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1、490American Society of HematologyGlossary of Molecular Biology TerminologyKenneth Kaushansky,MD*This glossary is designed to help the reader with the ter-minology of molecular biology.Each year,the glossarywill be expanded to include new terms introduced in theEducation Program.The basic terminology
2、 of molecu-lar biology is also included.The glossary is divided intoseveral general sections.A cross-reference guide is in-cluded to direct readers to the terms they are interestedin.The hope is that this addition to the Education Pro-gram will further the understanding of those who areless familiar
3、 with the discipline of molecular biology.CROSS-REFERENCE GUIDETermSectionActinomycin D pulse experimentsVAdeno-associated viral vectorsVIIIAdenoviral vectorsVIIIALKXAllele-specific hybridizationXIAllele-specific PCRIVAML-1XAmphotropic virusVIIIAnaplastic lymphoma kinaseXAntisense oligonucleotidesVI
4、IIBasic helix-loop-helix proteinsVBcl-1XBcl-2XBcl-3XBcl-6X galactosidaseVBranched chain DNA signalamplification assayIIc-ablXc-fosXc-junXc-mybXc-mycXc-rasXTermSectionc-relXCalcium phosphateVICANXCATVcDNAIIcDNA bluntingIXcDNA library preparationIXcdkVcdkIVCFBIXChimeraplastyVIIIChitosan-DNAVIIIChloram
5、phenicol transferaseVChromatography,gel filtrationIVChromatography,ion exchangeIVChromatography,hydrophobicIVChromatography,affinityIVChromatography,high performanceliquid(HPLC)IVCis-acting factorsVCodonIIColor complementation assayXIComparative gene hybridizationIVCompetitive oligonucleotide hybrid
6、izationXIConcatamerizationVICyclin-dependent kinaseVContigVIICosmidIICpG nucleotideIICyclinsVDEAE dextranVIDEKXDideoxynucleotide(ddN)chaintermination sequencingIVDirectional cloningIXDNA(deoxyribonucleic acid)IIDNA methylasesIIIDNA microarraysIVDNA polymeraseIIIDNAse footprintingIVDNAse hypersensiti
7、vity site mappingIV*University of Washington School of Medicine,Division ofHematology,Box 357710,Seattle WA 98195-7710Hematology 2002491TermSectionEcotropic vectorsVIIIEcotropic virusVIIIElectroporationVIEndonucleaseIIIEnhancerVEpisomalVIIIETOXEvi-1XExonsVExonucleaseIIIFarnesyl protein transferaseII
8、IFasXFirst strand synthesisIXFISH(fluorescence in situ hybridization)IVFTPaseIIIGene knock-in experimentsVIIGene knock-out experimentsVIIHelix-turn-helixVHomologous recombinationVIIHox IIIXHPLCIVImmunoglobulin somatic hypermutationVIn situ hybridizationIVInitiation codonVInitiation complexVInterfero
9、n regulatory factorXIntronsVIRF-1XIRF-2XIsoschizomerIIIKinasesIIIKlenow fragmentIIIKOZAK sequenceVLCRVLeucine zipper proteinsVLibrary screeningIXLigasesIIILinkeringIXLiposomesVILocus control regionVLong terminal repeatVIIILuciferaseVMammalian protein kinasesIIIMaster switch genesVMaxXMaxam-Gilbert s
10、equencingIVMinimal residual diseaseIVMissense mutationVMLLXMobility shift(or band shift)assaysIVmRNAIIMutagenesis,site-specificIVTermSectionNested PCRIVNF-1XNick-translationIVNonsense mutationVNonviral transduction methodsVIIINorthern blottingIVNucleasesIIINucleosomesVORF(open reading frame)IIp53XPC
11、R(polymerase chain reaction)IVPhageIIPlasmidsIIPolyadenylationVPolylysine-ligand DNAIXPolymerasesIIIPositional variegationVIIIPost transcriptional regulationVProtein translationVProteomicsIVProteosomeVPseudotype retroviral vectorsIVPseudotyped virusesVIIIRandom primingIVRARXRbXRDA(representational d
12、ifference analysis)IXReal-time PCRIVReporter genesVRestriction endonucleaseIIIRestriction fragment length polymorphismXIRetinoic acid receptorXRetroviral vectorsVIIIReverse allele-specific hybridizationXIReverse geneticsIXReverse PCRIVReverse transcriptaseIIIRFLPXIRibonucleaseIIIRiboprobesIVRibozyme
