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Role for perinuclear chromosome tethering in maintenance of genome stability

Nature volume 456, pages 667–670 (2008)Cite this article

Abstract

Repetitive DNA sequences, which constitute half the genome in some organisms, often undergo homologous recombination. This can instigate genomic instability resulting from a gain or loss of DNA1. Assembly of DNA into silent chromatin is generally thought to serve as a mechanism ensuring repeat stability by limiting access to the recombination machinery2. Consistent with this notion is the observation, in the budding yeast Saccharomyces cerevisiae, that stability of the highly repetitive ribosomal DNA (rDNA) sequences requires a Sir2-containing chromatin silencing complex that also inhibits transcription from foreign promoters and transposons inserted within the repeats by a process called rDNA silencing2,3,4,5. Here we describe a protein network that stabilizes rDNA repeats of budding yeast by means of interactions between rDNA-associated silencing proteins and two proteins of the inner nuclear membrane (INM). Deletion of either the INM or silencing proteins reduces perinuclear rDNA positioning, disrupts the nucleolus–nucleoplasm boundary, induces the formation of recombination foci, and destabilizes the repeats. In addition, artificial targeting of rDNA repeats to the INM suppresses the instability observed in cells lacking an rDNA-associated silencing protein that is typically required for peripheral tethering of the repeats. Moreover, in contrast to Sir2 and its associated nucleolar factors, the INM proteins are not required for rDNA silencing, indicating that Sir2-dependent silencing is not sufficient to inhibit recombination within the rDNA locus. These findings demonstrate a role for INM proteins in the perinuclear localization of chromosomes and show that tethering to the nuclear periphery is required for the stability of rDNA repeats. The INM proteins studied here are conserved and have been implicated in chromosome organization in metazoans6,7. Our results therefore reveal an ancient mechanism in which interactions between INM proteins and chromosomal proteins ensure genome stability.

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Figure 1: Protein network extending from rDNA to the nuclear envelope.
Figure 2: Role of perinuclear protein network at rDNA repeats.
Figure 3: Protein network tethers rDNA to the nuclear envelope.
Figure 4: Targeted perinuclear tethering promotes rDNA repeat stability.

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References

  1. Szostak, J. W. & Wu, R. Unequal crossing over in the ribosomal DNA of Saccharomyces cerevisiae . Nature 284, 426–430 (1980)

    Article  ADS  CAS  Google Scholar 

  2. Moazed, D. Common themes in mechanisms of gene silencing. Mol. Cell 8, 489–498 (2001)

    Article  CAS  Google Scholar 

  3. Straight, A. F. et al. Net1, a Sir2-associated nucleolar protein required for rDNA silencing and nucleolar integrity. Cell 97, 245–256 (1999)

    Article  CAS  Google Scholar 

  4. Bryk, M. et al. Transcriptional silencing of Ty1 elements in the RDN1 locus of yeast. Genes Dev. 11, 255–269 (1997)

    Article  CAS  Google Scholar 

  5. Smith, J. S. & Boeke, J. D. An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev. 11, 241–254 (1997)

    Article  CAS  Google Scholar 

  6. Capell, B. C. & Collins, F. S. Human laminopathies: nuclei gone genetically awry. Nature Rev. Genet. 7, 940–952 (2006)

    Article  CAS  Google Scholar 

  7. Reddy, K. L., Zullo, J. M., Bertolino, E. & Singh, H. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 452, 243–247 (2008)

    Article  ADS  CAS  Google Scholar 

  8. Nomura, M. Ribosomal RNA genes, RNA polymerases, nucleolar structures, and synthesis of rRNA in the yeast Saccharomyces cerevisiae . Cold Spring Harb. Symp. Quant. Biol. 66, 555–565 (2001)

    Article  CAS  Google Scholar 

  9. Keil, R. L. & Roeder, G. S. Cis-acting, recombination-stimulating activity in a fragment of the ribosomal DNA of S. cerevisiae . Cell 39, 377–386 (1984)

