title: Dynamic proteomics of human protein level and localization across the cell cycle.
abstract: Regulation of proteins across the cell cycle is a basic process in cell biology. It has been difficult to study this globally in human cells due to lack of methods to accurately follow protein levels and localizations over time. Estimates based on global mRNA measurements suggest that only a few percent of human genes have cell-cycle dependent mRNA levels. Here, we used dynamic proteomics to study the cell-cycle dependence of proteins. We used 495 clones of a human cell line, each with a different protein tagged fluorescently at its endogenous locus. Protein level and localization was quantified in individual cells over 24h of growth using time-lapse microscopy. Instead of standard chemical or mechanical methods for cell synchronization, we employed in-silico synchronization to place protein levels and localization on a time axis between two cell divisions. This non-perturbative synchronization approach, together with the high accuracy of the measurements, allowed a sensitive assay of cell-cycle dependence. We further developed a computational approach that uses texture features to evaluate changes in protein localizations. We find that 40% of the proteins showed cell cycle dependence, of which 11% showed changes in protein level and 35% in localization. This suggests that a broader range of cell-cycle dependent proteins exists in human cells than was previously appreciated. Most of the cell-cycle dependent proteins exhibit changes in cellular localization. Such changes can be a useful tool in the regulation of the cell-cycle being fast and efficient.
authors.affiliation: Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
authors.forename: Shlomit
authors.initials: S
authors.lastname: Farkash-Amar
authors.forename: Eran
authors.initials: E
authors.lastname: Eden
authors.forename: Ariel
authors.initials: A
authors.lastname: Cohen
authors.forename: Naama
authors.initials: N
authors.lastname: Geva-Zatorsky
authors.forename: Lydia
authors.initials: L
authors.lastname: Cohen
authors.forename: Ron
authors.initials: R
authors.lastname: Milo
authors.forename: Alex
authors.initials: A
authors.lastname: Sigal
authors.forename: Tamar
authors.initials: T
authors.lastname: Danon
authors.forename: Uri
authors.initials: U
authors.lastname: Alon
mesh_terms: D002453:Cell Cycle; D002460:Cell Line; D042522:DNA Replication Timing; D020869:Gene Expression Profiling; D006801:Humans; D011506:Proteins / Q000032:analysis / Q000235:genetics* / Q000378:metabolism; D040901:Proteomics; D059008:Time-Lapse Imaging
chemical_list: D011506:Proteins