13、sIIIRNA(Ribonucleic acid)IIRNA polymerase IIIIIRNA polymerase IIIIIIRNAse protection assayIVS1 nuclease analysisIVSCLXSecond strand synthesisIXSilencerVSouthern blottingIVSouthwestern blottingIVSplicingV492American Society of HematologyTermSectionSubtractive libraryIXTal-1XTATAVTelXTelomereIITelomer
14、aseIIITerminal deoxynucleotidylIIIThermostabile polymerasesIIITopoisomeraseIIITrans-acting factorsVTranscriptionVTranscription factorsVTranscriptional regulationVTransductionVITransfectionVITransgenic animalsVIIITransposonVIItRNAIIUbiquitinVViral-derived kinasesIIIViral-derived transduction vectorsV
15、IIIWestern blottingIVX-linked methylation patternsXIYACVIIYeast artificial chromosomeVIIYeast 2-hybrid screensIVZinc finger domain proteinsVII.NUCLEIC ACIDSDNA(deoxyribonucleic acid)The polymer constructedof successive nucleotides linked by phosphodiesterbonds.Some 3 x 109 nucleotides are contained
16、in thehuman haploid genome.During interphase,DNA existsin a nucleoprotein complex containing roughly equalamounts of histones and DNA,which interacts withnuclear matrix proteins.This complex is folded into abasic structure termed a nucleosome containing approxi-mately 150 base pairs.From this highly
17、 ordered struc-ture,DNA replication requires a complex process ofnicking,unfolding,replication,and splicing.In contrast,gene transcription requires nucleosomal re-organizationsuch that sites critical for the binding of transcriptionalmachinery reside at internucleosomal junctions.Branched chain DNA(
18、b-DNA)A method that exploitsthe formation of branched DNA to provide a sensitiveand specific assay for viral RNA or DNA.The assay isperformed in a microtiter format,in which partially ho-mologous oligodeoxynucleotides bind to target to cre-ate a branched DNA.Enzyme-labeled probes are thenbound to th
19、e branched DNA,and light output from achemiluminescence substrate is directly proportional tothe amount of starting target RNA.Standards providequantitation.The assay displays a 4 log dynamic rangeof detection,with greater sensitivity to changes in viralload than RT-PCR-based assays.It has been empl
20、oyedto quantitate levels of HIV,HCV,and HBV.RNA(ribonucleic acid)Three varieties of RNA are eas-ily identified in the mammalian cell.Most abundant isribosomal RNA(rRNA),which occurs in two sizes,28S(approximately 4600 nucleotides)and 18S(approxi-mately 1800 nucleotides);together they form the basicc
21、ore of the eukaryotic ribosome.Messenger RNA(mRNA)is the term used to describe the mature form ofthe primary RNA transcript of the individual gene onceit has been processed to eliminate introns and to containa polyadenylated tail.mRNA links the coding sequencepresent in the gene to the ribosome,wher
22、e it is trans-lated into a polypeptide sequence.Transfer RNA(tRNA)is the form of RNA used to shuttle successive aminoacids to the growing polypeptide chain.A tRNA mol-ecule contains an anti-codon,a three-nucleotide se-quence by which the tRNA molecule recognizes thecodon contained in the mRNA templa
23、te,and an adapteronto which the amino acid is attached.Codon Three successive nucleotides on an mRNA thatencode a specific amino acid in the polypeptide.Sixty-one codons encode the 20 amino acids,leading to codonredundancy,and three codons signal termination ofpolypeptide synthesis.ORF(open reading
24、frame)The term given to anystretch of a chromosome that could encode a polypep-tide sequence,i.e.,the region between a methioninecodon(ATG)that could serve to initiate protein transla-tion,and the inframe stop codon downstream of it.Sev-eral features of the ORF can be used to judge whether itactuall
25、y encodes an expressed protein,including itslength,the presence of a“Kozak”sequence upstream ofthe ATG(implying a ribosome might actually bind thereand initiate protein translation),whether the ORF existswithin the coding region of another gene,the presenceof exon/intron boundary sequences and their
