Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR

Abstract

Centromere-binding protein B (CENP-B) is a widely conserved DNA binding factor associated with heterochromatin and centromeric satellite repeats1. In fission yeast, CENP-B homologues have been shown to silence long terminal repeat (LTR) retrotransposons by recruiting histone deacetylases2. However, CENP-B factors also have unexplained roles in DNA replication3,4. Here we show that a molecular function of CENP-B is to promote replication-fork progression through the LTR. Mutants have increased genomic instability caused by replication-fork blockage that depends on the DNA binding factor switch-activating protein 1 (Sap1), which is directly recruited by the LTR. The loss of Sap1-dependent barrier activity allows the unhindered progression of the replication fork, but results in rearrangements deleterious to the retrotransposon. We conclude that retrotransposons influence replication polarity through recruitment of Sap1 and transposition near replication-fork blocks, whereas CENP-B counteracts this activity and promotes fork stability. Our results may account for the role of LTR in fragile sites, and for the association of CENP-B with pericentromeric heterochromatin and tandem satellite repeats.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: DNA damage in CENP-B mutants is suppressed by sap1 mutation.
Figure 2: Sap1 and CENP-B co-localize at the LTR of retrotransposons in vivo.
Figure 3: CENP-B promotes replication-fork progression through the Sap1-dependent barrier present at the LTR and prevents homologous recombination.
Figure 4: CENP-B and Sap1 have opposite effects on Tf2 stability.

Similar content being viewed by others

Accession codes

Data deposits

The sequences from the ChIP-seq experiments are deposited in Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra?term=SRA024710) under accession number SRA024710.

References

  1. Okada, T. et al. CENP-B controls centromere formation depending on the chromatin context. Cell 131, 1287–1300 (2007)

    Article  CAS  Google Scholar 

  2. Cam, H. P., Noma, K., Ebina, H., Levin, H. L. & Grewal, S. I. Host genome surveillance for retrotransposons by transposon-derived proteins. Nature 451, 431–436 (2008)

    Article  ADS  CAS  Google Scholar 

  3. Murakami, Y., Huberman, J. A. & Hurwitz, J. Identification, purification, and molecular cloning of autonomously replicating sequence-binding protein 1 from fission yeast Schizosaccharomyces pombe . Proc. Natl Acad. Sci. USA 93, 502–507 (1996)

    Article  ADS  CAS  Google Scholar 

  4. Locovei, A. M., Spiga, M. G., Tanaka, K., Murakami, Y. & D’Urso, G. The CENP-B homolog, Abp1, interacts with the initiation protein Cdc23 (MCM10) and is required for efficient DNA replication in fission yeast. Cell Div. 1, 27 (2006)

    Article  Google Scholar 

  5. Lee, J. K., Huberman, J. A. & Hurwitz, J. Purification and characterization of a CENP-B homologue protein that binds to the centromeric K-type repeat DNA of Schizosaccharomyces pombe . Proc. Natl Acad. Sci. USA 94, 8427–8432 (1997)

    Article  ADS  CAS  Google Scholar 

  6. Baum, M. & Clarke, L. Fission yeast homologs of human CENP-B have redundant functions affecting cell growth and chromosome segregation. Mol. Cell. Biol. 20, 2852–2864 (2000)

    Article  CAS  Google Scholar 

  7. Irelan, J. T., Gutkin, G. I. & Clarke, L. Functional redundancies, distinct localizations and interactions among three fission yeast homologs of centromere protein-B. Genetics 157, 1191–1203 (2001)

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Irvine, D. V. et al. Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing. Genome Res. 19, 1077–1083 (2009)

    Article  CAS  Google Scholar 

  9. de Lahondes, R., Ribes, V. & Arcangioli, B. Fission yeast Sap1 protein is essential for chromosome stability. Eukaryot. Cell 2, 910–921 (2003)

    Article  CAS  Google Scholar 

  10. Mejia-Ramirez, E., Sanchez-Gorostiaga, A., Krimer, D. B., Schvartzman, J. B. & Hernandez, P. The mating type switch-activating protein Sap1 is required for replication fork arrest at the rRNA genes of fission yeast. Mol. Cell. Biol. 25, 8755–8761 (2005)

    Article  CAS  Google Scholar 

  11. Krings, G. & Bastia, D. Sap1p binds to Ter1 at the ribosomal DNA of Schizosaccharomyces pombe and causes polar replication fork arrest. J. Biol. Chem. 280, 39135–39142 (2005)

    Article  CAS  Google Scholar 

  12. Noguchi, C. & Noguchi, E. Sap1 promotes the association of the replication fork protection complex with chromatin and is involved in the replication checkpoint in Schizosaccharomyces pombe . Genetics 175, 553–566 (2007)

    Article  CAS  Google Scholar 

  13. Szilard, R. K. et al. Systematic identification of fragile sites via genome-wide location analysis of gamma-H2AX. Nature Struct. Mol. Biol. 17, 299–305 (2010)

