Target type: biologicalprocess
The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA. [GOC:mah]
Nucleosome assembly is a fundamental process in eukaryotic cells, involving the packaging of DNA around histone proteins to form the basic unit of chromatin. The process is highly regulated and involves a series of steps, including:
1. **Histone synthesis and modification:** Histones are synthesized in the cytoplasm and transported to the nucleus. They undergo various post-translational modifications, such as acetylation, methylation, and phosphorylation, which influence their ability to bind DNA and contribute to the regulation of gene expression.
2. **Histone chaperones:** These proteins assist in the proper folding and assembly of histones, preventing their aggregation and facilitating their interaction with DNA. Some key chaperones include:
* **CAF-1:** Deploys newly synthesized histones to replication forks during DNA replication.
* **NAP1:** Delivers histones to nucleosomes during DNA repair and transcription.
* **ASF1:** Aids in the exchange of histones during transcription.
3. **DNA binding:** Histones contain positively charged amino acids that interact electrostatically with the negatively charged DNA molecule. The core histone octamer (two copies each of H2A, H2B, H3, and H4) forms a disc-shaped structure around which 147 base pairs of DNA are wrapped in approximately 1.65 turns.
4. **Nucleosome formation:** The DNA-histone complex forms a nucleosome, the basic repeating unit of chromatin. The linker histone H1 binds to the linker DNA between nucleosomes, contributing to the compaction of chromatin.
5. **Chromatin higher-order structure:** Nucleosomes are further assembled into higher-order structures, including the 30-nm fiber and the metaphase chromosome. These structures are essential for packaging the vast amount of DNA within the nucleus and regulating gene expression.
6. **Nucleosome remodeling:** Nucleosome positioning and accessibility are dynamic, constantly adjusting to accommodate various cellular processes. Specialized enzymes called ATP-dependent chromatin remodelers use the energy from ATP hydrolysis to reposition or remove nucleosomes, allowing access to DNA for processes like transcription, replication, and DNA repair.
7. **Nucleosome assembly factors:** Specific factors, like the histone acetyltransferase (HAT) complex, are crucial for nucleosome formation and chromatin assembly. They help to regulate the positioning and stability of nucleosomes, ultimately impacting gene expression.
In summary, nucleosome assembly is a multi-step process involving the interaction of histones, DNA, and various regulatory factors. This intricate process ensures proper DNA packaging, contributes to the regulation of gene expression, and facilitates essential cellular processes.'
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| Protein | Definition | Taxonomy |
|---|---|---|
| ATPase family AAA domain-containing protein 2 | An ATPase family AAA domain-containing protein 2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q6PL18] | Homo sapiens (human) |
| ATPase family AAA domain-containing protein 2B | An ATPase family AAA domain-containing protein 2B that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9ULI0] | Homo sapiens (human) |
| Protein-arginine deiminase type-4 | A protein-arginine deiminase type-4 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9UM07] | Homo sapiens (human) |
| Histone-lysine N-methyltransferase SMYD3 | A histone-lysine N-methyltransferase SMYD3 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9H7B4] | Homo sapiens (human) |
| Histone-binding protein RBBP4 | A histone-binding protein RBBP4 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q09028] | Homo sapiens (human) |
| Bromodomain-containing protein 2 | A bromodomain-containing protein 2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P25440] | Homo sapiens (human) |
| Nucleophosmin | A nucleophosmin that is encoded in the genome of human. [PRO:DNx, UniProtKB:P06748] | Homo sapiens (human) |