    Article  CAS  Google Scholar 

  10. Brewer, B. J. & Fangman, W. L. A replication fork barrier at the 3′ end of yeast ribosomal RNA genes. Cell 55, 637–643 (1988)

    Article  CAS  Google Scholar 

  11. Kobayashi, T. & Ganley, A. R. Recombination regulation by transcription-induced cohesin dissociation in rDNA repeats. Science 309, 1581–1584 (2005)

    Article  ADS  CAS  Google Scholar 

  12. Visintin, R., Hwang, E. S. & Amon, A. Cfi1 prevents premature exit from mitosis by anchoring Cdc14 phosphatase in the nucleolus. Nature 398, 818–823 (1999)

    Article  ADS  CAS  Google Scholar 

  13. Shou, W. et al. Exit from mitosis is triggered by Tem1-dependent release of the protein phosphatase Cdc14 from nucleolar RENT complex. Cell 97, 233–244 (1999)

    Article  CAS  Google Scholar 

  14. Huang, J. & Moazed, D. Association of the RENT complex with nontranscribed and coding regions of rDNA and a regional requirement for the replication fork block protein Fob1 in rDNA silencing. Genes Dev. 17, 2162–2176 (2003)

    Article  CAS  Google Scholar 

  15. Rabitsch, K. P. et al. Kinetochore recruitment of two nucleolar proteins is required for homolog segregation in meiosis I. Dev. Cell 4, 535–548 (2003)

    Article  CAS  Google Scholar 

  16. Huang, J. et al. Inhibition of homologous recombination by a cohesin-associated clamp complex recruited to the rDNA recombination enhancer. Genes Dev. 20, 2887–2901 (2006)

    Article  CAS  Google Scholar 

  17. Gottlieb, S. & Esposito, R. E. A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNA. Cell 56, 771–776 (1989)

    Article  CAS  Google Scholar 

  18. Fritze, C. E., Verschueren, K., Strich, R. & Easton Esposito, R. Direct evidence for SIR2 modulation of chromatin structure in yeast rDNA. EMBO J. 16, 6495–6509 (1997)

    Article  CAS  Google Scholar 

  19. Smith, J. S., Caputo, E. & Boeke, J. D. A genetic screen for ribosomal DNA silencing defects identifies multiple DNA replication and chromatin-modulating factors. Mol. Cell. Biol. 19, 3184–3197 (1999)

    Article  CAS  Google Scholar 

  20. King, M. C., Lusk, C. P. & Blobel, G. Karyopherin-mediated import of integral inner nuclear membrane proteins. Nature 442, 1003–1007 (2006)

    Article  ADS  CAS  Google Scholar 

  21. Brachner, A., Reipert, S., Foisner, R. & Gotzmann, J. LEM2 is a novel MAN1-related inner nuclear membrane protein associated with A-type lamins. J. Cell Sci. 118, 5797–5810 (2005)

    Article  CAS  Google Scholar 

  22. Rodriguez-Navarro, S., Igual, J. C. & Perez-Ortin, J. E. SRC1: an intron-containing yeast gene involved in sister chromatid segregation. Yeast 19, 43–54 (2002)

    Article  CAS  Google Scholar 

  23. Hellemans, J. et al. Loss-of-function mutations in LEMD3 result in osteopoikilosis, Buschke–Ollendorff syndrome and melorheostosis. Nature Genet. 36, 1213–1218 (2004)

    Article  CAS  Google Scholar 

  24. Bione, S. et al. Identification of a novel X-linked gene responsible for Emery–Dreifuss muscular dystrophy. Nature Genet. 8, 323–327 (1994)

    Article  CAS  Google Scholar 

  25. Kaeberlein, M., McVey, M. & Guarente, L. The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes Dev. 13, 2570–2580 (1999)

    Article  CAS  Google Scholar 

  26. Gartenberg, M. R., Neumann, F. R., Laroche, T., Blaszczyk, M. & Gasser, S. M. Sir-mediated repression can occur independently of chromosomal and subnuclear contexts. Cell 119, 955–967 (2004)

