Cell cycle control of centromeric repeat transcription and heterochromatin assembly

Abstract

Heterochromatin in eukaryotic genomes regulates diverse chromosomal processes including transcriptional silencing1. However, in Schizosaccharomyces pombe RNA polymerase II (RNAPII) transcription of centromeric repeats is essential for RNA-interference-mediated heterochromatin assembly2,3,4,5. Here we study heterochromatin dynamics during the cell cycle and its effect on RNAPII transcription. We describe a brief period during the S phase of the cell cycle in which RNAPII preferentially transcribes centromeric repeats. This period is enforced by heterochromatin, which restricts RNAPII accessibility at centromeric repeats for most of the cell cycle. RNAPII transcription during S phase is linked to loading of RNA interference and heterochromatin factors such as the Ago1 subunit of the RITS complex6 and the Clr4 methyltransferase complex subunit Rik1 (ref. 7). Moreover, Set2, an RNAPII-associated methyltransferase8 that methylates histone H3 lysine 36 at repeat loci during S phase, acts in a pathway parallel to Clr4 to promote heterochromatin assembly. We also show that phosphorylation of histone H3 serine 10 alters heterochromatin during mitosis, correlating with recruitment of condensin that affects silencing of centromeric repeats. Our analyses suggest at least two distinct modes of heterochromatin targeting to centromeric repeats, whereby RNAPII transcription of repeats and chromodomain proteins bound to methylated histone H3 lysine 9 mediate recruitment of silencing factors. Together, these processes probably facilitate heterochromatin maintenance through successive cell divisions.

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Figure 1: Levels of heterochromatin-derived transcripts and RNAPII occupancy peak during S phase.
Figure 2: Heterochromatin limits RNAPII occupancy.
Figure 3: Cell-cycle-dependent changes in heterochromatin.
Figure 4: Heterochromatin assembly during S phase requires RNAPII-associated activities.

References

  1. 1

    Grewal, S. I. & Jia, S. Heterochromatin revisited. Nature Rev. Genet. 8, 35–46 (2007)

    CAS  Article  Google Scholar 

  2. 2

    Volpe, T. A. et al. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833–1837 (2002)

    CAS  Article  ADS  Google Scholar 

  3. 3

    Cam, H. P. et al. Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nature Genet. 37, 809–819 (2005)

    CAS  Article  Google Scholar 

  4. 4

    Djupedal, I. et al. RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing. Genes Dev. 19, 2301–2306 (2005)

    CAS  Article  Google Scholar 

  5. 5

    Kato, H. et al. RNA polymerase II is required for RNAi-dependent heterochromatin assembly. Science 309, 467–469 (2005)

    CAS  Article  ADS  Google Scholar 

  6. 6

    Verdel, A. et al. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303, 672–676 (2004)

    CAS  Article  ADS  Google Scholar 

  7. 7

    Jia, S., Kobayashi, R. & Grewal, S. I. Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin. Nature Cell Biol. 7, 1007–1013 (2005)

    CAS  Article  Google Scholar 

  8. 8

    Morris, S. A. et al. Histone H3 K36 methylation is associated with transcription elongation in Schizosaccharomyces pombe . Eukaryot. Cell 4, 1446–1454 (2005)

    CAS  Article  Google Scholar 

  9. 9

    Hall, I. M. et al. Establishment and maintenance of a heterochromatin domain. Science 297, 2232–2237 (2002)

    CAS  Article  ADS  Google Scholar 

  10. 10

    Alfa, C., Fantes, P., Hyams, J., McLeod, M. & Warbrick, E. Experiments with Fission Yeast: A Laboratory Course Manual (Cold Sping Harbor Laboratory Press, Cold Spring Harbor, New York, 1993)

    Google Scholar 

  11. 11

    Kim, S. M. & Huberman, J. A. Regulation of replication timing in fission yeast. EMBO J. 20, 6115–6126 (2001)

    CAS  Article  Google Scholar 

  12. 12

    Nicolas, E. et al. Distinct roles of HDAC complexes in promoter silencing, antisense suppression and DNA damage protection. Nature Struct. Mol. Biol. 14, 372–380 (2007)

    CAS  Article  Google Scholar 

  13. 13

    Nakayama, J., Rice, J. C., Strahl, B. D., Allis, C. D. & Grewal, S. I. Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292, 110–113 (2001)

    CAS  Article  ADS  Google Scholar 

  14. 14

    Buhler, M., Verdel, A. & Moazed, D. Tethering RITS to a nascent transcript initiates RNAi- and heterochromatin-dependent gene silencing. Cell 125, 873–886 (2006)