26、 splicingsignals,and the presence of upstream sequences thatcould regulate expression of the putative gene.Plasmids Autonomously replicating circular DNA thatare passed epigenetically between bacteria or yeast.Inorder to propagate,plasmids must contain an origin ofreplication.Naturally occurring pla
27、smids transfer geneticinformation between hosts;of these,the genes encodingHematology 2002493resistance to a number of antibiotics are the most impor-tant clinically.The essential components of plasmids areused by investigators to introduce genes into bacteriaand yeast and to generate large amounts
28、of DNA formanipulation.Phage A virus of bacteria,phage such as lambda havebeen used to introduce foreign DNA into bacteria.Be-cause of its infectious nature,the transfection(introduc-tion)efficiency into the bacterial host is usually two or-ders of magnitude greater for phage over that of plas-mids.
29、Cosmid By combining the elements of phage and plas-mids,vectors can be constructed that carry up to 45 kbof foreign DNA.cDNA A complementary copy of a stretch of DNA pro-duced by recombinant DNA technology.Usually,cDNArepresents the mRNA of a given gene of interest.Telomere A repeating structure fou
30、nd at the end of chro-mosomes,serving to prevent recombination with free-ended DNA.Telomeres of sufficient length are requiredto maintain genetic integrity,and they are maintainedby telomerase.CpG This under-represented(i.e.50%of CMML cases.Consti-tutive activation of ras can mimic chronic stimulati
31、onby the corresponding lineage-specific growth factor.Hox 11 A homeobox containing transcription factor dis-rupted by translocation to the T cell receptor locus t(10;14)in 10%of cases of T cell ALL/lymphoblastic lymphoma.The Hox 11 gene is critical to the development of the spleenbut its role in hem
32、atopoiesis is unclear.Rhomb 2 Like Hox 11,Rhomb 2 is translocated in Tcell ALL/lymphoma associated with t(11;14).Rhomb 1may play a similar role in additional cases of T cell ALL.The Rhomb gene products are members of a family oftranscription factors,but as Rhomb 2 and Rhomb 1 donot contain DNA-bindi
33、ng domains,they are thought tobe involved in protein-protein interactions.Neither Rhomb2 or 1 are normally expressed in T cells;transformationinvolving these genes,like SCL or Hox 11 is thought to bedue to ectopic expression of the protein in T cells.ALK(anaplastic lymphoma kinase)A large propor-tio
34、n of Ki-1 positive lymphomas are characterized by at(2;5).The breakpoint involves nucleophosmin,a ubiq-uitously expressed gene,and ALK.The chimeric mRNAand protein are thought to be responsible for transfor-mation.ALK is a member of the insulin receptor familyof transmembrane receptor kinases,which
35、is not nor-mally expressed in hematopoietic tissues;the fusion geneis no longer membrane bound,which may underlie itspathogenesis.Evi-1 A transcription factor whose rearrangement int(3;21)is implicated as contributing to MDS.Over-expression of evi-1 blocks differentiation in response tohematopoietic
36、 growth factors.ETO Located on chromosome 8,ETO is involved in t(8:21)of AML type M2.Based on the presence of two zinc-fin-ger motifs.ETO possibly encodes a transcription factor,but its role in the pathogenesis of AML is unknown.AML-1 Located on chromosome 21,AML-1 is the fu-sion partner of ETO in t
37、(8:21).The gene is homologousto the runt gene of Drosophila and encodes a transcrip-tion factor.Normal hemopoietic targets include theCD13,GM-CSF,MPO,IL-3,and the T cell antigen re-ceptor promoters.AML-1 binds as a heterodimer,partnered with CBF.It is unclear if its mechanism ofaction is to enhance
