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positive regulation of gene expression via chromosomal CpG island demethylation
Definition
Target type: biologicalprocess
An epigenetic gene regulation mechanism that positively regulates gene expression by demethylation of cytosine residues in chromosomal CpG islands. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide and are often associated with the transcription start site of genes. [PMID:36150101, Wikipedia:Cpg_island]
Positive regulation of gene expression via chromosomal CpG island demethylation is a complex process that involves the removal of methyl groups from cytosine bases within CpG islands located in gene promoter regions. This demethylation event is often associated with increased gene expression and can be influenced by various factors, including developmental stage, environmental stimuli, and genetic predisposition.
The process typically involves the following steps:
1. Recognition and binding of DNA methyltransferases (DNMTs): DNMTs are a family of enzymes responsible for adding methyl groups to cytosine bases in DNA. In the context of demethylation, DNMTs can recognize and bind to CpG islands that are already methylated, potentially serving as a first step in the demethylation process.
2. Recruitment of Ten-Eleven Translocation (TET) enzymes: TET enzymes are dioxygenases that catalyze the oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). 5hmC is an intermediate in the demethylation pathway and serves as a substrate for further oxidation by TET enzymes.
3. Conversion of 5hmC to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC): TET enzymes can further oxidize 5hmC to 5fC and 5caC. These oxidized forms of cytosine are recognized and removed by the base excision repair (BER) pathway.
4. Excision of 5fC and 5caC by thymine DNA glycosylase (TDG): TDG is a DNA glycosylase that removes 5fC and 5caC from DNA.
5. Repair of the DNA gap by DNA polymerase and DNA ligase: After the removal of oxidized cytosines, the resulting DNA gap is repaired by DNA polymerase and DNA ligase.
6. Replication-dependent demethylation: During DNA replication, the newly synthesized strand does not inherit methylation patterns from the parental strand. This mechanism contributes to the overall demethylation process.
The demethylation process is tightly regulated and can be influenced by various signaling pathways and transcription factors. For instance, specific transcription factors can bind to demethylated CpG islands and activate gene expression. Furthermore, environmental factors, such as diet and stress, can also modulate the demethylation process.
Overall, positive regulation of gene expression via chromosomal CpG island demethylation is a crucial mechanism for controlling gene expression in response to various internal and external stimuli. Understanding the molecular mechanisms underlying this process is essential for developing therapeutic strategies targeting gene expression in diseases associated with aberrant DNA methylation patterns.'
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Proteins (4)
| Protein | Definition | Taxonomy |
|---|---|---|
| Single-stranded DNA cytosine deaminase | A single-stranded DNA cytosine deaminase that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9GZX7] | Homo sapiens (human) |
| Methylcytosine dioxygenase TET2 | A methylcytosine dioxygenase TET2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q6N021] | Homo sapiens (human) |
| DNA-(apurinic or apyrimidinic site) endonuclease | A DNA-(apurinic or apyrimidinic site) endonuclease that is encoded in the genome of human. [PRO:DNx, UniProtKB:P27695] | Homo sapiens (human) |
| N-glycosylase/DNA lyase | An N-glycosylase/DNA lyase that is encoded in the genome of human. [PRO:DNx, UniProtKB:O15527] | Homo sapiens (human) |
Compounds (57)
