Page last updated: 2024-10-24
lncRNA binding
Definition
Target type: molecularfunction
Binding to a long noncoding RNA (lncRNA). [PMID:25578728]
Long non-coding RNAs (lncRNAs) are RNA transcripts longer than 200 nucleotides that do not encode proteins. Despite lacking protein-coding potential, lncRNAs play diverse and crucial roles in cellular processes, including gene regulation, chromatin remodeling, and signal transduction. LncRNA binding, a central aspect of their function, involves the interaction of lncRNAs with various molecular partners, including proteins, DNA, and other RNA molecules. These interactions often lead to the modulation of target molecule activity, resulting in a wide range of cellular effects.
One primary function of lncRNA binding is to regulate gene expression. LncRNAs can act as scaffolds, bringing together different proteins and facilitating their interactions. For example, lncRNAs can recruit transcription factors or chromatin modifiers to specific genomic loci, thereby influencing gene transcription. They can also act as decoys, sequestering regulatory proteins away from their target genes, leading to gene silencing.
LncRNAs can also bind to DNA, affecting chromatin structure and accessibility. Some lncRNAs can interact with chromatin-modifying enzymes, directing their activity to specific genomic regions and influencing gene expression. Others can bind to DNA and block the binding of transcription factors, preventing gene activation.
In addition to protein and DNA interactions, lncRNAs can bind to other RNA molecules, including messenger RNAs (mRNAs), microRNAs (miRNAs), and other lncRNAs. LncRNA-mRNA interactions can regulate mRNA stability, translation, and localization, influencing protein production. LncRNA-miRNA interactions can modulate miRNA activity, influencing gene expression.
LncRNA binding can also play a role in signal transduction. LncRNAs can act as sensors of cellular signals, responding to changes in the cellular environment and modulating downstream signaling pathways. They can also act as messengers, relaying information from one cellular compartment to another.
Overall, lncRNA binding is a complex and dynamic process with a wide range of molecular functions. It is a key aspect of lncRNA-mediated regulation, influencing a multitude of cellular processes. Understanding the molecular mechanisms underlying lncRNA binding is essential for unraveling the roles of these enigmatic transcripts in health and disease.'
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Proteins (8)
| Protein | Definition | Taxonomy |
|---|---|---|
| DNA (cytosine-5)-methyltransferase 3A | A DNA (cytosine-5)-methyltransferase 3A that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9Y6K1] | Homo sapiens (human) |
| Protein phosphatase methylesterase 1 | A protein phosphatase methylesterase 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9Y570] | Homo sapiens (human) |
| Histone-lysine N-methyltransferase EZH2 | A histone-lysine N-methyltransferase EZH2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q15910] | Homo sapiens (human) |
| ELAV-like protein 1 | An ELAV-like protein 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q15717] | Homo sapiens (human) |
| Bromodomain-containing protein 3 | A bromodomain-containing protein 3 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q15059] | Homo sapiens (human) |
| Polycomb protein SUZ12 | A polycomb protein SUZ12 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q15022] | Homo sapiens (human) |
| Signal transducer and activator of transcription 3 | A signal transducer and activator of transcription 3 that is encoded in the genome of human. [PRO:WCB, UniProtKB:P40763] | Homo sapiens (human) |
| Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 | A sarcoplasmic/endoplasmic reticulum calcium ATPase 2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P16615] | Homo sapiens (human) |
Compounds (61)
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| 2,5-di-tert-butylhydroquinone | 2,5-di-tert-butylbenzene-1,4-diol : A member of the class of hydroquinones that is benzene-1,4-diol substituted by tert-butyl groups at position 2 and 5. | hydroquinones | |
| 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 |
