The Knowledge About HIV Based On Double-readability Language(DRL) (V3)
—-Hanfei Bao(包含飞)
%%%Adenosine:(腺苷)
%%%Angiogenesis:(血管再生)
%%%ArylHydrocarbonReceptor:(芳香碳氢化合物受体)
%%%AP-1:ActivatorProtein1:(激活蛋白l)
&&:AP1—isA—TranscriptionFactor–and–
((TranscriptionFactor—regulates—GeneExpression)—isStimulatedBy—StimulatingFactor)–and–(StimulatingFactor—hasExamples—(Cytokine–Or–GrowthFactor–Or–Stress–Or–BacterialInfection–Or–ViralInfection)):&&
%%%AP-1:BindingSite(AP-1结合位点，被称为TPA效应原件(TRE))
%%%AP3-L/NF-AT-BindingSite:(AP3-L/NF-AT结合位点)
%%%Apoptosis:Cell suicide based on the specialized cellular machinery to control cell number and eliminate cells that threaten the body([细胞]凋亡)
%%%ARNT:aryl hydrocarbon receptor nuclear translocator (芳香烃受体核转移子)
%%%ATF:Activating transcription factor(激活性转录因子)
&&:(ATF—isPhosphorylatedAtSite—Serine63OfATF)–and—(Serine63OfATF—isLoactedIn—KinaseInducibelDomain):&&
%%%\Cyclic AMP-dependent transcription factor ATF-1(环一磷酸腺苷依赖性激活性转录因子1)
&&:(ATF-1)—isEncodedBy—(ATF1-gene):&&
%%%ATF1Gene:(激活性转录因子1基因)
%%%ATF2:Activating transcription factor 2(激活性转录因子2)
%%%ATF2Gene:(ATF2 基因)
%%%ATF3:(激活性转录因子3)
%%%ATF4:(激活性转录因子4)
%%%ATF5:(激活性转录因子5)
%%%ATF6:(激活性转录因子6)
%%%ATF7:(激活性转录因子7)
%%%ATF-Family:Family of Activating transcription factor(激活性转录因子家族)
%%%ATF/CREB:activating transcription factor (ATF)/cyclic AMP response element binding protein (CREB)
%%%ATF/CREB-BindingSite:(ATF/CREB结合位点)
%%%ATF/CREB-Family:(ATF/CREB家族)
%%%ATF/CREB_BindingSiteVariant:(结合点突变)
%%%ATP:adenosine triphosphate(三磷酸腺苷)
%%%Bcl-3:B-cell lymphoma 3-encoded protein(B细胞淋巴瘤3-编码蛋白质)
%%%BondingBetweentTwoMolecules:(两个分子间的键合)
%%%\CovalentBonding:(共价键键合)
%%%bHLH-Domain:Basic helix-loop-helix domain:(基本螺旋-袢-螺旋域)
%%%BromodomainOfPCAF-Aacetylase:(P300/CBP-连接因子(PCAF)溴区结构域)
%%%BTEB:Basic Transcription Element-binding Protein(基础转录元件结合蛋白)
%%%\BTEB1:Basic Transcription Element-binding Protein 1 基础转录元件结合蛋白 1)
%%%bZIP:basic-region leucine zipper(基本区域亮氨酸拉链)
%%%DistalModulatoryRegion:(远距离调节区域)
%%%CAK: CDK-ActivatingKinase:(CDK-激活激酶)
%%%cAMP:cyclic adenosine monophosphate((单磷酸)环腺苷酸)
%%%cAMP-DependentProteinKinaseA: (环腺苷酸-依赖性蛋白激酶A)
%%%Calmodulin-DependentProteinKinaseI/II:(调钙蛋白依赖性蛋白激酶I/II)
%%%CCAAT:cytosine-cytosine-adenosine-adenosine-thymidine box motif(胞嘧啶-胞嘧啶-腺苷-腺腺苷-胸苷盒基元)
%%%Cdk:Cyclin Dependent Kinase(细胞周期蛋白依赖性激酶)
%%%\Cdk1: Cyclin Dependent Kinase 1(细胞周期蛋白依赖性激酶1)
%%%\Cdk2:Cyclin Dependent Kinase 2(细胞周期蛋白依赖性激酶2)
%%%\Cdk4:Cyclin Dependent Kinase 4(细胞周期蛋白依赖性激酶4)
%%%\Cdk6: Cyclin Dependent Kinase 6(细胞周期蛋白依赖性激酶6)
%%%\Cdk9: Cyclin Dependent Kinase 9(细胞周期蛋白依赖性激酶9)
%%%Cdk-Family:(Cdk家族)
%%%C/EBP:CCAAT/enhancer-binding protein(CCAAT/增强子-结合蛋白)