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| alpha-hydroxyglutarate | 2-hydroxyglutarate : A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of 2-hydroxyglutaric acid. 2-hydroxyglutaric acid : A 2-hydroxydicarboxylic acid that is glutaric acid in which one hydrogen alpha- to a carboxylic acid group is substituted by a hydroxy group. | 2-hydroxydicarboxylic acid; dicarboxylic fatty acid | metabolite; mouse metabolite |
| hydroxylamine | amino alcohol : An alcohol containing an amino functional group in addition to the alcohol-defining hydroxy group. | hydroxylamines | algal metabolite; bacterial xenobiotic metabolite; EC 1.1.3.13 (alcohol oxidase) inhibitor; EC 4.2.1.22 (cystathionine beta-synthase) inhibitor; EC 4.3.1.10 (serine-sulfate ammonia-lyase) inhibitor; nitric oxide donor; nucleophilic reagent |
| aurintricarboxylic acid | aurintricarboxylic acid : A member of the class of quinomethanes that is 3-methylidene-6-oxocyclohexa-1,4-diene-1-carboxylic acid in which the methylidene hydrogens are replaced by 4-carboxy-3-hydroxyphenyl groups. The trisodium salt is the biological stain 'chrome violet CG' while the triammonium salt is 'aluminon'. Aurintricarboxylic Acid: A dye which inhibits protein biosynthesis at the initial stages. The ammonium salt (aluminon) is a reagent for the colorimetric estimation of aluminum in water, foods, and tissues. | monohydroxybenzoic acid; quinomethanes; tricarboxylic acid | fluorochrome; histological dye; insulin-like growth factor receptor 1 antagonist |
| chelerythrine | chelerythrine : A benzophenanthridine alkaloid isolated from the root of Zanthoxylum simulans, Chelidonium majus L., and other Papaveraceae. | benzophenanthridine alkaloid; organic cation | antibacterial agent; antineoplastic agent; EC 2.7.11.13 (protein kinase C) inhibitor |
| deferoxamine | Deferoxamine: Natural product isolated from Streptomyces pilosus. It forms iron complexes and is used as a chelating agent, particularly in the mesylate form. desferrioxamine B : An acyclic desferrioxamine that is butanedioic acid in which one of the carboxy groups undergoes formal condensation with the primary amino group of N-(5-aminopentyl)-N-hydroxyacetamide and the second carboxy group undergoes formal condensation with the hydroxyamino group of N(1)-(5-aminopentyl)-N(1)-hydroxy-N(4)-[5-(hydroxyamino)pentyl]butanediamide. It is a siderophore native to Streptomyces pilosus biosynthesised by the DesABCD enzyme cluster as a high affinity Fe(III) chelator. | acyclic desferrioxamine | bacterial metabolite; ferroptosis inhibitor; iron chelator; siderophore |
| dequalinium | dequalinium : A quinolinium ion comprising decane in which one methyl hydrogen at each end of the molecule has been replaced by a 4-amino-2-methylquinolin-1-yl group. Dequalinium: A topical bacteriostat that is available as various salts. It is used in wound dressings and mouth infections and may also have antifungal action, but may cause skin ulceration. | quinolinium ion | antifungal agent; antineoplastic agent; antiseptic drug; mitochondrial NADH:ubiquinone reductase inhibitor |
| diphenyleneiodonium | dibenziodolium : An organic cation that is fluorene in which the methylene group is replaced by a positively charged iodine. diphenyleneiodonium: structure in first source; NADPH oxidase inhibitor | organic cation | |
| dipyridamole | dipyridamole : A pyrimidopyrimidine that is 2,2',2'',2'''-(pyrimido[5,4-d]pyrimidine-2,6-diyldinitrilo)tetraethanol substituted by piperidin-1-yl groups at positions 4 and 8 respectively. A vasodilator agent, it inhibits the formation of blood clots. Dipyridamole: A phosphodiesterase inhibitor that blocks uptake and metabolism of adenosine by erythrocytes and vascular endothelial cells. Dipyridamole also potentiates the antiaggregating action of prostacyclin. (From AMA Drug Evaluations Annual, 1994, p752) | piperidines; pyrimidopyrimidine; tertiary amino compound; tetrol | adenosine phosphodiesterase inhibitor; EC 3.5.4.4 (adenosine deaminase) inhibitor; platelet aggregation inhibitor; vasodilator agent |
