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Variability and memory of protein levels in human cells

Nature volume 444, pages 643–646 (2006)Cite this article

Abstract

Protein expression is a stochastic process that leads to phenotypic variation among cells1,2,3,4,5,6. The cell–cell distribution of protein levels in microorganisms has been well characterized7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23 but little is known about such variability in human cells. Here, we studied the variability of protein levels in human cells, as well as the temporal dynamics of this variability, and addressed whether cells with higher than average protein levels eventually have lower than average levels, and if so, over what timescale does this mixing occur. We measured fluctuations over time in the levels of 20 endogenous proteins in living human cells, tagged by the gene for yellow fluorescent protein at their chromosomal loci24. We found variability with a standard deviation that ranged, for different proteins, from about 15% to 30% of the mean. Mixing between high and low levels occurred for all proteins, but the mixing time was longer than two cell generations (more than 40 h) for many proteins. We also tagged pairs of proteins with two colours, and found that the levels of proteins in the same biological pathway were far more correlated than those of proteins in different pathways. The persistent memory for protein levels that we found might underlie individuality in cell behaviour and could set a timescale needed for signals to affect fully every member of a cell population.

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Figure 1: Protein level dynamics in individual cells.
Figure 2: Mixing-times of different proteins.
Figure 3: Mixing time correlates with variability.
Figure 4: Correlations between pairs of proteins CD-tagged with two fluorescent colours (YFP and mCherry) in the same cells.

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Acknowledgements

We thank the Kahn Family Foundation and the Israel Science Foundation for support. We thank J. Paulsson, J. Pedraza and A. Eldar for discussions of the manuscript, and A. Sharp and E. Ariel for flow cytometry assistance. R.M. thanks the Horowitz Complexity Science Foundation for support.

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Author notes

  1. Ron Milo

    Present address: Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, 02115, USA

  2. Alex Sigal, Ron Milo and Ariel Cohen: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel

    Alex Sigal, Ron Milo, Ariel Cohen, Naama Geva-Zatorsky, Yael Klein, Yuvalal Liron, Nitzan Rosenfeld, Tamar Danon, Natalie Perzov & Uri Alon

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Correspondence to Uri Alon.

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Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Notes

This file contains Supplementary Data, Supplementary Tables 1–4 and Supplementary Discussion. (PDF 208 kb)

Supplementary Figures

This file contains Supplementary Figures 1–5. (PDF 294 kb)

Supplementary Movie 1

Time-lapse movie of transmitted light images of the clone with YFP CD-tagged TOP1, from which frames were obtained for Figure 1b in the article. Movie duration is 100 hours (time-lapse: 1 frame per 10 minutes, each second of movie is ∼ 5 hours of cell growth). (MPG 7931 kb)

Supplementary Movie 2

Time-lapse movie of fluorescence images of the clone with YFP CD-tagged TOP1, shown in Video1, and from which frames were obtained for Figure 1b in the article. Movie duration is 100 hours (time-lapse: 1 frame per 10 minutes, each second of movie is ∼ 5 hours of cell growth). (MPG 2195 kb)

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Sigal, A., Milo, R., Cohen, A. et al. Variability and memory of protein levels in human cells. Nature 444, 643–646 (2006). https://doi.org/10.1038/nature05316

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