Page last updated: 2024-10-24

methyl-CpG binding

Definition

Target type: molecularfunction

Binding to a methylated cytosine/guanine dinucleotide. [GOC:jl, PMID:11746232]

Methyl-CpG binding proteins (MBDs) are a family of proteins that recognize and bind to methylated CpG dinucleotides in DNA. These proteins play a crucial role in various cellular processes, including gene regulation, DNA replication, and repair. The molecular function of methyl-CpG binding can be summarized as follows:

1. **DNA Recognition and Binding:** MBDs possess a conserved methyl-CpG binding domain (MBD) that specifically interacts with methylated cytosines within CpG dinucleotides. This interaction is highly specific and requires the presence of both a methylated cytosine and a guanine nucleotide.

2. **Chromatin Remodeling:** Binding of MBDs to methylated CpG sites can recruit other proteins involved in chromatin remodeling, such as histone deacetylases (HDACs) and histone methyltransferases (HMTs). These recruited proteins modify the structure of chromatin, making the DNA less accessible for transcription.

3. **Gene Silencing:** MBDs, through their interaction with chromatin remodeling complexes, can silence gene expression by preventing the recruitment of transcription factors and RNA polymerase II. This silencing mechanism is crucial for maintaining proper gene expression patterns and preventing inappropriate gene activation.

4. **DNA Replication and Repair:** MBDs also participate in DNA replication and repair processes. They can facilitate the accurate replication of methylated DNA, ensuring the inheritance of methylation patterns to daughter cells. Additionally, MBDs can help recruit repair enzymes to damaged DNA regions that contain methylated CpG sites.

5. **Development and Disease:** The dysregulation of methyl-CpG binding is linked to several developmental disorders and diseases, including cancer, neurodevelopmental disorders, and autoimmune diseases. Mutations in MBD genes can disrupt normal gene expression patterns and contribute to the pathogenesis of these conditions.

Overall, methyl-CpG binding proteins play a critical role in regulating gene expression, maintaining genomic stability, and influencing cellular processes. Their ability to recognize and bind to methylated CpG sites serves as a key mechanism for controlling the accessibility of DNA to transcription factors and other regulatory proteins.'
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Proteins (5)

ProteinDefinitionTaxonomy
Methylosome protein 50A methylosome protein WDR77 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9BQA1]Homo sapiens (human)
Protein arginine N-methyltransferase 1A protein arginine N-methyltransferase 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q99873]Homo sapiens (human)
E3 ubiquitin-protein ligase UHRF1An E3 ubiquitin-protein ligase UHRF1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q96T88]Homo sapiens (human)
DNA (cytosine-5)-methyltransferase 1A DNA (cytosine-5)-methyltransferase 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P26358]Homo sapiens (human)
Protein arginine N-methyltransferase 5A protein arginine N-methyltransferase 5 that is encoded in the genome of human. [PRO:DNx, UniProtKB:O14744]Homo sapiens (human)

Compounds (42)

CompoundDefinitionClassesRoles
fluorescitefluorescein (acid form) : A xanthene dye that is highly fluorescent and commonly used as a fluorescent tracer.benzoic acids;
cyclic ketone;
hydroxy monocarboxylic acid;
organic heterotricyclic compound;
phenols;
xanthene dye
fluorescent dye;
radioopaque medium
pentamidinepentamidine : A diether consisting of pentane-1,5-diol in which both hydroxyl hydrogens have been replaced by 4-amidinophenyl groups. A trypanocidal drug that is used for treatment of cutaneous leishmaniasis and Chagas disease.

Pentamidine: Antiprotozoal agent effective in trypanosomiasis, leishmaniasis, and some fungal infections; used in treatment of PNEUMOCYSTIS pneumonia in HIV-infected patients. It may cause diabetes mellitus, central nervous system damage, and other toxic effects.
aromatic ether;
carboxamidine;
diether
anti-inflammatory agent;
antifungal agent;
calmodulin antagonist;
chemokine receptor 5 antagonist;
EC 2.3.1.48 (histone acetyltransferase) inhibitor;
NMDA receptor antagonist;
S100 calcium-binding protein B inhibitor;
trypanocidal drug;
xenobiotic
procainamideprocainamide : A benzamide that is 4-aminobenzamide substituted on the amide N by a 2-(diethylamino)ethyl group. It is a pharmaceutical antiarrhythmic agent used for the medical treatment of cardiac arrhythmias.

Procainamide: A class Ia antiarrhythmic drug that is structurally-related to PROCAINE.
benzamidesanti-arrhythmia drug;
platelet aggregation inhibitor;
sodium channel blocker
saccharinsaccharin : A 1,2-benzisothiazole having a keto-group at the 3-position and two oxo substituents at the 1-position. It is used as an artificial sweetening agent.

