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Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint

Nature Genetics volume 44, pages 157–164 (2012)Cite this article

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Abstract

Exogenous double-stranded RNA (dsRNA) has been shown to exert homology-dependent effects at the level of both target mRNA stability and chromatin structure. Using C. elegans undergoing RNAi as an animal model, we have investigated the generality, scope and longevity of dsRNA-targeted chromatin effects and their dependence on components of the RNAi machinery. Using high-resolution genome-wide chromatin profiling, we found that a diverse set of genes can be induced to acquire locus-specific enrichment of histone H3 lysine 9 trimethylation (H3K9me3), with modification footprints extending several kilobases from the site of dsRNA homology and with locus specificity sufficient to distinguish the targeted locus from the other 20,000 genes in the C. elegans genome. Genetic analysis of the response indicated that factors responsible for secondary siRNA production during RNAi were required for effective targeting of chromatin. Temporal analysis revealed that H3K9me3, once triggered by dsRNA, can be maintained in the absence of dsRNA for at least two generations before being lost. These results implicate dsRNA-triggered chromatin modification in C. elegans as a programmable and locus-specific response defining a metastable state that can persist through generational boundaries.

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Figure 1: H3K9me3 profiles triggered by gene-specific dsRNAs.
Figure 2: H3K9me3 profiles triggered by dsRNAs that target different sections of the smg-1 locus.
Figure 3: Small RNA coverage profiles at the smg-1 locus after exposure to smg-1 dsRNA in various genetic backgrounds.
Figure 4: Multigenerational analyses of H3K9me3 and siRNAs at the RNAi target locus.
Figure 5: Time lag between initial dsRNA exposure and chromatin and siRNA responses.
Figure 6: A working model for dsRNA-triggered H3K9 methylation in C. elegans.

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Acknowledgements

We thank Z. Weng, P. Lacroute, A. Sidow, H. Zhang, J. Merker, D. Wu, K. Artiles, L. Gracey, A. Lamm, C. Mello, M. Stadler, R. Alcazar and J. Ni for help, suggestions and support. Funding for this study was provided by a grant from the US National Institutes of Health (R01-GM37706).

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  1. Shouhong Guang

    Present address: Current address: School of Life Sciences, University of Science & Technology of China, Hefei, China.,

Authors and Affiliations

  1. Department of Pathology, Stanford University School of Medicine, Stanford, California, USA

    Sam Guoping Gu, Julia Pak & Andrew Fire

  2. Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, USA

    Shouhong Guang & Scott Kennedy

  3. Department of Genetics, Stanford University School of Medicine, Stanford, California, USA

    Jay M Maniar & Andrew Fire

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Contributions

Experiments were conceived in discussions among all authors. Experiments and data analyses for Figure 1 were performed by S.G.G., J.P., J.M.M., S.G., S.K. and A.F. Experiments and data analyses for Figures 2, 3, 4 and 5 were performed by S.G.G., J.P. and A.F. Overall discussions of the data and implications involved all authors, and the manuscript was written by S.G.G. and A.F.

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Correspondence to Andrew Fire.

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Gu, S., Pak, J., Guang, S. et al. Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint. Nat Genet 44, 157–164 (2012). https://doi.org/10.1038/ng.1039

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