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The human CENP-A centromeric nucleosome-associated complex

Abstract

The basic element for chromosome inheritance, the centromere, is epigenetically determined in mammals. The prime candidate for specifying centromere identity is the array of nucleosomes assembled with CENP-A, the centromere-specific histone H3 variant. Here, we show that CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of three new human centromere proteins (CENP-M, CENP-N and CENP-T), along with CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Facilitates chromatin transcription (FACT) and nucleophosmin-1 (previously implicated in transcriptional chromatin remodelling and as a multifunctional nuclear chaperone, respectively) are absent from histone H3-containing nucleosomes, but are stably recruited to CENP-A nucleosomes independent of CENP-A NAC. Seven new CENP-A-nucleosome distal (CAD) centromere components (CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S) are identified as assembling on the CENP-A NAC. The CENP-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival despite continued centromere-derived mitotic checkpoint signalling.

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Figure 1: Purification of CENP-A nucleosomes.
Figure 2: CENP-A dependent centromere localization of four CENP-A nucleosome associated proteins.
Figure 3: Purification of the CENP-A NAC and identification of its associated CAD complex components.
Figure 4: Assembly of the CENP-A NAC requires CENP-M and CENP-N.
Figure 5: CENP-U(50) depletion causes mitotic errors without affecting the mitotic checkpoint.
Figure 6: Mitotic defects due to CENP-A NAC disruption by depletion of CENP-M, CENP-N or CENP-T.

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References

  1. Cleveland, D. W., Mao, Y. & Sullivan, K. F. Centromeres and kinetochores: from epigenetics to mitotic checkpoint signaling. Cell 112, 407–421 (2003).

    Article  CAS  Google Scholar 

  2. Amor, D. J., Kalitsis, P., Sumer, H. & Choo, K. H. Building the centromere: from foundation proteins to 3D organization. Trends Cell Biol. 14, 359–368 (2004).

    Article  CAS  Google Scholar 

  3. Amor, D. J. & Choo, K. H. Neocentromeres: role in human disease, evolution, and centromere study. Am. J. Hum. Genet. 71, 695–714 (2002).

    Article  Google Scholar 

  4. Henikoff, S. & Ahmad, K. Assembly of variant histones into chromatin. Annu. Rev. Cell Dev. Biol. 21, 133–153 (2005).

    Article  CAS  Google Scholar 

  5. Sullivan, B. A., Blower, M. D. & Karpen, G. H. Determining centromere identity: cyclical stories and forking paths. Nature Rev. Genet. 2, 584–596 (2001).

    Article  CAS  Google Scholar 

  6. Blower, M. D., Sullivan, B. A. & Karpen, G. H. Conserved organization of centromeric chromatin in flies and humans. Dev. Cell 2, 319–330 (2002).

    Article  CAS  Google Scholar 

  7. Black, B. E. et al. Structural determinants for generating centromeric chromatin. Nature 430, 578–82 (2004).

    Article  CAS  Google Scholar 

  8. Cheeseman, I. M., Drubin, D. G. & Barnes, G. Simple centromere, complex kinetochore: linking spindle microtubules and centromeric DNA in budding yeast. J. Cell Biol. 157, 199–203 (2002).

    Article  CAS  Google Scholar 

  9. McAinsh, A. D., Tytell, J. D. & Sorger, P. K. Structure, function and regulation of budding yeast kinetochores. Annu. Rev. Cell Dev. Biol. 19, 519–539 (2003).

    Article  CAS  Google Scholar 

  10. Howman, E. V. et al. Early disruption of centromeric chromatin organization in centromere protein A (Cenpa) null mice. Proc. Natl Acad. Sci. USA 97, 1148–1153 (2000).

    Article  CAS  Google Scholar 

  11. Fukagawa, T., Pendon, C., Morris, J. & Brown, W. CENP-C is necessary but not sufficient to induce formation of a functional centromere. EMBO J. 18, 4196–4209 (1999).

    Article  CAS  Google Scholar 

  12. Meluh, P. B. & Koshland, D. Evidence that the MIF2 gene of Saccharomyces cerevisiae encodes a centromere protein with homology to the mammalian centromere protein CENP-C. Mol. Biol. Cell 6, 793–807 (1995).

    Article  CAS  Google Scholar 

  13. Goshima, G., Kiyomitsu, T., Yoda, K. & Yanagida, M. Human centromere chromatin protein hMis12, essential for equal segregation, is independent of CENP-A loading pathway. J. Cell Biol. 160, 25–39 (2003).

    Article  CAS  Google Scholar 

  14. Goshima, G., Saitoh, S. & Yanagida, M. Proper metaphase spindle length is determined by centromere proteins Mis12 and Mis6 required for faithful chromosome segregation. Genes Dev. 13, 1664–1677 (1999).