&&:(C/EBP)—promotes—ExpressionOfGene:&&
%%%\C/EBPα:
%%%\C/EBPβ:
%%%\C/EBPγ:
%%%\C/EBPδ:
%%%\C/EBPε:
%%%\C/EBεζ:
%%%C/EBP-BindingSite:(CCAAT/增强子-结合蛋白结合位点)
%%%Cell:(细胞)
%%%CellSurvival:(细胞存活)
%%%\Long-livedLatentHIV-InfectedCell:(长期存活的HIV-感染细胞)
%%%\QuiescentMemoryT-Cell:(休止记忆T细胞)
%%%\Tissue-ResidentMacrophage:(组织内巨噬细胞)
%%%CellularTranscriptionFactor:(细胞转录因子)
%%%C-Fos:(为一种原癌基因)
&&:(C-Fos)—isA—(Proto-oncogene):&&
&&:(C-Fos)—isA—(HumanHomologOfRetroviralOncogene-(v-fos)):&&
&&:(C-Fos)—isFoundInAbnormality—Ratfibroblasts:&&
&&:(C-Fos)—isConsideredAs—TransformingGeneOf(FBJ-MSV):&&
&&:((c-Fos)–or–FosB–or–(Fra-1)–or–(Fra-2))—isA—FosFamilyOfTranscriptionFactor:&&
&&:(c-Fos)—isLocatedIn—ChromosomeRegion14Fromq21Toq31:&&
&&:(c-Fos)—isInvolvedIn—FormationOf(AP-1Complex):&&
&&:(AP-1Complex)—bindsAtGeneSite—(AP-1)SpecificSiteAtPromoterAndEnhancerRegionOfGene:&&
&&:(C-Fos)—isInvolvedIn—ManyCellarFunctions:&&
&&:(C-Fos)—isOverExpressedIn—SomeCancer:&&
%%%C-FosFamily:(c-Fos族)
%%%Chromatin:(染色质)
%%%ChromatinFiber:(染色质纤维)
%%%Chromosome:(染色体)
%%%Chromodomain:(染色质域或克罗莫结构域)
%%%C-JunFamily:(C-Jun族)
%%%CKIs:Cdk inhibitor proteins(Cdk抑制子蛋白)
%%%COUP-TF:chicken ovalbumin upstream promoter-transcription factor(鸡卵清蛋白上游启动子转录因子)
&&:(COUP-TF)—regulatesNegatively—ExpressionOfHIV1Gene:&&
&&:(COUP-TF)—isTransformedInto—DimerOf(COUP-TF):&&
%%%COUP-TF-BindingRegion:(COUP-TF结合区域)
%%%CodingSequence:(编码序列)
%%%CorePromoter:(核心启动子单位(-78 to -1))
%%%Cyclin:(细胞周期蛋白)
%%%\CyclinT1:
%%%Dementia:(痴呆)
%%%\HIV-AssociatedDementia:(HIV相关性痴呆)
%%%DC:Dendritic cell(树突细胞)
%%%DNA sequence:(DNA序列)
%%%\PlantPromoterSequence:(植物促进子序列)
%%%DRB:5,6-Dichloro-1-beta-D-ribofuranosylbenzimidazole(5,6-二氯-1-beta-D-呋喃糖苯并咪唑)
&&:DRB—inhibits—TranscriptionElongationByRNA-PolymeraseII:&&
&&:DRB—isAnalogueOf—Adenosine:&&
%%%DRL:Double-ReadabilityLanguage, and also called SLHMR standing for The Structured Language Readable To Human And Machine(SLHMR)(人机双读语言，又称人机可读性结构化语言)
%%%DSIF:DRB sensitivity inducing factor(DRB敏感性诱发因子)
&&:DSIF—isA—NELF:&&
%%%EnhancerElement(增强子单元(-105 to -79))
%%%Erythropoiesis(红细胞生成)
%%%FBJ-MSV:Finkel-Biskis-Jinkins murine osteogenic sarcoma virus(Finkel-Biskis-Jinkins鼠类骨源性肉瘤病毒)
%%%Fos-FamilyOfTranscriptionFactors:(转录因子Fos族)
%%%\FosB:
%%%\Fra-1:
%%%\Fra-2:
%%%Gene:(基因)
%%%\HIF1A-Gene:(HIF1A-基因)
&&:HIF1A-Gene—encodes—HIF-1Alpha:&&
%%%\ARNT-Gene:(ARNT–基因)
&&:ARNT-Gene—encodes—HIF-1Beta:&&
%%%\EPAS1-Gene: &&:EPAS1-Gene—encodes—HIF-2Alpha:&&
%%%\ARNT2-gene:
&&:ARNT2-Gene—encodes—HIF-2Beta:&&
%%%\HIF3A-Gene:
&&:HIF3A-Gene—encodes—HIF-3Alpha:&&
%%%\ARNTL-Gene:
&&:ARNTL-Gene—encodes—HIF-3Beta:&&
%%%Genome:(基因组)
