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Literature summary extracted from
- Mechanisms involved in the regulation of histone lysine demethylases (2008), Curr. Opin. Cell Biol., 20, 316-325 .
Inhibitors
| EC Number | Inhibitors | Comment | Organism | Structure |
|---|---|---|---|---|
| 1.14.11.67 | additional information | 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 | Drosophila melanogaster |
Localization
| EC Number | Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|---|
| 1.14.11.67 | chromatin | - |
Drosophila melanogaster | 785 | - |
| 1.14.11.67 | chromatin | - |
Caenorhabditis elegans | 785 | - |
| 1.14.11.67 | nucleus | - |
Drosophila melanogaster | 5634 | - |
| 1.14.11.67 | nucleus | - |
Caenorhabditis elegans | 5634 | - |
| 1.14.99.66 | chromatin | - |
Drosophila melanogaster | 785 | - |
| 1.14.99.66 | chromatin | - |
Mus musculus | 785 | - |
| 1.14.99.66 | chromatin | - |
Caenorhabditis elegans | 785 | - |
| 1.14.99.66 | nucleus | - |
Drosophila melanogaster | 5634 | - |
| 1.14.99.66 | nucleus | - |
Mus musculus | 5634 | - |
| 1.14.99.66 | nucleus | - |
Caenorhabditis elegans | 5634 | - |
Natural Substrates/ Products (Substrates)
| EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 1.14.11.67 | [histone H3]-N6,N6,N6-trimethyl-L-lysine 4 + 2-oxoglutarate + O2 | Drosophila melanogaster | - |
[histone H3]-N6,N6-dimethyl-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? |  |
| 1.14.11.67 | [histone H3]-N6,N6,N6-trimethyl-L-lysine 4 + 2-oxoglutarate + O2 | Caenorhabditis elegans | - |
[histone H3]-N6,N6-dimethyl-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.11.67 | [histone H3]-N6,N6-drimethyl-L-lysine 4 + 2-oxoglutarate + O2 | Drosophila melanogaster | - |
[histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.11.67 | [histone H3]-N6,N6-drimethyl-L-lysine 4 + 2-oxoglutarate + O2 | Caenorhabditis elegans | - |
[histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.99.66 | [histone H3]-N6,N6-dimethyl-L-lysine 4 + 2-oxoglutarate + O2 | Drosophila melanogaster | - |
[histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.99.66 | [histone H3]-N6,N6-dimethyl-L-lysine 4 + 2-oxoglutarate + O2 | Mus musculus | - |
[histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.99.66 | [histone H3]-N6,N6-dimethyl-L-lysine 4 + 2-oxoglutarate + O2 | Caenorhabditis elegans | - |
[histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.99.66 | [histone H3]-N6,N6-dimethyl-L-lysine 4 + 2-oxoglutarate + O2 | Mus musculus C57BL/6J | - |
[histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.99.66 | [histone H3]-N6-methyl-L-lysine 4 + 2-oxoglutarate + O2 | Drosophila melanogaster | - |
[histone H3]-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.99.66 | [histone H3]-N6-methyl-L-lysine 4 + 2-oxoglutarate + O2 | Mus musculus | - |
[histone H3]-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.99.66 | [histone H3]-N6-methyl-L-lysine 4 + 2-oxoglutarate + O2 | Caenorhabditis elegans | - |
[histone H3]-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.99.66 | [histone H3]-N6-methyl-L-lysine 4 + 2-oxoglutarate + O2 | Mus musculus C57BL/6J | - |
[histone H3]-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 1.14.11.67 | Caenorhabditis elegans | Q23541 | - |
- |
| 1.14.11.67 | Drosophila melanogaster | Q9VMJ7 | - |
- |
| 1.14.99.66 | Caenorhabditis elegans | Q9XWP6 | - |
- |
| 1.14.99.66 | Drosophila melanogaster | Q9VMJ7 | - |
- |
| 1.14.99.66 | Mus musculus | Q6ZQ88 | - |
- |
| 1.14.99.66 | Mus musculus C57BL/6J | Q6ZQ88 | - |
- |
Source Tissue
| EC Number | Source Tissue | Comment | Organism | Textmining |
|---|---|---|---|---|
| 1.14.11.67 | crop | - |
Drosophila melanogaster | - |
| 1.14.11.67 | germ cell | - |
Caenorhabditis elegans | - |
| 1.14.11.67 | malpighian tubule | - |
Drosophila melanogaster | - |
| 1.14.11.67 | additional information | JaridB expression during early embryonic developing germline, development time course microarray (GDS191) | Caenorhabditis elegans | - |
| 1.14.11.67 | ovary | - |
Drosophila melanogaster | - |
| 1.14.99.66 | brain | - |
Mus musculus | - |
| 1.14.99.66 | embryonic stem cell | - |
Mus musculus | - |
| 1.14.99.66 | germ cell | - |
Caenorhabditis elegans | - |