Saccharin: Flavoring agent and non-nutritive sweetener.
1,2-benzisothiazole;
N-sulfonylcarboxamide
environmental contaminant;
sweetening agent;
xenobiotic
vorinostatvorinostat : A dicarboxylic acid diamide comprising suberic (octanedioic) acid coupled to aniline and hydroxylamine. A histone deacetylase inhibitor, it is marketed under the name Zolinza for the treatment of cutaneous T cell lymphoma (CTCL).

Vorinostat: A hydroxamic acid and anilide derivative that acts as a HISTONE DEACETYLASE inhibitor. It is used in the treatment of CUTANEOUS T-CELL LYMPHOMA and SEZARY SYNDROME.
dicarboxylic acid diamide;
hydroxamic acid
antineoplastic agent;
apoptosis inducer;
EC 3.5.1.98 (histone deacetylase) inhibitor
suraminsuramin : A member of the class of phenylureas that is urea in which each of the amino groups has been substituted by a 3-({2-methyl-5-[(4,6,8-trisulfo-1-naphthyl)carbamoyl]phenyl}carbamoyl)phenyl group. An activator of both the rabbit skeletal muscle RyR1 and sheep cardiac RyR2 isoform ryanodine receptor channels, it has been used for the treatment of human African trypanosomiasis for over 100 years.

Suramin: A polyanionic compound with an unknown mechanism of action. It is used parenterally in the treatment of African trypanosomiasis and it has been used clinically with diethylcarbamazine to kill the adult Onchocerca. (From AMA Drug Evaluations Annual, 1992, p1643) It has also been shown to have potent antineoplastic properties.
naphthalenesulfonic acid;
phenylureas;
secondary carboxamide
angiogenesis inhibitor;
antinematodal drug;
antineoplastic agent;
apoptosis inhibitor;
EC 2.7.11.13 (protein kinase C) inhibitor;
GABA antagonist;
GABA-gated chloride channel antagonist;
purinergic receptor P2 antagonist;
ryanodine receptor agonist;
trypanocidal drug
alizarindihydroxyanthraquinonechromophore;
dye;
plant metabolite
7-amino-4-hydroxy-2-naphthalenesulfonic acid7-amino-4-hydroxy-2-naphthalenesulfonic acid : An aminonaphthalenesulfonic acid that is 2-naphthalenesulfonic acid substituted by an amino group at position 7 and a hydroxy group at position 4 respectively.

7-amino-4-hydroxy-2-naphthalenesulfonic acid: structure given in first source
aminonaphthalenesulfonic acid;
naphthols
metabolite
1-naphthol-8-amino-3,6-disulfonic acid1-naphthol-8-amino-3,6-disulfonic acid: dye and found in industrial waste
dichlonedichlone: structure
azacitidine5-azacytidine : An N-glycosyl-1,3,5-triazine that is 4-amino-1,3,5-triazin-2(1H)-one substituted by a beta-D-ribofuranosyl residue via an N-glycosidic linkage. An antineoplastic agent, it is used in the treatment of myeloid leukaemia.

Azacitidine: A pyrimidine analogue that inhibits DNA methyltransferase, impairing DNA methylation. It is also an antimetabolite of cytidine, incorporated primarily into RNA. Azacytidine has been used as an antineoplastic agent.
N-glycosyl-1,3,5-triazine;
nucleoside analogue
antineoplastic agent
methyl redmethyl red : An azo dye consisting of benzoic acid substituted at position 2 by a 4-[(dimethylamino)phenyl]diazenyl group.

methyl red: RN given refers to parent cpd; structure
s-adenosylmethionineacylcarnitine: structure in first source

S-adenosyl-L-methioninate : A sulfonium betaine that is a conjugate base of S-adenosyl-L-methionine obtained by the deprotonation of the carboxy group.
sulfonium betainehuman metabolite
epigallocatechin gallate(-)-epigallocatechin 3-gallate : A gallate ester obtained by the formal condensation of gallic acid with the (3R)-hydroxy group of (-)-epigallocatechin.

