Page last updated: 2024-10-24
rDNA heterochromatin
Definition
Target type: cellularcomponent
A region of heterochromatin located at the rDNA repeats in a chromosome. [GOC:mah, PMID:20661445]
rDNA heterochromatin is a specialized type of chromatin that is found in the nucleolus, a subnuclear structure that is responsible for ribosome biogenesis. The nucleolus is composed of three main components: the fibrillar center, the dense fibrillar component, and the granular component. rDNA heterochromatin is located primarily in the dense fibrillar component, where it is organized into a complex structure called the nucleolar organizer region (NOR). The NOR is a highly transcribed region of the genome that contains multiple copies of the genes that encode ribosomal RNA (rRNA). The rDNA genes are transcribed by RNA polymerase I, and the resulting rRNA transcripts are processed and assembled into ribosomes. rDNA heterochromatin is characterized by its highly repetitive nature, its dense packing, and its low level of gene expression. The repetitive nature of rDNA heterochromatin is due to the presence of multiple copies of the rDNA genes, which are clustered together in the NOR. The dense packing of rDNA heterochromatin is due to the presence of a variety of proteins that bind to the DNA and help to compact it. The low level of gene expression in rDNA heterochromatin is due to the fact that the rDNA genes are not actively transcribed in this region of the genome. rDNA heterochromatin plays an important role in the regulation of ribosome biogenesis. The dense packing of rDNA heterochromatin helps to prevent the transcription of rDNA genes that are not needed. In addition, the low level of gene expression in rDNA heterochromatin helps to ensure that rRNA is only produced when it is needed.'
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Proteins (3)
| Protein | Definition | Taxonomy |
|---|---|---|
| Bromodomain adjacent to zinc finger domain protein 2A | A 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-1 | An NAD-dependent protein deacetylase sirtuin-1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q96EB6] | Homo sapiens (human) |
| Histone-lysine N-methyltransferase SUV39H1 | A histone-lysine N-methyltransferase SUV39H1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:O43463] | Homo sapiens (human) |
Compounds (39)
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| niacinamide | nicotinamide : 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 i | bisindolylmaleimide I: a bis(indolyl)maleimide | ||
| bisindolylmaleimide v | bisindolylmaleimide V: used as a negative control compound for protein kinase C inhibition; structure in first source; | indoles | |
| entinostat | benzamides; carbamate ester; primary amino compound; pyridines; substituted aniline | antineoplastic agent; apoptosis inducer; EC 3.5.1.98 (histone deacetylase) inhibitor | |
| fenamic acid | fenamic 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 31-8220 | Ro 31-8220: a protein kinase C inhibitor | imidothiocarbamic ester; indoles; maleimides | EC 2.7.11.13 (protein kinase C) inhibitor |
| fenofibrate | benzochromenone; delta-lactone; naphtho-alpha-pyrone | platelet aggregation inhibitor; Sir2 inhibitor | |
| suramin | suramin : 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 |
| nad | NAD | geroprotector | |
| gliotoxin | gliotoxin : 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 acid | 4-tert-butylbenzoic acid: RN given refers to parent cpd | alkylbenzene | |
| suramin sodium | suramin 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 salt | 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 |
| toxoflavin | toxoflavin : 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 |
| paullone | paullone : 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-adenosylhomocysteine | S-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 |
| hyperforin | hyperforin : 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 c | surfactin 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 |
| resveratrol | trans-resveratrol : A resveratrol in which the double bond has E configuration. | resveratrol | antioxidant; phytoalexin; plant metabolite; quorum sensing inhibitor; radical scavenger |
| CHIC-35 | CHIC-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)benzamide | 3-(1-azepanylsulfonyl)-N-(3-bromphenyl)benzamide: a sirtuin 2 inhibitor; structure in first source | ||
| CAY10591 | CAY10591: a SIRT1 NAD-dependent histone deacetylase activator | quinoxaline derivative | |
| sirtinol | aldimine; benzamides; naphthols | anti-inflammatory agent; EC 3.5.1.98 (histone deacetylase) inhibitor; Sir2 inhibitor | |
| verticillins | verticillins: 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)) | ||
| cambinol | cambinol: inhibitor of human silent information regulator 2 enzymes; structure in first source | ||
| (4-chlorophenyl)-[4-(8-nitro-5-quinolinyl)-1-piperazinyl]methanone | N-arylpiperazine | ||
| ex 527 | 6-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 | |
| panobinostat | panobinostat : 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 c | oblongifolin C: has antineoplastic activity; isolated from Garcinia yunnanensis; structure in first source | ||
| chetomin | |||
| quisinostat | indoles | ||
| srt1460 | SRT1460: small molecule activator of SIRT1 as therapeutics for the treatment of type 2 diabetes; structure in first source | ||
| srt1720 | |||
| srt2183 | SRT2183: small molecule activator of SIRT1 as therapeutics for the treatment of type 2 diabetes; structure in first source | ||
| tenovin-6 | tenovin-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-1215 | ricolinostat: an HDAC6 inhibitor; structure in first source | pyrimidinecarboxylic acid | |
| gsk343 | GSK343 : 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 |
| aristoforin | Aristoforin: derivative of hyperforin, is a potent anticancer agent; structure in first source | ||
| n-(3-((2-hydroxynaphthalen-1-ylmethylene)amino)phenyl)-2-phenylpropionamide |