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A multistep epigenetic switch enables the stable inheritance of DNA methylation states

Nature Genetics volume 39, pages 269–275 (2007)Cite this article

Abstract

In many prokaryotes and eukaryotes, DNA methylation at cis-regulatory sequences determines whether gene expression is on or off. Stable inheritance of these expression states is required in bacterial pathogenesis, cancer and developmental pathways1,2. Here we delineate the factors that control the stability of these states by using the agn43 gene in Escherichia coli as a model system. Systematic disruption of this system shows that a functional switch requires the presence of several, rarely occupied, intermediate states that separate the 'on' and 'off' states. Cells that leave the on and off state enter different intermediate states, where there is a strong bias that drives cells back to their original state. The intermediate states therefore act as buffers that prevent back and forth switching. This mechanism of generating multiple states is an alternative to feedback regulation3,4,5, and its general principle should be applicable to the analysis of other epigenetic switches and the design of synthetic circuits.

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Figure 1: Genetic amplification system for measuring agn43 expression and switching.
Figure 2: Deletions of the agn43 cis-regulatory region.
Figure 3: Deletion mapping of sequences upstream of the agn43 promoter.
Figure 4: Sequences necessary for maintaining the off state.
Figure 5: Molecular model of the steps involved in agn43 on-off switching.
Figure 6: Simulation of agn43 switching.

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Acknowledgements

We thank E.A. Oakenfull for logistical assistance; M. Thattai for discussions and assistance with data analysis; M. van der Woude for bacterial strains and plasmids; R. Lutz and H. Bujard for pZ expression plasmids; and A. Becskei, S.V. Godoy and J.M. Pedraza for suggestions and comments. This work was supported by grants from the National Science Foundation (PHY-0548484) and the National Institutes of Health (R01-GM077183).

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Authors and Affiliations

  1. Department of Physics, Massachusetts Institute of Technology, Cambridge, 02139, Massachusetts, USA

    Han N Lim & Alexander van Oudenaarden

  2. Department of Integrative Biology, University of California, Berkeley, 94720, California, USA

    Han N Lim

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Correspondence to Han N Lim.

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Supplementary information

Supplementary Fig. 1

Cis-regulatory deletion strains. (PDF 25 kb)

Supplementary Table 1

Bacterial strains and plasmids. (PDF 85 kb)

Supplementary Table 2

Oligonucleotide sequences. (PDF 32 kb)

Supplementary Methods (PDF 46 kb)

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Lim, H., van Oudenaarden, A. A multistep epigenetic switch enables the stable inheritance of DNA methylation states. Nat Genet 39, 269–275 (2007). https://doi.org/10.1038/ng1956

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