Transcript Abundance in Yeast Varies over Six Orders of Magnitude*
- From the Department of Biological Chemistry, School of Medicine, University of California, Davis, California 95616
Abstract
In the current era of functional genomics, it is remarkable that the intracellular range of transcript abundance is largely unknown. For the yeast Saccharomyces cerevisiae, hybridization-based complexity analysis and SAGE analysis showed that the majority of yeast mRNAs are present at one or fewer copies per cell; however, neither method provides an accurate estimate of the full range of low abundance transcripts. Here we examine the range of intracellular transcript abundance in yeast using kinetically monitored, reverse transcriptase-initiated PCR (kRT-PCR). Steady-state transcript levels encoded by all 65 genes on the left arm of chromosome III and 185 transcription factor genes are quantitated. Abundant transcripts encoded by glycolytic genes, previously quantitated by kRT-PCR, are present at a few hundred copies per cell whereas genes encoding physiologically important transcription factors are expressed at levels as low as one-thousandth transcript per cell. Of the genes assessed, only the silent mating type loci,HML and HMR, are transcriptionally silent. The results show that transcript abundance in yeast varies over six orders of magnitude. Finally, kRT-PCR, cDNA microarray, and high density oligonucleotide array assays are compared for their ability to detect and quantitate the complete yeast transcriptome.
Footnotes
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↵* This work was supported by National Institutes of Health Grant R01-HG1736.The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
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↵‡ To whom correspondence should be addressed: Dept. of Biological Chemistry, School of Medicine, University of California, One Shields Ave., Davis, CA 95616. Tel.: 530-752-8378; Fax: 530-752-3516; E-mail: mjholland@ucdavis.edu.
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Published, JBC Papers in Press, March 6, 2002, DOI 10.1074/jbc.C200101200
- Abbreviations:
- SAGE
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serial analysis of gene expression
- kRT-PCR
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kinetically monitored, reverse transcriptase-initiated PCR
- Tricine
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N-[2-hydroxy-1,1-bis(hydroxymethyl)ethyl]glycine
- ORF
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open reading frame
- TBP
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TATA-binding protein
- TAF
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TBP-associated factor
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- Received February 15, 2002.
- Revision received March 4, 2002.
- The American Society for Biochemistry and Molecular Biology, Inc.
