Page last updated: 2024-10-24

chromatin silencing complex

Definition

Target type: cellularcomponent

Any protein complex that mediates changes in chromatin structure that result in transcriptional silencing. [GOC:mah]

Chromatin silencing complexes are multi-protein assemblies that play a crucial role in regulating gene expression by repressing transcription. They are often associated with heterochromatin, a densely packed form of chromatin characterized by its low gene expression levels. These complexes can be found in various cellular compartments, including the nucleus, where they interact with DNA and other regulatory elements to silence gene expression. Key components of chromatin silencing complexes include:

1. **Histone Modifiers:** These enzymes modify the N-terminal tails of histone proteins, which are the core components of nucleosomes. Modifications can include methylation, acetylation, phosphorylation, and ubiquitination. These modifications can either promote or inhibit gene expression by influencing the accessibility of DNA to transcription factors. For example, histone deacetylases (HDACs) remove acetyl groups from histones, leading to a more condensed chromatin state and gene repression.
2. **DNA Methyltransferases (DNMTs):** These enzymes catalyze the addition of methyl groups to cytosine bases in DNA, primarily at CpG dinucleotides. DNA methylation is associated with gene silencing and is often found in regions of heterochromatin. DNMTs can establish or maintain methylation patterns during development and in response to environmental cues.
3. **Chromatin Remodelers:** These complexes use ATP hydrolysis to reposition nucleosomes along DNA, thereby altering chromatin structure and accessibility. They can either facilitate or inhibit transcription factor binding, depending on their activity and the context of the DNA sequence.
4. **Transcriptional Repressors:** These proteins directly bind to DNA or interact with other components of the silencing complex to block transcription initiation or elongation. They can recruit other silencing factors or alter chromatin structure to inhibit gene expression.

The specific composition of chromatin silencing complexes varies depending on the organism, cell type, and specific genes targeted for silencing. However, the core principles of their function remain consistent: they modulate chromatin structure, alter histone modifications, and directly inhibit transcription to achieve silencing.'
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Proteins (6)

ProteinDefinitionTaxonomy
Bromodomain adjacent to zinc finger domain protein 2AA bromodomain adjacent to zinc finger domain protein 2A that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9UIF9]Homo sapiens (human)
NAD-dependent protein deacetylase sirtuin-1An NAD-dependent protein deacetylase sirtuin-1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q96EB6]Homo sapiens (human)
NAD-dependent protein deacetylase sirtuin-2An NAD-dependent protein deacetylase sirtuin-2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q8IXJ6]Homo sapiens (human)
Histone-lysine N-methyltransferase EZH2A histone-lysine N-methyltransferase EZH2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q15910]Homo sapiens (human)
Polycomb protein SUZ12A polycomb protein SUZ12 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q15022]Homo sapiens (human)
Histone-lysine N-methyltransferase SUV39H1A histone-lysine N-methyltransferase SUV39H1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:O43463]Homo sapiens (human)

Compounds (54)

CompoundDefinitionClassesRoles
niacinamidenicotinamide : A pyridinecarboxamide that is pyridine in which the hydrogen at position 3 is replaced by a carboxamide group.pyridine alkaloid;
pyridinecarboxamide;
vitamin B3
anti-inflammatory agent;
antioxidant;
cofactor;
EC 2.4.2.30 (NAD(+) ADP-ribosyltransferase) inhibitor;
EC 3.5.1.98 (histone deacetylase) inhibitor;
Escherichia coli metabolite;
geroprotector;
human urinary metabolite;
metabolite;
mouse metabolite;
neuroprotective agent;
Saccharomyces cerevisiae metabolite;
Sir2 inhibitor
bisindolylmaleimide ibisindolylmaleimide I: a bis(indolyl)maleimide
2-(1-(2-(1-methylpyrrolidino)ethyl)-1h-indol-3-yl)maleimidebisindolylmaleimide II: protein kinase C inhibitor; see also bisindolylmaleimide I
bisindolylmaleimide ivindoles;
maleimides
bisindolylmaleimide vbisindolylmaleimide V: used as a negative control compound for protein kinase C inhibition; structure in first source;indoles
go 6976indolocarbazole;
organic heterohexacyclic compound
EC 2.7.11.13 (protein kinase C) inhibitor
idebenone1,4-benzoquinones;
primary alcohol
antioxidant;
ferroptosis inhibitor
nsc 664704kenpaullone : An indolobenzazepine that is paullone in which the hydrogen at position 9 is replaced by a bromo substituent. It is an ATP-competitive inhibitor of cyclin-dependent kinases (CDKs) and glycogen synthase kinase 3beta (GSK3beta).