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| azathioprine | azathioprine : A thiopurine that is 6-mercaptopurine in which the mercapto hydrogen is replaced by a 1-methyl-4-nitroimidazol-5-yl group. It is a prodrug for mercaptopurine and is used as an immunosuppressant, prescribed for the treatment of inflammatory conditions and after organ transplantation and also for treatment of Crohn's didease and MS. Azathioprine: An immunosuppressive agent used in combination with cyclophosphamide and hydroxychloroquine in the treatment of rheumatoid arthritis. According to the Fourth Annual Report on Carcinogens (NTP 85-002, 1985), this substance has been listed as a known carcinogen. (Merck Index, 11th ed) | aryl sulfide; C-nitro compound; imidazoles; thiopurine | antimetabolite; antineoplastic agent; carcinogenic agent; DNA synthesis inhibitor; hepatotoxic agent; immunosuppressive agent; prodrug |
| leflunomide | leflunomide : A monocarboxylic acid amide obtained by formal condensation of the carboxy group of 5-methyl-1,2-oxazole-4-carboxylic acid with the anilino group of 4-(trifluoromethyl)aniline. The prodrug of teriflunomide. Leflunomide: An isoxazole derivative that inhibits dihydroorotate dehydrogenase, the fourth enzyme in the pyrimidine biosynthetic pathway. It is used an immunosuppressive agent in the treatment of RHEUMATOID ARTHRITIS and PSORIATIC ARTHRITIS. | (trifluoromethyl)benzenes; isoxazoles; monocarboxylic acid amide | antineoplastic agent; antiparasitic agent; EC 1.3.98.1 [dihydroorotate oxidase (fumarate)] inhibitor; EC 3.1.3.16 (phosphoprotein phosphatase) inhibitor; hepatotoxic agent; immunosuppressive agent; non-steroidal anti-inflammatory drug; prodrug; pyrimidine synthesis inhibitor; tyrosine kinase inhibitor |
| ly 303511 | LY 303511: inhibitor of phosphatidylinositol 3-kinase | N-arylpiperazine | |
| 2-(4-morpholinyl)-8-phenyl-4h-1-benzopyran-4-one | 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one: specific inhibitor of phosphatidylinositol 3-kinase; structure in first source | chromones; morpholines; organochlorine compound | autophagy inhibitor; EC 2.7.1.137 (phosphatidylinositol 3-kinase) inhibitor; geroprotector |
| mesalamine | mesalamine : A monohydroxybenzoic acid that is salicylic acid substituted by an amino group at the 5-position. Mesalamine: An anti-inflammatory agent, structurally related to the SALICYLATES, which is active in INFLAMMATORY BOWEL DISEASE. It is considered to be the active moiety of SULPHASALAZINE. (From Martindale, The Extra Pharmacopoeia, 30th ed) | amino acid; aromatic amine; monocarboxylic acid; monohydroxybenzoic acid; phenols | non-steroidal anti-inflammatory drug |
| prazosin | prazosin : A member of the class of piperazines that is piperazine substituted by a furan-2-ylcarbonyl group and a 4-amino-6,7-dimethoxyquinazolin-2-yl group at positions 1 and 4 respectively. Prazosin: A selective adrenergic alpha-1 antagonist used in the treatment of HEART FAILURE; HYPERTENSION; PHEOCHROMOCYTOMA; RAYNAUD DISEASE; PROSTATIC HYPERTROPHY; and URINARY RETENTION. | aromatic ether; furans; monocarboxylic acid amide; piperazines; quinazolines | alpha-adrenergic antagonist; antihypertensive agent; EC 3.4.21.26 (prolyl oligopeptidase) inhibitor |
| imatinib | aromatic amine; benzamides; N-methylpiperazine; pyridines; pyrimidines | antineoplastic agent; apoptosis inducer; tyrosine kinase inhibitor | |
| streptonigrin | pyridines; quinolone | antimicrobial agent; antineoplastic agent | |
| sulfamethoxazole | sulfamethoxazole : An isoxazole (1,2-oxazole) compound having a methyl substituent at the 5-position and a 4-aminobenzenesulfonamido group at the 3-position. Sulfamethoxazole: A bacteriostatic antibacterial agent that interferes with folic acid synthesis in susceptible bacteria. Its broad spectrum of activity has been limited by the development of resistance. (From Martindale, The Extra Pharmacopoeia, 30th ed, p208) | isoxazoles; substituted aniline; sulfonamide; sulfonamide antibiotic | antibacterial agent; antiinfective agent; antimicrobial agent; drug allergen; EC 1.1.1.153 [sepiapterin reductase (L-erythro-7,8-dihydrobiopterin forming)] inhibitor; EC 2.5.1.15 (dihydropteroate synthase) inhibitor; environmental contaminant; epitope; P450 inhibitor; xenobiotic |
