Peter J.

Russell
AmolecularApproach2ndEdition

CHAPTER 10
Genomics

editedbyYueWenWangPh.D.
Dept.ofAgronomy,NTU

Chapter9slide

StructuralGenomics
1. TheadventofDNAsequencingtechniqueschangedexperimental
biology,andautomationhasenhancedtherateofchange.
2. Genomicsisthedevelopmentandapplicationoftechniquesfor:
a. Mappingchromosomes.
b. Sequencinggenomes.
c. Computationalanalysisofentiregenomes.

3. Subfieldsofgenomicsare:
a. Structuralgenomics,thegeneticandphysicalmappingandsequencing
ofchromosomes.
b. Functionalgenomics,comprehensiveanalysisofgenefunctionsandof
nongenesequencesinentiregenomes.
c. Comparativegenomics,comparisonofentiregenomesacrossspecies,
lookingatfunctionsandevolutionaryrelationships.

4. Thissectionfocusesonstructuralgenetics,specificallygenome
sequencing.

Chapter9slide

SequencingGenome
1.Genomeprojectsusetwogeneralapproaches:
a.Themappingapproachdividesthegenomeinto
segmentswithgeneticandphysicalmapping,refines
themapofeachsegment,andfinallysequencesthe
DNA.
b.Ashotgunapproachbreaksthegenomeinto
random,overlappingfragments,andsequenceseach
fragment.Basedonoverlaps,thesequencesare
assembledbycomputer.Anadvantageisthatphysical
mappingisnotrequired.

Chapter9slide

GenomeSequencingUsingaMappingApproach
1. Geneticandphysicalmapsaremadefirstto
providemarkersforsequencing.Examples
illustratethelogicofthisapproachinthehuman
genomeproject.

Chapter9slide

GeneticMappingofaGenome
1. Geneticmapsareconstructedforeachchromosomeusing
geneticcrossesandpedigreeanalysis.Anydetectable
allelecanmarkalocusonthechromosome,andcrossing
overindicatesthedistancebetweenmarkergenes.
2. Highdensitygeneticmappinghasbeenimportantinthe
HumanGenomeProject(HGP).Someaspectsofthis
procedure:
a. Asequencetaggedsite(STS)isauniquegenomicDNAsequence
usedasageneticmarker.Shorttandemrepeats(STRs)areused
extensivelyforSTSmapping,butnonpolymorphicmarkersare
alsoused.
b. PolymorphicSTRsarethebestDNAmarkersforgenerating
geneticmapsofSTSs.

Chapter9slide

PhysicalMappingofaGenome
1. Geneticmapsgeneratedforsomespecies(e.g.,E.coli)aresufficienttobegin
sequencing,butinhumanseventhedetailedgeneticmapdescribedabovelacks
therequiredresolution.Therefore,aphysicalmapderiveddirectlyfrom
genomicDNAratherthananalysisofrecombinantshasbeengenerated.
2. Inhumansthereare24physicalmapsfortheautosomesplusXandY.Types
ofphysicalmapsarepresentedinorderofincreasingresolution:
a. Cytogeneticmapsofchromosomalbandingpatterns(Chapter16)
b. Fluorescentinsituhybridization(FISH)maps(Chapter16)
c. Restrictionmaps
i. Restrictionenzymesthatcutarerarelyused,dueeithertoalarge(78bp)
recognitionsequenceortoscarcityoftherecognitionsequenceintheDNAunder
study.
ii.Themapforevenararelycuttingrestrictionenzymeisverycomplex,andsofar
hasbeenobtainedforonlythesmallesthumanchromosome(chromosome21was
mappedwithNotI).
d. Radiationhybridmaps(Chapter16)

