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RNAi triggered by specialized machinery silences developmental genes and retrotransposons


RNA interference (RNAi) is a conserved mechanism in which small interfering RNAs (siRNAs) guide the degradation of cognate RNAs, but also promote heterochromatin assembly at repetitive DNA elements such as centromeric repeats1,2. However, the full extent of RNAi functions and its endogenous targets have not been explored. Here we show that, in the fission yeast Schizosaccharomyces pombe, RNAi and heterochromatin factors cooperate to silence diverse loci, including sexual differentiation genes, genes encoding transmembrane proteins, and retrotransposons that are also targeted by the exosome RNA degradation machinery. In the absence of the exosome, transcripts are processed preferentially by the RNAi machinery, revealing siRNA clusters and a corresponding increase in heterochromatin modifications across large domains containing genes and retrotransposons. We show that the generation of siRNAs and heterochromatin assembly by RNAi is triggered by a mechanism involving the canonical poly(A) polymerase Pla1 and an associated RNA surveillance factor Red1, which also activate the exosome. Notably, siRNA production and heterochromatin modifications at these target loci are regulated by environmental growth conditions, and by developmental signals that induce gene expression during sexual differentiation. Our analyses uncover an interaction between RNAi and the exosome that is conserved in Drosophila, and show that differentiation signals modulate RNAi silencing to regulate developmental genes.

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Figure 1: siRNA clusters and RNAi-dependent assembly of heterochromatin at gene-containing regions.
Figure 2: Tf2 retrotransposons produce siRNAs and show RNAi-dependent heterochromatin formation.
Figure 3: RNAi and heterochromatin factors act in an overlapping manner with the exosome to silence genes located in HOODs.
Figure 4: Specialized machinery triggers RNAi to regulate developmental genes and silence retroelements.

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Gene Expression Omnibus

Data deposits

Microarray and sequencing data are available at the NCBI Gene Expression Omnibus (GEO) repository under the accession number GSE41643.


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We thank M. Zofall and K. Zhang for contributions, J. Barrowman for editing the manuscript, M. Yamamoto for the pla1-37 strain, E. Lei for the Drosophila rrp6 mutant, B. Walker and M. Pineda for their help in sequencing, and Grewal laboratory members for discussions. This study used the Helix Systems and the Biowulf Linux cluster at the National Institutes of Health. This work was supported by the Intramural Research Program of the National Institutes of Health, National Cancer Institute.

Author information




S.Y. and S.I.S.G. designed the experiments. F.Z., R.T.F., S.Y. and G.B.R. prepared the library of small RNA for deep sequencing. S.M. processed the deep-sequencing data. S.Y., S.M. and S.I.S.G. analysed the data. F.E.R.-T. and S.Y. carried out ChIP-chip. Y.R. performed the Drosophila genetic crosses. S.Y. performed all other experiments, if not stated. S.I.S.G. wrote the paper with input from all of the authors.

Corresponding author

Correspondence to Shiv I. S. Grewal.

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The authors declare no competing financial interests.

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Yamanaka, S., Mehta, S., Reyes-Turcu, F. et al. RNAi triggered by specialized machinery silences developmental genes and retrotransposons. Nature 493, 557–560 (2013).

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