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Modeling chromatin fibre folding for human embryonic stem cells

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  • Francesca Maggioni
  • Marida Bertocchi
  • Ettore Mosca
  • Rolland Reinbold
  • Ileana Zucchi

Abstract

In this study we analyze the chromatin state of human pluripotent stem cells by geometric modelling of fibre conformation. The model takes into account local structure of chromatin organized into euchromatin, permissive for gene activation, and heterochromatin, transcriptionally silenced. Euchromatin modelled using linear DNA while heterochromatin by means of a solenoid structure in which DNA winds onto six nucleosome spools per turn. Two geometric models are presented and are compared in terms of geometric quantities. The models are tested using in vivo data generated from chromatin immunoprecipitation human from embryonic stem cells. This study provides insight into and tools for identifying the relationships between chromosome geometry and epigenomic processes associated with chromatin remodeling, cellular reprograming and maintenance of cellular pluripotency.

Suggested Citation

  • Francesca Maggioni & Marida Bertocchi & Ettore Mosca & Rolland Reinbold & Ileana Zucchi, 2013. "Modeling chromatin fibre folding for human embryonic stem cells," Working Papers (2013-) 1301_qum, University of Bergamo, Department of Management, Economics and Quantitative Methods.
    • Handle: RePEc:brg:newwpa:1301_qum
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    File URL: http://aisberg.unibg.it/bitstream/10446/28874/1/wpMEQ_qm_1-2013.pdf
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    References listed on IDEAS

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    1. Thomas Schalch & Sylwia Duda & David F. Sargent & Timothy J. Richmond, 2005. "X-ray structure of a tetranucleosome and its implications for the chromatin fibre," Nature, Nature, vol. 436(7047), pages 138-141, July.
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