Chapter9slide

e. Clonecontig(contigshortenedformofcontiguous)maps
i.Apartialrestrictiondigestproducesasetoflarge,overlappingDNAs,whichare
clonedintoYACvectorcutwithacompatiblerestrictionenzyme.Shearingmay
alsobeusedtomakehighmolecularweightDNAthatisbluntendclonedinto
aYAC.
ii.AnentiregenomeorasinglechromosomemayberepresentedinaYACclone
library.
iii.YACclonesarethenassembledintoamapeitherbymatchingwithaFISH
generatedchromosomemaporbyDNAfingerprintingandassemblybasedon
overlaps.NonpolymorphicSTSsareespeciallyusefulforYACcontigmapping
(Figure10.1).
iv.Acompletelibraryshouldyieldacompletecontigmapthatindicatestheorderin
whichtheclonedfragmentsoccurinthechromosome.
v.ProblemsarisewhensomeoftheYACinsertscontainDNAfrommorethanone
chromosomallocation.ThishascomplicatedeffortsatgeneratingaYACcontig
mapofhumanchromosomes.
vi.Manylabshaveswitchedtobacterialartificialchromosome(BAC)vectorswith
acapacityof300kbandtheabilitytoreplicateinE.coliasaresourcefortheir
sequencingprojects.

Chapter9slide

Fig. 10.1 A representative YAC contig map assembled by STS mapping

Peter J. Russell, iGenetics: Copyright Pearson Education, Inc., publishing as Benjamin Cummings.

Chapter9slide

GeneratingtheSequenceofaGenome
1. Whenahighresolutionmapisavailable,sequencingispossible.Briefly:
a. Dideoxysequencingisused.DNAissynthesizedfromatemplate,andterminates
withincorporationofafluorescentlylabeledddNTP.
b. Allfourreactions(ddA,ddG,ddC,andddT)occurinthesametube.EachddNTP
carriesadifferentfluorescentlabel.
c. Productsareseparatedelectrophoretically,coloredbandsaredetectedwithlasers,
andthedataareconvertedtoacomputersequencefile.
d. PCRbasedsequencingusesoneoligonucleotideprimerandthermostableDNA
polymerase.Theadvantagesofthisapproachare:
i. DoublestrandedDNAissequenceddirectly.
ii.OnlyasmallamountoftemplateDNAisrequired.

2. Onesequencingreactionislimitedtoabout500nucleotides,andforaccurate
sequencesbothstrandsmustbesequencedseveraltimes.
3. Progressonthehumangenomeandotherprojectshasbeenacceleratedby
improvedtechnologiesforsequencingandanalysis.

Chapter9slide

4. HumangenomesequencingbythemappingapproachusedBACs,buta
BACinsertisfartoolargetosequenceinonereaction.Instead,the
insertswereeachsequencedusingashotgunapproach:
a. Eachinsertiscutfromthevector,shearedintofragmentsthatwillbe
partiallyoverlapping,andclonedintoaplasmidvector.
b. Eachsubcloneissequenced,andoverlapsareusedbyacomputerto
assemblethedataintoonecontiguoussequencerepresentingtheBAC
insert.
c. UsingthechromosomalmapforBACclones,theBACinsert
sequencesareputinordertoyieldthecompletechromosome
sequence.

5. Intheory,sequencingcontigsforatotallengthof6.58timesthe
genomewillspanmorethan99.8percentofthegenomicsequence.
6. Inpractice,theHGPdiditssequencingseventimesover,andhas
obtained97percentofthegenome.

Chapter9slide

GenomeSequencingUsingaDirectShotgun
Approach
Animation:DirectShotgunSequencingofGenomes
1. Theshotgunapproachobtainsagenomicsequenceby
breakingthegenomeintooverlappingfragmentsfor
cloningandsequencing.Acomputeristhenusedto
assemblethegenomicsequence.
2. Advancesthathavemadethisapproachpracticalforlarge
genomesinclude:
a. Bettercomputeralgorithmsforassemblingsequences.
b. Automationintheactualsequencing.

