Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate 英文参考文献.docVIP

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Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate 英文参考文献.doc

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Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate 英文参考文献

Krouketal.GenomeBiology2010,11:R123 /content/11/12/R123 RESEARCH OpenAccess Predictivenetworkmodelingofthehigh- resolutiondynamicplanttranscriptomein responsetonitrate GabrielKrouk1,2,PiotrMirowski3,YannLeCun3,DennisEShasha3,GloriaMCoruzzi1* Abstract Background:Nitrate,actingasbothanitrogensourceandasignalingmolecule,controlsmanyaspectsofplant development.However,genenetworksinvolvedinplantadaptationtofluctuatingnitrateenvironmentshavenot yetbeenidentified. Results:Hereweusetime-seriestranscriptomedatatodeciphergenerelationshipsandconsequentlytobuild coreregulatorynetworksinvolvedinArabidopsisrootadaptationtonitrateprovision.Theexperimentalapproach hasbeentomonitorgenome-wideresponsestonitrateat3,6,9,12,15and20minutesusingAffymetrixATH1 genechips.Thishigh-resolutiontimecourseanalysisdemonstratedthatthepreviouslyknownprimarynitrate responseisactuallyprecededbyaveryfastgeneexpressionmodulation,involvinggenesandfunctionsneededto prepareplantstouseorreducenitrate.Astate-spacemodelinferredfromthismicroarraytime-seriesdata successfullypredictsgenebehaviorinunlearntconditions. Conclusions:Theexperimentsandmethodsallowustoproposeatemporalworkingmodelfornitrate-driven genenetworks.Thisnetworkmodelistestedbothinsilicoandexperimentally.Forexample,theover-expressionof apredictedgenehubencodingatranscriptionfactorinducedearlyinthecascadeindeedleadstothe modificationofthekineticnitrateresponseofsentinelgenessuchasNIR,NIA2,andNRT1.1,andseveralother transcriptionfactors.Thepotentialnitrate/hormoneconnectionsimplicatedbythistime-seriesdataarealso evaluated. Background published [5-12]. Meta-analysis ofmicroarray data sets Higherplants,whichconstituteamainentryofnitrogen from several different labs demonstrated that at least a intothefoodchain,acquirenitrogenmainlyasnitrate tenth of the genome can potentially be regulated by (NO3-).Soilconcentrationsofthismineralioncanfluc- nitrogenprovision,dependingonthecontext[2,9,13,14]. tuatedramaticallyintherhizosphere, o