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Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome

Abstract

The organization of eukaryotic genomes into distinct structural and functional domains is important for the regulation and transduction of genetic information. Here, we investigated heterochromatin and euchromatin profiles of the entire fission yeast genome and explored the role of RNA interference (RNAi) in genome organization. Histone H3 methylated at Lys4, which defines euchromatin, was not only distributed across most of the chromosomal landscape but was also present at the centromere core, the site of kinetochore assembly. In contrast, histone H3 methylated at Lys9 and its interacting protein Swi6/HP1, which define heterochromatin, coated extended domains associated with a variety of repeat elements and small islands corresponding to meiotic genes. Notably, RNAi components were distributed throughout all these heterochromatin domains, and their localization depended on Clr4/Suv39h histone methyltransferase. Sequencing of small interfering RNAs (siRNAs) associated with the RITS RNAi effector complex identified hot spots of siRNAs, which mapped to a diverse array of elements in these RNAi-heterochromatin domains. We found that Clr4/Suv39h predominantly silenced repeat elements whose derived transcripts, transcribed mainly by RNA polymerase II, serve as a source for siRNAs. Our analyses also uncover an important role for the RNAi machinery in maintaining genomic integrity.

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Figure 1: Genome maps of H3K4me, H3K9me and Swi6.
Figure 2: H3K4me and H3K9me have mutually exclusive localization patterns across major heterochromatic domains and at other genetic elements in the S. pombe genome.
Figure 3: RNAi components are distributed throughout heterochromatic domains.
Figure 4: Clusters of siRNA hot spots reside in heterochromatic domains occupied by RNAi components.
Figure 5: RNAi and heterochromatin machineries dynamically target IRC elements.
Figure 6: Heterochromatin and RNAi distribution at subtelomere I.
Figure 7: Distribution of heterochromatin and RNAi components at tandem rDNA.
Figure 8: Transcripts silenced by Clr4 serve as precursors for RITS-associated siRNAs.

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Acknowledgements

We thank K. Shirahige, Y. Katou and M. Kawano for contributions; M. Lichten, B. Paterson and K. Noma for critical reading; and other members of the laboratory of S.I.S.G. for discussions. T.S. is a JSPS Research Fellow in Biomedical and Behavioral Research at the US National Institutes of Health. This study used the high-performance computational capabilities of the Helix Systems at the National Institutes of Health (http://helix.nih.gov).

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Correspondence to Shiv I S Grewal.

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Supplementary information

Supplementary Fig. 1

Scatter plots of H3K9me and H3K4me ChIP-on-chip analyses. (PDF 29 kb)

Supplementary Fig. 2

RITS and Rdp1 distribute throughout the silent mating-type interval. (PDF 29 kb)

Supplementary Fig. 3

SPAC212.11 transcription is regulated by RNAi and heterochromatin machineries. (PDF 66 kb)

Supplementary Table 1

Increased frequency of mitotic recombination at tandem rDNA in RNAi and clr4 mutants. (PDF 21 kb)

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Cam, H., Sugiyama, T., Chen, E. et al. Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nat Genet 37, 809–819 (2005). https://doi.org/10.1038/ng1602

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