Chapter9slide

3. ApioneerofthisapproachisJ.CraigVenter,whoseCeleraGenomicshasalso
sequenced(5fold)thehumangenometo97%,withcompleteassemblyofthe
fragmentsexceptforgapscausedbythemissing3%.
4. Directshotgunsequencinginvolves(Figure10.2):
a. Mechanicalshearingandcloningofsmall(about2kb)genomicDNA
fragments.
b. Sequencingabout500bponeachendoftheinsertDNA.Sequencesinthe
centeroftheclonedDNAareobtainedfromanoverlappingcloneratherthan
directly.
c. Computeranalysisgivesthesequenceofmostofthegenome,withgapscaused
bysequencesmissingfromthelibrary.
d. Asecondlibraryismadewithlarger(about10kb)randomfragments,allowing
resolutionofrepeatedsequences.
5. AdvancesinautomatedDNAsequencingandcomputeralgorithmsforsequence
analysisallowthewholegenomeapproachtobeusedwithevenlargegenomes.
BACmapsareoftenalsopartoftheseprojects.
6. Assemblingandfinishinggenomesequencesrequiresarrangingsequencesinthe
ordertheyarefoundinthegenomeandthenfinishingthedetailsofthesequence
(<1error/10,000bases).

Chapter9slide

Fig. 10.2 The direct shotgun approach to obtaining the genomic DNA sequence of an
organism

Peter J. Russell, iGenetics: Copyright Pearson Education, Inc., publishing as Benjamin Cummings.

Chapter9slide

SelectedExamplesofGenomesSequenced
1. Followingisadiscussionofsomegenomesthat
havebeensequenced,withtherationalefortheir
selection.

Chapter9slide

BacterialGenomes
1. Haemophilusinfluenzae,thefirstcellularorganismtohaveitsgenome
sequenced,wasselectedforitstypicalbacterialgenomesizeanditsGC
contentclosetohumans(Figure10.3).
a. Nogeneticorphysicalmapexisted,soashotgunapproachwasused.
b. TheH.influenzaegenomeis1.83Mb.
c. Annotationofthesequenceinvolvedcomputeranalysistofindsignificant
sequences,including:
i. 1,743openreadingframes(ORFs),regionswithnostopcodonina
particularreadingframe.Arbitrarily,ORFsthatareover100codonsare
consideredlikelytoencodeproteins.
ii.Repeatedsequences.
iii.Operons.
iv.Transposableelements.
d. 736ofthepredictedgeneshavenoroleassignment,meaningthatno
functionisyetverifiedforthem.

Chapter9slide

Fig. 10.3 The annotated genome of H. influenzae

Peter J. Russell, iGenetics: Copyright Pearson Education, Inc., publishing as Benjamin Cummings.

Chapter9slide

2. Escherichiacoliwasselectedbecauseitisan
importantmodelsystemformolecularbiology,
genetics,andbiotechnology,aswellasacommon
bacteriuminanimalintestinesandthe
environment.
a. Ashotgunapproachwasused.
b. Thegenomeis4.64MbwithaGCcontentof50.8
percent.
c. Analysisofthegenomesequenceshowsthat87.8
percentofthegenomeismadeupofORFs.
d. Of4,288ORFs,38percentareofunknownfunction.

Chapter9slide

ArchaeonGenomes
1. Methanococcusjannaschiiisananaerobic,hyperthermophilic
methanogenthatreducesCO2tomethane.
a. Ashotgunapproachwasused.
b. Thegenomehasthreeparts:
i. Alargecircularchromosomeofabout1.66Mb,with1,682ORFs.
ii.Acircularextrachromosomalelement(ECE)ofabout58kb,with44
ORFs.
iii.AsmallercircularECEofabout17kb,with12ORFs.

2. AnalysisofthesequenceconfirmsArchaeasuniquetaxonomic
position,showingthat:
a. MostM.jannaschiigenesinvolvedinenergyproduction,metabolism,and
celldivisionaresimilartothoseofeubacteria.
b. MostofthegenesinvolvedinDNAreplication,transcription,
andtranslationaresimilartothoseofeukaryotes..