%%%Glycolysis:(糖酵解)
%%%GLS:gag leading sequence:(gag引导序列)
%%%GTF:General transcription factor:(通用转录因子)
%%%GrammaticalConcept:(语法概念)
%%%\Which:representing the previous adascent concept
%%%HAT:Histone Acetyltransferase(组蛋白乙酰转移酶)
%%%HDAC:Histone Deacetylases(组蛋白去乙酰化酶)
%%%HIF:hypoxia-inducible factor (低氧诱导因子)
%%%\HIF-1:hypoxia-inducible factor 1(低氧诱导因子1)
&&:HIF-1—isA—ROSTF:&&
&&HIF-1—isA—SubfamilyOfPAS:&&
%%%\\HIF-1Alpha:hypoxia-inducible factor 1 with alpha subunit
%%%\\HIF-1Beta:aryl hydrocarbon receptor nuclear translocator
%%%\HIF-2:(低氧诱导因子2)
%%%\\HIF-2Alpha:endothelial PAS domain protein 1
%%%\\HIF-2Beta:aryl hydrocarbon receptor nuclear translocator 2
%%%\HIF-3:(低氧诱导因子3)
%%%\\HIF-3Alpha:hypoxia inducible factor 3, alpha subunit
%%%\\HIF-3Beta:aryl hydrocarbon receptor nuclear translocator 3
&&:HIF—regulates—(Glycolysis–or–MitochondrialOxygenConsumption–or–Erythropoiesis–or–Angiogenesis–or–CellSurvival):&&
%%%HIV-1:Human Immunodeficiency Virus Type 1(人类免疫缺陷病毒1型)
%%%HRE:hypoxia response element (HRE) motif(低氧应答原件)
%%%Hypoxia(低氧状态)
&&:Hypoxia—isEquivalentOf—HypoxicCondition:&&
%%%HypoxicCondition(低氧环境)
%%%KDRL: Knowledge Expressed by DRL(以DRL形式表达的知识)
%%%LTR-Region: Long Terminal Repeat region(长的末端重复区)
%%%\LTR-RegionOfHIV:(HIV长的末端重复区)
%%%\5’LTR:(5’端长末端重复区)
%%%\3’LTR:(3’端长末端重复区)
&&:LTR—hasFunction—InsertionOfHIV1GeneticMaterialIntoHostGenome:&&
&&:LTR—isloatedAt—BothEndsOfRetrotransposon:&&
&&:LTR—containsPhysically—(U3–and–R–and–U5):&&
&&:U3—containsPhysically—(Modulatory–and–E–and–Basal):&&
&&:Modulatory—containsphysicallyAndSequentially—(Sp–and–GATAOf5–and–NFAT–and–C/EBP–and–NFAT–and–AP-1–and–GATA–and–C/EBP–and–USF–Ets–and–AP-1–and–C/EBP):&&
&&:E—containsphysicallyAndSequentially—(NF-kBOf2):&&
&&:Basal—containsphysicallyAndSequentially—(SpOf3–and–TATA):&&
&&:R—containsphysicallyAndSequentially—(NF-kB–and–TAR–and–NF-kB):&&
&&:U5—containsphysicallyAndSequentially—(AP-1Of3–and–NFAT):&&
%%%Lysines:(赖氨酸)
%%%Ligand:(配位体)
%%%Methylation:(甲基化)
%%%\DNAMethylation:(DNA甲基化)
%%%MitochondrialOxygenConsumption:(线粒体氧消耗)
%%%NELF:negative elongation factor(负性延长因子)
%%%NMP:nuclear matrix protein(核基质蛋白)
%%%NRE:negative modulatory region(负调节区,from -340 to -184)
%%%Nucleosomes(核小体)
%%%PAS-Domain:Per-Arnt-Sim (PAS) domain (一种被称为”尼龙搭扣”的生物大分子的基序(mottif))
&&:PAS-Domain—is-A—PhysicalForceOrMechanicalStructureInBiomacromolecule:&&
%%%PCAF:p300/CBP associated factor(p300/CBP结合因子)
%%%PCAF BRD:p300/CBP associated factor bromodomain (p300/CBP结合因子布罗姆结构域)
%%%PhysicalForceOrMechanicalStructure(力或力学结构)
%%%\PhysicalForceOrMechanicalStructureInBiomacromolecule(生物大分子中的力或力学结构)
%%%Proto-oncogene:(原癌基因)
