A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells

Tony Ly, Yasmeen Ahmad, Adam Shlien, Dominique Soroka, Allie Mills, Michael J. Emanuele, Michael R Stratton, Angus I Lamond

Research output: Contribution to journalArticlepeer-review

Abstract

Technological advances have enabled the analysis of cellular protein and RNA levels with unprecedented depth and sensitivity, allowing for an unbiased re-evaluation of gene regulation during fundamental biological processes. Here, we have chronicled the dynamics of protein and mRNA expression levels across a minimally perturbed cell cycle in human myeloid leukemia cells using centrifugal elutriation combined with mass spectrometry-based proteomics and RNA-Seq, avoiding artificial synchronization procedures. We identify myeloid-specific gene expression and variations in protein abundance, isoform expression and phosphorylation at different cell cycle stages. We dissect the relationship between protein and mRNA levels for both bulk gene expression and for over similar to 6000 genes individually across the cell cycle, revealing complex, genespecific patterns. This data set, one of the deepest surveys to date of gene expression in human cells, is presented in an online, searchable database, the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd/).

Original languageEnglish
Article number01630
Number of pages36
JournaleLIFE
Volume3
DOIs
Publication statusPublished - 4 Mar 2014

Keywords

  • messenger-rna
  • quantitative proteomics
  • transcriptional regulation
  • saccharomyces-cerevisiae
  • phosphorylation site
  • protein abundance
  • dna-replication
  • transgenic mice
  • animal-cells
  • rar-alpha

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