Chapter9slide

EukaryoticGenomes
1. Saccharomycescerevisiaeisamodeleukaryoteformany
typesofresearch.Itwasthefirsteukaryoticgenometobe
completelysequenced(Figure10.4).
a. Themappingapproachwasused.
b. The16chromosomegenomeis12Mb.Anestimated969kb
ofrepeatedsequencesaremissingfromthepublished
sequence.
c. Analysisreveals6,183ORFs,233withintrons.
d. ORFsmakeupabout70percentofthetotalgenome,and
about13havenoknownfunction.

Chapter9slide

2. Caenorhabditiselegans,anematode,hasbeenimportantin
bothgeneticandmolecularstudyofembryogenesis,
morphogenesis,development,nervedevelopmentand
function,aging,andbehavior(Figure10.5).
a. Thenearlycompletegenomesequencespans97Mb
distributedbetweensixchromosomes(fiveautosomesand
anXchromosome).
b. Analysisshows:
i.Thegenomeis100.3Mb
ii.Thereare20,443geneswith1,270thatdonotencode
proteins.

Chapter9slide

3. Drosophilamelanogaster,thefruitfly,hasbeenimportant
inbothclassicalgeneticsandthemoleculargeneticsof
development.
a. Sequencingusedthedirectshotgunapproach,supportedby
clonebasedsequencingandaBACderivedphysicalmap.
b. Thegenomeis118.4Mb.Another13(60Mb)iscurrently
unclonableheterochromatinlocatednearcentromeres.
c. Thereare14,015genes.Comparisonwithgenomic
sequencesfromotherspeciesindicates:
i.Drosophilahasabouttwicethenumberofgenesfound
inS.cerevisiae.
ii.Of289genesknowntobeinvolvedinhumandisease,
Drosophilahashomologsfor177..

Chapter9slide

4. Arabidopsisthalianawasthefirstfloweringplanttobe
sequenced,andisanimportantmodelforgeneticand
molecularbiologyofplants.
a. Thegenomeis120Mbwithabout25,900genes.
b. ArabidopsishasabouttwicethenumberofgenesasDrosophila.
c. ThenumberofgenesinArabidopsisisnearthelowerestimates
ofthehumangenenumber.
d. About100Arabidopsisgeneshavehumanhomologs,including
genesforbreastcancerandcysticfibrosis.
e. Ongoingworkisfocusedondefiningfunctionsofallgenes,
determininggeneregulation,andunderstandingthefatesofgene
productproteins.

Chapter9slide

5. HomosapiensDNAfromavarietyofanonymousdonorshasbeen
sequenced.Thehumangenomesequencedoesnotexactlymatchthe
genomeofanyhumanbeing.
a. AworkingdraftofthehumangenomewasannouncedinJune2000jointly
by:
i. FrancisCollinsfortheNationalHumanGenomeResearchInstitute.
ii.J.CraigVenterofCeleraGenomics.
b. ByJune2000,thesequencingefforthadgenerated7foldcoverageofthe
genome,withabout50percentofthegenomesequenceconsideredtobenear
finished,and24percentcompletelyfinished.
c. Thesequencingapproaches:
i. TheHumanGenomeSequencingProjectConsortiumfocusedonsequencing
thegenericheuchromatinregions,ignoringthegenerallyunclonable
heterochromatin,usingexistinggeneticandphysicalmaps.
ii.CeleraGenomicsusedshotgunsequencingfollowedbyaverylarge
computercalculationlookingforoverlapsintherandomDNAfragments
(enoughtorepresent4.6foldcoverageofthehumangenome).Shotgun
assemblyresultswereverifiedbycomparisonwithBACclonesequences
availableinpublicdatabases.
d. ThenextstepintheHumanGenomeProjectisannotatingthesequence,
analyzingitsgenesandotherfeatures.
Chapter9slide

6. Musmusculus(mouse)andRattusnorvegicus
(rat)genomeshavealsobeensequenced(Figure
10.6).
a. Thehumangenomeislargest,followedbyratandthen
mouse.
b. Allthreehaveaboutthesamenumberofgenes.
c. Rodentsserveasmodelsformammalianphysiology,
andabout99percentofthegenesinmouseandrat
havedirecthumancounterparts.