| sulfapyridine | sulfapyridine : A sulfonamide consisting of pyridine with a 4-aminobenzenesulfonamido group at the 2-position. Sulfapyridine: Antibacterial, potentially toxic, used to treat certain skin diseases. | pyridines; substituted aniline; sulfonamide; sulfonamide antibiotic | antiinfective agent; dermatologic drug; drug allergen; environmental contaminant; xenobiotic |
| trimethoprim | trimethoprim : An aminopyrimidine antibiotic whose structure consists of pyrimidine 2,4-diamine and 1,2,3-trimethoxybenzene moieties linked by a methylene bridge. Trimethoprim: A pyrimidine inhibitor of dihydrofolate reductase, it is an antibacterial related to PYRIMETHAMINE. It is potentiated by SULFONAMIDES and the TRIMETHOPRIM, SULFAMETHOXAZOLE DRUG COMBINATION is the form most often used. It is sometimes used alone as an antimalarial. TRIMETHOPRIM RESISTANCE has been reported. | aminopyrimidine; methoxybenzenes | antibacterial drug; diuretic; drug allergen; EC 1.5.1.3 (dihydrofolate reductase) inhibitor; environmental contaminant; xenobiotic |
| ferrocin c | N-methyl-2-quinolone: structure in first source | ||
| streptomycin | antibiotic antifungal drug; antibiotic fungicide; streptomycins | antibacterial drug; antifungal agrochemical; antimicrobial agent; antimicrobial drug; bacterial metabolite; protein synthesis inhibitor | |
| n-benzoyl-l-arginine | N-benzoyl-L-arginine : An N-acyl-L-arginine that is L-arginine in which one of the hydrogens attached to the alpha-amino group has been replaced by a benzoyl group. N-benzoyl-L-arginine: RM given refers to (l)-isomer; structure | benzamides; N-acyl-L-arginine | |
| benzoylarginine ethyl ester | benzoylarginine ethyl ester: used as substrate for trypsin; RN given refers to parent cpd | ||
| przewaquinone d | przewaquinone D: isolated from root of Salvia przewalskii; structure given in first source; RN given refers to the trans- isomer, przewaquinone D | ||
| methotrexate | dicarboxylic acid; monocarboxylic acid amide; pteridines | abortifacient; antimetabolite; antineoplastic agent; antirheumatic drug; dermatologic drug; DNA synthesis inhibitor; EC 1.5.1.3 (dihydrofolate reductase) inhibitor; immunosuppressive agent | |
| benzoyl l-arginine methyl ester | benzoyl L-arginine methyl ester: RN given refers to (L-Arg)-isomer | ||
| n(alpha)-benzoylarginineamide | N(alpha)-benzoylarginineamide: RN given refers to parent cpd(S)-isomer | ||
| clindamycin | clindamycin : A carbohydrate-containing antibiotic that is the semisynthetic derivative of lincomycin, a natural antibiotic. Clindamycin: An antibacterial agent that is a semisynthetic analog of LINCOMYCIN. | ||
| zithromax | azithromycin : A macrolide antibiotic useful for the treatment of bacterial infections. Azithromycin: A semi-synthetic macrolide antibiotic structurally related to ERYTHROMYCIN. It has been used in the treatment of Mycobacterium avium intracellulare infections, toxoplasmosis, and cryptosporidiosis. | macrolide antibiotic | antibacterial drug; environmental contaminant; xenobiotic |
| pd 173955 | PD 173955: inhibits src family-selective tyrosine kinase; structure in first source | aryl sulfide; dichlorobenzene; methyl sulfide; pyridopyrimidine | tyrosine kinase inhibitor |
| scutellarein | scutellarein : Flavone substituted with hydroxy groups at C-4', -5, -6 and -7. scutellarein: aglycone of scutellarin from Scutellaria baicalensis; carthamidin is 2S isomer of scutellarein; do not confuse with isoscutellarein and/or isocarthamidin which are respective regioisomers, or with the scutelarin protein | tetrahydroxyflavone | metabolite |
| ellagic acid | catechols; cyclic ketone; lactone; organic heterotetracyclic compound; polyphenol | antioxidant; EC 1.14.18.1 (tyrosinase) inhibitor; EC 2.3.1.5 (arylamine N-acetyltransferase) inhibitor; EC 2.4.1.1 (glycogen phosphorylase) inhibitor; EC 2.5.1.18 (glutathione transferase) inhibitor; EC 2.7.1.127 (inositol-trisphosphate 3-kinase) inhibitor; EC 2.7.1.151 (inositol-polyphosphate multikinase) inhibitor; EC 2.7.4.6 (nucleoside-diphosphate kinase) inhibitor; EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor; EC 5.99.1.2 (DNA topoisomerase) inhibitor; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor; food additive; fungal metabolite; geroprotector; plant metabolite; skin lightening agent | |
