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The establishment of gene silencing at single-cell resolution

Nature Genetics volume 41, pages 800–806 (2009)Cite this article

Abstract

The establishment of silencing in Saccharomyces cerevisiae is similar to heterochromatin formation in multicellular eukaryotes. Previous batch culture studies determined that the de novo establishment of silencing initiates during S phase and continues for up to five cell divisions for completion. To track silencing phenotypically, we developed an assay that introduces Sir3 protein into individual sir3Δ mutant cells synchronously and then detects the onset of silencing with single-cell resolution. Silencing was completed within the first one to two cell divisions in most cells queried. Moreover, we uncovered unexpected complexity in the contributions of a histone acetyltransferase (Sas2), two histone methytransferases (Dot1 and Set1) and one histone demethylase (Jhd2) to the dynamics of silencing. Our findings showed that removal of methyl modifications at H3K4 and H3K79 were important steps in silent chromatin formation and that Jhd2 and Set1 had competing roles in the process.

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Figure 1: A pedigree assay to measure the establishment of silencing as a function of cell divisions.
Figure 2: Strain 1 (JRY88828) and strain 2 (JRY8829) fusion products established silencing after one to three cell divisions.
Figure 3: Sir3-overexpression studies.
Figure 4: Silencing of cells with mutations in chromatin modifying enzymes.
Figure 5: Loss of DOT1 enhanced the sir1Δ loss-of-silencing phenotype.

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Acknowledgements

We thank F. Li, C. Hale, O. Zill, M. Gartenberg and K. Struhl for helpful contributions and wonderful discussions. Also, thanks to O. Zill, J. Kuei, J. Babiarz and L. Lombardi for strains and reagents. Finally, thanks to J. O for her hard work and contributions. This work was supported by a National Science Foundation Pre-Doctoral Fellowship to E.A. Osborne and by grants from the National Institute of Health (GM31105 to J.R.).

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Authors and Affiliations

  1. Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA

    Erin A Osborne

  2. Division of Biostatistics at the School of Public Health, University of California, Berkeley, Berkeley, California, USA

    Sandrine Dudoit

  3. California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, USA

    Sandrine Dudoit & Jasper Rine

  4. Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA

    Jasper Rine

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  1. Erin A Osborne
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  2. Sandrine Dudoit
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  3. Jasper Rine
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Contributions

E.A.O. and J.R. conceived of and designed this study. E.A.O. conducted the study. E.A.O. and S.D. performed statistical analysis. E.A.O. wrote the manuscript with contributions from J.R. and S.D. E.A.O. and J.R. obtained funding for the study.

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Correspondence to Jasper Rine.

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Osborne, E., Dudoit, S. & Rine, J. The establishment of gene silencing at single-cell resolution. Nat Genet 41, 800–806 (2009). https://doi.org/10.1038/ng.402

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