Chapter9slide

InsightsfromGenomeAnalysis:Genome
SizesandGeneDensities
1. Genomescanbecomparedforgenesand
intergenicregions.
2. TheCvalueparadoxsaysthereisnorelationship
betweentheamountofhaploidDNAandthe
complexityoftheorganism.
3. Genedensity(numberofgenesperlengthof
DNA)variesbetweenorganisms.

Chapter9slide

GenomesofBacteria
1. Therangeofsequencedbacterialgenomesis0.58mB
(Mycoplasmagenitalium)to9.11Mb(Bradyrhizobium
japonicum)(Table10.1).
2. Genedensitiesinbacterialgenomesaresimilar,12kb.
Examples:
a. Mycoplasmagenitaliumhasonegeneper1.15kb.
b. E.colihasagenedensityofonegeneper1.05kb.

3. Bacterialgenesarepackeddenselyinthechromosome.In
bothBacteriaandArchaea8590percentofthegenome
istypicallycodingDNA.

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Chapter9slide

GenomesofArchaea
1. Archaeaaregenerallyextremophileswithregardtoconditionssuchas
temperature,pressure,pH,metalions,orsalt.
2. SimilaritieswithBacteriainclude:
a. Morphology(rods,spheres,spirals).
b. Lackofintronsinproteincodinggenes.
c. Highgenedensity.

3. SimilaritieswithEukaryainclude:
a. Genesforreplication,transcription,andtranslation.
b. IntronsintRNAgenes.

4. Archaeagenomesrangewidely,from1.56Mb(Thermoplasma
acidophilum)to5.75Mb(Methanosarcinaacetivorans).

Chapter9slide

GenomesofEukarya
1. IncreasinggenomicDNAcontenttendstocorrelatewith
increasingcomplexity,butthereisnotadirect
relationship.Forexample:
a. TheinsectsDrosophilamelanogaster(fruitfly)andLocusta
migratoria(locust)havesimilarcomplexity,butthelocust
genomesizeis50thatoffruitfly.
b. Thelocustgenomeistwicethesizeofthemousegenome.

2. Differencesingenedensityaccountformanydifferences
ingenomesize.Forexample:
a. Fruitflyhasanaverageofonegeneper13kbofgenome.
b. Locusthasanaverageofonegeneper365kbofgenome.

3. Eukaryagenerallyhaslowergenedensityandmore
variabilitythanBacteriaorArchaea.Therangeislarge,
withatrendofincreasinggenedensitywithincreasing
complexity(Figure10.7).

Chapter9slide

Fig. 10.7 Regions of the chromosome of E. coli, yeast, fruit fly, and human, showing the
differences in gene density

Chapter9slide

4. Genesarenotdistributedevenlyinthechromosome.
Someregionsaregenerich,whileothersaregenedeserts
(1Mbwithoutagene).
5. Themajorityoftheeukaryoticgenomeisintergenic
regions,andinhumansthesearemostlyrepetitiveDNA.
a. Findinggenesinthisgenesparsegenomeisoftendifficult.
b. Thepufferfish(Fugurubripes)isusedasamodelvertebrate
becauseithasagenedensity8foldhigherthanhumans
andmanyofitsgenesarehomologoustohumangenes
(Figure10.8).

