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Intronic RNAs mediate EZH2 regulation of epigenetic targets

Nature Structural & Molecular Biology volume 19, pages 664–670 (2012)Cite this article

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Abstract

Epigenetic deregulation at a number of genomic loci is one of the hallmarks of cancer. A role for some RNA molecules in guiding repressive polycomb complex PRC2 to specific chromatin regions has been proposed. Here we use an in vivo cross-linking method to detect and identify direct PRC2-RNA interactions in human cancer cells, revealing a number of intronic RNA sequences capable of binding to the core component EZH2 and regulating the transcriptional output of its genomic counterpart. Overexpression of EZH2-bound intronic RNA for the H3K4 methyltransferase gene SMYD3 is concomitant with an increase in EZH2 occupancy throughout the corresponding genomic fragment and is sufficient to reduce levels of the endogenous transcript and protein, resulting in reduced growth capability in cell culture and animal models. These findings reveal the role of intronic RNAs in fine-tuning gene expression regulation at the level of transcriptional control.

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Figure 1: CLIP identifies a number of EZH2-interacting RNAs from within the introns of chromatin modifier genes.
Figure 2: CLIP-tag RNAs reveal chromatin-binding sites for EZH2 and reveal transcriptionally repressed gene targets.
Figure 3: Overexpression of intronic RNA CLIP tags downregulate endogenous gene expression through a mechanism that requires EZH2.
Figure 4: SMYD3 1-kb intronic sequence alone is capable of reducing proliferation in in vivo assays.

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Acknowledgements

This work was supported by the Ministerio de Ciencia e Innovación (MICINN), grant numbers BFU2008-04131 (S.G.) and SAF2011-22803 (M.E.), the European Research Council (ERC) Epigenetic Disruption of Non-Coding RNAs in Human Cancer (EPINORC) Advanced grant (to M.E.), Cellex Foundation, the Health and Science Departments of the Catalan Government (Generalitat de Catalunya) and Fondo de Investigaciones Sanitarias grant PI08-1345 (M.E.). S.G. is funded by the Ramón y Cajal Research Program (MICINN). A.P. is a Sara Borrell postdoctoral fellow. M.E. is an ICREA Research Professor.

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Authors and Affiliations

  1. Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain

    Sònia Guil, Marta Soler, Anna Portela, Jordi Carrère, Elena Fonalleras, Antonio Gómez & Manel Esteller

  2. Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Spain

    Alberto Villanueva

  3. Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain

    Manel Esteller

  4. Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain

    Manel Esteller

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  1. Sònia Guil
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Contributions

S.G., M.E., M.S., J.C., A.P. and A.V. designed the experiments. S.G., M.S., J.C., A.P., E.F. and A.V. conducted the experiments. A.G. carried out the CLIP–seq bioinformatics analysis. M.E. and S.G. evaluated the results and wrote the manuscript.

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Correspondence to Sònia Guil or Manel Esteller.

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Guil, S., Soler, M., Portela, A. et al. Intronic RNAs mediate EZH2 regulation of epigenetic targets. Nat Struct Mol Biol 19, 664–670 (2012). https://doi.org/10.1038/nsmb.2315

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