Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

Christine Vogel, Raquel De Sousa Abreu, Daijin Ko, Shu Yun Le, Bruce A. Shapiro, Suzanne C. Burns, Devraj Sandhu, Daniel R. Boutz, Edward M. Marcotte, Luiz O. Penalva

Research output: Contribution to journalArticlepeer-review

475 Scopus citations


Transcription, mRNA decay, translation and protein degradation are essential processes during eukaryotic gene expression, but their relative global contributions to steady-state protein concentrations in multi-cellular eukaryotes are largely unknown. Using measurements of absolute protein and mRNA abundances in cellular lysate from the human Daoy medulloblastoma cell line, we quantitatively evaluate the impact of mRNA concentration and sequence features implicated in translation and protein degradation on protein expression. Sequence features related to translation and protein degradation have an impact similar to that of mRNA abundance, and their combined contribution explains two-thirds of protein abundance variation. mRNA sequence lengths, amino-acid properties, upstream open reading frames and secondary structures in the 5′2 untranslated region (UTR) were the strongest individual correlates of protein concentrations. In a combined model, characteristics of the coding region and the 3′2UTR explained a larger proportion of protein abundance variation than characteristics of the 5′2UTR. The absolute protein and mRNA concentration measurements for >1000 human genes described here represent one of the largest datasets currently available, and reveal both general trends and specific examples of post-transcriptional regulation.

Original languageEnglish (US)
Article number400
JournalMolecular Systems Biology
StatePublished - 2010


  • gene expression regulation
  • protein degradation
  • protein stability
  • translation

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Information Systems
  • Applied Mathematics
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Computational Theory and Mathematics


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