38、aberrant transcription or to blunttranscription by acting in a dominant negative fashion.CBF Located on chromosome 16,CBF is one of thefusion partners in the inv(16)associated with AML typeM4Eo.As with AML-1,it is unclear whether the alteredtranscription factor enhances or blocks transcription.MLL L
39、ocated on chromosome 11,MLL(mixed lineageleukemia)is frequently altered in ALL,1oAML,and es-pecially in AML secondary to the use of topoisomeraseII inhibitors.MLL is homologous to the trithorax geneof Drosophila and displays many features of a transcrip-tion factor and of a DNA methyl transferase.50
40、8American Society of HematologyTel A helix-loop-helix transcription factor fused to thePDGF-receptor in CMML t(5:12)and to other genesin AML or MDS.Like most other translocationoncogenes,the mechanism of leukemogenesis is un-known.More recently,a Tel/AML1 fusion gene repre-senting a t(12;21)has been
41、 found in a large number ofcases of childhood ALL.As the translocation is not de-tected by routine cytogenetics,molecular analysis(FISH,etc.)is required to identify this favorable chromosomalrearrangement.DEK Located on chromosome 6,DEK is involved int(6:9)of AML.This translocation is usually seen i
42、nyoung patients and carries a poor prognosis.Its normalfunction is unknown,but DEK localizes to the nucleus.CAN Located on chromosome 9,CAN is part of t(6:9).CAN forms part of the nuclear pore.As it has two dif-ferent fusion partners but a consistent phenotype,CANis likely the critical component of
43、t(6:9).Fas(CD95 or Apo-1)A transmembrane glycoproteinexpressed on a wide variety of primitive and mature he-matopoietic cells,which,upon binding to its naturalligand triggers programmed cell death.NF-1 The gene responsible for neurofibromatosis.Thenormal protein functions to negatively regulate rasp
44、roteins,key intermediates in cytokine-inducedcellular proliferation.XI.GENETIC SCREENINGX-linked methylation patterns Several loci present onthe X chromosome become highly methylated when in-active but remain unmethylated on the active X chro-mosome(Lyon hypothesis).Should a polymorphic sitefor a me
45、thylation-sensitive restriction endonuclease ex-ist at such an X-linked locus,one can distinguish be-tween the active and inactive X chromosome by the pat-tern of restriction endonuclease digestion of that gene.However,in order to be widely useful for determiningclonality of hematopoietic cells,the
46、allelic frequencymust be close to equality.Several X-linked genes meetthese criteria and include phosphoglycerate kinase(PGK),hypoxanthine phosphoribosyltransferase(HPRT),the human androgen receptor gene(HUMARA),and the hyper-variable DXS255 locus.Both Southern blotting and PCR methods can be applie
47、dto this type of analysis.RFLP(restriction fragment length polymorphism)Ifa mutation of one allele of a genetic locus either gener-ates or destroys a restriction endonuclease site,the het-erogeneity present within or very close to a gene of in-terest can be used to track which allele an individual h
48、asinherited from each parent.When genomic DNA is di-gested with a restriction enzyme that recognizes a poly-morphic site and then hybridized with a probe specificfor the gene of interest,the allelic pattern can be com-pared to that of a similar assessment of both parents.The presence of multiple fam
49、ily members allows a com-plete genetic pedigree to be constructed.For example,globin gene mutations such as sickle hemoglobin can beanalyzed.The 6 mutation in hemoglobin,which resultsin Hgb S,destroys an Mst II site.Therefore,a largerthan normal DNA fragment is generated by digestion ofgenomic DNA w
50、ith Mst II,which can be easily detectedby Southern blot hybridization.In this specific case,theMst II polymorphism is absolutely specific for the mu-tant gene and family studies are not necessary.If theRFLP had not been specific for the mutation,but onlyexisted close to the specific disease-producin