kenpaullone: inhibits CDK1/cyclin B; structure in first source
indolobenzazepine;
lactam;
organobromine compound
cardioprotective agent;
EC 2.7.11.22 (cyclin-dependent kinase) inhibitor;
EC 2.7.11.26 (tau-protein kinase) inhibitor;
geroprotector
entinostatbenzamides;
carbamate ester;
primary amino compound;
pyridines;
substituted aniline
antineoplastic agent;
apoptosis inducer;
EC 3.5.1.98 (histone deacetylase) inhibitor
fenamic acidfenamic acid : An aminobenzoic acid that is the N-phenyl derivative of anthranilic acid. It acts as a parent skeleton for the synthesis of several non-steroidal anti-inflammatory drugs.

fenamic acid: has chloride and potassium channel-blocking activity; RN given refers to parent cpd
aminobenzoic acid;
secondary amino compound
membrane transport modulator
ro 31-8220Ro 31-8220: a protein kinase C inhibitorimidothiocarbamic ester;
indoles;
maleimides
EC 2.7.11.13 (protein kinase C) inhibitor
fenofibratebenzochromenone;
delta-lactone;
naphtho-alpha-pyrone
platelet aggregation inhibitor;
Sir2 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
nadNADgeroprotector
gliotoxingliotoxin : A pyrazinoindole with a disulfide bridge spanning a dioxo-substituted pyrazine ring; mycotoxin produced by several species of fungi.

Gliotoxin: A fungal toxin produced by various species of Trichoderma, Gladiocladium fimbriatum, Aspergillus fumigatus, and Penicillium. It is used as an immunosuppressive agent.
dipeptide;
organic disulfide;
organic heterotetracyclic compound;
pyrazinoindole
antifungal agent;
EC 2.5.1.58 (protein farnesyltransferase) inhibitor;
immunosuppressive agent;
mycotoxin;
proteasome inhibitor
4-tert-butylbenzoic acid4-tert-butylbenzoic acid: RN given refers to parent cpdalkylbenzene
suramin sodiumsuramin sodium : An organic sodium salt that is the hexasodium salt of suramin. It is an FDA approved drug for African sleeping sickness and river blindness.organic sodium saltangiogenesis 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
toxoflavintoxoflavin : A pyrimidotriazine that is 1,6-dimethyl-1,5,6,7-tetrahydropyrimido[5,4-e][1,2,4]triazine with oxo groups at positions 5 and 7.

toxoflavin: azapteridine antibiotic; structure
carbonyl compound;
pyrimidotriazine
antibacterial agent;
antineoplastic agent;
apoptosis inducer;
bacterial metabolite;
toxin;
virulence factor;
Wnt signalling inhibitor
3-deazaneplanocin3-deazaneplanocin: S-adenosylhomocysteine hydrolase antagonist
tanshinonetanshinone: from root of Salvia miltiorrhiza Bunge; RN given refers to tanshinone I; cardioprotective agent and neuroprotective agentabietane diterpenoidanticoronaviral agent
przewaquinone dprzewaquinone D: isolated from root of Salvia przewalskii; structure given in first source; RN given refers to the trans- isomer, przewaquinone D
tanshinone ii atashinone IIA: a cardiovascular agent with antineoplastic activity; isolated from Salvia miltiorrhiza; structure in first sourceabietane diterpenoid
paullonepaullone : An indolobenzazepine that is 5,6,7,12-tetrahydroindolo[3,2-d][1]benzazepine carrying an oxo substituent at position 6.

paullone: structure in first source
indolobenzazepine;
lactam
EC 2.7.11.22 (cyclin-dependent kinase) inhibitor;
EC 2.7.11.26 (tau-protein kinase) inhibitor
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
hyperforinhyperforin : A cyclic terpene ketone that is a prenylated carbobicyclic acylphloroglucinol derivative produced by St. John's Wort, Hypericum perforatum.