%%%P-TEFb:positive transcription elongation factor b(阳性转录因子b)
%%%ROS:reactive oxygen species(活性氧类)
%%%\superoxide:(超氧化物())
%%%\hydrogen peroxide:(过氧化氢(H2O2))
%%%\hydroxyl radical:(羟基(OH))
%%%ROS-dependent pathway(活性氧类-依赖性通道)
%%%ROSTF:redox-sensitive transcription factor(氧化还原敏感性转录因子)
%%%RNS:reactive nitrogen species:(活性氮类)
%%%\NitricOxide:(一氧化氮(NO))
%%%\Peroxynitrite:(过氧化亚硝酸盐())
%%%SizeOfDistanceOfTimeOrSpace:(时空距离大小)
%%%\InfinitesimalDistanceOfTime:(无限小时间距离)
%%%\InfinitesimalDistanceOfSpace:(无限小空间距离)
%%%SOD:Superoxide Dismutase:(超氧物歧化酶)
%%%TAR:transactivating response element(反式激活效应元件,+1 to +59)
%%%Tat:Trans-Activator of Transcription(病毒反式转录因子)
%%%TBP:TATA box binding protein(TATA盒结合蛋白)
%%%TBP-associated factors:(TBP关联因子)
%%%Transcript cleavage factor:(转录子分裂因子)
%%%Transposon:(转座子)
%%%TranscriptionRegulation:(转录调节)
%%%\TranscriptionInitiation:(转录启动)
%%%\PolymeraseRecruitment:(多聚酶招募)
%%%\TranscriptionElongation:(转录延长)
%%%\ChromatinOrganization:(染色质组织)
%%%USF:Upstream stimulating factor(上游刺激因子)
&&:USF—mayStimulates—Transcription:&&
%%%UTR: Untranslated region(非翻译区)
%%%Vpr:Viral Protein R(一种病毒编码调节蛋白)
%%%YY1:nuclear motif-associated protein-1:(核基序关联蛋白)
%%%ZincFinger:(锌指结构)
%%%Ligand Binding:(配位体结合)
%%%\\ProteinLigandBinding:(蛋白质配位体结合)
%%%\\DNA-LigandBinding:(DNA配位体结合,指Target为DNA)
&&:ProteinLigandBinding—mayProduces—SignalAtSiteOnTargetProtein:&&
&&:ProteinLigandBinding—mayCauses—ChangeOfTargetProtein:&&
%%%ConceptRelatingToLigandBinding:
%%%\Ligand:(配位体)
%%%\\ProteinLigand:(蛋白质配位体)
%%%\Receptor:(受体)
%%%\TargetProtein:(目标蛋白)
&&:TargetProtein—equalsTo—Receptor:&&
%%%\ElectricCharge:(电荷)
%%%\Hydrophobicity:(疏水性)
%%%\MolecularStructure:(分子结构)
%%%\Association:(关联)
%%%\Dissociation:(离解，分开，脱离关系)
%%%\ChemicalConformationOrThreeDimensionalShapeOrientation:(三维构型改变)
%%%\Inhibitor:(抑制子)
%%%\Activator:(激活子)
%%%\Neurotransmitter:(神经递质)
%%%\Affinity:(亲和性)
%%%\\RateOfLigandBinding:(配位体结合速率)
%%%\SolventEffect:(溶剂效应。溶剂作用)
%%%\Non-covalentBinding:(非共价键结合)
%%%\ChemicalEnvironment:(化学环境)
&&:(Substance–or–Inhibitor–or–Activator–or–Neurotransmitter)—mayActAs—Ligand:&&
&&:(InteractionBetweenSubjectAndObject–and–ChemicalEnvironment)—Influences—RateOfLigandBinding:&&
%%%IntermolecularForce:(分子间力)
%%%\IonicBond:(离子键)
%%%\HydrogenBond:(氢键)
%%%\VDW:VanDerWaalsForce:(范德华力)
&&:(IonicBond–or–HydrogenBond–or–VanDerWaalsForce)—isA—IntermolecularForce:&&
%%%\CovalentBond:(共价键)
%%%LigandBinding:(配位键结合)
********after virion entering into host cell********
********The following knowledge is base on:********
********http://hivinsite.ucsf.edu/InSite?page=kb-00&doc=kb-02-01-01********
********Warner C. Greene, MD, PhD, University of California San Francisco********
********B. Matija Peterlin, MD, University of California San Francisco********
&&:VirionOfHIV-InsideCell—undergoes—UncoatingOfVirionOfHIV:&&
