenuation of isoforms KDM5B and KDM5C mRNA hampers embryo development to the blastocyst stage in fertilized, parthenogenetically activated and nuclear transfer embryos. Isoform KDM5B attenuation increases H3K4me2-3 levels on D3 embryos and H3K4 mono-, di- and trimethylation on D5 embryos.KDM5C attenuation increases H3K9me1 on D3 embryos, and H3K9me1 and H3K4me1 on D5 embryos. KDM5B and KDM5C attenuation affects DNA damage response and increases DNA double-strand breaks, and decreases development of UV-irradiated embryos
physiological function
demethylase KDM5A/JARID1A interacts with the haematopoietic-specific master transcription proteins SCL and GATA1 in red blood cells. A direct physical contact is obeserved between GATA1 and the second PHD domain of JARID1A
physiological function
in a murine 3T3-L1 preadipocyte differentiation model, KDM5A down-regulation inhibits 3T3-L1 preadipocyte differentiation. The KDM5A knockdown significantly upregulates the negative regulator of adipogenesis Wnt6, having increased levels of the H3K4me3 mark on its promoter. WNT6 knockdown significantly rescues adipogenesis inhibited by the KDM5A knockdown. Early transcription factor C/EBPbeta negatively regulates Wnt6 expression by binding to the Wnt6 gene promoter and repressing Wnt6 transcription. KDM5A interacts with C/EBPbeta and their interaction cooperatively inhibits Wnt6 transcription
physiological function
in dental pulp cells, KDM5A depletion results in greater alkaline phosphatase activity and more mineral deposition formation. The expression levels of the odontogenic markers DMP1, DSPP, OSX, and OCN are increased by KDM5A knockdown. KDM5A deficiency leads to a significant increment in total H3K4me3 levels, whereas no significant difference is found for H3K4 me2. H3K4me3 levels on the promoters of the odontogenic markers increase after KDM5A knockdown in dental pulp cells
physiological function
KDM5B is not a strong transcriptional repressor but rather a fine-tuning regulator of cell type-specific H3K4 methylation and transcript levels. The top up-regulated genes CYP1A1, CYP1B2, ALDH1A3 and AHRR are involved in the aryl hydrocarbon receptor (AhR) response
physiological function
knockout or inhibition of Jarid1b prevents the development of endothelial dysfunction in response to angiotensin AngII, accompanied by a loss of the inflammatory response to AngII. AngII induces the soluble epoxide hydrolase (sEH). Knockout or inhibition of Jarid1b prevents the AngII-mediated sEH induction. Jarid1b maintains the length of the 3'-untranslated region of the sEH mRNA, thereby increasing its stability and thus sEH protein expression
physiological function
the expression of STING, i.e. cyclic GMP-AMP synthase stimulator of interferon genes, is epigenetically suppressed by the histone H3K4 lysine demethylases KDM5B and KDM5C. The induction of STING expression by KDM5 blockade triggers a robust interferon response in a cytosolic DNA-dependent manner in breast cancer cells, resulting in resistance to infection by DNA and RNA viruses
physiological function
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The lysine-specific histone demethylase 1 is a chromatin modifying enzyme that specifically removes methyl groups from lysine 4 of histone 3 and induces transcriptional repression. Tightly regulated distribution for LSD1 in the brain of rats under ischemic insult, suggesting a critical role in neuron function, overview
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physiological function
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histone lysine methylation is an important epigenetic modification for gene expression in eukaryotic cells. Increased JMJ15 levels may regulate the gene expression program that enhances stress tolerance
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additional information
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active mark H3K4me3 disappear upon gamma-secretase inhibitor N-[N-(3,5-difluorophenylacetyl-L-alanyl)]-S-phenylglycine t-butyl ester treatment at the RBP-J-binding site of the genes Deltex-1, Hes-1, and CD25 enhancer, as well as at the promoter of preTa. The Notch target genes are down-regulated. After removal of GSI, the peak of H3K4me3 at the RBP-J-binding site reappears. H3K4 trimethylation at Notch target gene Deltex-1 is dynamic only at the RBP-J-binding sites