hyperforin: a prenylated acylphloroglucinol derivative; antibiotic component of novoimanine; psychoactive agent in St. John's wort; Russian; structure;
surfactin csurfactin C : A cyclodepsipeptide that is N-[(3R)-3-hydroxy-13-methyltetradecanoyl]-L-alpha-glutamyl-L-leucyl-D-leucyl-L-valyl-L-alpha-aspartyl-D-leucyl-L-leucine in which the C-terminal carboxy group has been lactonised by condensation with the alcoholic hydroxy group.cyclodepsipeptide;
lipopeptide antibiotic;
macrocyclic lactone
antibacterial agent;
antifungal agent;
antineoplastic agent;
antiviral agent;
metabolite;
platelet aggregation inhibitor;
surfactant
resveratroltrans-resveratrol : A resveratrol in which the double bond has E configuration.resveratrolantioxidant;
phytoalexin;
plant metabolite;
quorum sensing inhibitor;
radical scavenger
CHIC-35CHIC-35 : An organic heterotricyclic compound resulting from the formal fusion of the 2-3 bond of 5-chloroindole with the 2-3 bond of cycloheptanecarboxamide (the S enantiomer). It is a potent, cell-permeable, metabolically stable and selective inhibitor of the deacetylase SIRT1.aromatic compound;
organic heterotricyclic compound;
organochlorine compound;
primary carboxamide
EC 3.5.1.98 (histone deacetylase) inhibitor
3-(1-azepanylsulfonyl)-n-(3-bromphenyl)benzamide3-(1-azepanylsulfonyl)-N-(3-bromphenyl)benzamide: a sirtuin 2 inhibitor; structure in first source
CAY10591CAY10591: a SIRT1 NAD-dependent histone deacetylase activatorquinoxaline derivative
1,4-bis[2-(4-hydroxyphenyl)ethylamino]anthracene-9,10-dioneanthraquinone
sirtinolaldimine;
benzamides;
naphthols
anti-inflammatory agent;
EC 3.5.1.98 (histone deacetylase) inhibitor;
Sir2 inhibitor
verticillinsverticillins: 3 antibiotics isolated from imperfect fungus Verticillium: verticillin A, verticillin B (mono-3-hydroxymethyl analog of verticillin A), & verticillin C (differs from verticillin B in that 1 of dioxopiperazine rings has a trisulfide rather than a disulfide bridge; active against gram-positive bacteria & mycobacteria but not against gram-negative bacteria & fungi; RN given refers to cpd with unknown MF; structure (verticillins A & B))
cambinolcambinol: inhibitor of human silent information regulator 2 enzymes; structure in first source
(4-chlorophenyl)-[4-(8-nitro-5-quinolinyl)-1-piperazinyl]methanoneN-arylpiperazine
ex 5276-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide : A member of the class of carbazoles that is 2,3,4,9-tetrahydro-1H-carbazole which is substituted at position 1 by an aminocarbohyl group and at position 6 by a chlorine.

6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide: structure in first source
carbazoles;
monocarboxylic acid amide;
organochlorine compound
su 11248monocarboxylic acid amide;
pyrroles
angiogenesis inhibitor;
antineoplastic agent;
EC 2.7.10.1 (receptor protein-tyrosine kinase) inhibitor;
immunomodulator;
neuroprotective agent;
vascular endothelial growth factor receptor antagonist
panobinostatpanobinostat : A hydroxamic acid obtained by formal condensation of the carboxy group of (2E)-3-[4-({[2-(2-methylindol-3-yl)ethyl]amino}methyl)phenyl]prop-2-enoic acid with the amino group of hydroxylamine. A histone deacetylase inhibitor used (as its lactate salt) in combination with bortezomib and dexamethasone for the treatment of multiple myeloma.

Panobinostat: An indole and hydroxamic acid derivative that acts as a HISTONE DEACETYLASE inhibitor. It is used as an antineoplastic agent in combination with BORTEZOMIB and DEXAMETHASONE for the treatment of MULTIPLE MYELOMA.
cinnamamides;
hydroxamic acid;
methylindole;
secondary amino compound
angiogenesis modulating agent;
antineoplastic agent;
EC 3.5.1.98 (histone deacetylase) inhibitor
oblongifolin coblongifolin C: has antineoplastic activity; isolated from Garcinia yunnanensis; structure in first source
chetomin
quisinostatindoles
srt1460SRT1460: small molecule activator of SIRT1 as therapeutics for the treatment of type 2 diabetes; structure in first source
srt1720
srt2183SRT2183: small molecule activator of SIRT1 as therapeutics for the treatment of type 2 diabetes; structure in first source
tenovin-6tenovin-6 : A monocarboxylic acid amide obtained by formal condensation of the carboxy group of 5-(dimethylamino)pentanoic acid with the aromatic amino group of N-[(4-aminophenyl)carbamothioyl]-4-tert-butylbenzamide.monocarboxylic acid amide;
tertiary amino compound;
thioureas
antineoplastic agent;
p53 activator;
Sir2 inhibitor
i-bet726
acy-1215ricolinostat: an HDAC6 inhibitor; structure in first sourcepyrimidinecarboxylic acid
epz005687EPZ005687: inhibits EZH2 protein; structure in first sourceindazoles
epz-6438tazemetostat: a histone methyltransferase EZH2 inhibitor with antineoplastic activity
gsk-2816126GSK-2816126: inhibits EZH2 methyltransferase; structure in first sourcepiperazines;
pyridines
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
1-[(1R)-1-(1-ethylsulfonyl-4-piperidinyl)ethyl]-N-[(4-methoxy-6-methyl-2-oxo-1H-pyridin-3-yl)methyl]-2-methyl-3-indolecarboxamide(R)-1-(1-(1-(ethylsulfonyl)piperidin-4-yl)ethyl)-N-((4-methoxy-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-2-methyl-1H-indole-3-carboxamide: EZH2 inhibitorindolecarboxamide
aristoforinAristoforin: derivative of hyperforin, is a potent anticancer agent; structure in first source
n-(3-((2-hydroxynaphthalen-1-ylmethylene)amino)phenyl)-2-phenylpropionamide