Novel Low Abundance and Transient RNAs in Yeast Revealed by Tiling Microarrays and Ultra High–Throughput Sequencing Are Not Conserved Across Closely Related Yeast Species 英文参考文献.docVIP
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Novel Low Abundance and Transient RNAs in Yeast Revealed by Tiling Microarrays and Ultra High–Throughput Sequencing Are Not Conserved Across Closely Related Yeast Species 英文参考文献
NovelLowAbundanceandTransientRNAsinYeast
RevealedbyTilingMicroarraysandUltraHigh–
ThroughputSequencingAreNotConservedAcross
CloselyRelatedYeastSpecies
AlbertLee1.,KasperDanielHansen2.,JamesBullard2.,SandrineDudoit2,GavinSherlock1*
1DepartmentofGenetics,StanfordUniversity,Stanford,California,UnitedofStatesofAmerica,2DivisionofBiostatistics,SchoolofPublicHealth,UniversityofCalifornia
Berkeley,Berkeley,California,UnitedStatesofAmerica
Abstract
A complete description of the transcriptome of an organism is crucial for a comprehensive understanding of how it
functions and how its transcriptional networks are controlled, and may provide insights into the organism’s evolution.
DespitethestatusofSaccharomycescerevisiaeasarguablythemostwell-studiedmodeleukaryote,westilldonothaveafull
catalogorunderstandingofallitsgenes.InordertointerrogatethetranscriptomeofS.cerevisiaeforlowabundanceor
rapidly turned over transcripts, we deleted elements of the RNA degradation machinery with the goal of preferentially
increasing the relative abundance of such transcripts. We then used high-resolution tiling microarrays and ultra high–
throughputsequencing(UHTS)toidentify,map,andvalidateunannotatedtranscriptsthataremoreabundantintheRNA
degradation mutants relative to wild-type cells. We identified 365 currently unannotated transcripts, the majority
presumably representing low abundance or short-lived RNAs, of which 185 are previously unknown and unique to this
study. It is likely that many of these are cryptic unstable transcripts (CUTs), which are rapidly degraded and whose
function(s) within the cell are still unclear, while others may be novel functional transcripts. Of the 185 transcripts we
identifiedasnoveltoourstudy,greaterthan80percentcomefromregionsofthegenomethathavelowerconservation
scores amongst closely related yeast species than 85 percent of the verified ORFs in S. cerevisiae. Such regions of the
genomehavetypicallybeenlesswell-studied,andbydefinitiontranscriptsfromtheseregion
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