Letter | Published:

The Paf1 complex represses small-RNA-mediated epigenetic gene silencing

Nature volume 520, pages 248252 (09 April 2015) | Download Citation


RNA interference (RNAi) refers to the ability of exogenously introduced double-stranded RNA to silence expression of homologous sequences. Silencing is initiated when the enzyme Dicer processes the double-stranded RNA into small interfering RNAs (siRNAs). Small RNA molecules are incorporated into Argonaute-protein-containing effector complexes, which they guide to complementary targets to mediate different types of gene silencing, specifically post-transcriptional gene silencing and chromatin-dependent gene silencing1. Although endogenous small RNAs have crucial roles in chromatin-mediated processes across kingdoms, efforts to initiate chromatin modifications in trans by using siRNAs have been inherently difficult to achieve in all eukaryotic cells. Using fission yeast, here we show that RNAi-directed heterochromatin formation is negatively controlled by the highly conserved RNA polymerase-associated factor 1 complex (Paf1C). Temporary expression of a synthetic hairpin RNA in Paf1C mutants triggers stable heterochromatin formation at homologous loci, effectively silencing genes in trans. This repressed state is propagated across generations by the continual production of secondary siRNAs, independently of the synthetic hairpin RNA. Our data support a model in which Paf1C prevents targeting of nascent transcripts by the siRNA-containing RNA-induced transcriptional silencing complex and thereby epigenetic gene silencing, by promoting efficient transcription termination and rapid release of the RNA from the site of transcription. We show that although compromised transcription termination is sufficient to initiate the formation of bi-stable heterochromatin by trans-acting siRNAs, impairment of both transcription termination and nascent transcript release is imperative to confer stability to the repressed state. Our work uncovers a novel mechanism for small-RNA-mediated epigenome regulation and highlights fundamental roles for Paf1C and the RNAi machinery in building epigenetic memory.

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Primary accessions

Gene Expression Omnibus

Data deposits

Genome-wide data sets are deposited at GEO under the accession number GSE59171.


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We thank T. Iida for providing the plasmid encoding the ade6-hp construct, N. Laschet and R. Tsuji for technical assistance, S. Thiry for hybridizing tiling arrays, K. Jacobeit and S. Dessus-Babus for small RNA sequencing, T. Roloff for archiving data sets, M. Kirschmann for developing the Matlab script for colony counting, and A. Tuck for comments on the manuscript. This work was supported by funds from the Swiss National Science Foundation, the European Research Council, and the Boehringer Ingelheim Fonds. The Friedrich Miescher Institute for Biomedical Research is supported by the Novartis Research Foundation.

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Author notes

    • Katarzyna Maria Kowalik
    •  & Yukiko Shimada

    These authors contributed equally to this work.


  1. Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland

    • Katarzyna Maria Kowalik
    • , Yukiko Shimada
    • , Valentin Flury
    • , Michael Beda Stadler
    •  & Marc Bühler
  2. University of Basel, Petersplatz 10, 4003 Basel, Switzerland

    • Katarzyna Maria Kowalik
    • , Yukiko Shimada
    • , Valentin Flury
    • , Michael Beda Stadler
    •  & Marc Bühler
  3. Swiss Institute of Bioinformatics, Maulbeerstrasse 66, 4058 Basel, Switzerland

    • Michael Beda Stadler
  4. Eötvös Loránd University, Faculty of Sciences, Institute of Chemistry, 1/A Pázmány Péter sétány, Budapest 1117, Hungary

    • Julia Batki


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Y.S., K.M.K., V.F. and J.B. generated strains and performed experiments; Y.S. performed the sms screen; the genome-wide small RNA and gene expression data were analysed by K.M.K.; M.B.S. designed and performed the computational analysis of the mutant genome resequencing data; M.B. designed experiments and prepared the manuscript. All authors discussed the results and commented on the manuscript.

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A patent application has been filed.

Corresponding author

Correspondence to Marc Bühler.

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