&&:(UncoatingOfVirionOfHIV—possiblyInvoloves—PhosphorylationOfViralMatrixProtean)—isCatalysedBy—MitogenActivatedProteinKinase:&&
&&:UncoatingOfVirionOfHIV—mayInvolve—(CyclophilinA–and–Nef–Vif):&&
&&:Nef—associatesWith—UniversalProtonPump:&&
&&:(UniversalProtonPump—promotes—UncoatingOfVirionOfHIV)—isFacilitatedBy—(UniversalProtonPump—makesChangeIn—Local-pH):&&
&&:ViralReverseTranscriptionComplex—isComposedOf—(LysineTransFerRNA-Abbr-tRNALys–and–ViralReverseTranscriptase–and–Matrix–and–NucleocapsidProtein–and–ViralProteinR-AbbrVpr–and–HostProtein):&&
&&:((ViralReverseTranscriptionComplex—isReleasedFrom—Virion)–and—(ViralReverseTranscriptionComplex—isReleasedTo—CytoplasmOfHostCell))—isCarriedOutAfter—(VirionOfHIV-InsideCell—undergoes—UncoatingOfVirionOfHIV):&&
&&:(VirionOfHIV-InsideCell—undergoes—UncoatingOfVirionOfHIV)—isCarriedOutAfter—(Virion—MovesInto—CytoplasmOfHostCell):&&
&&:(ReverseTranscriptionComplex—adheresTo—ActinMicrofilament)—isModiatedBy—PhosphorylatedMatrix:&&
&&:ActinMicrofilament—isLocatedIn—CytoplasmOfCell:&&
&&:Vif—stabilizes—ReverseTranscriptionComplex:&&
&&:Vif—overcomes—(CEM15/APOBEC3G—desstabilizes—ReverseTranscriptionComplex):&&
&&:ReverseTranscription—creates—HIV-PreintegrationComplexAbbrPIC:&&
&&:HIV-PreintegrationComplexAbbrPIC—isComposedOf—(Double-StrandedViral-cDNA–and–Integrase–and–Matrix–and–Vpr–and–ReverseTranscriptase–and–HighMobilityGroupDNA-binding-CellularProteinAbbrHMGI(Y)):&&
&&:HIV-PreintegrationComplexAbbrPIC—mayMoveInCellPerhapsTrough—CytoskeletalStructure:&&
%%%StructureOfChromatin:
%%%CellReplication:
%%%CellularRepair:
%%%INI1/hSNF5-Gene:
%%%DevelopmentOfTumor:
&&:(IntegraseInteractor1AbbrINI1/hSNF5—changes—StructureOfChromatin)—facilitates—(Transcription–and–CellReplication–and–CellularRepair):&&
&&:IntegraseInteractor1AbbrINI1/hSNF5—isAComponentOf—SWI/SNF-ChromatinRemodelingComplex:&&
&&:INI1/hSNF5-Gene—suppresses—DevelopmentOfTumor:&&
********!!!!!********
%%%NuclearImportOfPIC:
%%%Matrix:
%%%NuclearLocalizationSignal:
%%%ImportinAlpha:
%%%ImportinBeta:
%%%NuclearImportPathway:
%%%NuclearImportSignal:
%%%NuclearPoreComplex:
%%%NondividingCell:
%%%NuclearImportPathway:
%%%TerminallyDifferentiatedMacrophage:
%%%NuclearImportOfPIC:
%%%ImportinSystem:
&& :HIV-1—canInfect—NondividingCell:&&
&&:HIV-1—canInfect—TerminallyDifferentiatedMacrophage:&&
&&:TerminallyDifferentiatedMacrophage—isA—NondividingCell:&&
&&:(Integrase–and–Matrix–and–Vpr)—mayPossiblyMediate—NuclearImportOfPIC:&&