| 2,3-dimethoxy-1,4-naphthoquinone | 2,3-dimethoxynaphthalene-1,4-dione : A naphthoquinone that is 1,4-naphthoquinone bearing two methoxy substituents at positions 2 and 3. Redox-cycling agent that induces intracellular superoxide anion formation and, depending on the concentration, induces cell proliferation, apoptosis or necrosis. Used to study the role of ROS in cell toxicity, apoptosis, and necrosis. | 1,4-naphthoquinones | |
| hycanthone | hycanthone : A thioxanthen-9-one compound having a hydroxymethyl substituent at the 1-position and a 2-[(diethylamino)ethyl]amino substituent at the 4-position. It was formerly used (particularly as the monomethanesulfonic acid salt) as a schistosomicide for individual or mass treatement of infection with Schistosoma haematobium and S. mansoni, but due to its toxicity and concern about possible carcinogenicity, it has been replaced by other drugs such as praziquantel. Hycanthone: Potentially toxic, but effective antischistosomal agent, it is a metabolite of LUCANTHONE. | thioxanthenes | mutagen; schistosomicide drug |
| hydralazine | hydralazine : The 1-hydrazino derivative of phthalazine; a direct-acting vasodilator that is used as an antihypertensive agent. Hydralazine: A direct-acting vasodilator that is used as an antihypertensive agent. | azaarene; hydrazines; ortho-fused heteroarene; phthalazines | antihypertensive agent; vasodilator agent |
| phenelzine | Phenelzine: One of the MONOAMINE OXIDASE INHIBITORS used to treat DEPRESSION; PHOBIC DISORDERS; and PANIC. | primary amine | |
| isocarboxazid | Isocarboxazid: An MAO inhibitor that is effective in the treatment of major depression, dysthymic disorder, and atypical depression. It also is useful in the treatment of panic disorder and the phobic disorders. (From AMA, Drug Evaluations Annual, 1994, p311) | benzenes | |
| isoniazid | Hydra: A genus of freshwater polyps in the family Hydridae, order Hydroida, class HYDROZOA. They are of special interest because of their complex organization and because their adult organization corresponds roughly to the gastrula of higher animals. hydrazide : Compounds derived from oxoacids RkE(=O)l(OH)m (l =/= 0) by replacing -OH by -NRNR2 (R groups are commonly H). (IUPAC). | carbohydrazide | antitubercular agent; drug allergen |
| beta-lapachone | beta-lapachone : A benzochromenone that is 3,4-dihydro-2H-benzo[h]chromene-5,6-dione substituted by geminal methyl groups at position 2. Isolated from Tabebuia avellanedae, it exhibits antineoplastic and anti-inflammatory activities. beta-lapachone: antineoplastic inhibitor of reverse transcriptase, DNA topoisomerase, and DNA polymerase | benzochromenone; orthoquinones | anti-inflammatory agent; antineoplastic agent; plant metabolite |
| mitoxantrone | mitoxantrone : A dihydroxyanthraquinone that is 1,4-dihydroxy-9,10-anthraquinone which is substituted by 6-hydroxy-1,4-diazahexyl groups at positions 5 and 8. Mitoxantrone: An anthracenedione-derived antineoplastic agent. | dihydroxyanthraquinone | analgesic; antineoplastic agent |
| nialamide | Nialamide: An MAO inhibitor that is used as an antidepressive agent. | organonitrogen compound; organooxygen compound | |
| protoporphyrin ix | protoporphyrin : A cyclic tetrapyrrole that consists of porphyrin bearing four methyl substituents at positions 3, 8, 13 and 17, two vinyl substituents at positions 7 and 12 and two 2-carboxyethyl substituents at positions 2 and 18. The parent of the class of protoporphyrins. protoporphyrin IX: RN given refers to parent cpd; structure in Merck Index, 9th ed, #7685 | ||
| sanguinarine | benzophenanthridine alkaloid : A specific group of isoquinoline alkaloids that occur only in higher plants and are constituents mainly of the Papaveraceae family. | alkaloid antibiotic; benzophenanthridine alkaloid; botanical anti-fungal agent | |
