An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data 英文参考文献.docVIP
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An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data 英文参考文献
AnAbundanceofUbiquitouslyExpressedGenes
RevealedbyTissueTranscriptomeSequenceData
DanielRamsko¨ld1,EricT.Wang2,ChristopherB.Burge2*,RickardSandberg1*
1Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden, 2Department of Biology, Massachusetts Institute of Technology, Cambridge,
Massachusetts,UnitedStatesofAmerica
Abstract
The parts of the genome transcribed by a cell or tissue reflect the biological processes and functions it carries out. We
characterizedthefeaturesofmammaliantissuetranscriptomesatthegenelevelthroughanalysisofRNAdeepsequencing
(RNA-Seq)dataacrosshumanandmousetissuesandcelllines.Weobservedthatroughly8,000protein-codinggeneswere
ubiquitouslyexpressed,contributingtoaround75%ofallmRNAsbymessagecopynumberinmosttissues.ThesemRNAs
encodedproteinsthatwereoftenintracellular,andtendedtobeinvolvedinmetabolism,transcription,RNAprocessingor
translation. In contrast, genes for secreted or plasma membrane proteins were generally expressed in only a subset of
tissues. The distribution of expression levels was broad but fairly continuous: no support was found for the concept of
distinct expression classes of genes. Expression estimates that included reads mapping to coding exons only correlated
betterwithqRT-PCRdatathanestimateswhichalsoincluded39untranslatedregions(UTRs).Muscleandliverhadtheleast
complextranscriptomes,inthattheyexpressedpredominantlyubiquitousgenesandalargefractionofthetranscriptscame
fromafewhighlyexpressedgenes,whereasbrain,kidneyandtestisexpressedmorecomplextranscriptomeswiththevast
majorityofgenesexpressedandrelativelysmallcontributionsfromthemostexpressedgenes.mRNAsexpressedinbrain
hadunusuallylong39UTRs,andmean39UTRlengthwashigherforgenesinvolvedindevelopment,morphogenesisand
signaltransduction,suggestingaddedcomplexityofUTR-basedregulationforthesegenes.Ourresultssupportamodelin
which variable exterior components feed into a large, densely connected core composed of ubiquitously expressed
intracellularproteins.
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