Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

Summary Data on absolute molecule numbers will empower the modeling, understanding, and comparison of cellular functions and biological systems. We quantified transcriptomes and proteomes in fission yeast during cellular proliferation and quiescence. This rich resource provides the first comprehensive reference for all RNA and most protein concentrations in a eukaryote under two key physiological conditions. The integrated data set supports quantitative biology and affords unique insights into cell regulation. Although mRNAs are typically expressed in a narrow range above 1 copy/cell, most long, noncoding RNAs, except for a distinct subset, are tightly repressed below 1 copy/cell. Cell-cycle-regulated transcription tunes mRNA numbers to phase-specific requirements but can also bring about more switch-like expression. Proteins greatly exceed mRNAs in abundance and dynamic range, and concentrations are regulated to functional demands. Upon transition to quiescence, the proteome changes substantially, but, in stark contrast to mRNAs, proteins do not uniformly decrease but scale with cell volume.

• Publication year

  2012

• Venue

  Cell

• Publication date

  2012-10-26

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1016/j.cell.2012.09.019PMID 23101633PMCID 3482660
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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  2011cited by this paper
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  2010influential reference
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  2009cited by this paper
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  2008influential reference
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  2008cited by this paper
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  2008influential reference
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  2008cited by this paper
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  2008cited by this paper
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  2007cited by this paper
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  2007cited by this paper
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  2007cited by this paper
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  2003cited by this paper
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  2003cited by this paper
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  2003influential reference
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  2002cited by this paper
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  2002cited by this paper
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  2002cited by this paper
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  2001cited by this paper
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  2001cited by this paper
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  1998cited by this paper
• Dissecting the regulatory circuitry of a eukaryotic genome.

  1998cited by this paper
• The protein responsible for the repeating structure of cytoplasmic poly(A)-ribonucleoprotein

  1983cited by this paper
• Ribosome Numbers in a Fission Yeast

  1965influential reference
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  1964cited by this paper
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