Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data 英文参考文献.docVIP

EvaluatingGeneExpressionDynamicsUsingPairwise RNAFISHData MatthieuWyart1,2,DavidBotstein1,3,NedS.Wingreen1,3 * 1Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America, 2Center for Soft Matter Research, New York University,NewYork,NewYork,UnitedStatesofAmerica,3DepartmentofMolecularBiology,PrincetonUniversity,Princeton,NewJersey,UnitedStatesofAmerica Abstract Recently,anovelapproachhasbeendevelopedtostudygeneexpressioninsinglecellswithhightimeresolutionusingRNA FluorescentInSituHybridization(FISH).ThetechniqueallowsindividualmRNAstobecountedwithhighaccuracyinwild- typecells,butrequirescellstobefixed;thus,eachcellprovidesonlya‘‘snapshot’’ofgeneexpression.Hereweshowhow and when RNA FISH data on pairs of genes can be used to reconstruct real-time dynamics from a collection of such snapshots. Using maximum-likelihood parameter estimation on synthetically generated, noisy FISH data, we show that dynamical programs of gene expression, such as cycles (e.g., the cell cycle) or switches between discrete states, can be accuratelyreconstructed.InthelimitthatmRNAsareproducedinshort-livedbursts,binarythresholdingoftheFISHdata providesarobustwayofreconstructingdynamics.Inthisregime,priorknowledgeofthetypeofdynamics–cycleversus switch–isgenerallyrequiredandadditionalconstraints,e.g.,fromtripletFISHmeasurements,mayalsobeneededtofully constrainallparameters.Asademonstration,weapplythethresholdingmethodtoRNAFISHdataobtainedfromsingle, unsynchronized cells of Saccharomyces cerevisiae. Our results support the existence of metabolic cycles and provide an estimate of global gene-expression noise. The approach to FISH data presented here can be applied in general to reconstruct dynamics from snapshots of pairs of correlated quantities including, for example, protein concentrations obtainedfromimmunofluorescenceassays. Citation: Wyart M, Botstein D,WingreenNS(2010)Evaluating Gene Expression DynamicsUsing Pairwise RNAFISH Data.