Chapter9slide

FunctionalGenomics
1. Functionalgenomicsanalyzesallgenesingenomestodeterminetheir
functionsandtheirgenecontrolandexpression.
2. Researchquestionsaboutgeneexpression,physiology,and
developmentcannowbeansweredatthegenomiclevel.
3. Currentfunctionalgenomicsreliesonmolecularbiologylabresearch
andsophisticatedcomputeranalysisbybioinformaticsresearchers.
4. Thisfusionofbiologywithmathandcomputerscienceisusedfor
manythings.Examples:
a. Findinggeneswithinagenomicsequence.
b. Aligningsequencesindatabasestodeterminematching.
c. Predictingstructureandfunctionofgeneproducts.
d. Describinginteractionsbetweengenesandgeneproductsinthecell,
betweencellsandbetweenorganisms.
e. Consideringphylogeneticrelationships. .

Chapter9slide

IdentifyingGenesinDNASequences
1. Annotationbeginstheprocessofassigning
functionstogenes,especiallyproteincoding
genes,usingcomputeralgorithmstosearchboth
strandsforORFs.Intronscomplicateanalysisof
eukaryoticgenes.
2. ORFsexistinallsizes,andnotallencode
proteins.Tofocusonsequencesmostlikelyto
encodeproteins,aminimumORFsizeis
arbitrarilysetandshortersequencesarenot
analyzed.

Chapter9slide

SequenceSimilaritySearchestoAssignGeneFunction
1. Computersareusedtofindhomologybetweensequencesinadatabase(e.g.,aBLAST
search).Similarityreflectsevolutionaryrelationshipsandoftensharedfunctions.
2. EitherDNAoraminoacidsequencescanbesearched,butaminoacidsyieldmore
specificinformation,sincethereare20possiblematches,ratherthanjustfour.Oftenno
convincingmatchisfound,dueinparttothelimitationsofcurrentdatabases.
3. Sometimesmatchesarefoundonlyatthedomainlevel,whenaregioninthenewprotein
matchesproteindomainsinthedatabase.Thisprovidescluestothenewproteins
functionandtheevolutionofitsgene.
4. Asdatabasesgrow,sodoesourknowledgeofgenefunctions.Thecurrentdistributionof
knowledgeaboutthegenesofyeastis(Figure9.14):
a. About30%ofthegeneshaveknownfunctions.
b. Oftheremaining70%ofORFs:
i.30%encodeaproteinthateitherhashomologytoprotein(s)ofknownfunction,orhas
domainsrelatedtofunctionallycharacterizeddomains.
ii.10%areFUN(functionunknown)genes.Theyhavehomologsindatabases,but
function(s)ofthehomologsareunknown.Groupsofhomologousgenesofunknown
functionareorphanfamilies.
iii.30%ofORFshavenohomologsinthedatabases.Theseinclude67%thatmaynot
actuallyencodeproteins.Theremaindermayrepresentgenesknownonlyinyeast,the
singleorphans.

5. Everygenomesequencedcontainsfunctionunknowngenes,butasdatabasesare
expandedtheproblemshoulddecrease.

Chapter9slide

Fig. 10.9 The distribution of predicted ORFs in the genome of yeast

Peter J. Russell, iGenetics: Copyright Pearson Education, Inc., publishing as Benjamin Cummings.

Chapter9slide

AssigningGeneFunctionExperimentally
1. Oneapproachtodetermininggenefunctionistodeletethegene,and
observethephenotypewhenthatgenesfunctionisknockedout.
PCRmaybeusedtoproduceandscreenageneknockout(Figure
10.10):
a. Usingknowngenomesequences,PCRprimersaredesignedto
constructanartificiallinearDNAdeletionmodule.Itconsistsof:
i. Thegenesequenceupstreamandthroughthestartcodon.
ii.AkanR(kanamycin)markergeneconferringresistanceto
achemical,G418.
iii.Thegenesequencedownstreamofandincludingthestopcodon.
b. TheamplifiedlinearDNAistransformedintoyeast,andG418
resistantcoloniesselected.ThesearegeneratedwhenthenewDNA
replacesthegeneofinterestinthegenomebyhomologous
recombination.
c. TheynowexpresskanRinsteadofthegeneunderstudy,producinga
lossoffunction(null)mutation.