    CAS  Article  Google Scholar 

  15. 15

    Fischle, W. et al. Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 438, 1116–1122 (2005)

    CAS  Article  ADS  Google Scholar 

  16. 16

    Hirota, T., Lipp, J. J., Toh, B. H. & Peters, J. M. Histone H3 serine 10 phosphorylation by Aurora B causes HP1 dissociation from heterochromatin. Nature 438, 1176–1180 (2005)

    CAS  Article  ADS  Google Scholar 

  17. 17

    Yamada, T., Fischle, W., Sugiyama, T., Allis, C. D. & Grewal, S. I. The nucleation and maintenance of heterochromatin by a histone deacetylase in fission yeast. Mol. Cell 20, 173–185 (2005)

    CAS  Article  Google Scholar 

  18. 18

    Nakayama, J., Klar, A. J. & Grewal, S. I. A chromodomain protein, Swi6, performs imprinting functions in fission yeast during mitosis and meiosis. Cell 101, 307–317 (2000)

    CAS  Article  Google Scholar 

  19. 19

    Hirano, T. Condensins: organizing and segregating the genome. Curr. Biol. 15, R265–R275 (2005)

    CAS  Article  Google Scholar 

  20. 20

    Sutani, T. et al. Fission yeast condensin complex: essential roles of non-SMC subunits for condensation and Cdc2 phosphorylation of Cut3/SMC4. Genes Dev. 13, 2271–2283 (1999)

    CAS  Article  Google Scholar 

  21. 21

    Giet, R. & Glover, D. M. Drosophila aurora B kinase is required for histone H3 phosphorylation and condensin recruitment during chromosome condensation and to organize the central spindle during cytokinesis. J. Cell Biol. 152, 669–682 (2001)

    CAS  Article  Google Scholar 

  22. 22

    Oliveira, R. A., Coelho, P. A. & Sunkel, C. E. The condensin I subunit Barren/CAP-H is essential for the structural integrity of centromeric heterochromatin during mitosis. Mol. Cell. Biol. 25, 8971–8984 (2005)

    CAS  Article  Google Scholar 

  23. 23

    Meyer, B. J. Sex in the wormcounting and compensating X-chromosome dose. Trends Genet. 16, 247–253 (2000)

    CAS  Article  Google Scholar 

  24. 24

    Saka, Y. et al. Fission yeast cut3 and cut14, members of a ubiquitous protein family, are required for chromosome condensation and segregation in mitosis. EMBO J. 13, 4938–4952 (1994)

    CAS  Article  Google Scholar 

  25. 25

    Zofall, M. & Grewal, S. I. HULC, a histone H2B ubiquitinating complex, modulates heterochromatin independent of histone methylation in fission yeast. J. Biol. Chem. 282, 14065–14072 (2007)

    CAS  Article  Google Scholar 

  26. 26

    Horn, P. J., Bastie, J. N. & Peterson, C. L. A. Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation. Genes Dev. 19, 1705–1714 (2005)

    CAS  Article  Google Scholar 

  27. 27

    Schramke, V. et al. RNA-interference-directed chromatin modification coupled to RNA polymerase II transcription. Nature 435, 1275–1279 (2005)

    CAS  Article  ADS  Google Scholar 

  28. 28

    Li, B., Carey, M. & Workman, J. L. The role of chromatin during transcription. Cell 128, 707–719 (2007)

    CAS  Article  Google Scholar 

  29. 29

    Motamedi, M. R. et al. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119, 789–802 (2004)

    CAS  Article  Google Scholar 

  30. 30

    Murzina, N., Verreault, A., Laue, E. & Stillman, B. Heterochromatin dynamics in mouse cells: interaction between chromatin assembly factor 1 and HP1 proteins. Mol. Cell 4, 529–540 (1999)

    CAS  Article  Google Scholar 

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Acknowledgements

We thank M. Yanagida for strains, and B. Strahl and C. D. Allis for antibodies. We also thank K. Tomita and X. Chen for technical help, T. Fischer for help with microarray data analysis, and other members of the Grewal laboratory for discussions. This research was supported by the Intramural Research Program of the National Institutes of Health, National Cancer Institute.

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Correspondence to Shiv I. S. Grewal.

Supplementary information

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This file contains Supplementary Figures 1-10 with Legends. The Supplementary Figures show results from conventional ChIP, RT-PCR, serial dilution and Northern analyses that complement data presented in primary Figures 1-4. (PDF 847 kb)

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Chen, E., Zhang, K., Nicolas, E. et al. Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature 451, 734–737 (2008). https://doi.org/10.1038/nature06561

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