Effect of capsid confinement on the chromatin organization of the SV40 minichromosome

Gadiel Saper, Stanislav Kler, Roi Asor, Ariella Oppenheim, Uri Raviv, Daniel Harries*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

29 Scopus citations


Using small-angle X-ray scattering, we determined the three-dimensional packing architecture of the minichromosome confined within the SV40 virus. In solution, the minichromosome, composed of closed circular dsDNA complexed in nucleosomes, was shown to be structurally similar to cellular chromatin. In contrast, we find a unique organization of the nanometrically encapsidated chromatin, whereby minichromosomal density is somewhat higher at the center of the capsid and decreases towards the walls. This organization is in excellent agreement with a coarse-grained computer model, accounting for tethered nucleosomal interactions under viral capsid confinement. With analogy to confined liquid crystals, but contrary to the solenoid structure of cellular chromatin, our simulations indicate that the nucleosomes within the capsid lack orientational order. Nucleosomes in the layer adjacent to the capsid wall, however, align with the boundary, thereby inducing a 'molten droplet' state of the chromatin. These findings indicate that nucleosomal interactions suffice to predict the genome organization in polyomavirus capsids and underscore the adaptable nature of the eukaryotic chromatin architecture to nanoscale confinement.

Original languageAmerican English
Pages (from-to)1569-1580
Number of pages12
JournalNucleic Acids Research
Issue number3
StatePublished - Feb 2013

Bibliographical note

Funding Information:
The authors thank the SOLEIL synchrotron, SWING beam-line and J. Perez; ESRF, beam-line ID02 and J. Gummel, S. Callow and T. Naryanan; and Elettra, 5.2L SAXS beam-line, and H. Amenitsch, for discussions and help with SAXS data acquisition. R.A. thanks the Hebrew University Nanocenter for a fellowship support. The Fritz Haber Center is supported by the Minerva foundation, Munich, Germany. G.S., S.K., A.O., U.R. and D.H. designed research; G.S., S.K., U.R. and D.H. preformed research; G.S. and R.A. analyzed data; G.S., A.O., U.R. and D.H wrote the article.


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