| 1.14.99.66 | germ cell | H3K4me2 levels are higher in the primordial germ cells of heterozygous females | Drosophila melanogaster | - |
| 1.14.99.66 | additional information | KDM1 expression during early embryonic developing germline, development time course microarray (GDS191) | Caenorhabditis elegans | - |
| 1.14.99.66 | additional information | large scale transcriptome analysis of C57BL/6J (GDS868) | Mus musculus | - |
| 1.14.99.66 | pituitary gland cell line | - |
Mus musculus | - |
| 1.14.99.66 | testis | KDM1/LSD1 shows relatively higher levels of expression in mouse testis and related tissues, complementing the observed lower levels of H3K4me2 in these tissues | Mus musculus | - |
| 1.14.99.66 | thymus | - |
Mus musculus | - |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 1.14.11.67 | additional information | no activity with H3K4me1 | Drosophila melanogaster | ? | - |
? | |
| 1.14.11.67 | additional information | no activity with H3K4me1 | Caenorhabditis elegans | ? | - |
? | |
| 1.14.11.67 | [histone H3]-N6,N6,N6-trimethyl-L-lysine 4 + 2-oxoglutarate + O2 | - |
Drosophila melanogaster | [histone H3]-N6,N6-dimethyl-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.11.67 | [histone H3]-N6,N6,N6-trimethyl-L-lysine 4 + 2-oxoglutarate + O2 | - |
Caenorhabditis elegans | [histone H3]-N6,N6-dimethyl-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.11.67 | [histone H3]-N6,N6-drimethyl-L-lysine 4 + 2-oxoglutarate + O2 | - |
Drosophila melanogaster | [histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.11.67 | [histone H3]-N6,N6-drimethyl-L-lysine 4 + 2-oxoglutarate + O2 | - |
Caenorhabditis elegans | [histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.99.66 | additional information | the fly KDM1 protein has in vitro demethylase activity for H3K4me2/1 | Drosophila melanogaster | ? | - |
? | |
| 1.14.99.66 | [histone H3]-N6,N6-dimethyl-L-lysine 4 + 2-oxoglutarate + O2 | - |
Drosophila melanogaster | [histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.99.66 | [histone H3]-N6,N6-dimethyl-L-lysine 4 + 2-oxoglutarate + O2 | - |
Mus musculus | [histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.99.66 | [histone H3]-N6,N6-dimethyl-L-lysine 4 + 2-oxoglutarate + O2 | - |
Caenorhabditis elegans | [histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.99.66 | [histone H3]-N6,N6-dimethyl-L-lysine 4 + 2-oxoglutarate + O2 | - |
Mus musculus C57BL/6J | [histone H3]-N6-methyl-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.99.66 | [histone H3]-N6-methyl-L-lysine 4 + 2-oxoglutarate + O2 | - |
Drosophila melanogaster | [histone H3]-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.99.66 | [histone H3]-N6-methyl-L-lysine 4 + 2-oxoglutarate + O2 | - |
Mus musculus | [histone H3]-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.99.66 | [histone H3]-N6-methyl-L-lysine 4 + 2-oxoglutarate + O2 | - |
Caenorhabditis elegans | [histone H3]-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
| 1.14.99.66 | [histone H3]-N6-methyl-L-lysine 4 + 2-oxoglutarate + O2 | - |
Mus musculus C57BL/6J | [histone H3]-L-lysine 4 + succinate + formaldehyde + CO2 | - |
? | |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 1.14.11.67 | Jarid1 | - |
Drosophila melanogaster |
| 1.14.11.67 | JaridB | - |
Caenorhabditis elegans |
| 1.14.11.67 | KDM5 | - |
Drosophila melanogaster |
| 1.14.11.67 | KDM5B | - |
Caenorhabditis elegans |
| 1.14.11.67 | Lid | - |
Drosophila melanogaster |
| 1.14.11.67 | lysine-specific demethylase | - |
Drosophila melanogaster |
| 1.14.11.67 | lysine-specific demethylase | - |
Caenorhabditis elegans |
| 1.14.11.67 | RBR-2 | - |
Caenorhabditis elegans |
| 1.14.99.66 | CG9088 | - |
Drosophila melanogaster |
| 1.14.99.66 | KDM1 | - |
Drosophila melanogaster |
| 1.14.99.66 | KDM1 | - |
Caenorhabditis elegans |
| 1.14.99.66 | KDM1A | - |
Mus musculus |
| 1.14.99.66 | Lid | - |
Drosophila melanogaster |
| 1.14.99.66 | LSD1 | - |
Mus musculus |
| 1.14.99.66 | LSD1 | - |
Caenorhabditis elegans |
| 1.14.99.66 | SPR-5 | - |
Caenorhabditis elegans |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 1.14.11.67 | evolution | 5 isozymes of enzyme Jarid/KDM5 (Jarid1A-D and Jarid2) in Caenorhabditis elegans, overview | Caenorhabditis elegans |
