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Defects in RNA quality control factors reveal RNAi-independent nucleation of heterochromatin

Nature Structural & Molecular Biology volume 18, pages 1132–1138 (2011)Cite this article

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Abstract

Heterochromatin assembly at Schizosaccharomyces pombe centromeres involves a self-reinforcing loop mechanism wherein chromatin-bound RNAi factors facilitate targeting of Clr4–Rik1 methyltransferase. However, the initial nucleation of heterochromatin has remained elusive. We show that cells lacking Mlo3, a protein involved in mRNP biogenesis and RNA quality control, assemble functional heterochromatin in RNAi-deficient cells. Heterochromatin restoration is linked to RNA surveillance because loss of Mlo3-associated TRAMP also rescues heterochromatin defects of RNAi mutants. mlo3Δ, which causes accumulation of bidirectional repeat-transcripts, restores Rik1 enrichment at repeats and triggers de novo heterochromatin formation in the absence of RNAi. RNAi-independent heterochromatin nucleation occurs at selected euchromatic loci that show upregulation of antisense RNAs in mlo3Δ cells. We find that the exosome RNA degradation machinery acts parallel to RNAi to promote heterochromatin formation at centromeres. These results suggest that RNAi-independent mechanisms exploit transcription and non-coding RNAs to nucleate heterochromatin.

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Figure 1: mlo3Δ restores functional heterochromatin at centromeres in the ago1Δ mutant.
Figure 2: tfs1Δ restores centromeric heterochromatin in ago1Δ cells.
Figure 3: tfs1Δ and mlo3Δ differentially suppress heterochromatin defects in clr3Δ ago1Δ double mutant cells.
Figure 4: Loss of RNA surveillance factor TRAMP restores centromeric heterochromatin in ago1Δ cells.
Figure 5: Rrp6 acts parallel to RNAi to mediate heterochromatin formation and silencing at centromeres.
Figure 6: mlo3Δ restores Rik1 enrichment at centromeric repeats and triggers de novo heterochromatin formation in the absence of RNAi.
Figure 7: RNAi-independent heterochromatin formation occurs at euchromatic loci in mlo3Δ cells.

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Acknowledgements

We are thankful to D. Eick (Helmholtz Center Munich) for the gift of phospho (Ser2) RNAPII antibody, R. Dhar and N. Krogan (University of California, San Francisco) for strains, J. Dhakshnamoorthy, N. Komissarova and S. Mehta for helpful contributions, and members of the Grewal laboratory for discussions. This research was supported by the Intramural Research Program of the US National Institutes of Health, National Cancer Institute, Center for Cancer Research.

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  1. Eesin Chen

    Present address: Present address: Department of Biochemistry, National University of Singapore, Singapore.,

  2. Francisca E Reyes-Turcu and Ke Zhang: These authors contributed equally to this work.

Authors and Affiliations

  1. Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA

    Francisca E Reyes-Turcu, Ke Zhang, Martin Zofall, Eesin Chen & Shiv I S Grewal

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Contributions

F.E.R.-T., K.Z. and S.I.S.G. designed the research. K.Z., F.E.R.-T. and M.Z. conducted the experiments. E.C. contributed the reagents. F.E.R.-T., K.Z. and S.I.S.G. analyzed the data. F.E.R.-T. and S.I.S.G. wrote the paper. F.E.R.-T., K.Z. and S.I.S.G. edited the paper.

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Correspondence to Shiv I S Grewal.

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Reyes-Turcu, F., Zhang, K., Zofall, M. et al. Defects in RNA quality control factors reveal RNAi-independent nucleation of heterochromatin. Nat Struct Mol Biol 18, 1132–1138 (2011). https://doi.org/10.1038/nsmb.2122

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