Bài giảng Biology - Chapter 19: Eukaryotic Genomes: Organization, Regulation, and Evolution

Chapter 19Eukaryotic Genomes: Organization, Regulation, and EvolutionOverview: How Eukaryotic Genomes Work and EvolveIn eukaryotes, the DNA-protein complex, called chromatinIs ordered into higher structural levels than the DNA-protein complex in prokaryotesFigure 19.1Both prokaryotes and eukaryotesMust alter their patterns of gene expression in response to changes in environmental conditionsConcept 19.1: Chromatin structure is based on successive levels of DNA packingEukaryotic DNAIs precisely combined with a large amount of proteinEukaryotic chromosomesContain an enormous amount of DNA relative to their condensed lengthNucleosomes, or “Beads on a String”Proteins called histonesAre responsible for the first level of DNA packing in chromatinBind tightly to DNAThe association of DNA and histonesSeems to remain intact throughout the cell cycleIn electron micrographsUnfolded chromatin has the appearance of beads on a stringEach “bead” is a nucleosomeThe basic unit of DNA packingFigure 19.2 a2 nm10 nmDNA double helixHistonetailsHis-tonesLinker DNA(“string”)Nucleosome(“bad”)Histone H1(a) Nucleosomes (10-nm fiber)Nucleosome30 nm(b) 30-nm fiberHigher Levels of DNA PackingThe next level of packingForms the 30-nm chromatin fiberFigure 19.2 bThe 30-nm fiber, in turnForms looped domains, making up a 300-nm fiberFigure 19.2 cProtein scaffold300 nm(c) Looped domains (300-nm fiber)LoopsScaffoldIn a mitotic chromosomeThe looped domains themselves coil and fold forming the characteristic metaphase chromosomeFigure 19.2 d700 nm1,400 nm(d) Metaphase chromosomeIn interphase cellsMost chromatin is in the highly extended form called euchromatinConcept 19.2: Gene expression can be regulated at any stage, but the key step is transcriptionAll organismsMust regulate which genes are expressed at any given timeDuring development of a multicellular organismIts cells undergo a process of specialization in form and function called cell differentiationDifferential Gene ExpressionEach cell of a multicellular eukaryoteExpresses only a fraction of its genesIn each type of differentiated cellA unique subset of genes is expressedMany key stages of gene expressionCan be regulated in eukaryotic cellsFigure 19.3SignalNUCLEUSChromatinChromatin modification:DNA unpacking involvinghistone acetylation andDNA demethlationGeneDNAGene availablefor transcriptionRNAExonTranscriptionPrimary transcriptRNA processingTransport to cytoplasmIntronCapmRNA in nucleusTailCYTOPLASMmRNA in cytoplasmDegradationof mRNATranslationPolypetideCleavageChemical modificationTransport to cellulardestinationActive proteinDegradation of proteinDegraded proteinRegulation of Chromatin StructureGenes within highly packed heterochromatinAre usually not expressedHistone ModificationChemical modification of histone tailsCan affect the configuration of chromatin and thus gene expressionFigure 19.4a(a) Histone tails protrude outward from a nucleosomeChromatin changesTranscriptionRNA processingmRNA degradationTranslationProtein processingand degradationDNAdouble helixAmino acidsavailablefor chemicalmodificationHistonetailsHistone acetylationSeems to loosen chromatin structure and thereby enhance transcriptionFigure 19.4 b(b) Acetylation of histone tails promotes loose chromatin structure that permits transcriptionUnacetylated histonesAcetylated histonesDNA MethylationAddition of methyl groups to certain bases in DNAIs associated with reduced transcription in some speciesEpigenetic InheritanceEpigenetic inheritanceIs the inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequenceRegulation of Transcription InitiationChromatin-modifying enzymes provide initial control of gene expressionBy making a region of DNA either more or less able to bind the transcription machineryOrganization of a Typical Eukaryotic GeneAssociated with most eukaryotic genes are multiple control elementsSegments of noncoding DNA that help regulate transcription by binding certain proteinsFigure 19.5Enhancer(distal control elements)Proximalcontrol elementsDNAUpstreamPromoterExonIntronExonIntronPoly-A signalsequenceExonTerminationregionTranscriptionDownstreamPoly-AsignalExonIntronExonIntronExonPrimary RNAtranscript(pre-mRNA)5Intron RNARNA processing:Cap and tail added;introns excised andexons spliced togetherCoding segmentPPPGmRNA5 Cap5 UTR(untranslatedregion)StartcodonStopcodon3 UTR(untranslatedregion)Poly-AtailChromatin changesTranscriptionRNA processingmRNAdegradationTranslationProtein processingand degradationCleared 3 endof primarytransportThe Roles of Transcription FactorsTo initiate transcriptionEukaryotic RNA polymerase requires the assistance of proteins called transcription factorsEnhancers and Specific Transcription