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RNA-interference-directed chromatin modification coupled to RNA polymerase II transcription

Nature volume 435, pages 1275–1279 (2005)Cite this article

A Retraction to this article was published on 13 October 2005

Abstract

RNA interference (RNAi) acts on long double-stranded RNAs (dsRNAs) in a variety of eukaryotes to generate small interfering RNAs that target homologous messenger RNA, resulting in their destruction. This process is widely used to ‘knock-down’ the expression of genes of interest to explore phenotypes1,2,3. In plants3,4,5, fission yeast6,7,8, ciliates9,10, flies11 and mammalian cells12,13, short interfering RNAs (siRNAs) also induce DNA or chromatin modifications at the homologous genomic locus, which can result in transcriptional silencing or sequence elimination14. siRNAs may direct DNA or chromatin modification by siRNA–DNA interactions at the homologous locus4,5. Alternatively, they may act by interactions between siRNA and nascent transcript15,16. Here we show that in fission yeast (Schizosaccharomyces pombe), chromatin modifications are only directed by RNAi if the homologous DNA sequences are transcribed. Furthermore, transcription by exogenous T7 polymerase is not sufficient. Ago1, a component of the RNAi effector RISC/RITS complex, associates with target transcripts and RNA polymerase II. Truncation of the regulatory carboxy-terminal domain (CTD) of RNA pol II disrupts transcriptional silencing, indicating that, like other RNA processing events17,18,19, RNAi-directed chromatin modification is coupled to transcription.

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Figure 1: Transcription of siRNA target is required to effect silent chromatin assembly.
Figure 2: Transcription by T7 polymerase is not sufficient for RNAi-directed chromatin modification.
Figure 3: RNA pol II CTD truncation affects centromeric silent chromatin.
Figure 4: Association of Ago1 with chromatin is RNase sensitive and dependent on transcription and pol II.

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Acknowledgements

We thank members of the Allshire laboratory for advice, discussion and comments on the manuscript; E. Bayne for the model; P. Dunoyer and O. Voinnet for help with siRNA detection; T. Jenuwein for anti-H3K9me2 serum; and other members of the EC FP6 ‘The Epigenome’ Network for input. This research was supported by funding from the Wellcome Trust to R.C.A., who is a Wellcome Trust Principal Research Fellow.

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Authors and Affiliations

  1. Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, King's Buildings, University of Edinburgh, EH9 3JR, Edinburgh, UK

    Vera Schramke, Daniel M. Sheedy & Robin C. Allshire

  2. Cold Spring Harbor Laboratory, Watson School of Biological Sciences, 1 Bungtown Road, Cold Spring Harbor, New York, 11724, USA

    Ahmet M. Denli & Gregory J. Hannon

  3. Karolinska Institutet, Department of Biosciences/Department of Natural Sciences, University College Sodertorn, Alfred Nobel's Allé 7, S-141 89, Huddinge, Sweden

    Carolina Bonila & Karl Ekwall

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  1. Vera Schramke
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Correspondence to Robin C. Allshire.

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This contains Supplementary Figures S1-S3 and Supplementary Tables 1-3 (DOC 299 kb)

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Schramke, V., Sheedy, D., Denli, A. et al. RNA-interference-directed chromatin modification coupled to RNA polymerase II transcription. Nature 435, 1275–1279 (2005). https://doi.org/10.1038/nature03652

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