Dynamic simulation of active/inactive chromatin domains

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. © Springer 2005.