&&:(Matrix–or–Vpr)—shuttlesBetween—(CellNucleus–and–Cytoplasm):&&
&&:Matrix—containsPhysically—CanonicalNuclearLocalizationSignal:&&
&&:Integrase—containsPhysically—NuclearLocalizationSignal:&&
&&:NuclearLocalizationSignal—isRecognizedBy—(ImportinAlpha–and–ImportinBeta):&&
&&:(NuclearImportPathway–and–NuclearImportSignal)—isComponentOf—NuclearImportPathway):&&
&&:HIV-VprGeneProduct—containsPhysically—NoncanonicalNuclearTargetingSignal:&&
********!!!!!********
********References********
********1.Warner C. Greene,B. Matija Peterlin:Molecular Insights Into HIV Biology, http://hivinsite.ucsf.edu/InSite?page=kb-00&doc=kb-02-01-01********
********2.Das S. Integrase interactor 1 in health and disease, By Das S.https://www.ncbi.nlm.nih.gov/pubmed/25772157********
&&:Tat—mayIncreasesSignificantly—RateOfViralGeneExpression:&&
&&:((Tat—bindsTo—RNA-StemLoopStructureOfTAR)–and–(Tat—recruitsSthToSth—(CellularCyclinDependentKinase9AbbrCdk9,RNA-StemLoopStructureOfTAR)))—underConditionOf—(Tat—existsWith—CyclinT1AlsoNameCycT1):&&
%%%PositiveTranscriptionElongationFactor-bComplexAbbrP-TEFbComplex
&&:((CellularCyclinDependentKinase9AbbrCdk9—canCatalyze—PhosphorylationOfC-TerminalDomainOfRNAPII)—existsInStructureOf—PositiveTranscriptionElongationFactor-bComplexAbbrP-TEFbComplex)—marks—StartOfElongationOfEukaryoticTranscription:&&
%%%TranscriptionOfDNA-ToSynthesizePrecursorOf-mRNA
%%%TranscriptionOfDNA-ToSynthesizePrecursorOf-snRNA
%%%TranscriptionOfDNA-ToSynthesizePrecursorOf-microRNA
&&:RNA-PolymeraseIIAbbrRNAPII—existsInStrctureOf—EukaryoticCell:&&
&&:RNA-PolymeraseIIAbbrRNAPII—canCatalyze—TranscriptionOfDNA-ToSynthesizePrecursorOf-mRNA:&&
&&:RNA-PolymeraseIIAbbrRNAPII—canCatalyze—TranscriptionOfDNA-ToSynthesizePrecursorOf-snRNA:&&
&&:RNA-PolymeraseIIAbbrRNAPII—canCatalyze—TranscriptionOfDNA-ToSynthesizePrecursorOf-microRNA:&&
&&:RNA-PolymeraseII—isRecruitedTo—CorePromoter:&&
&&:GeneralTranscriptionFactorAbbrGTF—isRecruitedTo—CorePromoter:&&
&&:TranscriptionCoFactor—isRecruitedTo—CorePromoter:&&
&&:RNA-PolymeraseII—catalysesTranscriptionOfDNAInto—ProteinCodingRNA:&&
&&:RNA-PolymeraseII—catalysesTranscriptionOfDNAInto—NonProteinCodingRNA:&&
&&:LongNonCodingRNA—isA—NonProteinCodingRNA:&&
&&:miRNA—isA—NonProteinCodingRNA:&&
&&:Ribosome—isA—NonProteinCodingRNA:&&
&&:iRNA—isA—NonProteinCodingRNA:&&
&&:RegulatoryRNA—isA—NonProteinCodingRNA:&&
&&:InitiatorElementAbbrInrAlsoNameInitiatorMotif—isLocatedAt—TranscriptionStartSiteOfGeneOfEukaryocyte:&&
&&:InitiatorElementAbbrInrAlsoNameInitiatorMotif—isPartOf—CorePromoter:&&