Chapter9slide

Fig. 10.10 Creating a gene knockout in yeast

Peter J. Russell, iGenetics: Copyright Pearson Education, Inc., publishing as Benjamin Cummings.

Chapter9slide

2. MolecularscreeningwithspecificprimersandPCRis
usedtoconfirmthatadeletionoccurredintheORFof
interest.Adeletionresultsinnoprimingwithprimers
directedtowardthatregion,andmaybeconfirmedby
showinginsertionofaselectablemarker(e.g.,kanR).
3. Theyeastknockout(YKO)projectsystematicallydeleted
eachyeastgene.Someresults:
a. Essentialgenesgivealethalphenotype.
b. About4,200ofyeasts6,200genesarenonessential,andyield
viableknockoutmutants.
c. Oftheviableknockouts,abouthalfshowadetectablephenotype
andhalfdonot.

4. Nullallelesarewidelyusedtoinvestigategenefunctions.
Miceknockoutsareusedtostudygeneswithhuman
analogs.

Chapter9slide

DescribingPatternsofGeneExpression
1. Genomicsequencingmakesitpossibleto
determineallgenesthatareexpressedinacellby
analyzingthetotalRNAtranscriptsofthecell,its
transcriptome.Thetranscriptomeisanindicator
ofcellphenotypeandfunction.Similarly,the
completesetofproteinsinacellisitsproteome.

Chapter9slide

TheTranscriptome
Animation:AnalysisofGeneExpressionUsingDNAMicroarrays

1. Thetranscriptomechangesasthecellrespondsto
stimulusandmovesthroughitscellcycle,andsoisatool
forunderstandingcellularfunction.
2. Probearraysareusedtostudygeneexpression.Yeast
sporulationisoneexample:
a. Yeastsporulationproducesfourhaploidspores,andinvolves
fourstages,eachassociatedwithitsowntranscripts(Figure
10.11).
i.DNAreplicationandrecombination.
ii.Meiosis.
iii.MeiosisII.
iv.Sporematuration.

Chapter9slide

Fig. 10.11 Global gene expression analysis of yeast sporulation using a DNA
microarray

Peter J. Russell, iGenetics: Copyright Pearson Education, Inc., publishing as Benjamin Cummings.

Chapter9slide

b. SamplesofmRNAtakenatintervalsduringsporulationwere
convertedtocDNAsandanalyzedonmicroarraysofPCRamplified
ORFsequences.Theresultswerecorrelatedwithcellularevents
c. ControlcDNAwasmadefrompreinductionmRNAs,andlabeled
green.ThecDNAsfrompostinductionmRNAswerelabeledred.
Microarrayswereprobedwithamixofboth,andresultswere
interpretedasfollows:
i. Redspotsindicateageneinducedduringsporulation.
ii.Greenspotsindicateagenerepressedduringsporulation.
iii.Yellowspotsmarkgeneswhoseexpressionisunchangedduring
sporulation.
d. Resultsshowmorethan1,000geneswithalteredexpressionduring
sporulation,about12repressedandtheother12notrepressed.
Patternsofexpressionovertimebecomeapparentinthistypeof
experiment.

Chapter9slide

3. DNAmicroarraysarenowwidelyused,althoughstillexpensive.Examplesof
studiesthatcurrentlyusethistechnology:
a. ChangesinDrosophilageneexpressionduringmorphogenesis.
b. Humancancersandtheircharacteristicpatternsofgeneexpression(transcriptional
fingerprints)thatrevealdistinctionsbetweendifferenttypesofcancer.
c. Screeningforgeneticdiseases,especiallythoseresultingfromoneofmanyalleles.
Apatientsblood,forexample,canbescreenedforhundredsofpossiblemutations
intheBRCA1andBRCA2genesassociatedwithbreastcancer.