| niclosamide | niclosamide : A secondary carboxamide resulting from the formal condensation of the carboxy group of 5-chlorosalicylic acid with the amino group of 2-chloro-4-nitroaniline. It is an oral anthelmintic drug approved for use against tapeworm infections. Niclosamide: An antihelmintic that is active against most tapeworms. (From Martindale, The Extra Pharmacopoeia, 30th ed, p48) | benzamides; C-nitro compound; monochlorobenzenes; salicylanilides; secondary carboxamide | anthelminthic drug; anticoronaviral agent; antiparasitic agent; apoptosis inducer; molluscicide; piscicide; STAT3 inhibitor |
| procainamide | procainamide : 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. | benzamides | anti-arrhythmia drug; platelet aggregation inhibitor; sodium channel blocker |
| dichlone | dichlone: structure | ||
| oleanolic acid | hydroxy monocarboxylic acid; pentacyclic triterpenoid | plant metabolite | |
| nitazoxanide | nitazoxanide: a 5-nitrothiazolyl derivative used for a broad range of intestinal parasitic infections including CRYPTOSPORIDIUM and GIARDIA; it is a redox-active nitrothiazolyl-salicylamide prodrug | benzamides; carboxylic ester | |
| 5,5'-methylenedisalicylic acid | 5,5'-methylenedisalicylic acid: inhibits attachment of ribosomes to microsomal membranes; RN given refers to parent cpd; structure in first source & Merck Index, 9th ed, #5934 | ||
| 3-deazaneplanocin | 3-deazaneplanocin: S-adenosylhomocysteine hydrolase antagonist | ||
| loganin | beta-D-glucoside; cyclopentapyran; enoate ester; iridoid monoterpenoid; methyl ester; monosaccharide derivative; secondary alcohol | anti-inflammatory agent; EC 3.1.1.7 (acetylcholinesterase) inhibitor; EC 3.2.1.20 (alpha-glucosidase) inhibitor; EC 3.4.23.46 (memapsin 2) inhibitor; neuroprotective agent; plant metabolite | |
| paxilline | paxilline : An indole diterpene alkaloid with formula C27H33NO4 isolated from Penicillium paxilli. It is a potent inhibitor of large conductance Ca2(+)- and voltage-activated K(+) (BK)-type channels. paxilline: structure given in first source; RN given refers to (2R-(2alpha,4bbeta,6aalpha,12bbeta,12calpha,14abeta))-isomer | diterpene alkaloid; enone; organic heterohexacyclic compound; terpenoid indole alkaloid; tertiary alcohol | anticonvulsant; Aspergillus metabolite; EC 3.6.3.8 (Ca(2+)-transporting ATPase) inhibitor; genotoxin; geroprotector; mycotoxin; Penicillium metabolite; potassium channel blocker |
| tanshinone | tanshinone: from root of Salvia miltiorrhiza Bunge; RN given refers to tanshinone I; cardioprotective agent and neuroprotective agent | abietane diterpenoid | anticoronaviral agent |
| tetrahydrocurcumin | tetrahydrocurcumin : A beta-diketone that is curcumin in which both of the double bonds have been reduced to single bonds. | beta-diketone; diarylheptanoid; polyphenol | metabolite |
| przewaquinone d | przewaquinone D: isolated from root of Salvia przewalskii; structure given in first source; RN given refers to the trans- isomer, przewaquinone D | ||
| 5,8-dihydroxy-3-methyl-4-(9h)-naphtho(2,3-c)furanone | 5,8-dihydroxy-3-methyl-4-(9H)-naphtho(2,3-c)furanone: isolated from Micromonospora sp. KY7123; structure given in first source | ||
| cryptotanshinone | cryptotanshinone: from Salvia miltiorrhiza | abietane diterpenoid | anticoronaviral agent |
| ar-turmerone | (+)-(S)-ar-turmerone : A sesquiterpenoid that is 2-methylhept-2-en-4-one substituted by a 4-methylphenyl group at position 6. It has been isolated from Peltophorum dasyrachis. ar-turmerone: potent antivenom against snake bites; isolated form Curcuma longa; structure given in first source | enone; sesquiterpenoid | EC 3.1.1.7 (acetylcholinesterase) inhibitor; plant metabolite |
| sweroside | glycoside | ||
| tanshinone ii a | tashinone IIA: a cardiovascular agent with antineoplastic activity; isolated from Salvia miltiorrhiza; structure in first source | abietane diterpenoid | |
| nsc 74859 | NSC 74859: inhibits Stat3 binding activity; structure in first source S3I-201 : An amidobenzoic acid obtained by formal condensation of the carboxy group of [(4-methylbenzene-1-sulfonyl)oxy]acetic acid with the amino group of 4-amino-2-hydroxybenzoic acid. | amidobenzoic acid; monohydroxybenzoic acid; tosylate ester | STAT3 inhibitor |
| telocinobufagin | telocinobufagin: structure | steroid lactone | |
| tizoxanide | tizoxanide: major metabolite of nitazoxanide; structure in first source | salicylamides | |
| bardoxolone methyl | methyl 2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oate: structure in first source | cyclohexenones | |
| 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 |