&&:InitiatorElementAbbrInrAlsoNameInitiatorMotif—directs—TranscriptionInitiation:&&
&&:RNA—includesLogically—NonProteinCodingRNA:&&
&&:RNA—includesLogically—ProteinCodingRNA:&&
&&:RNA-PolymeraseII—isA—RNA-Polymerase:&&
&&:RNA-Polymerase—binds—Promoter:&&
&&:RNA-Polymerase—binds—ResponseElement:&&
&&:TranscriptionFactor—binds—ResponseElement:&&
&&:ResponseElement—isPartOf—Promoter:&&
&&:RNA-Polymerase—isRecruitedTo—TranscriptionFactor:&&
&&:Activator—isA—TranscriptionFactor:&&
&&:Reprssor—isA—TranscriptionFactor:&&
&&:Enhancer—isA—RegulatoryRegion:&&
&&:Silencer—isA—RegulatoryRegion:&&
&&:BoundaryElement—isA—RegulatoryRegion:&&
&&:Insulator—isA—RegulatoryRegion:&&
&&:(Promoter—cooperatesWith—RegulatoryRegion)—leadsTo—(TranscriptionFactor—recruits—RNA-Polymerase):&&
&&:5′LongTerminalRepeatOfHIVAbbrLTR-OfHIV—dominantlyRegulates—TranscriptionOfHIV:&&
&&:5′LongTerminalRepeatOfHIVAbbrLTR-OfHIV—containStructurely—(TatActivatingRegionAbbrTAR–and–Promotor–and–Enhancer–and—NegativeRegulatoryElement):&&
&&:((TatActivatingRegionAbbrTAR—forms—RNA-StemLoop)—underContextOf—NascentRNA)–and–(RNA-StemLoop—binds—VirusEncodedTransactivatorAbbrTatEncodedByVirus):&&
&&:((Promotor–or–Enhancer–or–ModulatoryElement)—recruits—HostTranscriptionFactor):&&
&&:HostTranscriptionFactor—functionsAS—ActivatorProtein–or–RepressorProtein–or–AdapterProtein:&&
&&:((AP-1–or–C/EBPb–or–NFAT–or–Ets/PU.1–or–TCF/LEF-1)—Transactivates—5′LongTerminalRepeatOfHIVAbbrLTR-OfHIV)—induces—TranscriptionOfHIV:&&
&&:(CorePromoter–or–ProximalPromoter–or–DistalPromoter)—isPartOf—Promoter:&&
&&:DistalPrpmoter—isLocatedUpStreamFrom—ProximalPromoter:&&
&&:ProximalPromoter—isLocatedUpStreamFrom—CorePromoter:&&
&&:CorePromoter—containsPhysically—(RNAPolymeraseBindingSite–and–TATA-Box–and–TranscriptionStartSiteAbbrTSS):&&
&&:RNA-Polymerase—hasSubtype—(RNA-PolymeraseI–and–RNA-PolymeraseII–and–RNA-PolymeraseIII):&&
&&:RNA-PolymeraseI—encodesFor—RiboSomalRNA-Abbr-rRNA:&&
&&:RNA-PolymeraseII—encodesFor—MessengerRNA-Abbr-mRNA:&&
&&:RNA-PolymeraseIII—encodesFor—TransforRNA-Abbr-tRNA:&&
********https://www.addgene.org/mol-bio-reference/promoter-background/********
********https://www.hindawi.com/journals/mbi/2012/614120/********
********Mechanisms of HIV Transcriptional Regulation and Their Contribution to Latency********
********Gillian M. Schiralli Lester and Andrew J. Henderson********
%%%CisActingTranscriptionalRegulatoryDNA-Element(同分子作用转录调节DNA元素)
%%%TransActingTranscriptionalRegulatoryDNA-Element(跨分子作用转录调节DNA元素)
&&:CisActingTranscriptionalRegulatoryDNA-Element—containsPhysically—(FamilyOfPromoter–and–FamilyOfDistalRegulatoryElement):&&