FactorsProximal control elementsAre located close to the promoterDistal control elements, groups of which are called enhancersMay be far away from a gene or even in an intronDistal controlelementActivatorsEnhancerPromoterGeneTATAboxGeneraltranscriptionfactorsDNA-bendingproteinGroup ofMediator proteinsRNAPolymerase IIRNAPolymerase IIRNA synthesisTranscriptionInitiation complexChromatin changesTranscriptionRNA processingmRNAdegradationTranslationProtein processingand degradation A DNA-bending proteinbrings the bound activatorscloser to the promoter.Other transcription factors,mediator proteins, and RNApolymerase are nearby.2 Activator proteins bindto distal control elementsgrouped as an enhancer in the DNA. This enhancer hasthree binding sites.1 The activators bind tocertain general transcriptionfactors and mediatorproteins, helping them forman active transcriptioninitiation complex on the promoter.3An activatorIs a protein that binds to an enhancer and stimulates transcription of a geneFigure 19.6Some specific transcription factors function as repressorsTo inhibit expression of a particular geneSome activators and repressorsAct indirectly by influencing chromatin structureCombinatorial Control of Gene ActivationA particular combination of control elementsWill be able to activate transcription only when the appropriate activator proteins are presentFigure 19.7a, bEnhancerPromoterControlelementsAlbumingeneCrystallingeneLiver cellnucleusLens cellnucleusAvailableactivatorsAvailableactivatorsAlbumingeneexpressedAlbumingene notexpressedCrystallin genenot expressedCrystallin geneexpressed(a)(b)Liver cellLens cellCoordinately Controlled GenesUnlike the genes of a prokaryotic operonCoordinately controlled eukaryotic genes each have a promoter and control elementsThe same regulatory sequencesAre common to all the genes of a group, enabling recognition by the same specific transcription factorsMechanisms of Post-Transcriptional RegulationAn increasing number of examplesAre being found of regulatory mechanisms that operate at various stages after transcriptionRNA ProcessingIn alternative RNA splicingDifferent mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as intronsFigure 19.8Chromatin changesTranscriptionRNA processingmRNAdegradationTranslationProtein processingand degradationExonsDNAPrimaryRNAtranscriptmRNARNA splicingormRNA DegradationThe life span of mRNA molecules in the cytoplasmIs an important factor in determining the protein synthesis in a cellIs determined in part by sequences in the leader and trailer regionsRNA interference by single-stranded microRNAs (miRNAs)Can lead to degradation of an mRNA or block its translationFigure 19.95Chromatin changesTranscriptionRNA processingmRNAdegradationTranslationProtein processingand degradationDegradation of mRNAORBlockage of translationTarget mRNAmiRNAProteincomplexDicerHydrogenbond The micro-RNA (miRNA)precursor foldsback on itself,held togetherby hydrogenbonds.12 An enzymecalled Dicer movesalong the double-stranded RNA, cutting it intoshorter segments.2 One strand ofeach short double-stranded RNA isdegraded; the otherstrand (miRNA) thenassociates with acomplex of proteins.3 The boundmiRNA can base-pairwith any targetmRNA that containsthe complementarysequence.4 The miRNA-proteincomplex prevents geneexpression either bydegrading the targetmRNA or by blockingits translation.5Initiation of TranslationThe initiation of translation of selected mRNAsCan be blocked by regulatory proteins that bind to specific sequences or structures of the mRNAAlternatively, translation of all the mRNAs in a cellMay be regulated simultaneouslyProtein Processing and DegradationAfter translationVarious types of protein processing, including cleavage and the addition of chemical groups, are subject to controlProteasomesAre giant protein complexes that bind protein molecules and degrade themFigure 19.10Chromatin changesTranscriptionRNA processingmRNAdegradationTranslationProtein processingand degradationUbiquitinProtein tobe degradedUbiquinatedproteinProteasomeProteasomeand ubiquitinto be recycledProteinfragments(peptides)Protein entering aproteasome Multiple ubiquitin mol-ecules are attached to a proteinby enzymes in the cytosol.1 The ubiquitin-tagged proteinis recognized by a proteasome,which unfolds the protein andsequesters it within a central cavity.2 Enzymatic components of theproteasome cut the protein intosmall peptides, which can befurther degraded by otherenzymes in the cytosol.3Concept 19.3: Cancer results from genetic changes that affect cell cycle controlThe gene regulation systems that go wrong during cancerTurn out to be the very same systems that play important roles in embryonic developmentTypes of Genes Associated with CancerThe genes that normally regulate cell