    Article  CAS  Google Scholar 

  27. Guacci, V., Hogan, E. & Koshland, D. Chromosome condensation and sister chromatid pairing in budding yeast. J. Cell Biol. 125, 517–530 (1994)

    Article  CAS  Google Scholar 

  28. Torres-Rosell, J. et al. The Smc5–Smc6 complex and SUMO modification of Rad52 regulates recombinational repair at the ribosomal gene locus. Nature Cell Biol. 9, 923–931 (2007)

    Article  CAS  Google Scholar 

  29. Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature 425, 737–741 (2003)

    Article  ADS  CAS  Google Scholar 

  30. Moazed, D. & Johnson, D. A deubiquitinating enzyme interacts with SIR4 and regulates silencing in S. cerevisiae . Cell 86, 667–677 (1996)

    Article  CAS  Google Scholar 

  31. Haas, W. et al. Optimization and use of peptide mass measurement accuracy in shotgun proteomics. Mol. Cell. Proteomics 5, 1326–1337 (2006)

    Article  CAS  Google Scholar 

  32. Buker, S. M. et al. Two different Argonaute complexes are required for siRNA generation and heterochromatin assembly in fission yeast. Nature Struct. Mol. Biol. 14, 200–207 (2007)

    Article  CAS  Google Scholar 

  33. Beausoleil, S. A., Villen, J., Gerber, S. A., Rush, J. & Gygi, S. P. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. Nature Biotechnol. 24, 1285–1292 (2006)

    Article  CAS  Google Scholar 

  34. Kurdistani, S. K. & Grunstein, M. In vivo protein–protein and protein–DNA crosslinking for genomewide binding microarray. Methods 31, 90–95 (2003)

    Article  CAS  Google Scholar 

  35. Oakes, M., Siddiqi, I., Vu, L., Aris, J. & Nomura, M. Transcription factor UAF, expansion and contraction of ribosomal DNA (rDNA) repeats, and RNA polymerase switch in transcription of yeast rDNA. Mol. Cell. Biol. 19, 8559–8569 (1999)

    Article  CAS  Google Scholar 

  36. Libuda, D. E. & Winston, F. Amplification of histone genes by circular chromosome formation in Saccharomyces cerevisiae . Nature 443, 1003–1007 (2006)

    Article  ADS  CAS  Google Scholar 

Download references

Acknowledgements

We thank C. Yip, T. Walz, J. Huang, M. Bühler, D. Koshland, A. Palazzo, D. E. Libuda, F. Winston, L. Vasiljeva, S. Buratowski, J. E. Warner, C. Anderson, G. A. Beltz, M. Lisby, T. Daniel, L. Ding and the Harvard NeuroDiscovery Optical Imaging Center for technical assistance or materials, and T. Rapoport, T. Iida, M. Motamedi, A. Johnson, M. Onishi, E. Gerace, S. Buker, M. Halic and members of the Moazed laboratory for helpful discussions and comments. This work was supported by the National Institutes of Health and the Howard Hughes Medical Institute (D.M.), and the Canadian Institutes of Health Research Institute of Aging (K.M.). D.M. is a scholar of the Leukemia and Lymphoma Society.

Author Contributions K.M. and D.M. designed experiments and wrote the paper. K.M. and J.S. performed LC–MS/MS analyses. K.M. performed the other experiments. S.P.G. provided mass spectrometry expertise and equipment.

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  1. Howard Hughes Medical Institute and,,

    Karim Mekhail & Danesh Moazed

  2. Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA,

    Karim Mekhail, Jan Seebacher, Steven P. Gygi & Danesh Moazed

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  1. Karim Mekhail
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Correspondence to Danesh Moazed.

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Mekhail, K., Seebacher, J., Gygi, S. et al. Role for perinuclear chromosome tethering in maintenance of genome stability. Nature 456, 667–670 (2008). https://doi.org/10.1038/nature07460

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