| bosutinib | 4-((2,4-dichloro-5-methoxyphenyl)amino)-6-methoxy-7-(3-(4-methyl-1-piperazinyl)propoxy)-3-quinolinecarbonitrile: a Src kinase inhibitor; structure in first source | aminoquinoline; aromatic ether; dichlorobenzene; N-methylpiperazine; nitrile; tertiary amino compound | antineoplastic agent; tyrosine kinase inhibitor |
| 6h-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepine-6-acetamide, 4-(4-chlorophenyl)-n-(4-hydroxyphenyl)-2,3,9-trimethyl-, (6s)- | organonitrogen heterocyclic compound; organosulfur heterocyclic compound | ||
| crizotinib | crizotinib : A 3-[1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-[1-(piperidin-4-yl)pyrazol-4-yl]pyridin-2-amine that has R configuration at the chiral centre. The active enantiomer, it acts as a kinase inhibitor and is used for the treatment of patients with locally advanced or metastatic non-small cell lung cancer (NSCLC) Crizotinib: A piperidine and aminopyridine derivative that acts as an inhibitor of RECEPTOR PROTEIN-TYROSINE KINASES, including ANAPLASTIC LYMPHOMA KINASE (ALK) and HEPATOCYTE GROWTH FACTOR RECEPTOR (HGFR; c-Met). It is used in the treatment of NON-SMALL CELL LUNG CANCER. | 3-[1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-[1-(piperidin-4-yl)pyrazol-4-yl]pyridin-2-amine | antineoplastic agent; biomarker; EC 2.7.10.1 (receptor protein-tyrosine kinase) inhibitor |
| az 505 | AZ 505: an SMYD2 inhibitor; structure in first source | ||
| n-alpha-benzoyl-n5-(2-chloro-1-iminoethyl)-l-ornithine amide | benzenes | ||
| jq1 compound | carboxylic ester; organochlorine compound; tert-butyl ester; thienotriazolodiazepine | angiogenesis inhibitor; anti-inflammatory agent; antineoplastic agent; apoptosis inducer; bromodomain-containing protein 4 inhibitor; cardioprotective agent; ferroptosis inducer | |
| gsk525762a | molibresib: mimicks acetylated histones; structure in first source | benzodiazepine | |
| LSM-6732 | organonitrogen heterocyclic compound; organosulfur heterocyclic compound; tert-butyl ester | ||
| gsk1210151a | GSK1210151A: inhibitor of the BET family of proteins; structure in first source | imidazoquinoline | |
| i-bet726 | |||
| tetracycline | tetracycline : A broad-spectrum polyketide antibiotic produced by the Streptomyces genus of actinobacteria. Tetracycline: A naphthacene antibiotic that inhibits AMINO ACYL TRNA binding during protein synthesis. | ||
| chlortetracycline | chlortetracycline : A member of the class of tetracyclines with formula C22H23ClN2O8 isolated from Streptomyces aureofaciens. Chlortetracycline: A TETRACYCLINE with a 7-chloro substitution. | ||
| minocycline | minocycline : A tetracycline analogue having a dimethylamino group at position 7 and lacking the methyl and hydroxy groups at position 5. Minocycline: A TETRACYCLINE analog, having a 7-dimethylamino and lacking the 5 methyl and hydroxyl groups, which is effective against tetracycline-resistant STAPHYLOCOCCUS infections. | ||
| ceritinib | ceritinib : A member of the class of aminopyrimidines that is 2,6-diamino-5-chloropyrimidine in which the amino groups at positions 2 and 6 are respectively carrying 2-methoxy-4-(piperidin-4-yl)-5-methylphenyl and 2-(isopropylsulfonyl)phenyl substituents. Used for the treatment of ALK-positive metastatic non-small cell lung cancer. ceritinib: an anaplastic lymphoma kinase inhibitor | aminopyrimidine; aromatic ether; organochlorine compound; piperidines; secondary amino compound; sulfone | antineoplastic agent; EC 2.7.10.1 (receptor protein-tyrosine kinase) inhibitor |
| epz-6438 | tazemetostat: a histone methyltransferase EZH2 inhibitor with antineoplastic activity | ||
| 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 |
| MZ1 | organic molecular entity | ||
| rvx 208 | apabetalone: a bromodomain and extra-terminal domain protein (BET) inhibitor; prevents interactions between BET proteins and acetyl-lysine residues on histone tails to modify epigenetic regulation |