epigallocatechin gallate: a steroid 5alpha-reductase inhibitor and antimutagen in green tea (Camellia sinensis)
flavans;
gallate ester;
polyphenol
antineoplastic agent;
antioxidant;
apoptosis inducer;
geroprotector;
Hsp90 inhibitor;
neuroprotective agent;
plant metabolite
hexamidinehexamidine : A polyether that is the bis(4-guanidinophenyl) ether of hexane-1,6-diol.aromatic ether;
guanidines;
polyether
antimicrobial agent;
antiseptic drug
sinefunginadenosines;
non-proteinogenic alpha-amino acid
antifungal agent;
antimicrobial agent
5,5'-methylenedisalicylic acid5,5'-methylenedisalicylic acid: inhibits attachment of ribosomes to microsomal membranes; RN given refers to parent cpd; structure in first source & Merck Index, 9th ed, #5934
fluorone blackfluorone Black: structure
c.i. direct red 23C.I. Direct Red 23: azo dye; structure in first source
s-tubercidinylhomocysteine
furamidinefuramidine: RN given refers to parent cpd; WR 199385 refers to di-HCl; pafuramidine is a prodrug of this
6-bromo-3-(bromomethyl)-7-methyl-2,3,7-trichloro-1-octene6-bromo-3-(bromomethyl)-7-methyl-2,3,7-trichloro-1-octene: structure given in first sourcemonoterpenoid;
organobromine compound;
organochlorine compound
algal metabolite;
antineoplastic agent;
marine metabolite
s-adenosyl-3-thiopropylamineS-adenosyl-3-thiopropylamine : A thioadenosine that is adenosine in which the hydroxy group at C-5' is replaced by a 3-aminopropyl group.

S-adenosyl-3-thiopropylamine: decarboxylated S-adenosylhomocysteine; RN given refers to parent cpd
organic sulfide;
primary amino compound;
thioadenosine
n(4)-adenosyl-n(4)-methyl-2,4-diaminobutanoic acid
nsc 401077NSC 401077: inhibits DNA methyltransferase DNMT1; structure in first source
s-adenosylhomocysteineS-adenosyl-L-homocysteine : An organic sulfide that is the S-adenosyl derivative of L-homocysteine.

S-Adenosylhomocysteine: 5'-S-(3-Amino-3-carboxypropyl)-5'-thioadenosine. Formed from S-adenosylmethionine after transmethylation reactions.
adenosines;
amino acid zwitterion;
homocysteine derivative;
homocysteines;
organic sulfide
cofactor;
EC 2.1.1.72 [site-specific DNA-methyltransferase (adenine-specific)] inhibitor;
EC 2.1.1.79 (cyclopropane-fatty-acyl-phospholipid synthase) inhibitor;
epitope;
fundamental metabolite
5'-methylthioadenosine5'-methylthioadenosine: structure

5'-S-methyl-5'-thioadenosine : Adenosine with the hydroxy group at C-5' substituted with a methylthio (methylsulfanyl) group.
thioadenosinealgal metabolite;
Escherichia coli metabolite;
human metabolite;
mouse metabolite;
Saccharomyces cerevisiae metabolite
decitabine2'-deoxyribonucleoside
rg108RG108: DNA methyltransferase inhibitor; structure in first sourceindolyl carboxylic acid
genistein7-hydroxyisoflavonesantineoplastic agent;
EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor;
geroprotector;
human urinary metabolite;
phytoestrogen;
plant metabolite;
tyrosine kinase inhibitor
stilbamidinestilbamidine: RN given refers to parent cpd
mbx 1090
psammaplin apsammaplin A: isolated from marine sponges Poecillastra and Jaspis; structure in second source
sgi-1027SGI-1027: inhibits DNA methyltransferase 1; structure in first source
bix 01294piperidines
unc 0638UNC 0638: inhibits lysine methyltransferases G9a and GLP; structure in first sourcequinazolines
(5-bromo-3-pyridinyl)-[4-(1-pyrrolidinyl)-1-piperidinyl]methanonearomatic carboxylic acid;
pyridinemonocarboxylic acid
epz004777N-glycosyl compound
entecavirbenzamides;
N-acylpiperidine
gsk343GSK343 : A member of the class of indazoles that is 1-isopropyl-1H-indazole-4-carboxamide in which the nitrogen of the carboxamide group is substituted by a (6-methyl-2-oxo-4-propyl-1,2-dihydropyridin-3-yl)methyl group and in which the indazole ring is substituted at position 6 by a 2-(4-methylpiperazin-1-yl)pyridin-4-yl group. A highly potent and selective EZH2 inhibitor (IC50 = 4 nM).

GSK343: an EZH2 methyltransferase inhibitor
aminopyridine;
indazoles;
N-alkylpiperazine;
N-arylpiperazine;
pyridone;
secondary carboxamide
antineoplastic agent;
apoptosis inducer;
EC 2.1.1.43 (enhancer of zeste homolog 2) inhibitor
6,7-dimethoxy-2-(pyrrolidin-1-yl)-n-(5-(pyrrolidin-1-yl)pentyl)quinazolin-4-amine6,7-dimethoxy-2-(pyrrolidin-1-yl)-N-(5-(pyrrolidin-1-yl)pentyl)quinazolin-4-amine: a SETD8 inhibitor; structure in first source
gsk3235025GSK3235025: an inhibitor of protein arginine methyltransferase-5 (PRMT5); structure in first source