| bisabolol | Kamillosan: drug combination containing chamomile and bisabolol; used to treat dermatitis | sesquiterpenoid | |
| ganoderic acid a | triterpenoid | ||
| piplartine | piplartine: Antineoplastic Agent, Phytogenic; alkaloid from Piper; structure in first source | cinnamamides; dicarboximide | |
| rg108 | RG108: DNA methyltransferase inhibitor; structure in first source | indolyl carboxylic acid | |
| curcumin | curcumin : A beta-diketone that is methane in which two of the hydrogens are substituted by feruloyl groups. A natural dyestuff found in the root of Curcuma longa. Curcumin: A yellow-orange dye obtained from tumeric, the powdered root of CURCUMA longa. It is used in the preparation of curcuma paper and the detection of boron. Curcumin appears to possess a spectrum of pharmacological properties, due primarily to its inhibitory effects on metabolic enzymes. | aromatic ether; beta-diketone; diarylheptanoid; enone; polyphenol | anti-inflammatory agent; antifungal agent; antineoplastic agent; biological pigment; contraceptive drug; dye; EC 1.1.1.205 (IMP dehydrogenase) inhibitor; EC 1.1.1.21 (aldehyde reductase) inhibitor; EC 1.1.1.25 (shikimate dehydrogenase) inhibitor; EC 1.6.5.2 [NAD(P)H dehydrogenase (quinone)] inhibitor; EC 1.8.1.9 (thioredoxin reductase) inhibitor; EC 2.7.10.2 (non-specific protein-tyrosine kinase) inhibitor; EC 3.5.1.98 (histone deacetylase) inhibitor; flavouring agent; food colouring; geroprotector; hepatoprotective agent; immunomodulator; iron chelator; ligand; lipoxygenase inhibitor; metabolite; neuroprotective agent; nutraceutical; radical scavenger |
| stattic | 1-benzothiophenes; C-nitro compound; sulfone | antineoplastic agent; radiosensitizing agent; STAT3 inhibitor | |
| stx-0119 | STX-0119: antineoplastic; structure in first source | ||
| quercetin | 7-hydroxyflavonol; pentahydroxyflavone | antibacterial agent; antineoplastic agent; antioxidant; Aurora kinase inhibitor; chelator; EC 1.10.99.2 [ribosyldihydronicotinamide dehydrogenase (quinone)] inhibitor; geroprotector; phytoestrogen; plant metabolite; protein kinase inhibitor; radical scavenger | |
| genistein | 7-hydroxyisoflavones | antineoplastic agent; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor; geroprotector; human urinary metabolite; phytoestrogen; plant metabolite; tyrosine kinase inhibitor | |
| andrographolide | carbobicyclic compound; gamma-lactone; labdane diterpenoid; primary alcohol; secondary alcohol | anti-HIV agent; anti-inflammatory drug; antineoplastic agent; metabolite | |
| nifuroxazide | nifuroxazide: structure | benzoic acids | |
| hylin | |||
| 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 | ||
| 2-acetylfuranonaphthoquinone | 2-acetylfuranonaphthoquinone: has antineoplastic activity; structure in first source | ||
| 5,15-diphenylporphine | 5,15-diphenylporphine: structure in first source | ||
| wp1066 | |||
| Dihydrotanshinone I | dihydrotanshinone I: extracted from Radix Salviae | abietane diterpenoid | anticoronaviral agent |
| azd 1480 | |||
| sgi-1027 | SGI-1027: inhibits DNA methyltransferase 1; structure in first source | ||
| biselyngbyaside | biselyngbyaside: antineoplastic from the marine cyanobacterium Lyngbya sp.; structure in first source | ||
| amz 30 | |||
| 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 | |||
| bp-1-102 | BP-1-102: a STAT3 inhibitor; structure in first source | ||
| epz005687 | EPZ005687: inhibits EZH2 protein; structure in first source | indazoles | |
| epz-6438 | tazemetostat: a histone methyltransferase EZH2 inhibitor with antineoplastic activity | ||
| gsk-2816126 | GSK-2816126: inhibits EZH2 methyltransferase; structure in first source | piperazines; pyridines | |
| 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 |
| 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 inhibitor | indolecarboxamide | |
| phaeosphaeride a | phaeosphaeride A: inhibits STAT3-dependent signaling; structure in first source | ||
| hydrazinocurcumin | hydrazinocurcumin : A pyrazole obtained by cyclocodensation of the two carbonyl groups of curcumin with hydrazine. hydrazinocurcumin: structure in first source | aromatic ether; olefinic compound; polyphenol; pyrazoles | angiogenesis modulating agent; antineoplastic agent; EC 2.3.1.48 (histone acetyltransferase) inhibitor; EC 2.7.11.1 (non-specific serine/threonine protein kinase) inhibitor |
| alpha-cyclopiazonic acid | alpha-cyclopiazonic acids | ||
| 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 |