growth and division during the cell cycleInclude genes for growth factors, their receptors, and the intracellular molecules of signaling pathwaysOncogenes and Proto-OncogenesOncogenesAre cancer-causing genesProto-oncogenesAre normal cellular genes that code for proteins that stimulate normal cell growth and divisionA DNA change that makes a proto-oncogene excessively activeConverts it to an oncogene, which may promote excessive cell division and cancerFigure 19.11Proto-oncogeneDNATranslocation or transposition:gene moved to new locus,under new controlsGene amplification:multiple copies of the genePoint mutationwithin a controlelementPoint mutationwithin the geneOncogeneOncogeneNormal growth-stimulatingprotein in excessHyperactive ordegradation-resistant proteinNormal growth-stimulatingprotein in excessNormal growth-stimulatingprotein in excessNewpromoterTumor-Suppressor GenesTumor-suppressor genesEncode proteins that inhibit abnormal cell divisionInterference with Normal Cell-Signaling PathwaysMany proto-oncogenes and tumor suppressor genesEncode components of growth-stimulating and growth-inhibiting pathways, respectivelyFigure 19.12a(a) Cell cycle–stimulating pathway.This pathway is triggered by a growthfactor that binds to its receptor in theplasma membrane. The signal is relayed to a G protein called Ras. Like all G proteins, Rasis active when GTP is bound to it. Ras passesthe signal to a series of protein kinases.The last kinase activates a transcriptionactivator that turns on one or more genes for proteins that stimulate the cell cycle. If amutation makes Ras or any other pathway component abnormally active, excessive celldivision and cancer may result.12435GTPRasRasGTPHyperactiveRas protein(product ofoncogene)issues signalson its ownNUCLEUSGene expressionProtein thatstimulatesthe cell cyclePPPPMUTATIONPDNAPThe Ras protein, encoded by the ras geneIs a G protein that relays a signal from a growth factor receptor on the plasma membrane to a cascade of protein kinases2ReceptorTranscriptionfactor (activator)5G protein3Protein kinases(phosphorylationcascade)41 Growth factorThe p53 gene encodes a tumor-suppressor proteinThat is a specific transcription factor that promotes the synthesis of cell cycle–inhibiting proteinsFigure 19.12bUVlightDNADefective ormissingtranscriptionfactor, such asp53, cannotactivatetranscriptionMUTATIONProtein thatinhibitsthe cell cyclepathway, DNA damage is an intracellularsignal that is passed via protein kinasesand leads to activation of p53. Activatedp53 promotes transcription of the gene for aprotein that inhibits the cell cycle. Theresulting suppression of cell division ensuresthat the damaged DNA is not replicated.Mutations causing deficiencies in anypathway component can contribute to thedevelopment of cancer.(b) Cell cycle–inhibiting pathway. In this132Protein kinases23Activeformof p53DNA damagein genome1Mutations that knock out the p53 geneCan lead to excessive cell growth and cancerFigure 19.12cEFFECTS OF MUTATIONSProteinoverexpressedCell cycleoverstimulatedIncreased celldivisionCell cycle notinhibitedProtein absentEffects of mutations. Increased cell division, possibly leading to cancer, can result if the cell cycle is overstimulated, as in (a), or not inhibited when it normally would be, as in (b). (c)The Multistep Model of Cancer DevelopmentNormal cells are converted to cancer cellsBy the accumulation of multiple mutations affecting proto-oncogenes and tumor-suppressor genesA multistep model for the development of colorectal cancerFigure 19.13ColonColon wallNormal colonepithelial cellsSmall benigngrowth (polyp)Larger benigngrowth (adenoma)Malignant tumor(carcinoma)2 Activation ofras oncogene 3 Loss oftumor-suppressorgene DCC 4 Loss oftumor-suppressorgene p53 5 Additionalmutations1 Loss of tumor-suppressorgene APC (orother) Certain virusesPromote cancer by integration of viral DNA into a cell’s genomeInherited Predisposition to CancerIndividuals who inherit a mutant oncogene or tumor-suppressor alleleHave an increased risk of developing certain types of cancerConcept 19.4: Eukaryotic genomes can have many noncoding DNA sequences in addition to genesThe bulk of most eukaryotic genomesConsists of noncoding DNA sequences, often described in the past as “junk DNA”However, much evidence is accumulatingThat noncoding DNA plays important roles in the cellThe Relationship Between Genomic Composition and Organismal ComplexityCompared with prokaryotic genomes, the genomes of eukaryotesGenerally are largerHave longer genesContain a much greater amount of noncoding DNA both associated with genes and between genesNow that the complete sequence of the human genome is availableWe know what makes up most of the 98.5% that does not code for proteins, rRNAs, or tRNAsFigure 19.14Exons (regions of genes codingfor protein, rRNA, tRNA) (1.5%)RepetitiveDNA thatincludestransposableelementsand relatedsequences(44%)Introns andregulatorysequences(24%)UniquenoncodingDNA (15%)RepetitiveDNAunrelated totransposableelements(about 15%)Alu elements(10%)Simple sequenceDNA (3%)Large-segmentduplications (5-6%)Transposable Elements and Related SequencesThe first evidence for wandering DNA segmentsCame from geneticist Barbara McClintock’s breeding experiments with Indian cornFigure 19.15TransposonNew copy oftransposonTransposonis copiedDNA of genomeInsertionMobile transposon(a) Transposon movement (“copy-and-paste” mechanism)RetrotransposonNew copy ofretrotransposonDNA of genomeRNAReversetranscriptase(b) Retrotransposon movementInsertionMovement of Transposons and RetrotransposonsEukaryotic transposable elements are of two typesTransposons, which move within a genome by means of a DNA intermediateRetrotransposons, which move by means of an RNA intermediateFigure 19.16a, bSequences Related to Transposable ElementsMultiple copies of transposable elements and sequences related to themAre scattered throughout the eukaryotic genomeIn humans and other primatesA large portion of transposable element–related DNA consists of a family of similar sequences called Alu elementsOther Repetitive DNA, Including Simple Sequence DNASimple sequence DNAContains many copies of tandemly repeated short sequencesIs common in centromeres and telomeres, where it probably plays structural roles in the chromosomeGenes and Multigene FamiliesMost eukaryotic genesAre present in one copy per haploid set of chromosomesThe rest of the genomeOccurs in multigene families, collections of identical or very similar genesDNARNA transcriptsNon-transcribedspacerTranscription unitDNA18S5.8S28SrRNA5.8S28S18SSome multigene familiesConsist of identical DNA sequences, usually clustered tandemly, such as those that code for RNA productsFigure 19.17a Part of the ribosomal RNA gene familyThe classic examples of multigene families of nonidentical genesAre two related families of genes that encode globinsFigure 19.17b The human -globin and -globin gene families-GlobinHemeHemoglobin-Globin-Globin gene family-Globin gene familyChromosome 16Chromosome 11EmbryoFetusand adultEmbryoFetusAdultGA 2121Concept 19.5: Duplications, rearrangements, and mutations of DNA contribute to genome evolutionThe basis of change at the genomic level is mutationWhich underlies much of genome evolutionDuplication of Chromosome SetsAccidents in cell divisionCan lead to extra copies of all or part of a genome, which may then diverge if one set accumulates sequence changesDuplication and Divergence of DNA SegmentsUnequal crossing over during prophase I of meiosisCan result in one chromosome with a deletion and another with a duplication of a particular geneFigure 19.18NonsisterchromatidsTransposableelementGeneIncorrect pairingof two homologuesduring meiosisCrossoverandEvolution of Genes with Related Functions: The Human Globin GenesThe genes encoding the various globin proteinsEvolved from one common ancestral globin gene, which duplicated and divergedFigure 19.19Ancestral globin gene2 121GA-Globin gene familyon chromosome 16 -Globin gene familyon chromosome 11Evolutionary timeDuplication ofancestral geneMutation inboth copiesTransposition todifferent chromosomesFurther duplicationsand mutationsSubsequent duplications of these genes and random mutationsGave rise to the present globin genes, all of which code for oxygen-binding proteinsThe similarity in the amino acid sequences of the various globin proteinsSupports this model of gene duplication and mutationTable 19.1Evolution of Genes with Novel FunctionsThe copies of some duplicated genesHave diverged so much during evolutionary time that the functions of their encoded proteins are now substantially differentRearrangements of Parts of Genes: Exon Duplication and Exon ShufflingA particular exon within a geneCould be duplicated on one chromosome and deleted from the homologous chromosomeIn exon shufflingErrors in meiotic recombination lead to the occasional mixing and matching of different exons either within a gene or between two nonallelic genesFigure 19.20EGFEGFEGFEGFEpidermal growthfactor gene with multipleEGF exons (green)FFFFFibronectin gene with multiple“finger” exons (orange)ExonshufflingExonduplicationExonshufflingKFEGFKKPlasminogen gene with a“kfingle” exon (blue)Portions of ancestral genesTPA gene as it exists todayHow Transposable Elements Contribute to Genome EvolutionMovement of transposable elements or recombination between copies of the same elementOccasionally generates new sequence combinations that are beneficial to the organismSome mechanismsCan alter the functions of genes or their patterns of expression and regulation