additional information
five solvent-exposed regions in c-JMJ703 structure, including P195-K199, S224-R261, R288-S295, T329-Y349, and Q363-V377. Three key residues, H394, E396, and H482, are perfectly conserved in JMJD2 proteins. They chelated Fe(II) in them active site through their hydrophilic side chains. The methyl group binding pocket of JmjC domain is unique among methylated peptide binding proteins due to the polar rather than hydrophobic environment
additional information
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five solvent-exposed regions in c-JMJ703 structure, including P195-K199, S224-R261, R288-S295, T329-Y349, and Q363-V377. Three key residues, H394, E396, and H482, are perfectly conserved in JMJD2 proteins. They chelated Fe(II) in them active site through their hydrophilic side chains. The methyl group binding pocket of JmjC domain is unique among methylated peptide binding proteins due to the polar rather than hydrophobic environment
additional information
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stable overexpression of N-terminally HA-tagged Fbxl10 in murine embryonic fibroblasts leads to an increase in cell and nuclear size and changes the transcriptome, but with no effect on proliferation, mitosis, and apoptosis or global histone marks, quantitative real-time PCR expression analysis
additional information
enzyme KDM5A uses distinct domains to associate with the SIN3B and NuRD complexes
additional information
enzyme KDM5B contains multiple conserved chromatin-associated domains, including three PHD fingers. The first and third, but not the second, PHD finger of KDM5B possess histone binding activities. The PHD1 finger is highly specific for unmodified histone H3 (H3K4me0), whereas the PHD3 finger shows preference for the trimethylated histone mark H3K4me3, but also binds H3K4me0. Mechanism of H3K4me0 recognition by PHD1, the H3K4me0 binding mode is conserved overview. KDM5B inhibits the migration and invasion abilities of MDA-MB 231 breast cancer cells, and binding of the PHD1 finger to H3K4me0 is required to suppress cell migration
additional information
minimal requirements for enzymatic activity of the KDM5 family is the linked JmjNJmjC domain coupled with the immediate C-terminal helical zinc-binding domain
additional information
minimal requirements for enzymatic activity of the KDM5 family is the linked JmjNJmjC domain coupled with the immediate C-terminal helical zinc-binding domain
additional information
minimal requirements for enzymatic activity of the KDM5 family is the linked JmjNJmjC domain coupled with the immediate C-terminal helical zinc-binding domain
additional information
minimal requirements for enzymatic activity of the KDM5 family is the linked JmjNJmjC domain coupled with the immediate C-terminal helical zinc-binding domain, hypothetical modeling of the N-terminal half of KDM5, overview
additional information
minimal requirements for enzymatic activity of the KDM5 family is the linked JmjNJmjC domain coupled with the immediate C-terminal helical zinc-binding domain, hypothetical modeling of the N-terminal half of KDM5, overview
additional information
minimal requirements for enzymatic activity of the KDM5 family is the linked JmjNJmjC domain coupled with the immediate C-terminal helical zinc-binding domain, hypothetical modeling of the N-terminal half of KDM5, overview
additional information
KDM1/LSD1-mediated H3K4me2 demethylation and epigenetic regulation model. Model for demethylase regulation by expression, interacting proteins and local chromatin environment
additional information
KDM1/LSD1-mediated H3K4me2 demethylation and epigenetic regulation model. Model for demethylase regulation by expression, interacting proteins and local chromatin environment
additional information
overexpression of CG3654 shows no significant effect on the levels of H3K4me3, H3K9me3, H3K27me3, H3K36me3 and H4K20me3
additional information
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overexpression of CG3654 shows no significant effect on the levels of H3K4me3, H3K9me3, H3K27me3, H3K36me3 and H4K20me3