    Article  CAS  Google Scholar 

  14. Aguilar-Arnal, L., Marsellach, F. X. & Azorin, F. The fission yeast homologue of CENP-B, Abp1, regulates directionality of mating-type switching. EMBO J. 27, 1029–1038 (2008)

    Article  CAS  Google Scholar 

  15. Arcangioli, B. & Klar, A. J. A novel switch-activating site (SAS1) and its cognate binding factor (SAP1) required for efficient mat1 switching in Schizosaccharomyces pombe . EMBO J. 10, 3025–3032 (1991)

    Article  CAS  Google Scholar 

  16. Deshpande, A. M. & Newlon, C. S. DNA replication fork pause sites dependent on transcription. Science 272, 1030–1033 (1996)

    Article  ADS  CAS  Google Scholar 

  17. Ghazvini, M., Ribes, V. & Arcangioli, B. The essential DNA-binding protein sap1 of Schizosaccharomyces pombe contains two independent oligomerization interfaces that dictate the relative orientation of the DNA-binding domain. Mol. Cell. Biol. 15, 4939–4946 (1995)

    Article  CAS  Google Scholar 

  18. Guo, Y. & Levin, H. L. High-throughput sequencing of retrotransposon integration provides a saturated profile of target activity in Schizosaccharomyces pombe . Genome Res. 20, 239–248 (2010)

    Article  CAS  Google Scholar 

  19. Segurado, M., Gomez, M. & Antequera, F. Increased recombination intermediates and homologous integration hot spots at DNA replication origins. Mol. Cell 10, 907–916 (2002)

    Article  CAS  Google Scholar 

  20. Meister, P. et al. Nuclear factories for signalling and repairing DNA double strand breaks in living fission yeast. Nucleic Acids Res. 31, 5064–5073 (2003)

    Article  CAS  Google Scholar 

  21. Sehgal, A., Lee, C. Y. & Espenshade, P. J. SREBP controls oxygen-dependent mobilization of retrotransposons in fission yeast. PLoS Genet. 3, e131 (2007)

    Article  Google Scholar 

  22. Kupiec, M. & Petes, T. D. Allelic and ectopic recombination between Ty elements in yeast. Genetics 119, 549–559 (1988)

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Gomez, E. B., Nugent, R. L., Laria, S. & Forsburg, S. L. Schizosaccharomyces pombe histone acetyltransferase Mst1 (KAT5) is an essential protein required for damage response and chromosome segregation. Genetics 179, 757–771 (2008)

    Article  CAS  Google Scholar 

  24. 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 

  25. Roguev, A. et al. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science 322, 405–410 (2008)

    Article  ADS  CAS  Google Scholar 

  26. Ton-Hoang, B. et al. Single-stranded DNA transposition is coupled to host replication. Cell 142, 398–408 (2010)

    Article  CAS  Google Scholar 

  27. Wong, L. H. & Choo, K. H. Evolutionary dynamics of transposable elements at the centromere. Trends Genet. 20, 611–616 (2004)

    Article  CAS  Google Scholar 

  28. Putnam, C. D., Hayes, T. K. & Kolodner, R. D. Specific pathways prevent duplication-mediated genome rearrangements. Nature 460, 984–989 (2009)

    Article  ADS  CAS  Google Scholar 

  29. Wallis, J. W., Chrebet, G., Brodsky, G., Rolfe, M. & Rothstein, R. A hyper-recombination mutation in S. cerevisiae identifies a novel eukaryotic topoisomerase. Cell 58, 409–419 (1989)

    Article  CAS  Google Scholar 

  30. Lemoine, F. J., Degtyareva, N. P., Lobachev, K. & Petes, T. D. Chromosomal translocations in yeast induced by low levels of DNA polymerase a model for chromosome fragile sites. Cell 120, 587–598 (2005)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank the Martienssen laboratory, V. Aranda, E. Mejia-Ramirez and F. Antequera for technical advice and discussions, and R. Allshire, E. Noguchi, M. O’Connell, P. Espenshade and the National BioResource Project (T. Nakamura, Japan) for strains. This work was supported by National Institutes of Health grant RO1GM076396 to R.A.M., Cancer Research UK grant C9546/A6517 to J.B., l’Agence Nationale de la Recherche grant ANR-06-BLAN-0271 to B.A., a National Health and Medical Research Council C.J. Martin Fellowship to D.V.I. and a Postdoctoral Fellowship from the Spanish Ministry of Education to M.Z.

Author information

Authors and Affiliations

Authors

Contributions

M.Z., B.A. and R.A.M. designed the experiments presented and wrote the paper. M.Z. performed and analysed the experiments. M.W.V. provided bioinformatic analysis. D.G. and D.V.I. provided strains. S.W. and J.B. performed additional experiments.

Corresponding author

Correspondence to Robert A. Martienssen.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Table 1, Supplementary Figures 1-11 with legends, Supplementary Methods and additional references. (PDF 9247 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zaratiegui, M., Vaughn, M., Irvine, D. et al. CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR. Nature 469, 112–115 (2011). https://doi.org/10.1038/nature09608

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature09608

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing