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CENP-C directs a structural transition of CENP-A nucleosomes mainly through sliding of DNA gyres

Nature Structural & Molecular Biology volume 23, pages 204208 (2016) | Download Citation

Abstract

The histone H3 variant CENP-A is incorporated into nucleosomes that mark centromere location. We have recently reported that CENP-A nucleosomes, compared with their H3 counterparts, confer an altered nucleosome shape. Here, using a single-molecule fluorescence resonance energy transfer (FRET) approach with recombinant human histones and centromere DNA, we found that the nucleosome shape change directed by CENP-A is dominated by lateral passing of two DNA gyres (gyre sliding). A nonhistone centromere protein, CENP-C, binds and reshapes the nucleosome, sliding the DNA gyres back to positions similar to those in canonical nucleosomes containing conventional histone H3. The model that we generated to explain the CENP-A–nucleosome transition provides an example of a shape change imposed by external binding proteins and has notable implications for understanding of the epigenetic basis of the faithful inheritance of centromere location on chromosomes.

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Acknowledgements

We thank K. Gupta (University of Pennsylvania) for advice on modeling, C. Davey (Nanyang Technical University) and U. Surana (Agency for Science, Technology and Research, Singapore) for advice on ENA experiments and D. Cleveland (University of California, San Diego), K. Luger (University of Colorado) and A. Straight (Stanford University) for plasmids. This work was supported by US National Institutes of Health grants GM082989 (B.E.B.) and GM097286 (T.-H.L.), and a postdoctoral fellowship from the American Cancer Society (N.S.). We acknowledge support from a University of Pennsylvania Genetics Training Grant (US National Institutes of Health grant GM008216 supporting S.J.F.).

Author information

Author notes

    • Nikolina Sekulic

    Present address: Biotechnology Centre of Oslo, Department of Chemistry, University of Oslo, Oslo, Norway.

    • Samantha J Falk
    •  & Jaehyoun Lee

    These authors contributed equally to this work.

Affiliations

  1. Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

    • Samantha J Falk
    • , Nikolina Sekulic
    •  & Ben E Black
  2. Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA.

    • Jaehyoun Lee
    • , Michael A Sennett
    •  & Tae-Hee Lee

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Contributions

S.J.F., J.L., N.S., T.-H.L. and B.E.B. designed experiments. M.A.S. performed preliminary experiments that informed the design of the study. S.J.F. and J.L. performed experiments. S.J.F., J.L., N.S., T.-H.L. and B.E.B. analyzed data. N.S. performed modeling. S.J.F., J.L., N.S., T.-H.L. and B.E.B. wrote and edited the paper. T.-H.L. and B.E.B. directed the study.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Tae-Hee Lee or Ben E Black.

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    CENP-C binding causes structural changes that reshape the entire CENP-A nucleosome

    Front and side views of the structural transitions that occur in the CENP-A nucleosome when it is bound by CENP-C. Before CENP-C binding, the (CENP-A–H4)2 heterotetramer is both rotated and compacted, causing the H2A– H2B heterodimers to move outward and away from each other. This movement is coupled to the DNA wrapping the histone octamer, which tightens around the dyad and laterally pushes the DNA gyres past one another. Upon CENP-C binding, the (CENP-A–H4)2 heterotetramer rotates outward, allowing the H2A–H2B heterodimers to move closer together and the DNA around the dyad to loosen, which in turn causes the DNA gyres to slide away from each other.

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DOI

https://doi.org/10.1038/nsmb.3175

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