| tyrphostin a9 | alkylbenzene | geroprotector | |
| 1-naphthaldehyde | 1-naphthaldehyde : A naphthaldehyde with a formyl group at position 1. 1-naphthaldehyde: structure naphthaldehyde : An aldehyde in which the organyl group is a naphthyl group. | naphthaldehyde | mouse metabolite |
| pyrazolanthrone | anthra[1,9-cd]pyrazol-6(2H)-one : A member of the class of anthrapyrazoles that is anthra[1,9-cd]pyrazole substituted at position 6 by an oxo group. An inhibitor of c-Jun N-terminal kinase. pyrazolanthrone: JNK (c-Jun N-terminal kinase) inhibitor; structure in first source | anthrapyrazole; aromatic ketone; cyclic ketone | antineoplastic agent; c-Jun N-terminal kinase inhibitor; geroprotector |
| hydralazine hydrochloride | hydralazine hydrochloride : The hydrochloride salt of hydralazine; a direct-acting vasodilator that is used as an antihypertensive agent. | hydrochloride | antihypertensive agent; vasodilator agent |
| lucanthone | lucanthone : A thioxanthen-9-one compound having a methyl substituent at the 1-position and a 2-[(diethylamino)ethyl]amino substituent at the 4-position. Formerly used for the treatment of schistosomiasis. It is a prodrug, being metabolised to hycanthone. Lucanthone: One of the SCHISTOSOMICIDES, it has been replaced largely by HYCANTHONE and more recently PRAZIQUANTEL. (From Martindale The Extrapharmacopoeia, 30th ed., p46) | thioxanthenes | adjuvant; antineoplastic agent; EC 5.99.1.2 (DNA topoisomerase) inhibitor; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor; mutagen; photosensitizing agent; prodrug; schistosomicide drug |
| 2,3,5-trimethylquinol | 2,3,5-trimethylhydroquinone : A member of the class of hydroquinones that is hydroquinone substituted by methyl groups at positions 2, 3 and 5. 2,3,5-trimethylquinol: reducing agent | hydroquinones; methylbenzene | |
| idarubicin | Idarubicin: An orally administered anthracycline antineoplastic. The compound has shown activity against BREAST NEOPLASMS; LYMPHOMA; and LEUKEMIA. | anthracycline antibiotic; deoxy hexoside; monosaccharide derivative | |
| mitoxantrone hydrochloride | hydrochloride | antineoplastic agent | |
| flupirtine | flupirtine: RN given refers to parent cpd without isomeric designation | aminopyridine | |
| masoprocol | masoprocol : The meso-form of nordihydroguaiaretic acid. An antioxidant found in the creosote bush, Larrea divaricata, it is a potent lipoxygenase inhibitor that interferes with arachidonic acid metabolism. It also inhibits (though to a lesser extent) formyltetrahydrofolate synthetase, carboxylesterase, and cyclooxygenase. Masoprocol: A potent lipoxygenase inhibitor that interferes with arachidonic acid metabolism. The compound also inhibits formyltetrahydrofolate synthetase, carboxylesterase, and cyclooxygenase to a lesser extent. It also serves as an antioxidant in fats and oils. | nordihydroguaiaretic acid | antineoplastic agent; hypoglycemic agent; lipoxygenase inhibitor; metabolite |
| 7-nitro-1h-indole-2-carboxylic acid | 7-nitro-1H-indole-2-carboxylic acid: acts on AP endonuclease, 3'-phosphodiesterase, and 3'-phosphatase activities of APE1; structure in first source | ||
| 3,3',4,4',5,5'-hexabromobiphenyl | |||
| 6-hydroxydopa | 6-hydroxydopa: RN given refers to cpd without isomeric designation | non-proteinogenic alpha-amino acid | |
| tanshinone ii a | tashinone IIA: a cardiovascular agent with antineoplastic activity; isolated from Salvia miltiorrhiza; structure in first source | abietane diterpenoid | |
| 2-(4-aminophenyl)quinoline | 2-(4-aminophenyl)quinoline: used for imaging tau protein; structure in first source | ||
| 5-carboxy-8-hydroxyquinoline | 5-carboxy-8-hydroxyquinoline: a JmjC histone demethylase inhibitor; structure in first source | quinolines | |
| 1,3,6-trimethylpyrimido[5,4-e][1,2,4]triazine-5,7-dione | pyrimidotriazine | ||