    Article  CAS  Google Scholar 

  15. Liu, S. T. et al. Human CENP-I specifies localization of CENP-F, MAD1 and MAD2 to kinetochores and is essential for mitosis. Nature Cell Biol. 5, 341–345 (2003).

    Article  CAS  Google Scholar 

  16. Nishihashi, A. et al. CENP-I is essential for centromere function in vertebrate cells. Dev. Cell 2, 463–476 (2002).

    Article  CAS  Google Scholar 

  17. Fukagawa, T. et al. CENP-H, a constitutive centromere component, is required for centromere targeting of CENP-C in vertebrate cells. EMBO J. 20, 4603–4617 (2001).

    Article  CAS  Google Scholar 

  18. Bomont, P., Maddox, P., Shah, J. V., Desai, A. B. & Cleveland, D. W. Unstable microtubule capture at kinetochores depleted of the centromere-associated protein CENP-F. EMBO J. 24, 3927–3939 (2005).

    Article  CAS  Google Scholar 

  19. Mao, Y., Desai, A. & Cleveland, D. W. Microtubule capture by CENP-E silences BubR1-dependent mitotic checkpoint signaling. J. Cell Biol. 170, 873–880 (2005).

    Article  CAS  Google Scholar 

  20. Obuse, C. et al. Proteomics analysis of the centromere complex from HeLa interphase cells: UV-damaged DNA binding protein 1 (DDB-1) is a component of the CEN-complex, while BMI-1 is transiently co-localized with the centromeric region in interphase. Genes Cells 9, 105–120 (2004).

    Article  CAS  Google Scholar 

  21. Cheeseman, I. M. et al. Implication of a novel multiprotein Dam1p complex in outer kinetochore function. J. Cell Biol. 155, 1137–1145 (2001).

    Article  CAS  Google Scholar 

  22. Smith, S. & Stillman, B. Stepwise assembly of chromatin during DNA replication in vitro. EMBO J. 10, 971–980 (1991).

    Article  CAS  Google Scholar 

  23. Jackson, V. In vivo studies on the dynamics of histone–DNA interaction: evidence for nucleosome dissolution during replication and transcription and a low level of dissolution independent of both. Biochemistry 29, 719–731 (1990).

    Article  CAS  Google Scholar 

  24. Shelby, R. D., Vafa, O. & Sullivan, K. F. Assembly of CENP-A into centromeric chromatin requires a cooperative array of nucleosomal DNA contact sites. J. Cell Biol. 136, 501–513 (1997).

    Article  CAS  Google Scholar 

  25. Eickbush, T. H. & Moudrianakis, E. N. The histone core complex: an octamer assembled by two sets of protein-protein interactions. Biochemistry 17, 4955–4964 (1978).

    Article  CAS  Google Scholar 

  26. Masumoto, H., Masukata, H., Muro, Y., Nozaki, N. & Okazaki, T. A human centromere antigen (CENP-B) interacts with a short specific sequence in alphoid DNA, a human centromeric satellite. J. Cell Biol. 109, 1963–1973 (1989).

    Article  CAS  Google Scholar 

  27. Verreault, A., Kaufman, P. D., Kobayashi, R. & Stillman, B. Nucleosome assembly by a complex of CAF-1 and acetylated histones H3/H4. Cell 87, 95–104 (1996).

    Article  CAS  Google Scholar 

  28. Tagami, H., Ray-Gallet, D., Almouzni, G. & Nakatani, Y. Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. Cell 116, 51–61 (2004).

    Article  CAS  Google Scholar 

  29. Maison, C. & Almouzni, G. HP1 and the dynamics of heterochromatin maintenance. Nature Rev. Mol. Cell Biol. 5, 296–304 (2004).

    Article  CAS  Google Scholar 

  30. Sarma, K. & Reinberg, D. Histone variants meet their match. Nature Rev. Mol. Cell Biol. 6, 139–149 (2005).

    Article  CAS  Google Scholar 

  31. Hanissian, S. H. et al. cDNA cloning and characterization of a novel gene encoding the MLF1-interacting protein MLF1IP. Oncogene 23, 3700–3707 (2004).

    Article  CAS  Google Scholar 

  32. Minoshima, Y. et al. The constitutive centromere component CENP-50 is required for recovery from spindle damage. Mol. Cell Biol. 25, 10315–10328 (2005).

    Article  CAS  Google Scholar 

  33. Bierie, B., Edwin, M., Joseph Melenhorst, J. & Hennighausen, L. The proliferation associated nuclear element (PANE1) is conserved between mammals and fish and preferentially expressed in activated lymphoid cells. Gene Expr. Patterns 4, 389–395 (2004).