| 1.14.11.67 | evolution | 5 isozymes of enzyme Jarid/KDM5 (Jarid1A-D and Jarid2) in Drosophila melanogaster, overview | Drosophila melanogaster |
| 1.14.11.67 | malfunction | analysis of demethylase developmental expression patterns and mutant/knockdown phenotypes, overview | Caenorhabditis elegans |
| 1.14.11.67 | 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 | Drosophila melanogaster |
| 1.14.11.67 | 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 | Drosophila melanogaster |
| 1.14.11.67 | 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 | Caenorhabditis elegans |
| 1.14.11.67 | additional information | KDM1/LSD1-mediated H3K4me2 demethylation and epigenetic regulation model. Model for demethylase regulation by expression, interacting proteins and local chromatin environment | Drosophila melanogaster |
| 1.14.11.67 | additional information | KDM1/LSD1-mediated H3K4me2 demethylation and epigenetic regulation model. Model for demethylase regulation by expression, interacting proteins and local chromatin environment | Caenorhabditis elegans |
| 1.14.11.67 | 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 | Drosophila melanogaster |
| 1.14.11.67 | 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 | Caenorhabditis elegans |
| 1.14.99.66 | malfunction | a KDM1 mutant is embryonic lethal, analysis of demethylase developmental expression patterns and mutant/knockdown phenotypes, overview | Mus musculus |
| 1.14.99.66 | malfunction | a KDM1 mutant T08D10.2 shows extended lifespan, analysis of demethylase developmental expression patterns and mutant/knockdown phenotypes, overview | Caenorhabditis elegans |
| 1.14.99.66 | malfunction | mutations of the fly KDM1 homolog lead to sex-specific embryonic lethality and sterility in the surviving (primarily female) offspring, likely due to defects in ovary development, a KDM1 mutant shows female sterility, analysis of demethylase developmental expression patterns and mutant/knockdown phenotypes, overview | Drosophila melanogaster |
| 1.14.99.66 | 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. KDM1/LSD1 is linked to an ERalpha-mediated gene activation program in a ligand-dependent manner, with approximately 58% of ERalpha + promoters also exhibiting KDM1/LSD1 recruitment. 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 | Drosophila melanogaster |
| 1.14.99.66 | 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. KDM1/LSD1 is linked to an ERalpha-mediated gene activation program in a ligand-dependent manner, with approximately 58% of ERalpha + promoters also exhibiting KDM1/LSD1 recruitment. 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 | Mus musculus |
| 1.14.99.66 | 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. KDM1/LSD1 is linked to an ERalpha-mediated gene activation program in a ligand-dependent manner, with approximately 58% of ERalpha + promoters also exhibiting KDM1/LSD1 recruitment. 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 | Caenorhabditis elegans |
| 1.14.99.66 | additional information | KDM1/LSD1-mediated H3K4me2 demethylation and epigenetic regulation model. Model for demethylase regulation by expression, interacting proteins and local chromatin environment | Drosophila melanogaster |
| 1.14.99.66 | additional information | KDM1/LSD1-mediated H3K4me2 demethylation and epigenetic regulation model. Model for demethylase regulation by expression, interacting proteins and local chromatin environment | Mus musculus |
| 1.14.99.66 | additional information | KDM1/LSD1-mediated H3K4me2 demethylation and epigenetic regulation model. Model for demethylase regulation by expression, interacting proteins and local chromatin environment | Caenorhabditis elegans |
| 1.14.99.66 | 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. Conserved role for KDM1 in meiosis and germ cell development. 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 | Drosophila melanogaster |
| 1.14.99.66 | 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. Conserved role for KDM1 in meiosis and germ cell development. 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 | Mus musculus |
| 1.14.99.66 | 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 | Caenorhabditis elegans |
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