| IPA-3 | IPA-3 : An organic disulfide obtained by oxidative dimerisation of 1-sulfanylnaphthalen-2-ol. | naphthols; organic disulfide | EC 2.7.11.1 (non-specific serine/threonine protein kinase) inhibitor |
| 2-[[2-methyl-5-(3-methyl-4-oxo-1-phthalazinyl)phenyl]sulfonylamino]acetic acid ethyl ester | alpha-amino acid ester | ||
| (2'-(4-aminophenyl)-(2,5'-bi-1h-benzimidazol)-5-amine) | benzimidazoles | ||
| nemadipine-a | nemadipine-A : A dihydropyridine that is that is 1,4-dihydropyridine which is substituted at positions 2 and 6 by methyl groups, at positions 3 and 5 by ethoxycarbonyl groups, and at position 4 by a pentafluorophenyl group. An L-type calcium channel alpha1-subunit antagonist. When exposed to the microscopic soil nematode Caenorhabditis elegans, nemadipine-A induces a variety of defects including those affecting morphology and egg laying. nemadipine-A: structure in first source | dicarboxylic acids and O-substituted derivatives; diester; dihydropyridine; ethyl ester; pentafluorobenzenes | calcium channel blocker |
| 5-[[(1-cyclohexyl-5-tetrazolyl)thio]methyl]-3-phenyl-1,2,4-oxadiazole | oxadiazole; ring assembly | ||
| oxalylglycine | N-oxalylglycine : An amino dicarboxylic acid that is iminodiacetic acid with an oxo substituent. It is used as an inhibitor of alpha-ketoglutarate dependent (EC 1.14.11.*) enzymes. oxalylglycine: structure given in first source | amino dicarboxylic acid; N-acylglycine | EC 1.14.11.* (oxidoreductase acting on paired donors, 2-oxoglutarate as one donor, incorporating 1 atom each of oxygen into both donors) inhibitor |
| 2-[[5-(dimethylsulfamoyl)-1H-indol-3-yl]methylidene]propanedioic acid diethyl ester | indoles | ||
| 1,6-dimethyl-3-propylpyrimido[5,4-e][1,2,4]triazine-5,7-dione | pyrimidotriazine | ||
| ro 41-0960 | |||
| myricetin | 7-hydroxyflavonol; hexahydroxyflavone | antineoplastic agent; antioxidant; cyclooxygenase 1 inhibitor; food component; geroprotector; hypoglycemic agent; plant metabolite | |
| tectochrysin | tectochrysin : A monohydroxyflavone that is flavone substituted by a hydroxy group at position 4 and a methoxy group at position 7 respectively. tectochrysin: structure in first source | monohydroxyflavone; monomethoxyflavone | antidiarrhoeal drug; antineoplastic agent; plant metabolite |
| casein kinase ii | Casein Kinase II: A ubiquitous casein kinase that is comprised of two distinct catalytic subunits and dimeric regulatory subunit. Casein kinase II has been shown to phosphorylate a large number of substrates, many of which are proteins involved in the regulation of gene expression. | ||
| ag 538 | AG 538: an IGF-1 receptor kinase inhibitor; structure in first source | ||
| e 3330 | E 3330: structure given in first source; MW 378.47 | ||
| 2-(2-methoxyanilino)-8-[(3-methyl-1-piperidinyl)-oxomethyl]-[1,3,4]thiadiazolo[2,3-b]quinazolin-5-one | N-acylpiperidine | ||
| CDN1163 | CDN1163 : A secondary carboxamide resulting from the formal condensation of the carboxy group of 4-isopropoxybenzoic acid with the primary amino group of 2-methylquinolin-8-amine. An allosteric activator of sarco/endoplasmic reticulum Ca(2+)-ATPase (SERCA). CDN1163: a SERCA2 activator with antidiabetic activity; structure in first source | aromatic ether; quinolines; secondary carboxamide | SERCA activator |
| N-[3-(1,3-benzothiazol-2-yl)-5,6-dihydro-4H-thieno[2,3-c]pyrrol-2-yl]acetamide | benzothiazoles | ||
| hispidin | hispidin : Fungal metabolite first found in basidiomycete Inonotus hispidus (formerly Polyporus hispidus). hispidin: metabolite of Basidiomycete Polyporus hispidus | 2-pyranones; catechols | antioxidant; EC 2.7.11.13 (protein kinase C) inhibitor; fungal metabolite |
| thiolactomycin | thiolactomycin: from actinomycetes; structure given in first source | ||
| galloflavin | galloflavin: structure in first source | ||
| 4-[[(4-oxo-1,5,6,7-tetrahydrocyclopenta[d]pyrimidin-2-yl)thio]methyl]benzoic acid methyl ester | benzoate ester |