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1、UpdateonGeneExpressionAnalysis,Proteomics,andNetworkDiscoveryGeneExpressionAnalysis,Proteomics,andNetworkDiscovery1SachaBaginsky,LarsHennig,PhilipZimmermann,andWilhelmGruissem*DepartmentofBiologyandZurich-BaselPlantScienceCenter,ETHZurichUniversitatstrasse2,8129Zurich,SwitzerlandTechnologicaladvance
2、sinbiologicalexperimenta-tionarenowenablingresearcherstoinvestigatelivingsystemsonanunprecedentedscalebystudyingge-nomes,proteomes,ormolecularnetworksintheirentirety.Genomicstechnologieshaveledtoaparadigmshiftinbiologicalexperimentationbecausetheymeasure(pro?lemostorevenallcomponentsofoneclass(e.g.t
3、ranscripts,proteins,etc.inahighlyparallelway.Whethergeneexpressionanalysisusingmicro-arrays,proteomeandmetabolomeanalysisusingmassspectrometry,orlarge-scalescreensforgeneticinteractions,high-throughputpro?lingtechnologiesprovidearichsourceofquantitativebiologicalinformationthatallowsresearcherstomov
4、ebeyondareductionistapproachbybothintegratingandun-derstandinginteractionsbetweenmultiplecompo-nentsincellsandorganisms(Fig.1;forarecentupdateofbioinformaticstools,seePitzschkeandHirt,2010.Currently,mostgenomicsexperimentsinvoIvepro?lingtranscripts,proteins,ormetabolites.Increasingeffortstocomplemen
5、tmoleculardatawithphenotypicinformationwillfurtheradvanceourun-derstandingofthequantitativerelationshipsbetweenmoleculesindirectingsystemsbehaviorandfunction.InthefollowingUpdatewewillbrie?yreviewrecentadvancesinthe?eldandhighlightadvantagesandlimitationsofcurrentapproachestodevelopmodelsofgenetican
6、dmolecularnetworksthataimtodescribeemergentpropertiesofplantsystems.GENOMICSTECHNOLOGIES:THEPOWEROFGENOME-SCALEQUANTITATIVEDATARESOLUTIONPROFILINGTRANSCRIPTOMESTranscriptpro?lingoffersthelargestcoverageandawidedynamicrangeofgeneexpressioninformationandcanoftenbeperformedgenomewide.Micro-arraysarecur
7、rentlymostpopularfortranscriptpro?lingandcanbereadilyaffordedbymanylaboratories.Variouscommercialandacademicmicro-arrayplatformsexistthatvaryingenomecoverage,availability,speci?city,andsensitivity(TableI.Micro-arraysmanufacturedbyAffymetrixareprobablymostcommonlyusedinplantbiology(Redmanetal.,2004;R
8、ehraueretal.,2010,butcommercialarraysfromAgilentorarraysfromtheacademicCompleteArabi-dopsisTranscriptomeMicroArray(CATMAconsor-tiumareoftenusedaswell(forreview,seeBuschandLohmann,2007.Serialanalysisofgeneexpression(SAGEandmassivelyparallelsignaturesequencing(MPSSarewell-establishedalternativestomicr
9、oar-rays.Bothtechniquescanbesuperiortomicroarraysbecausetheydonotdependonpriorprobeselection.Morerecently,directsequencingoftranscriptsbyhigh-throughputsequencingtechnologies(RNA-SeqhasbecomeanadditionalalternativetomicroarraysandissupersedingSAGEandMPSS(BuschandLohmann,2007.LikeSAGEandMPPS,RNA-Seqd
10、oesnotdependongenomeannotationforpriorprobeselectionandavoidsbiasesintroduceddur-inghybridizationofmicroarrays.Ontheotherhand,RNA-Seqposesnovelalgorithmicandlogisticchal-lenges,andcurrentwet-labRNA-Seqstrategiesre-quirelengthylibrarypreparationprocedures.Therefore,RNA-Seqisthemethodofchoiceinproject
11、susingnonmodelorganismsandfortranscriptdiscov-eryandgenomeannotation.Becauseoftheirrobustsampleprocessingandanalysispipelines,oftenmicro-arraysarestillapreferablechoiceforprojectsthatinvoIvelargenumbersofsamplesforpro?lingtranscriptsinmodelorganismswithwell-annotatedge-nomes.ToolssuchasGenevestigato
12、r(Hruzetal.,2008andMapMan(Usadeletal.,2009allowresearcherstoorganizelargegeneexpressiondatasetsandanalyzethemforrelationalnetworkswithinasingleexperi-mentoracrossmanyexperiments(contextualmeta-analysis.PROFILINGEPIGENOMESANDTRANSCRIPTIONFACTORBINDINGMuchcontrolofgeneexpressionoccursattheleveloftrans
13、cription,andinformationongenomewidechromatinpro?les(epigenomesandtranscriptionfactorbindingtopromotersisneededtodecipher1ThisworkwassupportedbytheEuropeanUnion(EUFrameworkProgram6,AGRON-OMICS;grantno.LSHG-CT006-)37704,theSwissNationalScieneeFoundation,CTI(SwissInnovationPromotionAgency,ETHZurich,and
14、theFunctionalGenomicsCenterZurichforourpro?lingexperiments.*Correspondingauthor;e-mailwgruissemethz.ch.Theauthorresponsiblefordistributionofmaterialsintegratothe?ndingspresentedinthisarticleinaccordancewiththepolicydescribedintheInstructionsforAuthors(www.plantphysiol.orgis:WilhelmGruissem(wgruissem
15、ethz.ch.www.plantphysiol.org/cgi/doi/10.1104/pp.109.150433theinherentlogicoftranscriptionalregulation.Chromatinimmunoprecipitation(ChIPcoupledtomicroarrayanalysis(ChIP-chiporhigh-throughputsequencing(ChIP-Seqcangeneratesuchdata.Inplants,DNAmethylation,repressiveandactivatingchromatinmarks,aswellashi
16、stonevariantshavebeenmappedontothegenome(forreview,seeZhang,2008,butbecausesuchmarksareexpectedtodifferbetweencelltypesanddevelopmentalstages,moretargetedepigenomepro?lingisneededinthefuture.TargetedanalysisofDNAmethylationduringseeddevelopment,forinstance,revealedunexpectedgenome-widedemethylation(Gehringetal.,2009;Hsiehetal.,2009.ChIP-chipwasalsousedforglobalmappingofbindingsitesoftranscriptionfactorssuchasTGA2andSEPALLATA3andtore?nede?nitionsofbindingmotfsthatwerepr