&&:FamilyOfDistalRegulatoryElement—containsPhysically—(Enhancer–and–Silencer–and–Insulator–and–LocusControlRegionAbbrLCR):&&
********Glenn A. Maston, Sara K. Evans, and Michael R. Green********
********“Transcriptional Regulatory Elements in the Human Genome”********
********http://web.stanford.edu/class/cs273a/papers.spr07/09/txRegulationReview.pdf********
&&:TransActingElement—isA—DNA-Sequence:&&
&&:TransActingElement—containsPhysically—GenesForTranscriptionOfOtherGene:&&
&&:GenesForTranscriptionOfOtherGene—encodesFor—ProteinForTranscriptionOfGene:&&
&&:GenesForTranscriptionOfOtherGene—encodesFor—microRNAForTranscriptionOfGene:&&
&&:TranscriptionInitiationComplex—consisteOf—(PromoterSequence–and–DNA-BindingProtein):&&
&&:CisActingElement—isA—DNA-Sequence:&&
&&:CisActingElement—isLocatedIn—VicinityOfStructuralPortionOfGene:&&
&&:ResponseElement—isA–CisActingElemen:&&
&&:TransActingFactor—isA—Protein:&&
&&:TransActingFactor—combines—CisActingElement:&&
&&:TransActingFactor—controls—ExpressionOfGene:&&
&&:ExpressionOfGene—isFunctionOf—Gene:&&
&&:TransActingFactor—isExpressedByGeneUnderContextOf—SpecificTissue:&&
&&:TransActingFactor—isExpressedByGeneUnderContextOf—SpecificStageOfDevelopmentOfOrganism:&&
&&:TransActingFactor—controlsExpressionOfGeneUnderContextOf—Phosphorylation:&&
&&:TransActingFactor—controlsExpressionOfGeneUnderContextOf—BeingActivatedByLigandBinding:&&
&&:TransActingFactor—controlsExpressionOfGeneUnderContextOf—EffectOfEnvironmentSignal:&&
********References********
********https://www.ndsu.edu/pubweb/~mcclean/plsc731/cis-trans/cis-trans6.htm********
********Copyright ? 1998. Phillip McClean********
&&:GTF-FLNM-GeneralTranscriptionFactor isA TF-FLNM-TranscriptionFactor-AlsoNameSequenceSpecificDNA-BindingFactor:&&
&&:(TFIIA-FLNM-TranscriptionFactorII-A–or–TFIIB-FLNM-TranscriptionFactorII-B–or–TFIID-FLNM-TranscriptionFactorII-D–or–TFIIE-FLNM-TranscriptionFactorII-E–or–TFIIF-FLNM-TranscriptionFactorII-F–or–TFIIH-FLNM-TranscriptionFactorII-H)—isA—GTF-FLNM-GeneralTranscriptionFactor:&&
&&:UpstreamTranscriptionFactor isA TF-FLNM-TranscriptionFactor-AlsoNameSequenceSpecificDNA-BindingFactor:&&
&&:(Otc1-FLNM-OctamerTranscriptionFactor1–or–Sp1-FLNM-SpecificityProtein1–or–C/EBP-FLNM-CCAAT/EnhancerBindingProteinBeta–or–AP-1-FLNM-ActivatorProtein1–or–NF-1-FLNM-NeurofibromatosisType1–or–ATF/CREB-FLNM-ActivatingTranscriptionFactor/cAMP-ResponseElementBindingProtein–or–HSF-FLNM-HeatShockFactor–or–bHLH-FLNM-BasicHelixLoopHelix)—isA—UpstreamTranscriptionFactor:&&
********Reference: https://en.wikipedia.org/wiki/Transcription_factor********
********edited 2018-02-08,02-09,03-14,-16,-20,04-01********
