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. 2005 Dec;31(3-4):351–363. doi: 10.1007/s10867-005-7286-3

Dynamic Simulation of Active/Inactive Chromatin Domains

Jens Odenheimer 1,✉, Gregor Kreth 2, Dieter W Heermann 1
PMCID: PMC3456343  PMID: 23345903

Abstract

In the present study a model for the compactification of the 30 nm chromatin fibre into higher order structures is suggested. The idea is that basically every condensing agent (HMG/SAR, HP1, cohesin, condensin, DNA–DNA interaction …) can be modeled as an effective attractive potential of specific chain segments. This way the formation of individual 1 Mbp sized rosettes from a linear chain could be observed. We analyse how the size of these rosettes depends on the number of attractive segments and on the segment length. It turns out that 8–20 attractive segments per 1 Mbp domain produces rosettes of 300–800 nm in diameter. Furthermore, our results show that the size of the rosettes is relatively insensitive to the segment length.

Key words: chromatin structure, simulation, condensing agents, rosette structure, virtual microscopy, molecular dynamics, modeling

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