4. Pharmacogenomicsstudieshowtheindividualsgenomeaffectsthebodys
responsetomedication,withthehopeofeventuallytailoringtreatmenttothe
patientsgeneticfactors.
a. Basedinbiochemistry,pharmacogenomicsdevelopsdrugsassociatedwithRNA
moleculesandproteinsassociatedwithgenesanddiseases.
b. Thisnewapproachhasfewsuccessestodate,butoneexampleisindevelopingtests
todetectpatientswithdeficientcytochromep450(CYP)liverenzymes,whoare
susceptibletodrugoverdose.

Chapter9slide

TheProteome
1. Proteomicsiscatalogingandanalysisoftheproteome,orcompleteset
ofexpressedproteinsinacellatagiventime.Proteomicsfocuseson
whichproteinsaremadeandinwhatquantities,andtheirinteractions
withotherproteins.
2. Goalsofproteomicsareto:
a. Identifyeveryproteinintheproteome.
b. Developadatabasewiththesequenceofeachprotein.
c. Analyzeproteinlevelsindifferentcelltypesandstagesof
development.

3. Proteinidentificationandsequencingisverycomplex.Celera
Genomicsisinvolvedinidentification,sequencing,andcomputer
analysisofthedata.
4. Proteomecomplexityfarexceedsgenomecomplexity,dueto:
a. AlternativeRNAsplicing.
b. Posttranslationalmodificationsofproteins.

Chapter9slide

5. Conventionalproteomeanalysisuses2Dacrylamidegelelectrophoresisand
massspectrometry,butisneithersensitiveenoughtodetectlowlevelsnorable
toanalyzemanyproteinsatonce.
6. Proteinarrays,similartoDNAmicroarrays,areusedtodetect,quantify,and
characterizeproteinsonalargescale.Automationallowslargenumbersof
measurementsinparallel.
a. Proteinsarefixedonasolidsubstrate(glass,membrane,ormicrotiterplate).
b. Targetproteinsarelabeledfluorescently.
c. Bindingtoimmobilizedprobearrayisdetectedbylaser,anddataareanalyzedvia
computer.
d. Twotypesofproteinarraysarecommonlyused:
i. Acapturearrayisasetofantibodiesboundtoasurfaceandusedtodetectlabeled
targetmoleculesfromcells.Capturearraysareusedindiagnosisandinprotein
expressionprofiling.
ii.Alargescaleproteinarrayusespurifiedproteinsfromanexpressionlibrary,
spottedontoasubstrateandusedtodetectlabeledtargetmoleculesforbiological
functionsincludingproteinproteinordrugtargetinteractions.

Chapter9slide

ComparativeGenomics
iActivity:PersonalizedPrescriptionsforCancer
Patients
1. Comparativegenomicsprovidesawaytostudy
functionsofhumangenesbyworkingwithnon
humanhomologs.Genesandtheirarrangement
alsoprovidevaluablecluestoevolutionary
relationshipsbetweenorganisms.

Chapter9slide

EthicsandtheHumanGenomeProject
1. Theabilitytoidentifyhumangenesraisescomplexethicalissues
involvingtherighttoinformationaboutonesowngenome,accessto
genomicinformationbyemployers,insurancecompaniesand
governmentagencies,andconcernsabouttheabilitytodiagnosebut
nottreatgeneticdisorders.
2. FederalagenciesfundingtheHGPdevote35%oftheirbudgetsto
studyofethical,legalandsocialissues(ELSI),producingtheworlds
largestbioethicsprogram.AreascurrentlyemphasizedbytheELSI
program:
a. Privacyofgeneticinformation.
b. Appropriateuseofgeneticinformationintheclinicalsetting.
c. Fairuseofgeneticinformation.
d. Professionalandpubliceducation.

Chapter9slide