    Article  CAS  Google Scholar 

  34. Cheeseman, I. M. & Desai, A. A combined approach for the localization and tandem affinity purification of protein complexes from metazoans. Sci. STKE DOI:10.1126/stke.2662005pl1 (2005).

  35. Earnshaw, W. C. et al. Molecular cloning of cDNA for CENP-B, the major human centromere autoantigen. J. Cell Biol. 104, 817–829 (1987).

    Article  CAS  Google Scholar 

  36. Saitoh, H. et al. CENP-C, an autoantigen in scleroderma, is a component of the human inner kinetochore plate. Cell 70, 115–125 (1992).

    Article  CAS  Google Scholar 

  37. Sugata, N., Munekata, E. & Todokoro, K. Characterization of a novel kinetochore protein, CENP-H. J. Biol. Chem. 274, 27343–27346 (1999).

    Article  CAS  Google Scholar 

  38. Orphanides, G., Wu, W. H., Lane, W. S., Hampsey, M. & Reinberg, D. The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins. Nature 400, 284–288 (1999).

    Article  CAS  Google Scholar 

  39. Okuwaki, M., Matsumoto, K., Tsujimoto, M. & Nagata, K. Function of nucleophosmin/B23, a nucleolar acidic protein, as a histone chaperone. FEBS Lett. 506, 272–276 (2001).

    Article  CAS  Google Scholar 

  40. Okuda, M. The role of nucleophosmin in centrosome duplication. Oncogene 21, 6170–6174 (2002).

    Article  CAS  Google Scholar 

  41. Brummelkamp, T. R., Bernards, R. & Agami, R. A system for stable expression of short interfering RNAs in mammalian cells. Science 296, 550–553 (2002).

    Article  CAS  Google Scholar 

  42. Regnier, V. et al. CENP-A is required for accurate chromosome segregation and sustained kinetochore association of BubR1. Mol. Cell Biol. 25, 3967–3981 (2005).

    Article  CAS  Google Scholar 

  43. Chen, R. H., Shevchenko, A., Mann, M. & Murray, A. W. Spindle checkpoint protein Xmad1 recruits Xmad2 to unattached kinetochores. J. Cell Biol. 143, 283–295 (1998).

    Article  CAS  Google Scholar 

  44. Shah, J. V. et al. Dynamics of centromere and kinetochore proteins; implications for checkpoint signaling and silencing. Curr. Biol. 14, 942–952 (2004).

    CAS  PubMed  Google Scholar 

  45. Zinkowski, R. P., Meyne, J. & Brinkley, B. R. The centromere–kinetochore complex: a repeat subunit model. J. Cell Biol. 113, 1091–1110 (1991).

    Article  CAS  Google Scholar 

  46. Hayashi, T. et al. Mis16 and Mis18 are required for CENP-A loading and histone deacetylation at centromeres. Cell 118, 715–729 (2004).

    Article  CAS  Google Scholar 

  47. Belotserkovskaya, R. et al. FACT facilitates transcription-dependent nucleosome alteration. Science 301, 1090–1093 (2003).

    Article  CAS  Google Scholar 

  48. Yoda, K., Morishita, S. & Hashimoto, K. Histone variant CENP-A purification, nucleosome reconstitution. Methods Enzymol. 375, 253–269 (2004).

    Article  CAS  Google Scholar 

  49. MacCoss, M. J. et al. Shotgun identification of protein modifications from protein complexes and lens tissue. Proc. Natl Acad. Sci. USA 99, 7900–7905 (2002).

    Article  CAS  Google Scholar 

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Acknowledgements

The authors thank T. Fukagawa, I. Cheeseman, J. Shah, P. Maddox, K. Weis, F. Furnari and K. Yoda for generously providing reagents and assistance; D. Young and the University of California at San Diego (UCSD) Cancer Center for flow cytometry and the Oegema and Desai laboratorys for use of spinning disk confocal and deconvolution microscopes. This work has been supported by grants from the National Institutes of Health (NIH) to D.W.C. (GM 29513) and J.R.Y. (RR11823). D.R.F. has been supported by a postdoctoral fellowship from the NIH and B.E.B. has been supported by a postdoctoral fellowship from the American Cancer Society and in part by a Career Award in the Biomedical Sciences from the Burroughs Welcome Fund. D.W.C. receives salary support from the Ludwig Institute for Cancer Research.

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Correspondence to Don W. Cleveland.

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Foltz, D., Jansen, L., Black, B. et al. The human CENP-A centromeric nucleosome-associated complex. Nat Cell Biol 8, 458–469 (2006). https://doi.org/10.1038/ncb1397

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