title: A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells.
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 ∼6000 genes individually across the cell cycle, revealing complex, gene-specific 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/). DOI: http://dx.doi.org/10.7554/eLife.01630.001.
authors.affiliation: Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom.
authors.forename: Tony
authors.initials: T
authors.lastname: Ly
authors.forename: Yasmeen
authors.initials: Y
authors.lastname: Ahmad
authors.forename: Adam
authors.initials: A
authors.lastname: Shlien
authors.forename: Dominique
authors.initials: D
authors.lastname: Soroka
authors.forename: Allie
authors.initials: A
authors.lastname: Mills
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Emanuele
authors.forename: Michael R
authors.initials: MR
authors.lastname: Stratton
authors.forename: Angus I
authors.initials: AI
authors.lastname: Lamond
mesh_terms: D002453:Cell Cycle; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism*; D045744:Cell Line, Tumor; D002469:Cell Separation / Q000379:methods; D048429:Cell Size; D002498:Centrifugation; D002853:Chromatography, Liquid; D030562:Databases, Protein; D020869:Gene Expression Profiling / Q000379:methods; D015973:Gene Expression Regulation, Leukemic; D006801:Humans; D007951:Leukemia, Myeloid / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D010766:Phosphorylation; D040901:Proteomics / Q000379:methods; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D053719:Tandem Mass Spectrometry; D013997:Time Factors; D014162:Transfection
chemical_list: D018797:Cell Cycle Proteins; D012333:RNA, Messenger
keywords: RNA-Seq; cell cycle; mass spectrometry; proteomics; transcriptomics