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Literature summary for 1.14.11.69 extracted from

  • Liang, C.Y.; Hsu, P.H.; Chou, D.F.; Pan, C.Y.; Wang, L.C.; Huang, W.C.; Tsai, M.D.; Lo, W.S.
    The histone H3K36 demethylase Rph1/KDM4 regulates the expression of the photoreactivation gene PHR1 (2011), Nucleic Acids Res., 39, 4151-4165.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
gene rph1 Saccharomyces cerevisiae

Protein Variants

Protein Variants Comment Organism
H235A catalytically deficient mutant Saccharomyces cerevisiae

General Stability

General Stability Organism
the JmjN domain is important in maintaining protein stability and the repressive effect of Rph1 Saccharomyces cerevisiae

Inhibitors

Inhibitors Comment Organism Structure
additional information expression of GTT1, UGX2, CTT1, and HSP26 is highly induced by H2O2 treatment and causes the dissociation of Rph1 from the promoters of these genes Saccharomyces cerevisiae

Localization

Localization Comment Organism GeneOntology No. Textmining
chromatin Rph1 is associated with a specific chromatin locus. Release of Rph1 from chromatin also required the phosphorylation at S652 Saccharomyces cerevisiae 785
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nucleus
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Saccharomyces cerevisiae 5634
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Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2 Saccharomyces cerevisiae
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histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
-
?
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2 Saccharomyces cerevisiae BY4742
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histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
-
?
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2 Saccharomyces cerevisiae
-
histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
-
?
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2 Saccharomyces cerevisiae BY4742
-
histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
-
?
additional information Saccharomyces cerevisiae Rph1 is a histone demethylase specific to tri-methylated-H3K36. Rph1 binds to the URS of PHR1 through ZF domains and modulates chromatin modifications in specific regions of the PHR1 promoter ?
-
?
additional information Saccharomyces cerevisiae BY4742 Rph1 is a histone demethylase specific to tri-methylated-H3K36. Rph1 binds to the URS of PHR1 through ZF domains and modulates chromatin modifications in specific regions of the PHR1 promoter ?
-
?

Organism

Organism UniProt Comment Textmining
Saccharomyces cerevisiae
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-
-
Saccharomyces cerevisiae
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gene rph1
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Saccharomyces cerevisiae BY4742
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gene rph1
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Posttranslational Modification

Posttranslational Modification Comment Organism
phosphoprotein Rph1 is phosphorylated under oxidative stress, which leads to Rph1 dissociation and transcriptional activation. Rad53 may be the key kinase essential for Rph1 phosphorylation on oxidative stress with H2O2 treatment Saccharomyces cerevisiae
phosphoprotein the crucial checkpoint protein Rad53 acts as an upstream regulator of Rph1 and dominates the phosphorylation of Rph1 that is required for efficient PHR1 expression and the dissociation of Rph1. Release of Rph1 from chromatin also required the phosphorylation at S652 Saccharomyces cerevisiae

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2
-
Saccharomyces cerevisiae histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
-
?
histone H3-N6,N6,N6-trimethyl-L-lysine36 + 2-oxoglutarate + O2
-
Saccharomyces cerevisiae BY4742 histone H3-N6,N6-dimethyl-L-lysine36 + succinate + formaldehyde + CO2
-
?
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
-
Saccharomyces cerevisiae histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
-
?
histone H3-N6,N6-dimethyl-L-lysine36 + 2-oxoglutarate + O2
-
Saccharomyces cerevisiae BY4742 histone H3-N6-methyl-L-lysine36 + succinate + formaldehyde + CO2
-
?
additional information Rph1 is a histone demethylase specific to tri-methylated-H3K36. Rph1 binds to the URS of PHR1 through ZF domains and modulates chromatin modifications in specific regions of the PHR1 promoter Saccharomyces cerevisiae ?
-
?
additional information Rph1 is a histone demethylase specific to tri-methylated-H3K36. Rph1 binds to the URS of PHR1 through ZF domains and modulates chromatin modifications in specific regions of the PHR1 promoter Saccharomyces cerevisiae BY4742 ?
-
?

Synonyms

Synonyms Comment Organism
histone H3K36 demethylase
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Saccharomyces cerevisiae
Rph1/KDM4
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Saccharomyces cerevisiae

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
30
-
assay at Saccharomyces cerevisiae

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8
-
assay at Saccharomyces cerevisiae

Expression

Organism Comment Expression
Saccharomyces cerevisiae checkpoint kinase Rad53 negatively modulates Rph1 protein level down
Saccharomyces cerevisiae the crucial checkpoint protein Rad53 acts as an upstream regulator of Rph1 and dominates the phosphorylation of Rph1 that is required for efficient PHR1 expression and the dissociation of Rph1 down
Saccharomyces cerevisiae Rph1 is phosphorylated under oxidative stress, which leads to Rph1 dissociation and transcriptional activation. Rad53 may be the key kinase essential for Rph1 phosphorylation on oxidative stress with H2O2 treatment up

General Information

General Information Comment Organism
evolution Rph1 is a histone demethylase containing a Jumonji C (JmjC) domain and belongs to the C2H2 zinc-finger protein family Saccharomyces cerevisiae
malfunction histone H3K36A mutant shows increased UV sensitivity. Deletion of rph1 leads to approximately 2fold enhancement of PHR1 under normal conditions. Overexpression of Rph1 reduces the expression of PHR1 and increased UV sensitivity. The catalytically deficient mutant H235A of Rph1 diminishes the repressive transcriptional effect on PHR1 expression, which indicates that histone demethylase activity contributes to transcriptional repression Saccharomyces cerevisiae
malfunction more than 75% of Rph1-regulated genes show increased expression in the rph1-deletion mutant Saccharomyces cerevisiae
additional information Rph1 is a labile protein, and Rad53 negatively modulates Rph1 protein level. The JmjN domain is important in maintaining protein stability and the repressive effect of Rph1. Binding motif 5'-CCCCTWA-3', which resembles the stress re­sponse element, is overrepresented in the promoters of Rph1-repressed genes. JmjN and ZF domains of Rph1 are required for its function. Rph1 binds to gene promoters and is dissociated with DNA damage Saccharomyces cerevisiae
physiological function histone H3K36 demethylase Rph1/KDM4 regulates the expression of the photoreactivation gene PHR1, the demethylation at H3K36 is linked to UV sensitivity. Overexpression of Rph1 and H3K36A mutant reduced histone acetylation at the URS, which implies a crosstalk between histone demethylation and acetylation at the PHR1 promoter. Rph1 is a repressor of the DNA repair gene PHR1. Rph1 is dissociated from the PHR1 promoter in response to DNA damage. Rad53 regulates the expression of PHR1 and dissociation of Rph1 in response to DNA damage. Activated Rad53 complex phosphorylates Rph1 and S652A-mutated Rph1 impairs the dissociation in response to DNA damage Saccharomyces cerevisiae
physiological function Rph1 might be a regulatory node connecting different signal­ing pathways responding to environmental stresses. Rph1 is mainly a transcriptional repressor. Rph1-regulated genes respond to DNA damage and environmental stress. Microarray analysis, overview Saccharomyces cerevisiae